diff --git a/latest/cases/00027/l3v2/heta-code/output.heta b/latest/cases/00027/l3v2/heta-code/output.heta new file mode 100644 index 000000000..55e144934 --- /dev/null +++ b/latest/cases/00027/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.534; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 100; + diff --git a/latest/cases/00027/l3v2/json/output.json b/latest/cases/00027/l3v2/json/output.json new file mode 100644 index 000000000..376eaa6b5 --- /dev/null +++ b/latest/cases/00027/l3v2/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "0.534" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 100 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + } +] \ No newline at end of file diff --git a/latest/cases/00027/output.heta b/latest/cases/00027/output.heta index bf3983d0c..eca983c2d 100644 --- a/latest/cases/00027/output.heta +++ b/latest/cases/00027/output.heta @@ -42,18 +42,13 @@ where they appear in expressions. */ -volume #defineUnit { units: litre, }; -area #defineUnit { units: metre^2, }; -length #defineUnit { units: metre, }; -substance #defineUnit { units: mole, }; -time #defineUnit { units: second, }; -t @TimeScale { }; +t @TimeScale { units: second, }; -compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 0.534; +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.534; -S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; -S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; reaction1 := compartment * k__reaction1_local * S1; diff --git a/latest/cases/00057/l3v2/heta-code/output.heta b/latest/cases/00057/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9f30a3d03 --- /dev/null +++ b/latest/cases/00057/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 3e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment * k__reaction2_local * S2; + +k__reaction1_local @Const { } = 1; +k__reaction2_local @Const { } = 2; + diff --git a/latest/cases/00057/l3v2/json/output.json b/latest/cases/00057/l3v2/json/output.json new file mode 100644 index 000000000..fabad2d80 --- /dev/null +++ b/latest/cases/00057/l3v2/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "3e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k__reaction2_local * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + } +] \ No newline at end of file diff --git a/latest/cases/00057/output.heta b/latest/cases/00057/output.heta index b8b804fe1..47eab9cbf 100644 --- a/latest/cases/00057/output.heta +++ b/latest/cases/00057/output.heta @@ -37,19 +37,14 @@ where they appear in expressions. */ -volume #defineUnit { units: litre, }; -area #defineUnit { units: metre^2, }; -length #defineUnit { units: metre, }; -substance #defineUnit { units: mole, }; -time #defineUnit { units: second, }; -t @TimeScale { }; +t @TimeScale { units: second, }; -compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; -S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 3e-4 / compartment; -S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; -S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 3e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment; reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; reaction1 := compartment * k__reaction1_local * S1; diff --git a/latest/cases/00058/l3v2/heta-code/output.heta b/latest/cases/00058/l3v2/heta-code/output.heta index dc4e7960f..547004a16 100644 --- a/latest/cases/00058/l3v2/heta-code/output.heta +++ b/latest/cases/00058/l3v2/heta-code/output.heta @@ -11,7 +11,8 @@ S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compart reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; reaction1 := compartment * k * S1; reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; -reaction2 := compartment * k * S2; +reaction2 := compartment * k__reaction2_local * S2; +k__reaction2_local @Const { } = 2; k @Const 'k' { } = 1; diff --git a/latest/cases/00058/l3v2/json/output.json b/latest/cases/00058/l3v2/json/output.json index ee0248a6e..6af213510 100644 --- a/latest/cases/00058/l3v2/json/output.json +++ b/latest/cases/00058/l3v2/json/output.json @@ -62,12 +62,17 @@ ], "reversible": false }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, { "class": "Reaction", "id": "reaction2", "title": "reaction2", "assignments": { - "ode_": "compartment * k * S2" + "ode_": "compartment * k__reaction2_local * S2" }, "actors": [ { diff --git a/latest/cases/00058/output.heta b/latest/cases/00058/output.heta index ce425dc6b..ba55bfdb0 100644 --- a/latest/cases/00058/output.heta +++ b/latest/cases/00058/output.heta @@ -52,7 +52,8 @@ S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compart reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; reaction1 := compartment * k * S1; reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; -reaction2 := compartment * k * S2; +reaction2 := compartment * k__reaction2_local * S2; +k__reaction2_local @Const { } = 2; k @Const 'k' { } = 1; diff --git a/latest/cases/00101/l2v5/heta-code/output.heta b/latest/cases/00101/l2v5/heta-code/output.heta new file mode 100644 index 000000000..57599f6b6 --- /dev/null +++ b/latest/cases/00101/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-15 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00101/l2v5/index.heta b/latest/cases/00101/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00101/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00101/l2v5/json/output.json b/latest/cases/00101/l2v5/json/output.json new file mode 100644 index 000000000..d82ccc8a1 --- /dev/null +++ b/latest/cases/00101/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00101/l3v2/heta-code/output.heta b/latest/cases/00101/l3v2/heta-code/output.heta new file mode 100644 index 000000000..41bdeb49c --- /dev/null +++ b/latest/cases/00101/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-15 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00101/l3v2/index.heta b/latest/cases/00101/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00101/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00101/l3v2/json/output.json b/latest/cases/00101/l3v2/json/output.json new file mode 100644 index 000000000..94f57b810 --- /dev/null +++ b/latest/cases/00101/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00101/model-sbml-l2v5.xml b/latest/cases/00101/model-sbml-l2v5.xml new file mode 100644 index 000000000..3a18f4d83 --- /dev/null +++ b/latest/cases/00101/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00101/model-sbml-l3v2.xml b/latest/cases/00101/model-sbml-l3v2.xml new file mode 100644 index 000000000..5bf1e3407 --- /dev/null +++ b/latest/cases/00101/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00101/output.heta b/latest/cases/00101/output.heta new file mode 100644 index 000000000..801c0f4a5 --- /dev/null +++ b/latest/cases/00101/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one 2D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-15 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00101/synopsis.txt b/latest/cases/00101/synopsis.txt new file mode 100644 index 000000000..5ea3cb88e --- /dev/null +++ b/latest/cases/00101/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with four species in one 2D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00102/l2v5/heta-code/output.heta b/latest/cases/00102/l2v5/heta-code/output.heta new file mode 100644 index 000000000..98db6bc73 --- /dev/null +++ b/latest/cases/00102/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00102/l2v5/index.heta b/latest/cases/00102/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00102/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00102/l2v5/json/output.json b/latest/cases/00102/l2v5/json/output.json new file mode 100644 index 000000000..91781bc2b --- /dev/null +++ b/latest/cases/00102/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00102/l3v2/heta-code/output.heta b/latest/cases/00102/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1b94d180b --- /dev/null +++ b/latest/cases/00102/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00102/l3v2/index.heta b/latest/cases/00102/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00102/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00102/l3v2/json/output.json b/latest/cases/00102/l3v2/json/output.json new file mode 100644 index 000000000..8d54608c7 --- /dev/null +++ b/latest/cases/00102/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00102/model-sbml-l2v5.xml b/latest/cases/00102/model-sbml-l2v5.xml new file mode 100644 index 000000000..bb0909e4f --- /dev/null +++ b/latest/cases/00102/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00102/model-sbml-l3v2.xml b/latest/cases/00102/model-sbml-l3v2.xml new file mode 100644 index 000000000..96acf908a --- /dev/null +++ b/latest/cases/00102/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00102/output.heta b/latest/cases/00102/output.heta new file mode 100644 index 000000000..6a0ec9e18 --- /dev/null +++ b/latest/cases/00102/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one 1D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00102/synopsis.txt b/latest/cases/00102/synopsis.txt new file mode 100644 index 000000000..a7acf5b65 --- /dev/null +++ b/latest/cases/00102/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with four species in one 1D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00103/l2v5/heta-code/output.heta b/latest/cases/00103/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6df579648 --- /dev/null +++ b/latest/cases/00103/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-4; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1e-4; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 2e-4; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00103/l2v5/index.heta b/latest/cases/00103/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00103/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00103/l2v5/json/output.json b/latest/cases/00103/l2v5/json/output.json new file mode 100644 index 000000000..c1b923056 --- /dev/null +++ b/latest/cases/00103/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00103/l3v2/heta-code/output.heta b/latest/cases/00103/l3v2/heta-code/output.heta new file mode 100644 index 000000000..67665e95a --- /dev/null +++ b/latest/cases/00103/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-4; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00103/l3v2/index.heta b/latest/cases/00103/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00103/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00103/l3v2/json/output.json b/latest/cases/00103/l3v2/json/output.json new file mode 100644 index 000000000..22030932e --- /dev/null +++ b/latest/cases/00103/l3v2/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00103/model-sbml-l2v5.xml b/latest/cases/00103/model-sbml-l2v5.xml new file mode 100644 index 000000000..564986479 --- /dev/null +++ b/latest/cases/00103/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00103/model-sbml-l3v2.xml b/latest/cases/00103/model-sbml-l3v2.xml new file mode 100644 index 000000000..f94e58685 --- /dev/null +++ b/latest/cases/00103/model-sbml-l3v2.xml @@ -0,0 +1,94 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00103/output.heta b/latest/cases/00103/output.heta new file mode 100644 index 000000000..21154bc10 --- /dev/null +++ b/latest/cases/00103/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one 0D compartment + and one function definition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +This model contains one 0-dimensional compartment called "compartment". +There are four species, S1, S2, S3 and S4, and two parameters, k1 and k2. + +The model contains a function called "multiply" that takes two numerical +arguments and multiplies them: + +[{width:25em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | +| multiply | x, y | $x * y$ |] + +The model contains two reactions defined as: + +[{width:25em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1, multiply(S1, S2))$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:25em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |mole^-1^ second^-1^ |] + +In this example, the compartment has its spatialDimensions attribute set to +a value of zero; i.e., the compartment represents a point, and therefore +cannot have a value for the %size% or %units% attributes. The quantities +of species located in the compartment must be treated as amounts and not +concentrations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-4; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00103/synopsis.txt b/latest/cases/00103/synopsis.txt new file mode 100644 index 000000000..e7b3dc056 --- /dev/null +++ b/latest/cases/00103/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one 0D compartment + and one function definition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +This model contains one 0-dimensional compartment called "compartment". +There are four species, S1, S2, S3 and S4, and two parameters, k1 and k2. + +The model contains a function called "multiply" that takes two numerical +arguments and multiplies them: + +[{width:25em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | +| multiply | x, y | $x * y$ |] + +The model contains two reactions defined as: + +[{width:25em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1, multiply(S1, S2))$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:25em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |mole^-1^ second^-1^ |] + +In this example, the compartment has its spatialDimensions attribute set to +a value of zero; i.e., the compartment represents a point, and therefore +cannot have a value for the %size% or %units% attributes. The quantities +of species located in the compartment must be treated as amounts and not +concentrations. + diff --git a/latest/cases/00104/l2v5/heta-code/output.heta b/latest/cases/00104/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c5763822f --- /dev/null +++ b/latest/cases/00104/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * multiply(k1, S1); +C_proc @Process { actors: = C, aux: {{"metaid":"rule1"}}, }; +C_proc := (-1) * C * p1; + +k1 @Record 'k1' { } .= 0.9; +p1 @Record 'p1' { } .= 0.1; + diff --git a/latest/cases/00104/l2v5/index.heta b/latest/cases/00104/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00104/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00104/l2v5/json/output.json b/latest/cases/00104/l2v5/json/output.json new file mode 100644 index 000000000..ed0ab1d84 --- /dev/null +++ b/latest/cases/00104/l2v5/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Process", + "id": "C_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * C * p1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00104/l3v2/heta-code/output.heta b/latest/cases/00104/l3v2/heta-code/output.heta new file mode 100644 index 000000000..86ecc1806 --- /dev/null +++ b/latest/cases/00104/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * multiply(k1, S1); +C_proc @Process { actors: = C, aux: {{"metaid":"rule1"}}, }; +C_proc := (-1) * C * p1; + +k1 @Const 'k1' { } = 0.9; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00104/l3v2/index.heta b/latest/cases/00104/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00104/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00104/l3v2/json/output.json b/latest/cases/00104/l3v2/json/output.json new file mode 100644 index 000000000..bacbf2c9e --- /dev/null +++ b/latest/cases/00104/l3v2/json/output.json @@ -0,0 +1,91 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.9 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Process", + "id": "C_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * C * p1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00104/model-sbml-l2v5.xml b/latest/cases/00104/model-sbml-l2v5.xml new file mode 100644 index 000000000..b0644a43f --- /dev/null +++ b/latest/cases/00104/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + -1 + C + p1 + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00104/model-sbml-l3v2.xml b/latest/cases/00104/model-sbml-l3v2.xml new file mode 100644 index 000000000..4c2975db6 --- /dev/null +++ b/latest/cases/00104/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + C + p1 + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00104/output.heta b/latest/cases/00104/output.heta new file mode 100644 index 000000000..8db17b5da --- /dev/null +++ b/latest/cases/00104/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using a functionDefinition and a rateRule to vary compartment size. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are two +species called S1 and S2 and two parameters called k1 and p1. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * multiply(k1,S1)$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C | $-p1 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * multiply(k1, S1); +C_proc @Process { actors: = C, aux: {{"metaid":"rule1"}}, }; +C_proc := (-1) * C * p1; + +k1 @Const 'k1' { } = 0.9; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00104/synopsis.txt b/latest/cases/00104/synopsis.txt new file mode 100644 index 000000000..a5a2a603a --- /dev/null +++ b/latest/cases/00104/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using a functionDefinition and a rateRule to vary compartment size. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are two +species called S1 and S2 and two parameters called k1 and p1. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * multiply(k1,S1)$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C | $-p1 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00105/l2v5/heta-code/output.heta b/latest/cases/00105/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bb7986a40 --- /dev/null +++ b/latest/cases/00105/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +C_proc @Process { actors: = C, aux: {{"metaid":"rule1"}}, }; +C_proc := (-1) * C * p1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.1; + diff --git a/latest/cases/00105/l2v5/index.heta b/latest/cases/00105/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00105/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00105/l2v5/json/output.json b/latest/cases/00105/l2v5/json/output.json new file mode 100644 index 000000000..580b4de5d --- /dev/null +++ b/latest/cases/00105/l2v5/json/output.json @@ -0,0 +1,165 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Process", + "id": "C_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * C * p1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00105/l3v2/heta-code/output.heta b/latest/cases/00105/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2a249393d --- /dev/null +++ b/latest/cases/00105/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +C_proc @Process { actors: = C, aux: {{"metaid":"rule1"}}, }; +C_proc := (-1) * C * p1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00105/l3v2/index.heta b/latest/cases/00105/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00105/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00105/l3v2/json/output.json b/latest/cases/00105/l3v2/json/output.json new file mode 100644 index 000000000..d7ac8eb66 --- /dev/null +++ b/latest/cases/00105/l3v2/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Process", + "id": "C_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * C * p1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00105/model-sbml-l2v5.xml b/latest/cases/00105/model-sbml-l2v5.xml new file mode 100644 index 000000000..be8ea10a5 --- /dev/null +++ b/latest/cases/00105/model-sbml-l2v5.xml @@ -0,0 +1,97 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + -1 + C + p1 + + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00105/model-sbml-l3v2.xml b/latest/cases/00105/model-sbml-l3v2.xml new file mode 100644 index 000000000..d00e7c4b4 --- /dev/null +++ b/latest/cases/00105/model-sbml-l3v2.xml @@ -0,0 +1,114 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + C + p1 + + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00105/output.heta b/latest/cases/00105/output.heta new file mode 100644 index 000000000..d33c8eb37 --- /dev/null +++ b/latest/cases/00105/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one varying compartment + and one functionDefinition +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are three +species called S1, S2 and S3 and three parameters called k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C | $-p1 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +C_proc @Process { actors: = C, aux: {{"metaid":"rule1"}}, }; +C_proc := (-1) * C * p1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00105/synopsis.txt b/latest/cases/00105/synopsis.txt new file mode 100644 index 000000000..aeadc7b01 --- /dev/null +++ b/latest/cases/00105/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in one varying compartment + and one functionDefinition +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are three +species called S1, S2 and S3 and three parameters called k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C | $-p1 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00106/l2v5/heta-code/output.heta b/latest/cases/00106/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b50407a39 --- /dev/null +++ b/latest/cases/00106/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +C_proc @Process { actors: = C, aux: {{"metaid":"rule1"}}, }; +C_proc := (-1) * C * p1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.1; + diff --git a/latest/cases/00106/l2v5/index.heta b/latest/cases/00106/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00106/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00106/l2v5/json/output.json b/latest/cases/00106/l2v5/json/output.json new file mode 100644 index 000000000..0b3d7e075 --- /dev/null +++ b/latest/cases/00106/l2v5/json/output.json @@ -0,0 +1,182 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Process", + "id": "C_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * C * p1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00106/l3v2/heta-code/output.heta b/latest/cases/00106/l3v2/heta-code/output.heta new file mode 100644 index 000000000..af46518c1 --- /dev/null +++ b/latest/cases/00106/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +C_proc @Process { actors: = C, aux: {{"metaid":"rule1"}}, }; +C_proc := (-1) * C * p1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00106/l3v2/index.heta b/latest/cases/00106/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00106/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00106/l3v2/json/output.json b/latest/cases/00106/l3v2/json/output.json new file mode 100644 index 000000000..41c4ba671 --- /dev/null +++ b/latest/cases/00106/l3v2/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Process", + "id": "C_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * C * p1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00106/model-sbml-l2v5.xml b/latest/cases/00106/model-sbml-l2v5.xml new file mode 100644 index 000000000..8f24df7f8 --- /dev/null +++ b/latest/cases/00106/model-sbml-l2v5.xml @@ -0,0 +1,100 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + -1 + C + p1 + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00106/model-sbml-l3v2.xml b/latest/cases/00106/model-sbml-l3v2.xml new file mode 100644 index 000000000..7a56e7762 --- /dev/null +++ b/latest/cases/00106/model-sbml-l3v2.xml @@ -0,0 +1,117 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + C + p1 + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00106/output.heta b/latest/cases/00106/output.heta new file mode 100644 index 000000000..7ec6b809a --- /dev/null +++ b/latest/cases/00106/output.heta @@ -0,0 +1,72 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one varying compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C | $-p1 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +C_proc @Process { actors: = C, aux: {{"metaid":"rule1"}}, }; +C_proc := (-1) * C * p1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00106/synopsis.txt b/latest/cases/00106/synopsis.txt new file mode 100644 index 000000000..6671f337e --- /dev/null +++ b/latest/cases/00106/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic two reactions with four species in one varying compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C | $-p1 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00107/l2v5/heta-code/output.heta b/latest/cases/00107/l2v5/heta-code/output.heta new file mode 100644 index 000000000..25add8119 --- /dev/null +++ b/latest/cases/00107/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.15 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00107/l2v5/index.heta b/latest/cases/00107/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00107/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00107/l2v5/json/output.json b/latest/cases/00107/l2v5/json/output.json new file mode 100644 index 000000000..354decf81 --- /dev/null +++ b/latest/cases/00107/l2v5/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00107/l3v2/heta-code/output.heta b/latest/cases/00107/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3b34cb838 --- /dev/null +++ b/latest/cases/00107/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00107/l3v2/index.heta b/latest/cases/00107/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00107/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00107/l3v2/json/output.json b/latest/cases/00107/l3v2/json/output.json new file mode 100644 index 000000000..dbaebb0d6 --- /dev/null +++ b/latest/cases/00107/l3v2/json/output.json @@ -0,0 +1,70 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00107/model-sbml-l2v5.xml b/latest/cases/00107/model-sbml-l2v5.xml new file mode 100644 index 000000000..68a1e9c49 --- /dev/null +++ b/latest/cases/00107/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00107/model-sbml-l3v2.xml b/latest/cases/00107/model-sbml-l3v2.xml new file mode 100644 index 000000000..e6eba765e --- /dev/null +++ b/latest/cases/00107/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00107/output.heta b/latest/cases/00107/output.heta new file mode 100644 index 000000000..65cba02ca --- /dev/null +++ b/latest/cases/00107/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment of non-unity size using a function to apply +the kinetic law. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Volume of compartment "compartment" |$ 2.3$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00107/synopsis.txt b/latest/cases/00107/synopsis.txt new file mode 100644 index 000000000..98af97f26 --- /dev/null +++ b/latest/cases/00107/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment of non-unity size using a function to apply +the kinetic law. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Volume of compartment "compartment" |$ 2.3$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00108/l2v5/heta-code/output.heta b/latest/cases/00108/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c0be27072 --- /dev/null +++ b/latest/cases/00108/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 2e-4 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00108/l2v5/index.heta b/latest/cases/00108/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00108/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00108/l2v5/json/output.json b/latest/cases/00108/l2v5/json/output.json new file mode 100644 index 000000000..7012b4bc6 --- /dev/null +++ b/latest/cases/00108/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00108/l3v2/heta-code/output.heta b/latest/cases/00108/l3v2/heta-code/output.heta new file mode 100644 index 000000000..511808db9 --- /dev/null +++ b/latest/cases/00108/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00108/l3v2/index.heta b/latest/cases/00108/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00108/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00108/l3v2/json/output.json b/latest/cases/00108/l3v2/json/output.json new file mode 100644 index 000000000..4332e9ca8 --- /dev/null +++ b/latest/cases/00108/l3v2/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00108/model-sbml-l2v5.xml b/latest/cases/00108/model-sbml-l2v5.xml new file mode 100644 index 000000000..b7144adb8 --- /dev/null +++ b/latest/cases/00108/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00108/model-sbml-l3v2.xml b/latest/cases/00108/model-sbml-l3v2.xml new file mode 100644 index 000000000..2bee677b9 --- /dev/null +++ b/latest/cases/00108/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00108/output.heta b/latest/cases/00108/output.heta new file mode 100644 index 000000000..14d7fb750 --- /dev/null +++ b/latest/cases/00108/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + of non-unity size using a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". +There are three species named S1, S2 and S3 and two parameters named k1 and k2. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 | $1.0 \x 10^-4$ | mole | +|Initial amount of S2 | $2.0 \x 10^-4$ | mole | +|Initial amount of S3 | $1.0 \x 10^-4$ | mole | +|Value of parameter k1 | $ 0.75$ | litre mole^-1^ second^-1^ | +|Value of parameter k2 | $ 0.25$ | second^-1^ | +|Volume of compartment "compartment":| $ 2.3$ | litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units where they appear in +expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00108/synopsis.txt b/latest/cases/00108/synopsis.txt new file mode 100644 index 000000000..58e127887 --- /dev/null +++ b/latest/cases/00108/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + of non-unity size using a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". +There are three species named S1, S2 and S3 and two parameters named k1 and k2. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 | $1.0 \x 10^-4$ | mole | +|Initial amount of S2 | $2.0 \x 10^-4$ | mole | +|Initial amount of S3 | $1.0 \x 10^-4$ | mole | +|Value of parameter k1 | $ 0.75$ | litre mole^-1^ second^-1^ | +|Value of parameter k2 | $ 0.25$ | second^-1^ | +|Volume of compartment "compartment":| $ 2.3$ | litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units where they appear in +expressions. + diff --git a/latest/cases/00109/l2v5/heta-code/output.heta b/latest/cases/00109/l2v5/heta-code/output.heta new file mode 100644 index 000000000..43969bfb6 --- /dev/null +++ b/latest/cases/00109/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 12.5; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 5e-4 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.002 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 750; +k2 @Record 'k2' { } .= 250; + diff --git a/latest/cases/00109/l2v5/index.heta b/latest/cases/00109/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00109/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00109/l2v5/json/output.json b/latest/cases/00109/l2v5/json/output.json new file mode 100644 index 000000000..c2c7185f8 --- /dev/null +++ b/latest/cases/00109/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "12.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "750" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "250" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00109/l3v2/heta-code/output.heta b/latest/cases/00109/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e9446aa6d --- /dev/null +++ b/latest/cases/00109/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 12.5; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00109/l3v2/index.heta b/latest/cases/00109/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00109/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00109/l3v2/json/output.json b/latest/cases/00109/l3v2/json/output.json new file mode 100644 index 000000000..d1e73a1ed --- /dev/null +++ b/latest/cases/00109/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "12.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 250 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00109/model-sbml-l2v5.xml b/latest/cases/00109/model-sbml-l2v5.xml new file mode 100644 index 000000000..36344b81f --- /dev/null +++ b/latest/cases/00109/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00109/model-sbml-l3v2.xml b/latest/cases/00109/model-sbml-l3v2.xml new file mode 100644 index 000000000..654e722c2 --- /dev/null +++ b/latest/cases/00109/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00109/output.heta b/latest/cases/00109/output.heta new file mode 100644 index 000000000..66c01add2 --- /dev/null +++ b/latest/cases/00109/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one varying compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 12.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 12.5; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00109/synopsis.txt b/latest/cases/00109/synopsis.txt new file mode 100644 index 000000000..cf1131a38 --- /dev/null +++ b/latest/cases/00109/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one varying compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 12.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00110/l2v5/heta-code/output.heta b/latest/cases/00110/l2v5/heta-code/output.heta new file mode 100644 index 000000000..328efaaf7 --- /dev/null +++ b/latest/cases/00110/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * S2 * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00110/l2v5/index.heta b/latest/cases/00110/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00110/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00110/l2v5/json/output.json b/latest/cases/00110/l2v5/json/output.json new file mode 100644 index 000000000..9cc73ceba --- /dev/null +++ b/latest/cases/00110/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * S2 * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00110/l3v2/heta-code/output.heta b/latest/cases/00110/l3v2/heta-code/output.heta new file mode 100644 index 000000000..aec1f1b9c --- /dev/null +++ b/latest/cases/00110/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * S2 * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00110/l3v2/index.heta b/latest/cases/00110/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00110/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00110/l3v2/json/output.json b/latest/cases/00110/l3v2/json/output.json new file mode 100644 index 000000000..4b3f6d777 --- /dev/null +++ b/latest/cases/00110/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * S2 * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00110/model-sbml-l2v5.xml b/latest/cases/00110/model-sbml-l2v5.xml new file mode 100644 index 000000000..7bb27ed34 --- /dev/null +++ b/latest/cases/00110/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + S2 + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + diff --git a/latest/cases/00110/model-sbml-l3v2.xml b/latest/cases/00110/model-sbml-l3v2.xml new file mode 100644 index 000000000..0737e224d --- /dev/null +++ b/latest/cases/00110/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + S2 + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + diff --git a/latest/cases/00110/output.heta b/latest/cases/00110/output.heta new file mode 100644 index 000000000..9f9fca23c --- /dev/null +++ b/latest/cases/00110/output.heta @@ -0,0 +1,73 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments with functionDefinitions. +componentTags: Compartment, FunctionDefinition, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are three species named S1, S2 and S3 and two parameters named k1 and +k2. Compartment "compartment" contains species S1 and S2. Compartment +"compartment"1 contains species S3. + +The model contains: +* 3 species (S1, S2, S3) +* 2 parameters (k1, k2) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * S2 * multiply(k1, S1)$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |] + +The first reaction occurs entirely in compartment "compartment", whereas +the second reaction occurs between a species in "compartment" and a species +in "compartment1". + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * S2 * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00110/synopsis.txt b/latest/cases/00110/synopsis.txt new file mode 100644 index 000000000..4e29a0c4e --- /dev/null +++ b/latest/cases/00110/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Reactions occurring between two compartments with functionDefinitions. +componentTags: Compartment, FunctionDefinition, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are three species named S1, S2 and S3 and two parameters named k1 and +k2. Compartment "compartment" contains species S1 and S2. Compartment +"compartment"1 contains species S3. + +The model contains: +* 3 species (S1, S2, S3) +* 2 parameters (k1, k2) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * S2 * multiply(k1, S1)$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |] + +The first reaction occurs entirely in compartment "compartment", whereas +the second reaction occurs between a species in "compartment" and a species +in "compartment1". + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00111/l2v5/heta-code/output.heta b/latest/cases/00111/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5336ec84e --- /dev/null +++ b/latest/cases/00111/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: substance/volume, compartment: compartment1, } .= 0.1 / compartment1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 7.5; +k3 @Record 'k3' { } .= 0.75; + diff --git a/latest/cases/00111/l2v5/index.heta b/latest/cases/00111/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00111/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00111/l2v5/json/output.json b/latest/cases/00111/l2v5/json/output.json new file mode 100644 index 000000000..0d57ba1a0 --- /dev/null +++ b/latest/cases/00111/l2v5/json/output.json @@ -0,0 +1,188 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "compartment * k3 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00111/l3v2/heta-code/output.heta b/latest/cases/00111/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b7e9b852f --- /dev/null +++ b/latest/cases/00111/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 7.5; +k3 @Const 'k3' { } = 0.75; + diff --git a/latest/cases/00111/l3v2/index.heta b/latest/cases/00111/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00111/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00111/l3v2/json/output.json b/latest/cases/00111/l3v2/json/output.json new file mode 100644 index 000000000..fd7f44bcb --- /dev/null +++ b/latest/cases/00111/l3v2/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "compartment * k3 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 7.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.75 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00111/model-sbml-l2v5.xml b/latest/cases/00111/model-sbml-l2v5.xml new file mode 100644 index 000000000..c17548df2 --- /dev/null +++ b/latest/cases/00111/model-sbml-l2v5.xml @@ -0,0 +1,110 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + + + + + + + + + + + compartment + k3 + S3 + S4 + + + + + + + diff --git a/latest/cases/00111/model-sbml-l3v2.xml b/latest/cases/00111/model-sbml-l3v2.xml new file mode 100644 index 000000000..29e7020af --- /dev/null +++ b/latest/cases/00111/model-sbml-l3v2.xml @@ -0,0 +1,127 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + + + + + + + + + + + compartment + k3 + S3 + S4 + + + + + + + diff --git a/latest/cases/00111/output.heta b/latest/cases/00111/output.heta new file mode 100644 index 000000000..f8bbdf76c --- /dev/null +++ b/latest/cases/00111/output.heta @@ -0,0 +1,81 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments with functionDefinitions. +componentTags: Compartment, FunctionDefinition, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are four species named S1, S2, S3 and S4 and three parameters named +k1, k2 and k3. Compartment "compartment" contains species S1 and S2. +Compartment "compartment1" contains species S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 3 parameters (k1, k2, k3) +* 2 compartments (compartment, compartment1) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * multiply(S1, S2)$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ | +| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |] + +The first reaction occurs entirely within compartment "compartment", the +second reaction occurs between a species in "compartment" and a species in +"compartment1", and the third reaction occurs entirely within +"compartment1". + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial amount of species S4 | $0.1$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $7.5$ | constant | +| Initial value of parameter k3 | $0.75$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 7.5; +k3 @Const 'k3' { } = 0.75; + diff --git a/latest/cases/00111/synopsis.txt b/latest/cases/00111/synopsis.txt new file mode 100644 index 000000000..55a34d499 --- /dev/null +++ b/latest/cases/00111/synopsis.txt @@ -0,0 +1,55 @@ + +category: Test +synopsis: Reactions occurring between two compartments with functionDefinitions. +componentTags: Compartment, FunctionDefinition, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are four species named S1, S2, S3 and S4 and three parameters named +k1, k2 and k3. Compartment "compartment" contains species S1 and S2. +Compartment "compartment1" contains species S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 3 parameters (k1, k2, k3) +* 2 compartments (compartment, compartment1) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * multiply(S1, S2)$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ | +| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |] + +The first reaction occurs entirely within compartment "compartment", the +second reaction occurs between a species in "compartment" and a species in +"compartment1", and the third reaction occurs entirely within +"compartment1". + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial amount of species S4 | $0.1$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $7.5$ | constant | +| Initial value of parameter k3 | $0.75$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00112/l2v5/heta-code/output.heta b/latest/cases/00112/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a2e83eb71 --- /dev/null +++ b/latest/cases/00112/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00112/l2v5/index.heta b/latest/cases/00112/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00112/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00112/l2v5/json/output.json b/latest/cases/00112/l2v5/json/output.json new file mode 100644 index 000000000..56caad374 --- /dev/null +++ b/latest/cases/00112/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S3 + (-1) * S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00112/l3v2/heta-code/output.heta b/latest/cases/00112/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8813d4b3b --- /dev/null +++ b/latest/cases/00112/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00112/l3v2/index.heta b/latest/cases/00112/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00112/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00112/l3v2/json/output.json b/latest/cases/00112/l3v2/json/output.json new file mode 100644 index 000000000..be8d663bd --- /dev/null +++ b/latest/cases/00112/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S3 + (-1) * S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00112/model-sbml-l2v5.xml b/latest/cases/00112/model-sbml-l2v5.xml new file mode 100644 index 000000000..93b2e014b --- /dev/null +++ b/latest/cases/00112/model-sbml-l2v5.xml @@ -0,0 +1,85 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment1 + k2 + + + S3 + + + -1 + S1 + + + + + + + + + diff --git a/latest/cases/00112/model-sbml-l3v2.xml b/latest/cases/00112/model-sbml-l3v2.xml new file mode 100644 index 000000000..714ac6cbd --- /dev/null +++ b/latest/cases/00112/model-sbml-l3v2.xml @@ -0,0 +1,102 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment1 + k2 + + + S3 + + + -1 + S1 + + + + + + + + + diff --git a/latest/cases/00112/output.heta b/latest/cases/00112/output.heta new file mode 100644 index 000000000..25d74f235 --- /dev/null +++ b/latest/cases/00112/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments with functionDefinitions. +componentTags: Compartment, FunctionDefinition, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are two species named S1 and S3 and two parameters named k1 and k2. +Compartment "compartment" contains species S1. Compartment "compartment1" +contains species S3. + +The model contains: +* 2 species (S1, S3) +* 2 parameters (k1, k2) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 -> S3 | $compartment * multiply(k1, S1)$ | +| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |] + +The reactions occur between the species within different compartments: + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00112/synopsis.txt b/latest/cases/00112/synopsis.txt new file mode 100644 index 000000000..617077c18 --- /dev/null +++ b/latest/cases/00112/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Reactions occurring between two compartments with functionDefinitions. +componentTags: Compartment, FunctionDefinition, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are two species named S1 and S3 and two parameters named k1 and k2. +Compartment "compartment" contains species S1. Compartment "compartment1" +contains species S3. + +The model contains: +* 2 species (S1, S3) +* 2 parameters (k1, k2) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 -> S3 | $compartment * multiply(k1, S1)$ | +| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |] + +The reactions occur between the species within different compartments: + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00113/l2v5/heta-code/output.heta b/latest/cases/00113/l2v5/heta-code/output.heta new file mode 100644 index 000000000..340502daa --- /dev/null +++ b/latest/cases/00113/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := multiply(k1, S1); + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00113/l2v5/index.heta b/latest/cases/00113/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00113/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00113/l2v5/json/output.json b/latest/cases/00113/l2v5/json/output.json new file mode 100644 index 000000000..fbdcfc1ee --- /dev/null +++ b/latest/cases/00113/l2v5/json/output.json @@ -0,0 +1,98 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00113/l3v2/heta-code/output.heta b/latest/cases/00113/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cffdce5a4 --- /dev/null +++ b/latest/cases/00113/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := multiply(k1, S1); + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00113/l3v2/index.heta b/latest/cases/00113/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00113/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00113/l3v2/json/output.json b/latest/cases/00113/l3v2/json/output.json new file mode 100644 index 000000000..bf72e5512 --- /dev/null +++ b/latest/cases/00113/l3v2/json/output.json @@ -0,0 +1,72 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00113/model-sbml-l2v5.xml b/latest/cases/00113/model-sbml-l2v5.xml new file mode 100644 index 000000000..d01412aaf --- /dev/null +++ b/latest/cases/00113/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S1 + + + + + + + diff --git a/latest/cases/00113/model-sbml-l3v2.xml b/latest/cases/00113/model-sbml-l3v2.xml new file mode 100644 index 000000000..911971e91 --- /dev/null +++ b/latest/cases/00113/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S1 + + + + + + + diff --git a/latest/cases/00113/output.heta b/latest/cases/00113/output.heta new file mode 100644 index 000000000..cb76e7958 --- /dev/null +++ b/latest/cases/00113/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic single forward reaction using functionDefinitions with two +species in a compartment where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := multiply(k1, S1); + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00113/synopsis.txt b/latest/cases/00113/synopsis.txt new file mode 100644 index 000000000..4ca412a5d --- /dev/null +++ b/latest/cases/00113/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic single forward reaction using functionDefinitions with two +species in a compartment where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00114/l2v5/heta-code/output.heta b/latest/cases/00114/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ddc2a01e1 --- /dev/null +++ b/latest/cases/00114/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 1.7; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00114/l2v5/index.heta b/latest/cases/00114/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00114/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00114/l2v5/json/output.json b/latest/cases/00114/l2v5/json/output.json new file mode 100644 index 000000000..eae9d2710 --- /dev/null +++ b/latest/cases/00114/l2v5/json/output.json @@ -0,0 +1,144 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00114/l3v2/heta-code/output.heta b/latest/cases/00114/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e03917589 --- /dev/null +++ b/latest/cases/00114/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 1.7; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00114/l3v2/index.heta b/latest/cases/00114/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00114/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00114/l3v2/json/output.json b/latest/cases/00114/l3v2/json/output.json new file mode 100644 index 000000000..d149860bc --- /dev/null +++ b/latest/cases/00114/l3v2/json/output.json @@ -0,0 +1,116 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00114/model-sbml-l2v5.xml b/latest/cases/00114/model-sbml-l2v5.xml new file mode 100644 index 000000000..0542d4727 --- /dev/null +++ b/latest/cases/00114/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00114/model-sbml-l3v2.xml b/latest/cases/00114/model-sbml-l3v2.xml new file mode 100644 index 000000000..4ea4e9b38 --- /dev/null +++ b/latest/cases/00114/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00114/output.heta b/latest/cases/00114/output.heta new file mode 100644 index 000000000..219e4c94e --- /dev/null +++ b/latest/cases/00114/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic reactions using functionDefinitions with three species in a compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * multiply(S1,S2)$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.7 $ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 1.7; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00114/synopsis.txt b/latest/cases/00114/synopsis.txt new file mode 100644 index 000000000..439c11c6c --- /dev/null +++ b/latest/cases/00114/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic reactions using functionDefinitions with three species in a compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * multiply(S1,S2)$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.7 $ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00115/l2v5/heta-code/output.heta b/latest/cases/00115/l2v5/heta-code/output.heta new file mode 100644 index 000000000..49f32f095 --- /dev/null +++ b/latest/cases/00115/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 1.3e+6; +k2 @Record 'k2' { } .= 3e+5; + diff --git a/latest/cases/00115/l2v5/index.heta b/latest/cases/00115/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00115/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00115/l2v5/json/output.json b/latest/cases/00115/l2v5/json/output.json new file mode 100644 index 000000000..2d3b94b87 --- /dev/null +++ b/latest/cases/00115/l2v5/json/output.json @@ -0,0 +1,163 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.3e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "3e+5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00115/l3v2/heta-code/output.heta b/latest/cases/00115/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9fe491397 --- /dev/null +++ b/latest/cases/00115/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 300000; + diff --git a/latest/cases/00115/l3v2/index.heta b/latest/cases/00115/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00115/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00115/l3v2/json/output.json b/latest/cases/00115/l3v2/json/output.json new file mode 100644 index 000000000..13e4a7d4e --- /dev/null +++ b/latest/cases/00115/l3v2/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1300000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 300000 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00115/model-sbml-l2v5.xml b/latest/cases/00115/model-sbml-l2v5.xml new file mode 100644 index 000000000..2e6bc0886 --- /dev/null +++ b/latest/cases/00115/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00115/model-sbml-l3v2.xml b/latest/cases/00115/model-sbml-l3v2.xml new file mode 100644 index 000000000..c3b203352 --- /dev/null +++ b/latest/cases/00115/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00115/output.heta b/latest/cases/00115/output.heta new file mode 100644 index 000000000..803b2efef --- /dev/null +++ b/latest/cases/00115/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions using functiondefinitions with four species in a compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * multiply(S1,S2)$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 300000; + diff --git a/latest/cases/00115/synopsis.txt b/latest/cases/00115/synopsis.txt new file mode 100644 index 000000000..912f14d1c --- /dev/null +++ b/latest/cases/00115/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions using functiondefinitions with four species in a compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * multiply(S1,S2)$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00116/l2v5/heta-code/output.heta b/latest/cases/00116/l2v5/heta-code/output.heta new file mode 100644 index 000000000..55bb6873e --- /dev/null +++ b/latest/cases/00116/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * S2; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00116/l2v5/index.heta b/latest/cases/00116/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00116/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00116/l2v5/json/output.json b/latest/cases/00116/l2v5/json/output.json new file mode 100644 index 000000000..189d3352b --- /dev/null +++ b/latest/cases/00116/l2v5/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00116/l3v2/heta-code/output.heta b/latest/cases/00116/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9d79cf491 --- /dev/null +++ b/latest/cases/00116/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * S2; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00116/l3v2/index.heta b/latest/cases/00116/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00116/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00116/l3v2/json/output.json b/latest/cases/00116/l3v2/json/output.json new file mode 100644 index 000000000..64d91763a --- /dev/null +++ b/latest/cases/00116/l3v2/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00116/model-sbml-l2v5.xml b/latest/cases/00116/model-sbml-l2v5.xml new file mode 100644 index 000000000..3dd87839e --- /dev/null +++ b/latest/cases/00116/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment + k2 + S2 + + + + + + + diff --git a/latest/cases/00116/model-sbml-l3v2.xml b/latest/cases/00116/model-sbml-l3v2.xml new file mode 100644 index 000000000..88d621207 --- /dev/null +++ b/latest/cases/00116/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment + k2 + S2 + + + + + + + diff --git a/latest/cases/00116/output.heta b/latest/cases/00116/output.heta new file mode 100644 index 000000000..475168207 --- /dev/null +++ b/latest/cases/00116/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions using functionDefinitions in one compartment, + with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. +Species S1 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1) * compartment$ | +| S2 -> S1 | $k2 * S2 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * S2; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00116/synopsis.txt b/latest/cases/00116/synopsis.txt new file mode 100644 index 000000000..407b07636 --- /dev/null +++ b/latest/cases/00116/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions using functionDefinitions in one compartment, + with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. +Species S1 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1) * compartment$ | +| S2 -> S1 | $k2 * S2 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00117/l2v5/heta-code/output.heta b/latest/cases/00117/l2v5/heta-code/output.heta new file mode 100644 index 000000000..fb1c3a827 --- /dev/null +++ b/latest/cases/00117/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := compartment * multiply(k2, S2); + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00117/l2v5/index.heta b/latest/cases/00117/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00117/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00117/l2v5/json/output.json b/latest/cases/00117/l2v5/json/output.json new file mode 100644 index 000000000..43a8729f1 --- /dev/null +++ b/latest/cases/00117/l2v5/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * multiply(k2, S2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00117/l3v2/heta-code/output.heta b/latest/cases/00117/l3v2/heta-code/output.heta new file mode 100644 index 000000000..39fd80371 --- /dev/null +++ b/latest/cases/00117/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := compartment * multiply(k2, S2); + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00117/l3v2/index.heta b/latest/cases/00117/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00117/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00117/l3v2/json/output.json b/latest/cases/00117/l3v2/json/output.json new file mode 100644 index 000000000..3db7e0b6a --- /dev/null +++ b/latest/cases/00117/l3v2/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * multiply(k2, S2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00117/model-sbml-l2v5.xml b/latest/cases/00117/model-sbml-l2v5.xml new file mode 100644 index 000000000..f88f971d5 --- /dev/null +++ b/latest/cases/00117/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment + + multiply + k2 + S2 + + + + + + + + diff --git a/latest/cases/00117/model-sbml-l3v2.xml b/latest/cases/00117/model-sbml-l3v2.xml new file mode 100644 index 000000000..92541780b --- /dev/null +++ b/latest/cases/00117/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment + + multiply + k2 + S2 + + + + + + + + diff --git a/latest/cases/00117/output.heta b/latest/cases/00117/output.heta new file mode 100644 index 000000000..4a7bb270b --- /dev/null +++ b/latest/cases/00117/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic two reactions using functionDefinitions in one compartment, + with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. +Species S2 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1) * compartment$ | +| S2 -> S1 | $multiply(k2,S2) * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := compartment * multiply(k2, S2); + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00117/synopsis.txt b/latest/cases/00117/synopsis.txt new file mode 100644 index 000000000..a5bf51fbc --- /dev/null +++ b/latest/cases/00117/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions using functionDefinitions in one compartment, + with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. +Species S2 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1) * compartment$ | +| S2 -> S1 | $multiply(k2,S2) * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00118/l2v5/heta-code/output.heta b/latest/cases/00118/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8e03ba016 --- /dev/null +++ b/latest/cases/00118/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * S2; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00118/l2v5/index.heta b/latest/cases/00118/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00118/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00118/l2v5/json/output.json b/latest/cases/00118/l2v5/json/output.json new file mode 100644 index 000000000..6a4d4ace2 --- /dev/null +++ b/latest/cases/00118/l2v5/json/output.json @@ -0,0 +1,125 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00118/l3v2/heta-code/output.heta b/latest/cases/00118/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f3c44976d --- /dev/null +++ b/latest/cases/00118/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * S2; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00118/l3v2/index.heta b/latest/cases/00118/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00118/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00118/l3v2/json/output.json b/latest/cases/00118/l3v2/json/output.json new file mode 100644 index 000000000..d75c5d032 --- /dev/null +++ b/latest/cases/00118/l3v2/json/output.json @@ -0,0 +1,97 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00118/model-sbml-l2v5.xml b/latest/cases/00118/model-sbml-l2v5.xml new file mode 100644 index 000000000..7a74d1dc1 --- /dev/null +++ b/latest/cases/00118/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment + k2 + S2 + + + + + + + diff --git a/latest/cases/00118/model-sbml-l3v2.xml b/latest/cases/00118/model-sbml-l3v2.xml new file mode 100644 index 000000000..23b07c23c --- /dev/null +++ b/latest/cases/00118/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment + k2 + S2 + + + + + + + diff --git a/latest/cases/00118/output.heta b/latest/cases/00118/output.heta new file mode 100644 index 000000000..d4d735436 --- /dev/null +++ b/latest/cases/00118/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions using functionDefinitions in one compartment, + with both species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. +Both species S1 and S2 are labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1) * compartment$ | +| S2 -> S1 | $k2 * S2 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * S2; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00118/synopsis.txt b/latest/cases/00118/synopsis.txt new file mode 100644 index 000000000..1be74668e --- /dev/null +++ b/latest/cases/00118/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions using functionDefinitions in one compartment, + with both species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. +Both species S1 and S2 are labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1) * compartment$ | +| S2 -> S1 | $k2 * S2 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00119/l2v5/heta-code/output.heta b/latest/cases/00119/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8b7906de5 --- /dev/null +++ b/latest/cases/00119/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: compartment, } .= 2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S3); + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00119/l2v5/index.heta b/latest/cases/00119/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00119/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00119/l2v5/json/output.json b/latest/cases/00119/l2v5/json/output.json new file mode 100644 index 000000000..2251bd51b --- /dev/null +++ b/latest/cases/00119/l2v5/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * multiply(S1, S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00119/l3v2/heta-code/output.heta b/latest/cases/00119/l3v2/heta-code/output.heta new file mode 100644 index 000000000..efbdb364e --- /dev/null +++ b/latest/cases/00119/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S3); + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00119/l3v2/index.heta b/latest/cases/00119/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00119/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00119/l3v2/json/output.json b/latest/cases/00119/l3v2/json/output.json new file mode 100644 index 000000000..55175d74a --- /dev/null +++ b/latest/cases/00119/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * multiply(S1, S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00119/model-sbml-l2v5.xml b/latest/cases/00119/model-sbml-l2v5.xml new file mode 100644 index 000000000..ae5ad547e --- /dev/null +++ b/latest/cases/00119/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + multiply + S1 + S3 + + + + + + + + diff --git a/latest/cases/00119/model-sbml-l3v2.xml b/latest/cases/00119/model-sbml-l3v2.xml new file mode 100644 index 000000000..19cae2031 --- /dev/null +++ b/latest/cases/00119/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + multiply + S1 + S3 + + + + + + + + diff --git a/latest/cases/00119/output.heta b/latest/cases/00119/output.heta new file mode 100644 index 000000000..8616f9b40 --- /dev/null +++ b/latest/cases/00119/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction using functionDefinitions + with three species in a compartment where the one species is constant. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. +Species S3 is labeled as constant and therefore does not vary. +The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * multiply(S1,S3) * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 2$ |mole | +|Value of parameter k1 |$ 1.5$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S3); + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00119/synopsis.txt b/latest/cases/00119/synopsis.txt new file mode 100644 index 000000000..ac9cc71d7 --- /dev/null +++ b/latest/cases/00119/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction using functionDefinitions + with three species in a compartment where the one species is constant. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. +Species S3 is labeled as constant and therefore does not vary. +The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * multiply(S1,S3) * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 2$ |mole | +|Value of parameter k1 |$ 1.5$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00120/l2v5/heta-code/output.heta b/latest/cases/00120/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cbc6b9a7f --- /dev/null +++ b/latest/cases/00120/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * multiply(S3, S4); + +k1 @Record 'k1' { } .= 1.7; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00120/l2v5/index.heta b/latest/cases/00120/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00120/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00120/l2v5/json/output.json b/latest/cases/00120/l2v5/json/output.json new file mode 100644 index 000000000..cf853e5fd --- /dev/null +++ b/latest/cases/00120/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * multiply(S3, S4)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00120/l3v2/heta-code/output.heta b/latest/cases/00120/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4e3b83127 --- /dev/null +++ b/latest/cases/00120/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * multiply(S3, S4); + +k1 @Const 'k1' { } = 1.7; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00120/l3v2/index.heta b/latest/cases/00120/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00120/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00120/l3v2/json/output.json b/latest/cases/00120/l3v2/json/output.json new file mode 100644 index 000000000..7e4a5f430 --- /dev/null +++ b/latest/cases/00120/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * multiply(S3, S4)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00120/model-sbml-l2v5.xml b/latest/cases/00120/model-sbml-l2v5.xml new file mode 100644 index 000000000..9492a906f --- /dev/null +++ b/latest/cases/00120/model-sbml-l2v5.xml @@ -0,0 +1,85 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + + multiply + S3 + S4 + + + + + + + + diff --git a/latest/cases/00120/model-sbml-l3v2.xml b/latest/cases/00120/model-sbml-l3v2.xml new file mode 100644 index 000000000..7358b59da --- /dev/null +++ b/latest/cases/00120/model-sbml-l3v2.xml @@ -0,0 +1,102 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + + multiply + S3 + S4 + + + + + + + + diff --git a/latest/cases/00120/output.heta b/latest/cases/00120/output.heta new file mode 100644 index 000000000..555216b38 --- /dev/null +++ b/latest/cases/00120/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reactions using functionDefinitions with four species in a compartment + where the one species is constant. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S4 is labeled as constant and therefore does not vary. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * multiply(S3,S4) * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Initial amount of S4 |$ 1.5$ |mole | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * multiply(S3, S4); + +k1 @Const 'k1' { } = 1.7; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00120/synopsis.txt b/latest/cases/00120/synopsis.txt new file mode 100644 index 000000000..9c8f51009 --- /dev/null +++ b/latest/cases/00120/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic reactions using functionDefinitions with four species in a compartment + where the one species is constant. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S4 is labeled as constant and therefore does not vary. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * multiply(S3,S4) * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Initial amount of S4 |$ 1.5$ |mole | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00121/l2v5/heta-code/output.heta b/latest/cases/00121/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ab3344134 --- /dev/null +++ b/latest/cases/00121/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: substance/volume, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Record 'k1' { } .= 1.3e+6; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00121/l2v5/index.heta b/latest/cases/00121/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00121/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00121/l2v5/json/output.json b/latest/cases/00121/l2v5/json/output.json new file mode 100644 index 000000000..c3d056e8a --- /dev/null +++ b/latest/cases/00121/l2v5/json/output.json @@ -0,0 +1,175 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.3e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00121/l3v2/heta-code/output.heta b/latest/cases/00121/l3v2/heta-code/output.heta new file mode 100644 index 000000000..834e7f46a --- /dev/null +++ b/latest/cases/00121/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00121/l3v2/index.heta b/latest/cases/00121/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00121/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00121/l3v2/json/output.json b/latest/cases/00121/l3v2/json/output.json new file mode 100644 index 000000000..aad40e4c0 --- /dev/null +++ b/latest/cases/00121/l3v2/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1300000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00121/model-sbml-l2v5.xml b/latest/cases/00121/model-sbml-l2v5.xml new file mode 100644 index 000000000..7b80d6bc0 --- /dev/null +++ b/latest/cases/00121/model-sbml-l2v5.xml @@ -0,0 +1,93 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00121/model-sbml-l3v2.xml b/latest/cases/00121/model-sbml-l3v2.xml new file mode 100644 index 000000000..7440bc7a9 --- /dev/null +++ b/latest/cases/00121/model-sbml-l3v2.xml @@ -0,0 +1,110 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00121/output.heta b/latest/cases/00121/output.heta new file mode 100644 index 000000000..913bb0049 --- /dev/null +++ b/latest/cases/00121/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic reactions with functionDefinitions with five species + in a compartment where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Species S5 is labeled as constant and therefore does not vary. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * multiply(S1,S2) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00121/synopsis.txt b/latest/cases/00121/synopsis.txt new file mode 100644 index 000000000..1ac6e87b3 --- /dev/null +++ b/latest/cases/00121/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic reactions with functionDefinitions with five species + in a compartment where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Species S5 is labeled as constant and therefore does not vary. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * multiply(S1,S2) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00122/l2v5/heta-code/output.heta b/latest/cases/00122/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2b237cd0c --- /dev/null +++ b/latest/cases/00122/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := add(k2, k3); + +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.2; +k3 @Record 'k3' { } .= 0.3; + diff --git a/latest/cases/00122/l2v5/index.heta b/latest/cases/00122/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00122/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00122/l2v5/json/output.json b/latest/cases/00122/l2v5/json/output.json new file mode 100644 index 000000000..ea8512140 --- /dev/null +++ b/latest/cases/00122/l2v5/json/output.json @@ -0,0 +1,128 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.3" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00122/l3v2/heta-code/output.heta b/latest/cases/00122/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2aaf9443c --- /dev/null +++ b/latest/cases/00122/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := add(k2, k3); + +k1 @Record 'k1' { } .= 1; + +k2 @Const 'k2' { } = 0.2; +k3 @Const 'k3' { } = 0.3; + diff --git a/latest/cases/00122/l3v2/index.heta b/latest/cases/00122/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00122/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00122/l3v2/json/output.json b/latest/cases/00122/l3v2/json/output.json new file mode 100644 index 000000000..df14f754b --- /dev/null +++ b/latest/cases/00122/l3v2/json/output.json @@ -0,0 +1,100 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.2 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.3 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00122/model-sbml-l2v5.xml b/latest/cases/00122/model-sbml-l2v5.xml new file mode 100644 index 000000000..4af0dcef9 --- /dev/null +++ b/latest/cases/00122/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + add + k2 + k3 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00122/model-sbml-l3v2.xml b/latest/cases/00122/model-sbml-l3v2.xml new file mode 100644 index 000000000..62da79488 --- /dev/null +++ b/latest/cases/00122/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + add + k2 + k3 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00122/output.heta b/latest/cases/00122/output.heta new file mode 100644 index 000000000..acc7e0303 --- /dev/null +++ b/latest/cases/00122/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species called S1 and S2; two constant parameters called k2 and k3 and one +varying parameters called k1. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0.2$ |second^-1^ | +|Value of parameter k3 |$ 0.3$ |lsecond^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := add(k2, k3); + +k1 @Record 'k1' { } .= 1; + +k2 @Const 'k2' { } = 0.2; +k3 @Const 'k3' { } = 0.3; + diff --git a/latest/cases/00122/synopsis.txt b/latest/cases/00122/synopsis.txt new file mode 100644 index 000000000..f8a8739aa --- /dev/null +++ b/latest/cases/00122/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species called S1 and S2; two constant parameters called k2 and k3 and one +varying parameters called k1. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0.2$ |second^-1^ | +|Value of parameter k3 |$ 0.3$ |lsecond^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00123/l2v5/heta-code/output.heta b/latest/cases/00123/l2v5/heta-code/output.heta new file mode 100644 index 000000000..dea065ae4 --- /dev/null +++ b/latest/cases/00123/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 5e-7 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2, k3); + +k1 @Record 'k1' { } .= 1e+6; +k2 @Record 'k2' { } .= 3e+5; +k3 @Record 'k3' { } .= 7e+5; +p1 @Record 'p1' { } .= 1; + diff --git a/latest/cases/00123/l2v5/index.heta b/latest/cases/00123/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00123/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00123/l2v5/json/output.json b/latest/cases/00123/l2v5/json/output.json new file mode 100644 index 000000000..5e8a84146 --- /dev/null +++ b/latest/cases/00123/l2v5/json/output.json @@ -0,0 +1,191 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "3e+5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "7e+5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00123/l3v2/heta-code/output.heta b/latest/cases/00123/l3v2/heta-code/output.heta new file mode 100644 index 000000000..610b749d8 --- /dev/null +++ b/latest/cases/00123/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 5e-7 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2, k3); + +k1 @Record 'k1' { } .= 1e+6; + +k2 @Const 'k2' { } = 300000; +k3 @Const 'k3' { } = 700000; +p1 @Const 'p1' { } = 1; + diff --git a/latest/cases/00123/l3v2/index.heta b/latest/cases/00123/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00123/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00123/l3v2/json/output.json b/latest/cases/00123/l3v2/json/output.json new file mode 100644 index 000000000..43fd381bc --- /dev/null +++ b/latest/cases/00123/l3v2/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1e+6" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 300000 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 700000 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00123/model-sbml-l2v5.xml b/latest/cases/00123/model-sbml-l2v5.xml new file mode 100644 index 000000000..ce83f9e51 --- /dev/null +++ b/latest/cases/00123/model-sbml-l2v5.xml @@ -0,0 +1,98 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + k2 + k3 + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00123/model-sbml-l3v2.xml b/latest/cases/00123/model-sbml-l3v2.xml new file mode 100644 index 000000000..f55f71c21 --- /dev/null +++ b/latest/cases/00123/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + k2 + k3 + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00123/output.heta b/latest/cases/00123/output.heta new file mode 100644 index 000000000..a383dc092 --- /dev/null +++ b/latest/cases/00123/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species called S1, S2, S3 and S4; three constant parameters called k2, k3 and +p1 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3) * p1$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k3 |$ 0.7 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 5e-7 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2, k3); + +k1 @Record 'k1' { } .= 1e+6; + +k2 @Const 'k2' { } = 300000; +k3 @Const 'k3' { } = 700000; +p1 @Const 'p1' { } = 1; + diff --git a/latest/cases/00123/synopsis.txt b/latest/cases/00123/synopsis.txt new file mode 100644 index 000000000..c642582c0 --- /dev/null +++ b/latest/cases/00123/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species called S1, S2, S3 and S4; three constant parameters called k2, k3 and +p1 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3) * p1$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k3 |$ 0.7 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00124/l2v5/heta-code/output.heta b/latest/cases/00124/l2v5/heta-code/output.heta new file mode 100644 index 000000000..179b6cb17 --- /dev/null +++ b/latest/cases/00124/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2 * p2, k3); + +k1 @Record 'k1' { } .= 1.7; +k2 @Record 'k2' { } .= 0.3; +k3 @Record 'k3' { } .= -0.1; +p1 @Record 'p1' { } .= 1; +p2 @Record 'p2' { } .= 1; + diff --git a/latest/cases/00124/l2v5/index.heta b/latest/cases/00124/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00124/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00124/l2v5/json/output.json b/latest/cases/00124/l2v5/json/output.json new file mode 100644 index 000000000..dd5cd9953 --- /dev/null +++ b/latest/cases/00124/l2v5/json/output.json @@ -0,0 +1,181 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "-0.1" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2 * p2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00124/l3v2/heta-code/output.heta b/latest/cases/00124/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f3b83d100 --- /dev/null +++ b/latest/cases/00124/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2 * p2, k3); + +k1 @Record 'k1' { } .= 1.7; + +k2 @Const 'k2' { } = 0.3; +k3 @Const 'k3' { } = -0.1; +p1 @Const 'p1' { } = 1; +p2 @Const 'p2' { } = 1; + diff --git a/latest/cases/00124/l3v2/index.heta b/latest/cases/00124/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00124/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00124/l3v2/json/output.json b/latest/cases/00124/l3v2/json/output.json new file mode 100644 index 000000000..06b836ef4 --- /dev/null +++ b/latest/cases/00124/l3v2/json/output.json @@ -0,0 +1,149 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": -0.1 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 1 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2 * p2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00124/model-sbml-l2v5.xml b/latest/cases/00124/model-sbml-l2v5.xml new file mode 100644 index 000000000..d56bd45f4 --- /dev/null +++ b/latest/cases/00124/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + + + k2 + p2 + + k3 + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00124/model-sbml-l3v2.xml b/latest/cases/00124/model-sbml-l3v2.xml new file mode 100644 index 000000000..4bebf128f --- /dev/null +++ b/latest/cases/00124/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + + + k2 + p2 + + k3 + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00124/output.heta b/latest/cases/00124/output.heta new file mode 100644 index 000000000..65b0270ed --- /dev/null +++ b/latest/cases/00124/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species called S1, S2 and S3; four constant parameters called k2, k3, p1 and +p2 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $p1* add(p2 * k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter k3 |$ -0.1$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Value of parameter p2 |$ 1$ |litre mole^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2 * p2, k3); + +k1 @Record 'k1' { } .= 1.7; + +k2 @Const 'k2' { } = 0.3; +k3 @Const 'k3' { } = -0.1; +p1 @Const 'p1' { } = 1; +p2 @Const 'p2' { } = 1; + diff --git a/latest/cases/00124/synopsis.txt b/latest/cases/00124/synopsis.txt new file mode 100644 index 000000000..afb9411d3 --- /dev/null +++ b/latest/cases/00124/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species called S1, S2 and S3; four constant parameters called k2, k3, p1 and +p2 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $p1* add(p2 * k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter k3 |$ -0.1$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Value of parameter p2 |$ 1$ |litre mole^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00125/l2v5/heta-code/output.heta b/latest/cases/00125/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5eea00b3c --- /dev/null +++ b/latest/cases/00125/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00125/l2v5/index.heta b/latest/cases/00125/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00125/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00125/l2v5/json/output.json b/latest/cases/00125/l2v5/json/output.json new file mode 100644 index 000000000..9d46c4401 --- /dev/null +++ b/latest/cases/00125/l2v5/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00125/l3v2/heta-code/output.heta b/latest/cases/00125/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b903bb682 --- /dev/null +++ b/latest/cases/00125/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00125/l3v2/index.heta b/latest/cases/00125/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00125/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00125/l3v2/json/output.json b/latest/cases/00125/l3v2/json/output.json new file mode 100644 index 000000000..4a951bfc4 --- /dev/null +++ b/latest/cases/00125/l3v2/json/output.json @@ -0,0 +1,70 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00125/model-sbml-l2v5.xml b/latest/cases/00125/model-sbml-l2v5.xml new file mode 100644 index 000000000..676284458 --- /dev/null +++ b/latest/cases/00125/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00125/model-sbml-l3v2.xml b/latest/cases/00125/model-sbml-l3v2.xml new file mode 100644 index 000000000..cbf43f134 --- /dev/null +++ b/latest/cases/00125/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00125/output.heta b/latest/cases/00125/output.heta new file mode 100644 index 000000000..0e92c5d3c --- /dev/null +++ b/latest/cases/00125/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic single reaction using functionDefinitions involving species + with a non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $multiply(k1,S1) * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00125/synopsis.txt b/latest/cases/00125/synopsis.txt new file mode 100644 index 000000000..c82efa25e --- /dev/null +++ b/latest/cases/00125/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic single reaction using functionDefinitions involving species + with a non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $multiply(k1,S1) * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00126/l2v5/heta-code/output.heta b/latest/cases/00126/l2v5/heta-code/output.heta new file mode 100644 index 000000000..10550109f --- /dev/null +++ b/latest/cases/00126/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * pow(S2, 2); + +k1 @Record 'k1' { } .= 0.35; +k2 @Record 'k2' { } .= 180; + diff --git a/latest/cases/00126/l2v5/index.heta b/latest/cases/00126/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00126/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00126/l2v5/json/output.json b/latest/cases/00126/l2v5/json/output.json new file mode 100644 index 000000000..98a7d7350 --- /dev/null +++ b/latest/cases/00126/l2v5/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * pow(S2, 2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.35" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "180" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00126/l3v2/heta-code/output.heta b/latest/cases/00126/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4b9aad7a1 --- /dev/null +++ b/latest/cases/00126/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * pow(S2, 2); + +k1 @Const 'k1' { } = 0.35; +k2 @Const 'k2' { } = 180; + diff --git a/latest/cases/00126/l3v2/index.heta b/latest/cases/00126/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00126/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00126/l3v2/json/output.json b/latest/cases/00126/l3v2/json/output.json new file mode 100644 index 000000000..9ff3fae0a --- /dev/null +++ b/latest/cases/00126/l3v2/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * pow(S2, 2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.35 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 180 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00126/model-sbml-l2v5.xml b/latest/cases/00126/model-sbml-l2v5.xml new file mode 100644 index 000000000..e5576343b --- /dev/null +++ b/latest/cases/00126/model-sbml-l2v5.xml @@ -0,0 +1,80 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment + k2 + + + S2 + 2 + + + + + + + + diff --git a/latest/cases/00126/model-sbml-l3v2.xml b/latest/cases/00126/model-sbml-l3v2.xml new file mode 100644 index 000000000..165455f09 --- /dev/null +++ b/latest/cases/00126/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + compartment + k2 + + + S2 + 2 + + + + + + + + diff --git a/latest/cases/00126/output.heta b/latest/cases/00126/output.heta new file mode 100644 index 000000000..471e94926 --- /dev/null +++ b/latest/cases/00126/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions using functionDefinitions involving species in one +compartment, with non-unity stoichiometries. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $multiply(k1,S1) * compartment$ | +| 2 S2 -> S1 | $k2 * S2 * S2 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.35$ |second^-1^ | +|Value of parameter k2 |$ 180$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * pow(S2, 2); + +k1 @Const 'k1' { } = 0.35; +k2 @Const 'k2' { } = 180; + diff --git a/latest/cases/00126/synopsis.txt b/latest/cases/00126/synopsis.txt new file mode 100644 index 000000000..bd7579a35 --- /dev/null +++ b/latest/cases/00126/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions using functionDefinitions involving species in one +compartment, with non-unity stoichiometries. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $multiply(k1,S1) * compartment$ | +| 2 S2 -> S1 | $k2 * S2 * S2 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.35$ |second^-1^ | +|Value of parameter k2 |$ 180$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00127/l2v5/heta-code/output.heta b/latest/cases/00127/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c2f5a3771 --- /dev/null +++ b/latest/cases/00127/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * S1 * S2 * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1000; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00127/l2v5/index.heta b/latest/cases/00127/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00127/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00127/l2v5/json/output.json b/latest/cases/00127/l2v5/json/output.json new file mode 100644 index 000000000..eadfe9005 --- /dev/null +++ b/latest/cases/00127/l2v5/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * S1 * S2 * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1000" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00127/l3v2/heta-code/output.heta b/latest/cases/00127/l3v2/heta-code/output.heta new file mode 100644 index 000000000..03cb26702 --- /dev/null +++ b/latest/cases/00127/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * S1 * S2 * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 1000; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00127/l3v2/index.heta b/latest/cases/00127/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00127/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00127/l3v2/json/output.json b/latest/cases/00127/l3v2/json/output.json new file mode 100644 index 000000000..b14e020a3 --- /dev/null +++ b/latest/cases/00127/l3v2/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * S1 * S2 * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00127/model-sbml-l2v5.xml b/latest/cases/00127/model-sbml-l2v5.xml new file mode 100644 index 000000000..8953d6b4e --- /dev/null +++ b/latest/cases/00127/model-sbml-l2v5.xml @@ -0,0 +1,81 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + S1 + S2 + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00127/model-sbml-l3v2.xml b/latest/cases/00127/model-sbml-l3v2.xml new file mode 100644 index 000000000..7f74ececa --- /dev/null +++ b/latest/cases/00127/model-sbml-l3v2.xml @@ -0,0 +1,98 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + S1 + S2 + + multiply + k1 + S1 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00127/output.heta b/latest/cases/00127/output.heta new file mode 100644 index 000000000..d1236d1da --- /dev/null +++ b/latest/cases/00127/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions using functionDefinitions with three species + in one compartment, with one species having a stoichiometry of 2. +componentTags: Compartment, Parameter, Reaction, Species, FunctionDefinition +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $multiply(k1,S1) * S1 * S2 * compartment$ | +| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.0 \x 10^3$ |litre^2^ mole^-2^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * S1 * S2 * multiply(k1, S1); +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 1000; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00127/synopsis.txt b/latest/cases/00127/synopsis.txt new file mode 100644 index 000000000..b95960e2e --- /dev/null +++ b/latest/cases/00127/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions using functionDefinitions with three species + in one compartment, with one species having a stoichiometry of 2. +componentTags: Compartment, Parameter, Reaction, Species, FunctionDefinition +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $multiply(k1,S1) * S1 * S2 * compartment$ | +| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.0 \x 10^3$ |litre^2^ mole^-2^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00128/l2v5/heta-code/output.heta b/latest/cases/00128/l2v5/heta-code/output.heta new file mode 100644 index 000000000..036ba447b --- /dev/null +++ b/latest/cases/00128/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.002 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 750; +k2 @Record 'k2' { } .= 250; + diff --git a/latest/cases/00128/l2v5/index.heta b/latest/cases/00128/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00128/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00128/l2v5/json/output.json b/latest/cases/00128/l2v5/json/output.json new file mode 100644 index 000000000..6f5ac8acf --- /dev/null +++ b/latest/cases/00128/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "750" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "250" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00128/l3v2/heta-code/output.heta b/latest/cases/00128/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2813bfb62 --- /dev/null +++ b/latest/cases/00128/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00128/l3v2/index.heta b/latest/cases/00128/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00128/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00128/l3v2/json/output.json b/latest/cases/00128/l3v2/json/output.json new file mode 100644 index 000000000..ae23ab245 --- /dev/null +++ b/latest/cases/00128/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 250 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00128/model-sbml-l2v5.xml b/latest/cases/00128/model-sbml-l2v5.xml new file mode 100644 index 000000000..f5f45c050 --- /dev/null +++ b/latest/cases/00128/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00128/model-sbml-l3v2.xml b/latest/cases/00128/model-sbml-l3v2.xml new file mode 100644 index 000000000..885dfd8f1 --- /dev/null +++ b/latest/cases/00128/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00128/output.heta b/latest/cases/00128/output.heta new file mode 100644 index 000000000..38540a735 --- /dev/null +++ b/latest/cases/00128/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions using functionDefinitions with four species in one compartment, + with non-unity stoichiometry +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * multiply(S1,S2) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := compartment * k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00128/synopsis.txt b/latest/cases/00128/synopsis.txt new file mode 100644 index 000000000..643ca8d91 --- /dev/null +++ b/latest/cases/00128/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions using functionDefinitions with four species in one compartment, + with non-unity stoichiometry +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * multiply(S1,S2) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00129/l2v5/build.log b/latest/cases/00129/l2v5/build.log new file mode 100644 index 000000000..a81ea81ce --- /dev/null +++ b/latest/cases/00129/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00129/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00129/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00129/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00129/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00129/l2v5/index.heta b/latest/cases/00129/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00129/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00129/l3v2/index.heta b/latest/cases/00129/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00129/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00129/model-sbml-l2v5.xml b/latest/cases/00129/model-sbml-l2v5.xml new file mode 100644 index 000000000..78693ec26 --- /dev/null +++ b/latest/cases/00129/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + 2 + p1 + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00129/synopsis.txt b/latest/cases/00129/synopsis.txt new file mode 100644 index 000000000..6f8a989f5 --- /dev/null +++ b/latest/cases/00129/synopsis.txt @@ -0,0 +1,41 @@ +category: Test +synopsis: Basic single forward reaction involving two species and a + stoichiometryMath element that uses a functionDefinition. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and p1. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> multiply(2, p1)S2 | $k1 * S1 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Value of parameter p1 |$ 1$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00130/l2v5/build.log b/latest/cases/00130/l2v5/build.log new file mode 100644 index 000000000..2ea40de1a --- /dev/null +++ b/latest/cases/00130/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00130/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00130/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00130/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00130/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00130/l2v5/index.heta b/latest/cases/00130/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00130/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00130/l3v2/index.heta b/latest/cases/00130/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00130/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00130/model-sbml-l2v5.xml b/latest/cases/00130/model-sbml-l2v5.xml new file mode 100644 index 000000000..2386601b0 --- /dev/null +++ b/latest/cases/00130/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + multiply + 2 + p1 + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00130/synopsis.txt b/latest/cases/00130/synopsis.txt new file mode 100644 index 000000000..bb05417b7 --- /dev/null +++ b/latest/cases/00130/synopsis.txt @@ -0,0 +1,88 @@ + + + +category: Test + +synopsis: Basic reactions with three species in a compartment + + involving a stoichiometryMath element that uses a functionDefinition. + +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, FunctionDefinition + +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry + +testType: TimeCourse + +levels: 2.1, 2.2, 2.3, 2.4, 2.5 + +generatedBy: Numeric + + + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + + +The model contains one compartment called "compartment". There are three + +species named S1, S2 and S3 and three parameters named k1, k2 and p1. The + +model contains two reactions defined as: + + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | + +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | + +| multiply(2, p1)S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + + + + + +The model contains one functionDefinition defined as: + + + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + + | multiply | x, y | $x * y$ |] + + + + + +The initial conditions are as follows: + + + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | + +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | + +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | + +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | + +|Value of parameter k1 |$ 1.7 \x 10^2$ |litre mole^-1^ second^-1^ | + +|Value of parameter k2 |$ 0.3$ |second^-1^ | + +|Value of parameter p1 |$ 1$ |dimensionless | + +|Volume of compartment "compartment" |$ 1$ |litre |] + + + +The species values are given as amounts of substance to make it easier to + +use the model in a discrete stochastic simulator, but (as per usual SBML + +principles) their symbols represent their values in concentration units + +where they appear in expressions. + + + diff --git a/latest/cases/00131/l2v5/build.log b/latest/cases/00131/l2v5/build.log new file mode 100644 index 000000000..4830e24b4 --- /dev/null +++ b/latest/cases/00131/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00131/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00131/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00131/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00131/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00131/l2v5/index.heta b/latest/cases/00131/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00131/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00131/l3v2/index.heta b/latest/cases/00131/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00131/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00131/model-sbml-l2v5.xml b/latest/cases/00131/model-sbml-l2v5.xml new file mode 100644 index 000000000..3221da530 --- /dev/null +++ b/latest/cases/00131/model-sbml-l2v5.xml @@ -0,0 +1,98 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + multiply + p1 + 2 + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00131/synopsis.txt b/latest/cases/00131/synopsis.txt new file mode 100644 index 000000000..719652e4f --- /dev/null +++ b/latest/cases/00131/synopsis.txt @@ -0,0 +1,44 @@ +category: Test +synopsis: Basic reactions with three species in a compartment + involving a stoichiometryMath element that uses a functionDefinition. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and three parameters named k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> (2 * p1)S1 + multiply(p1, 1 / 0.5)S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.7 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter p1 |$ 1$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00132/l2v5/heta-code/output.heta b/latest/cases/00132/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bdd245f66 --- /dev/null +++ b/latest/cases/00132/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.003 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k__reaction1_local, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment * k__reaction2_local * S2; + +k__reaction1_local @Const { } = 1; +k__reaction2_local @Const { } = 2; + diff --git a/latest/cases/00132/l2v5/index.heta b/latest/cases/00132/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00132/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00132/l2v5/json/output.json b/latest/cases/00132/l2v5/json/output.json new file mode 100644 index 000000000..01db0fc66 --- /dev/null +++ b/latest/cases/00132/l2v5/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.003 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k__reaction1_local, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k__reaction2_local * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00132/l3v2/heta-code/output.heta b/latest/cases/00132/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b5c6fb738 --- /dev/null +++ b/latest/cases/00132/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.003 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k__reaction1_local, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment * k__reaction2_local * S2; + +k__reaction1_local @Const { } = 1; +k__reaction2_local @Const { } = 2; + diff --git a/latest/cases/00132/l3v2/index.heta b/latest/cases/00132/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00132/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00132/l3v2/json/output.json b/latest/cases/00132/l3v2/json/output.json new file mode 100644 index 000000000..f1707c740 --- /dev/null +++ b/latest/cases/00132/l3v2/json/output.json @@ -0,0 +1,103 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.003 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k__reaction1_local, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k__reaction2_local * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00132/model-sbml-l2v5.xml b/latest/cases/00132/model-sbml-l2v5.xml new file mode 100644 index 000000000..9c8ad7110 --- /dev/null +++ b/latest/cases/00132/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k + S1 + + + + + + + + + + + + + + + + + + + + compartment + k + S2 + + + + + + + + + + diff --git a/latest/cases/00132/model-sbml-l3v2.xml b/latest/cases/00132/model-sbml-l3v2.xml new file mode 100644 index 000000000..7c51c0fe1 --- /dev/null +++ b/latest/cases/00132/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k + S1 + + + + + + + + + + + + + + + + + + + + compartment + k + S2 + + + + + + + + + + diff --git a/latest/cases/00132/output.heta b/latest/cases/00132/output.heta new file mode 100644 index 000000000..3af0e0e14 --- /dev/null +++ b/latest/cases/00132/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions using functionDefinitions with three species + and parameters local to reactions. +componentTags: Compartment, Species, Reaction, FunctionDefinition +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k,S1) * compartment,$ | +| S2 -> S3 | $k * S2 * compartment,$ |] + +Reaction S1 -> S2 defines one local parameter k. Reaction S2 -> S3 defines +another (different) local parameter k. + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$3.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of local parameter k |$ 1$ |second^-1^ | +|Value of local parameter k |$ 2$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.003 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k__reaction1_local, S1); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment * k__reaction2_local * S2; + +k__reaction1_local @Const { } = 1; +k__reaction2_local @Const { } = 2; + diff --git a/latest/cases/00132/synopsis.txt b/latest/cases/00132/synopsis.txt new file mode 100644 index 000000000..c529d57ff --- /dev/null +++ b/latest/cases/00132/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions using functionDefinitions with three species + and parameters local to reactions. +componentTags: Compartment, Species, Reaction, FunctionDefinition +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k,S1) * compartment,$ | +| S2 -> S3 | $k * S2 * compartment,$ |] + +Reaction S1 -> S2 defines one local parameter k. Reaction S2 -> S3 defines +another (different) local parameter k. + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$3.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of local parameter k |$ 1$ |second^-1^ | +|Value of local parameter k |$ 2$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00133/l2v5/heta-code/output.heta b/latest/cases/00133/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f7af8127c --- /dev/null +++ b/latest/cases/00133/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.003 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment * multiply(k__reaction2_local, S2); + +k @Record 'k' { } .= 1; + +k__reaction2_local @Const { } = 2; + diff --git a/latest/cases/00133/l2v5/index.heta b/latest/cases/00133/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00133/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00133/l2v5/json/output.json b/latest/cases/00133/l2v5/json/output.json new file mode 100644 index 000000000..d3696f9e3 --- /dev/null +++ b/latest/cases/00133/l2v5/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.003 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * multiply(k__reaction2_local, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00133/l3v2/heta-code/output.heta b/latest/cases/00133/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f3f12583b --- /dev/null +++ b/latest/cases/00133/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.003 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment * multiply(k__reaction2_local, S2); + +k__reaction2_local @Const { } = 2; +k @Const 'k' { } = 1; + diff --git a/latest/cases/00133/l3v2/index.heta b/latest/cases/00133/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00133/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00133/l3v2/json/output.json b/latest/cases/00133/l3v2/json/output.json new file mode 100644 index 000000000..7ca966bce --- /dev/null +++ b/latest/cases/00133/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.003 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * multiply(k__reaction2_local, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 1 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00133/model-sbml-l2v5.xml b/latest/cases/00133/model-sbml-l2v5.xml new file mode 100644 index 000000000..8157bd15e --- /dev/null +++ b/latest/cases/00133/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k + S1 + + + + + + + + + + + + + + + + compartment + + multiply + k + S2 + + + + + + + + + + + diff --git a/latest/cases/00133/model-sbml-l3v2.xml b/latest/cases/00133/model-sbml-l3v2.xml new file mode 100644 index 000000000..6f7804092 --- /dev/null +++ b/latest/cases/00133/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k + S1 + + + + + + + + + + + + + + + + compartment + + multiply + k + S2 + + + + + + + + + + + diff --git a/latest/cases/00133/output.heta b/latest/cases/00133/output.heta new file mode 100644 index 000000000..fb2006d69 --- /dev/null +++ b/latest/cases/00133/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic two reactions using functionDefinitions with three species + and parameters local to reactions. +componentTags: Compartment, Parameter, Species, Reaction, FunctionDefinition +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * compartmen$ | +| S2 -> S3 | $multiply(k,S2) * compartment,$ |] + +Reaction S2 -> S3 defines one local parameter k. This parameter shadows the +global parameter k and thus in reaction S2 -> S3 the value of the local +parameter must be used. + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$3.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k |$ 1$ |second^-1^ | +|Value of local parameter k |$ 2$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.003 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment * multiply(k__reaction2_local, S2); + +k__reaction2_local @Const { } = 2; +k @Const 'k' { } = 1; + diff --git a/latest/cases/00133/synopsis.txt b/latest/cases/00133/synopsis.txt new file mode 100644 index 000000000..76bada718 --- /dev/null +++ b/latest/cases/00133/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions using functionDefinitions with three species + and parameters local to reactions. +componentTags: Compartment, Parameter, Species, Reaction, FunctionDefinition +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * compartmen$ | +| S2 -> S3 | $multiply(k,S2) * compartment,$ |] + +Reaction S2 -> S3 defines one local parameter k. This parameter shadows the +global parameter k and thus in reaction S2 -> S3 the value of the local +parameter must be used. + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$3.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k |$ 1$ |second^-1^ | +|Value of local parameter k |$ 2$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00134/l2v5/heta-code/output.heta b/latest/cases/00134/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b6bf45cbc --- /dev/null +++ b/latest/cases/00134/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.003 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, modifiers: [S1], reversible: false, }; +reaction2 := compartment * multiply(S1__reaction2_local, S2); + +k @Record 'k' { } .= 2; + +S1__reaction2_local @Const { } = 1; + diff --git a/latest/cases/00134/l2v5/index.heta b/latest/cases/00134/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00134/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00134/l2v5/json/output.json b/latest/cases/00134/l2v5/json/output.json new file mode 100644 index 000000000..7ac7e7afb --- /dev/null +++ b/latest/cases/00134/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.003 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "S1__reaction2_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * multiply(S1__reaction2_local, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00134/l3v2/index.heta b/latest/cases/00134/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00134/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00134/model-sbml-l2v5.xml b/latest/cases/00134/model-sbml-l2v5.xml new file mode 100644 index 000000000..84986d194 --- /dev/null +++ b/latest/cases/00134/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k + S1 + + + + + + + + + + + + + + + + + + + compartment + + multiply + S1 + S2 + + + + + + + + + + + diff --git a/latest/cases/00134/output.heta b/latest/cases/00134/output.heta new file mode 100644 index 000000000..e5009d112 --- /dev/null +++ b/latest/cases/00134/output.heta @@ -0,0 +1,71 @@ +/* +category: Test +synopsis: Basic two reactions using functionDefinitions with three species + and parameters local to reactions. +componentTags: Compartment, Species, Parameter, Reaction, FunctionDefinition +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * compartmen$ | +| S2 -> S3 | $multiply(S1,S2) * compartment,$ |] + +Reaction S2 -> S3 defines one local parameter S1. This parameter shadows +the species S1 and thus in reaction S2 -> S3 the value of the local +parameter S1 must be used. + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$3.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k |$ 2$ |second^-1^ | +|Value of local parameter S1 |$ 1$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.003 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, modifiers: [S1], reversible: false, }; +reaction2 := compartment * multiply(S1__reaction2_local, S2); + +k @Record 'k' { } .= 2; + +S1__reaction2_local @Const { } = 1; + diff --git a/latest/cases/00134/synopsis.txt b/latest/cases/00134/synopsis.txt new file mode 100644 index 000000000..a6438c9ca --- /dev/null +++ b/latest/cases/00134/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions using functionDefinitions with three species + and parameters local to reactions. +componentTags: Compartment, Species, Parameter, Reaction, FunctionDefinition +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * compartmen$ | +| S2 -> S3 | $multiply(S1,S2) * compartment,$ |] + +Reaction S2 -> S3 defines one local parameter S1. This parameter shadows +the species S1 and thus in reaction S2 -> S3 the value of the local +parameter S1 must be used. + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$3.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k |$ 2$ |second^-1^ | +|Value of local parameter S1 |$ 1$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00135/l2v5/heta-code/output.heta b/latest/cases/00135/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ec77ec251 --- /dev/null +++ b/latest/cases/00135/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= k1 * S2; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00135/l2v5/index.heta b/latest/cases/00135/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00135/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00135/l2v5/json/output.json b/latest/cases/00135/l2v5/json/output.json new file mode 100644 index 000000000..631347e29 --- /dev/null +++ b/latest/cases/00135/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00135/l3v2/heta-code/output.heta b/latest/cases/00135/l3v2/heta-code/output.heta new file mode 100644 index 000000000..60f8580f8 --- /dev/null +++ b/latest/cases/00135/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00135/l3v2/index.heta b/latest/cases/00135/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00135/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00135/l3v2/json/output.json b/latest/cases/00135/l3v2/json/output.json new file mode 100644 index 000000000..e0347ae13 --- /dev/null +++ b/latest/cases/00135/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00135/model-sbml-l2v5.xml b/latest/cases/00135/model-sbml-l2v5.xml new file mode 100644 index 000000000..d209b9c63 --- /dev/null +++ b/latest/cases/00135/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00135/model-sbml-l3v2.xml b/latest/cases/00135/model-sbml-l3v2.xml new file mode 100644 index 000000000..8d6d95abd --- /dev/null +++ b/latest/cases/00135/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00135/output.heta b/latest/cases/00135/output.heta new file mode 100644 index 000000000..5b9833341 --- /dev/null +++ b/latest/cases/00135/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.125 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00135/synopsis.txt b/latest/cases/00135/synopsis.txt new file mode 100644 index 000000000..decefa461 --- /dev/null +++ b/latest/cases/00135/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.125 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00136/l2v5/heta-code/output.heta b/latest/cases/00136/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cbdfa402b --- /dev/null +++ b/latest/cases/00136/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= k2 / 100; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00136/l2v5/index.heta b/latest/cases/00136/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00136/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00136/l2v5/json/output.json b/latest/cases/00136/l2v5/json/output.json new file mode 100644 index 000000000..a0e0521a3 --- /dev/null +++ b/latest/cases/00136/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "k2 / 100" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00136/l3v2/heta-code/output.heta b/latest/cases/00136/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2d840cd4d --- /dev/null +++ b/latest/cases/00136/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00136/l3v2/index.heta b/latest/cases/00136/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00136/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00136/l3v2/json/output.json b/latest/cases/00136/l3v2/json/output.json new file mode 100644 index 000000000..88f85e373 --- /dev/null +++ b/latest/cases/00136/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00136/model-sbml-l2v5.xml b/latest/cases/00136/model-sbml-l2v5.xml new file mode 100644 index 000000000..4a567ca72 --- /dev/null +++ b/latest/cases/00136/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k2 + 100 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00136/model-sbml-l3v2.xml b/latest/cases/00136/model-sbml-l3v2.xml new file mode 100644 index 000000000..230a1ef3f --- /dev/null +++ b/latest/cases/00136/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + 100 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00136/output.heta b/latest/cases/00136/output.heta new file mode 100644 index 000000000..6464cf573 --- /dev/null +++ b/latest/cases/00136/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: InitialAssignments override any declared initial values. In this +case the value calculated by the initialAssignment is consistent with the +value declared. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00136/synopsis.txt b/latest/cases/00136/synopsis.txt new file mode 100644 index 000000000..9a71a19af --- /dev/null +++ b/latest/cases/00136/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: InitialAssignments override any declared initial values. In this +case the value calculated by the initialAssignment is consistent with the +value declared. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00137/l2v5/heta-code/output.heta b/latest/cases/00137/l2v5/heta-code/output.heta new file mode 100644 index 000000000..28da1e810 --- /dev/null +++ b/latest/cases/00137/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00137/l2v5/index.heta b/latest/cases/00137/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00137/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00137/l2v5/json/output.json b/latest/cases/00137/l2v5/json/output.json new file mode 100644 index 000000000..2135eee9b --- /dev/null +++ b/latest/cases/00137/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00137/l3v2/heta-code/output.heta b/latest/cases/00137/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5912a76b4 --- /dev/null +++ b/latest/cases/00137/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00137/l3v2/index.heta b/latest/cases/00137/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00137/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00137/l3v2/json/output.json b/latest/cases/00137/l3v2/json/output.json new file mode 100644 index 000000000..f73e1b9da --- /dev/null +++ b/latest/cases/00137/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00137/model-sbml-l2v5.xml b/latest/cases/00137/model-sbml-l2v5.xml new file mode 100644 index 000000000..0d75c0c98 --- /dev/null +++ b/latest/cases/00137/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00137/model-sbml-l3v2.xml b/latest/cases/00137/model-sbml-l3v2.xml new file mode 100644 index 000000000..c043b184e --- /dev/null +++ b/latest/cases/00137/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00137/output.heta b/latest/cases/00137/output.heta new file mode 100644 index 000000000..6c4b9edb0 --- /dev/null +++ b/latest/cases/00137/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00137/synopsis.txt b/latest/cases/00137/synopsis.txt new file mode 100644 index 000000000..bd04afed8 --- /dev/null +++ b/latest/cases/00137/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00138/l2v5/heta-code/output.heta b/latest/cases/00138/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0ce587696 --- /dev/null +++ b/latest/cases/00138/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1.125e-15 / compartment; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00138/l2v5/index.heta b/latest/cases/00138/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00138/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00138/l2v5/json/output.json b/latest/cases/00138/l2v5/json/output.json new file mode 100644 index 000000000..989108cc3 --- /dev/null +++ b/latest/cases/00138/l2v5/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.125e-15 / compartment", + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00138/l3v2/heta-code/output.heta b/latest/cases/00138/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b25fe3205 --- /dev/null +++ b/latest/cases/00138/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125e-15 / compartment; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00138/l3v2/index.heta b/latest/cases/00138/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00138/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00138/l3v2/json/output.json b/latest/cases/00138/l3v2/json/output.json new file mode 100644 index 000000000..82a7d7418 --- /dev/null +++ b/latest/cases/00138/l3v2/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.125e-15 / compartment", + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00138/model-sbml-l2v5.xml b/latest/cases/00138/model-sbml-l2v5.xml new file mode 100644 index 000000000..249b25b2f --- /dev/null +++ b/latest/cases/00138/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00138/model-sbml-l3v2.xml b/latest/cases/00138/model-sbml-l3v2.xml new file mode 100644 index 000000000..4d470eaf4 --- /dev/null +++ b/latest/cases/00138/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00138/output.heta b/latest/cases/00138/output.heta new file mode 100644 index 000000000..e1370d3f3 --- /dev/null +++ b/latest/cases/00138/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$1.125 \x 10^-15$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125e-15 / compartment; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00138/synopsis.txt b/latest/cases/00138/synopsis.txt new file mode 100644 index 000000000..bdf0e1dbd --- /dev/null +++ b/latest/cases/00138/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$1.125 \x 10^-15$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00139/l2v5/heta-code/output.heta b/latest/cases/00139/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4c3d78757 --- /dev/null +++ b/latest/cases/00139/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, } .= 1; +compartment := 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1.125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00139/l2v5/index.heta b/latest/cases/00139/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00139/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00139/l2v5/json/output.json b/latest/cases/00139/l2v5/json/output.json new file mode 100644 index 000000000..3bff4cebb --- /dev/null +++ b/latest/cases/00139/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1", + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00139/l3v2/heta-code/output.heta b/latest/cases/00139/l3v2/heta-code/output.heta new file mode 100644 index 000000000..34b61bfb4 --- /dev/null +++ b/latest/cases/00139/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 1; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00139/l3v2/index.heta b/latest/cases/00139/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00139/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00139/l3v2/json/output.json b/latest/cases/00139/l3v2/json/output.json new file mode 100644 index 000000000..d79ce96db --- /dev/null +++ b/latest/cases/00139/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1", + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00139/model-sbml-l2v5.xml b/latest/cases/00139/model-sbml-l2v5.xml new file mode 100644 index 000000000..1595efe54 --- /dev/null +++ b/latest/cases/00139/model-sbml-l2v5.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00139/model-sbml-l3v2.xml b/latest/cases/00139/model-sbml-l3v2.xml new file mode 100644 index 000000000..a7d126fbc --- /dev/null +++ b/latest/cases/00139/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00139/output.heta b/latest/cases/00139/output.heta new file mode 100644 index 000000000..f85623c1b --- /dev/null +++ b/latest/cases/00139/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $k1 / k1$ |] + +In this case the initial value declared for compartment "compartment" is +consistent with the value calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.125$ |mole | +|Value of parameter k1 |$ 0.75$ |any | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 1; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00139/synopsis.txt b/latest/cases/00139/synopsis.txt new file mode 100644 index 000000000..08cd51472 --- /dev/null +++ b/latest/cases/00139/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $k1 / k1$ |] + +In this case the initial value declared for compartment "compartment" is +consistent with the value calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.125$ |mole | +|Value of parameter k1 |$ 0.75$ |any | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00140/l2v5/heta-code/output.heta b/latest/cases/00140/l2v5/heta-code/output.heta new file mode 100644 index 000000000..15583f99b --- /dev/null +++ b/latest/cases/00140/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, } .= 5; +compartment := 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1.125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00140/l2v5/index.heta b/latest/cases/00140/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00140/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00140/l2v5/json/output.json b/latest/cases/00140/l2v5/json/output.json new file mode 100644 index 000000000..6ad9855f6 --- /dev/null +++ b/latest/cases/00140/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "5", + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00140/l3v2/heta-code/output.heta b/latest/cases/00140/l3v2/heta-code/output.heta new file mode 100644 index 000000000..25562a1a2 --- /dev/null +++ b/latest/cases/00140/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 5; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00140/l3v2/index.heta b/latest/cases/00140/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00140/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00140/l3v2/json/output.json b/latest/cases/00140/l3v2/json/output.json new file mode 100644 index 000000000..d3bfa0255 --- /dev/null +++ b/latest/cases/00140/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "5", + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00140/model-sbml-l2v5.xml b/latest/cases/00140/model-sbml-l2v5.xml new file mode 100644 index 000000000..0d4f89fd4 --- /dev/null +++ b/latest/cases/00140/model-sbml-l2v5.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00140/model-sbml-l3v2.xml b/latest/cases/00140/model-sbml-l3v2.xml new file mode 100644 index 000000000..85f79ed5a --- /dev/null +++ b/latest/cases/00140/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00140/output.heta b/latest/cases/00140/output.heta new file mode 100644 index 000000000..700527ecf --- /dev/null +++ b/latest/cases/00140/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $k1 / k1$ |] + +In this case the initial value declared for compartment "compartment" is +iconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.125$ |mole | +|Value of parameter k1 |$ 0.75$ |any | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 5; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00140/synopsis.txt b/latest/cases/00140/synopsis.txt new file mode 100644 index 000000000..ee84c91cb --- /dev/null +++ b/latest/cases/00140/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $k1 / k1$ |] + +In this case the initial value declared for compartment "compartment" is +iconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.125$ |mole | +|Value of parameter k1 |$ 0.75$ |any | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00141/l2v5/heta-code/output.heta b/latest/cases/00141/l2v5/heta-code/output.heta new file mode 100644 index 000000000..baedeeb69 --- /dev/null +++ b/latest/cases/00141/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, }; +compartment := 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1.125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00141/l2v5/index.heta b/latest/cases/00141/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00141/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00141/l2v5/json/output.json b/latest/cases/00141/l2v5/json/output.json new file mode 100644 index 000000000..3f13c1435 --- /dev/null +++ b/latest/cases/00141/l2v5/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00141/l3v2/heta-code/output.heta b/latest/cases/00141/l3v2/heta-code/output.heta new file mode 100644 index 000000000..db3c4f70c --- /dev/null +++ b/latest/cases/00141/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, }; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00141/l3v2/index.heta b/latest/cases/00141/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00141/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00141/l3v2/json/output.json b/latest/cases/00141/l3v2/json/output.json new file mode 100644 index 000000000..189b131eb --- /dev/null +++ b/latest/cases/00141/l3v2/json/output.json @@ -0,0 +1,76 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00141/model-sbml-l2v5.xml b/latest/cases/00141/model-sbml-l2v5.xml new file mode 100644 index 000000000..e69f6c39f --- /dev/null +++ b/latest/cases/00141/model-sbml-l2v5.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00141/model-sbml-l3v2.xml b/latest/cases/00141/model-sbml-l3v2.xml new file mode 100644 index 000000000..c16c7efc1 --- /dev/null +++ b/latest/cases/00141/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00141/output.heta b/latest/cases/00141/output.heta new file mode 100644 index 000000000..223961116 --- /dev/null +++ b/latest/cases/00141/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to assign value to the compartment. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $1$ |] + +In this case the initial value declared for compartment "compartment" is +consistent with the value calculated by the assignmentRule. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.125$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, }; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00141/synopsis.txt b/latest/cases/00141/synopsis.txt new file mode 100644 index 000000000..a386cbfe2 --- /dev/null +++ b/latest/cases/00141/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to assign value to the compartment. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $1$ |] + +In this case the initial value declared for compartment "compartment" is +consistent with the value calculated by the assignmentRule. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.125$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00142/l2v5/heta-code/output.heta b/latest/cases/00142/l2v5/heta-code/output.heta new file mode 100644 index 000000000..698350293 --- /dev/null +++ b/latest/cases/00142/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, } .= 1; +compartment := 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00142/l2v5/index.heta b/latest/cases/00142/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00142/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00142/l2v5/json/output.json b/latest/cases/00142/l2v5/json/output.json new file mode 100644 index 000000000..075980207 --- /dev/null +++ b/latest/cases/00142/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1", + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00142/l3v2/heta-code/output.heta b/latest/cases/00142/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1303bd82f --- /dev/null +++ b/latest/cases/00142/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 1; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00142/l3v2/index.heta b/latest/cases/00142/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00142/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00142/l3v2/json/output.json b/latest/cases/00142/l3v2/json/output.json new file mode 100644 index 000000000..bb385953d --- /dev/null +++ b/latest/cases/00142/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1", + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00142/model-sbml-l2v5.xml b/latest/cases/00142/model-sbml-l2v5.xml new file mode 100644 index 000000000..b288e21cb --- /dev/null +++ b/latest/cases/00142/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00142/model-sbml-l3v2.xml b/latest/cases/00142/model-sbml-l3v2.xml new file mode 100644 index 000000000..574b6dd61 --- /dev/null +++ b/latest/cases/00142/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00142/output.heta b/latest/cases/00142/output.heta new file mode 100644 index 000000000..93c32cc47 --- /dev/null +++ b/latest/cases/00142/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to assign value to the compartment. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $1$ |] + +In this case the initial value declared for compartment "compartment" is +consistent with the value calculated by the assignmentRule. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 1; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00142/synopsis.txt b/latest/cases/00142/synopsis.txt new file mode 100644 index 000000000..f37241765 --- /dev/null +++ b/latest/cases/00142/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to assign value to the compartment. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $1$ |] + +In this case the initial value declared for compartment "compartment" is +consistent with the value calculated by the assignmentRule. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00143/l2v5/heta-code/output.heta b/latest/cases/00143/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9e9bce3dc --- /dev/null +++ b/latest/cases/00143/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, } .= 5; +compartment := 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00143/l2v5/index.heta b/latest/cases/00143/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00143/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00143/l2v5/json/output.json b/latest/cases/00143/l2v5/json/output.json new file mode 100644 index 000000000..ed8f2883e --- /dev/null +++ b/latest/cases/00143/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "5", + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00143/l3v2/heta-code/output.heta b/latest/cases/00143/l3v2/heta-code/output.heta new file mode 100644 index 000000000..11058ef83 --- /dev/null +++ b/latest/cases/00143/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 5; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00143/l3v2/index.heta b/latest/cases/00143/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00143/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00143/l3v2/json/output.json b/latest/cases/00143/l3v2/json/output.json new file mode 100644 index 000000000..1ae86d1df --- /dev/null +++ b/latest/cases/00143/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "5", + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00143/model-sbml-l2v5.xml b/latest/cases/00143/model-sbml-l2v5.xml new file mode 100644 index 000000000..b6e5d5426 --- /dev/null +++ b/latest/cases/00143/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00143/model-sbml-l3v2.xml b/latest/cases/00143/model-sbml-l3v2.xml new file mode 100644 index 000000000..e4312347a --- /dev/null +++ b/latest/cases/00143/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00143/output.heta b/latest/cases/00143/output.heta new file mode 100644 index 000000000..468e3a21a --- /dev/null +++ b/latest/cases/00143/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to assign value to the compartment. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $1$ |] + +In this case the initial value declared for compartment "compartment" is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 5; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00143/synopsis.txt b/latest/cases/00143/synopsis.txt new file mode 100644 index 000000000..f7f22b4f8 --- /dev/null +++ b/latest/cases/00143/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to assign value to the compartment. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $1$ |] + +In this case the initial value declared for compartment "compartment" is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00144/l2v5/heta-code/output.heta b/latest/cases/00144/l2v5/heta-code/output.heta new file mode 100644 index 000000000..afca24fad --- /dev/null +++ b/latest/cases/00144/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, }; +compartment := 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00144/l2v5/index.heta b/latest/cases/00144/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00144/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00144/l2v5/json/output.json b/latest/cases/00144/l2v5/json/output.json new file mode 100644 index 000000000..8f9b109d7 --- /dev/null +++ b/latest/cases/00144/l2v5/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00144/l3v2/heta-code/output.heta b/latest/cases/00144/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0f7667d89 --- /dev/null +++ b/latest/cases/00144/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, }; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00144/l3v2/index.heta b/latest/cases/00144/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00144/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00144/l3v2/json/output.json b/latest/cases/00144/l3v2/json/output.json new file mode 100644 index 000000000..a02a1eff6 --- /dev/null +++ b/latest/cases/00144/l3v2/json/output.json @@ -0,0 +1,103 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "ode_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00144/model-sbml-l2v5.xml b/latest/cases/00144/model-sbml-l2v5.xml new file mode 100644 index 000000000..69ec43960 --- /dev/null +++ b/latest/cases/00144/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00144/model-sbml-l3v2.xml b/latest/cases/00144/model-sbml-l3v2.xml new file mode 100644 index 000000000..51f3f9e3d --- /dev/null +++ b/latest/cases/00144/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00144/output.heta b/latest/cases/00144/output.heta new file mode 100644 index 000000000..7dbb3e423 --- /dev/null +++ b/latest/cases/00144/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to assign value to the compartment. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $1$ |] + +In this case there is no initial value declared for compartment +"compartment". Thus the value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, }; +compartment := 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00144/synopsis.txt b/latest/cases/00144/synopsis.txt new file mode 100644 index 000000000..dc544d494 --- /dev/null +++ b/latest/cases/00144/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to assign value to the compartment. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to compartment "compartment": + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $1$ |] + +In this case there is no initial value declared for compartment +"compartment". Thus the value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00145/l2v5/heta-code/output.heta b/latest/cases/00145/l2v5/heta-code/output.heta new file mode 100644 index 000000000..560246ed1 --- /dev/null +++ b/latest/cases/00145/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.0125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 150; +k2 @Record 'k2' { } .= 5; +k2 := 5; + diff --git a/latest/cases/00145/l2v5/index.heta b/latest/cases/00145/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00145/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00145/l2v5/json/output.json b/latest/cases/00145/l2v5/json/output.json new file mode 100644 index 000000000..463666001 --- /dev/null +++ b/latest/cases/00145/l2v5/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "150" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5", + "ode_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00145/l3v2/heta-code/output.heta b/latest/cases/00145/l3v2/heta-code/output.heta new file mode 100644 index 000000000..643ffeae9 --- /dev/null +++ b/latest/cases/00145/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k2 @Record 'k2' { } .= 5; +k2 := 5; + +k1 @Const 'k1' { } = 150; + diff --git a/latest/cases/00145/l3v2/index.heta b/latest/cases/00145/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00145/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00145/l3v2/json/output.json b/latest/cases/00145/l3v2/json/output.json new file mode 100644 index 000000000..02c3f338f --- /dev/null +++ b/latest/cases/00145/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150 + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5", + "ode_": "5" + } + } +] \ No newline at end of file diff --git a/latest/cases/00145/model-sbml-l2v5.xml b/latest/cases/00145/model-sbml-l2v5.xml new file mode 100644 index 000000000..d14538ffc --- /dev/null +++ b/latest/cases/00145/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00145/model-sbml-l3v2.xml b/latest/cases/00145/model-sbml-l3v2.xml new file mode 100644 index 000000000..4ea8b0da1 --- /dev/null +++ b/latest/cases/00145/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00145/output.heta b/latest/cases/00145/output.heta new file mode 100644 index 000000000..5f7560ab6 --- /dev/null +++ b/latest/cases/00145/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions with three species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k2 | $5$ |] + +In this case the initial value declared for parameter k2 is consistent with +the value calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$1.25 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment "compartment" |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k2 @Record 'k2' { } .= 5; +k2 := 5; + +k1 @Const 'k1' { } = 150; + diff --git a/latest/cases/00145/synopsis.txt b/latest/cases/00145/synopsis.txt new file mode 100644 index 000000000..ebb8b125e --- /dev/null +++ b/latest/cases/00145/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with three species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k2 | $5$ |] + +In this case the initial value declared for parameter k2 is consistent with +the value calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$1.25 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment "compartment" |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00146/l2v5/heta-code/output.heta b/latest/cases/00146/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5a1906f32 --- /dev/null +++ b/latest/cases/00146/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.0125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 150; +k2 @Record 'k2' { } .= 0.005; +k2 := 5; + diff --git a/latest/cases/00146/l2v5/index.heta b/latest/cases/00146/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00146/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00146/l2v5/json/output.json b/latest/cases/00146/l2v5/json/output.json new file mode 100644 index 000000000..a0c56b3b8 --- /dev/null +++ b/latest/cases/00146/l2v5/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "150" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.005", + "ode_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00146/l3v2/heta-code/output.heta b/latest/cases/00146/l3v2/heta-code/output.heta new file mode 100644 index 000000000..70d4e72c4 --- /dev/null +++ b/latest/cases/00146/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k2 @Record 'k2' { } .= 0.005; +k2 := 5; + +k1 @Const 'k1' { } = 150; + diff --git a/latest/cases/00146/l3v2/index.heta b/latest/cases/00146/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00146/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00146/l3v2/json/output.json b/latest/cases/00146/l3v2/json/output.json new file mode 100644 index 000000000..257cc34c2 --- /dev/null +++ b/latest/cases/00146/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150 + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.005", + "ode_": "5" + } + } +] \ No newline at end of file diff --git a/latest/cases/00146/model-sbml-l2v5.xml b/latest/cases/00146/model-sbml-l2v5.xml new file mode 100644 index 000000000..a3958a7ff --- /dev/null +++ b/latest/cases/00146/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00146/model-sbml-l3v2.xml b/latest/cases/00146/model-sbml-l3v2.xml new file mode 100644 index 000000000..bca37ec28 --- /dev/null +++ b/latest/cases/00146/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00146/output.heta b/latest/cases/00146/output.heta new file mode 100644 index 000000000..ecf03986b --- /dev/null +++ b/latest/cases/00146/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Two reactions with three species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k2 | $5$ |] + +In this case the initial value declared for parameter k2 is inconsistent +with the value calculated by the assignmentRule. The calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$1.25 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.005$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k2 @Record 'k2' { } .= 0.005; +k2 := 5; + +k1 @Const 'k1' { } = 150; + diff --git a/latest/cases/00146/synopsis.txt b/latest/cases/00146/synopsis.txt new file mode 100644 index 000000000..75e587ea0 --- /dev/null +++ b/latest/cases/00146/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reactions with three species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k2 | $5$ |] + +In this case the initial value declared for parameter k2 is inconsistent +with the value calculated by the assignmentRule. The calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$1.25 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.005$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00147/l2v5/heta-code/output.heta b/latest/cases/00147/l2v5/heta-code/output.heta new file mode 100644 index 000000000..28890beab --- /dev/null +++ b/latest/cases/00147/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.0125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 150; +k2 @Record 'k2' { }; +k2 := 5; + diff --git a/latest/cases/00147/l2v5/index.heta b/latest/cases/00147/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00147/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00147/l2v5/json/output.json b/latest/cases/00147/l2v5/json/output.json new file mode 100644 index 000000000..63788412d --- /dev/null +++ b/latest/cases/00147/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "150" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "ode_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00147/l3v2/heta-code/output.heta b/latest/cases/00147/l3v2/heta-code/output.heta new file mode 100644 index 000000000..26b888ea0 --- /dev/null +++ b/latest/cases/00147/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k2 @Record 'k2' { }; +k2 := 5; + +k1 @Const 'k1' { } = 150; + diff --git a/latest/cases/00147/l3v2/index.heta b/latest/cases/00147/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00147/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00147/l3v2/json/output.json b/latest/cases/00147/l3v2/json/output.json new file mode 100644 index 000000000..5b18a3964 --- /dev/null +++ b/latest/cases/00147/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0125 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150 + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "ode_": "5" + } + } +] \ No newline at end of file diff --git a/latest/cases/00147/model-sbml-l2v5.xml b/latest/cases/00147/model-sbml-l2v5.xml new file mode 100644 index 000000000..15c93b4c5 --- /dev/null +++ b/latest/cases/00147/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00147/model-sbml-l3v2.xml b/latest/cases/00147/model-sbml-l3v2.xml new file mode 100644 index 000000000..97857f999 --- /dev/null +++ b/latest/cases/00147/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00147/output.heta b/latest/cases/00147/output.heta new file mode 100644 index 000000000..bac541bf6 --- /dev/null +++ b/latest/cases/00147/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions with three species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k2 | $5$ |] + +In this case there is no initial value declared for parameter k2. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$1.25 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ undeclared$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k2 @Record 'k2' { }; +k2 := 5; + +k1 @Const 'k1' { } = 150; + diff --git a/latest/cases/00147/synopsis.txt b/latest/cases/00147/synopsis.txt new file mode 100644 index 000000000..2c205fcb7 --- /dev/null +++ b/latest/cases/00147/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with three species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k2 | $5$ |] + +In this case there is no initial value declared for parameter k2. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$1.25 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ undeclared$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00148/l2v5/heta-code/output.heta b/latest/cases/00148/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f245da6a2 --- /dev/null +++ b/latest/cases/00148/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 0.75; +k1 := 0.75; + diff --git a/latest/cases/00148/l2v5/index.heta b/latest/cases/00148/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00148/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00148/l2v5/json/output.json b/latest/cases/00148/l2v5/json/output.json new file mode 100644 index 000000000..6353bd130 --- /dev/null +++ b/latest/cases/00148/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75", + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00148/l3v2/heta-code/output.heta b/latest/cases/00148/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e18867273 --- /dev/null +++ b/latest/cases/00148/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 0.75; +k1 := 0.75; + diff --git a/latest/cases/00148/l3v2/index.heta b/latest/cases/00148/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00148/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00148/l3v2/json/output.json b/latest/cases/00148/l3v2/json/output.json new file mode 100644 index 000000000..45b612536 --- /dev/null +++ b/latest/cases/00148/l3v2/json/output.json @@ -0,0 +1,64 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75", + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00148/model-sbml-l2v5.xml b/latest/cases/00148/model-sbml-l2v5.xml new file mode 100644 index 000000000..8e6a3603f --- /dev/null +++ b/latest/cases/00148/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + 0.75 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00148/model-sbml-l3v2.xml b/latest/cases/00148/model-sbml-l3v2.xml new file mode 100644 index 000000000..f8a68d0e6 --- /dev/null +++ b/latest/cases/00148/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.75 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00148/output.heta b/latest/cases/00148/output.heta new file mode 100644 index 000000000..64a0e7858 --- /dev/null +++ b/latest/cases/00148/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case the initial value declared for parameter k1 is consistent with +the value calculated by the assignmentRule. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 0.75; +k1 := 0.75; + diff --git a/latest/cases/00148/synopsis.txt b/latest/cases/00148/synopsis.txt new file mode 100644 index 000000000..a34f262c8 --- /dev/null +++ b/latest/cases/00148/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case the initial value declared for parameter k1 is consistent with +the value calculated by the assignmentRule. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00149/l2v5/heta-code/output.heta b/latest/cases/00149/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0eef1fabc --- /dev/null +++ b/latest/cases/00149/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 750; +k1 := 0.75; + diff --git a/latest/cases/00149/l2v5/index.heta b/latest/cases/00149/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00149/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00149/l2v5/json/output.json b/latest/cases/00149/l2v5/json/output.json new file mode 100644 index 000000000..f22904ebf --- /dev/null +++ b/latest/cases/00149/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "750", + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00149/l3v2/heta-code/output.heta b/latest/cases/00149/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c0049753d --- /dev/null +++ b/latest/cases/00149/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 750; +k1 := 0.75; + diff --git a/latest/cases/00149/l3v2/index.heta b/latest/cases/00149/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00149/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00149/l3v2/json/output.json b/latest/cases/00149/l3v2/json/output.json new file mode 100644 index 000000000..cc75f172b --- /dev/null +++ b/latest/cases/00149/l3v2/json/output.json @@ -0,0 +1,64 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "750", + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00149/model-sbml-l2v5.xml b/latest/cases/00149/model-sbml-l2v5.xml new file mode 100644 index 000000000..bfa7230b3 --- /dev/null +++ b/latest/cases/00149/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + 0.75 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00149/model-sbml-l3v2.xml b/latest/cases/00149/model-sbml-l3v2.xml new file mode 100644 index 000000000..0c85c4275 --- /dev/null +++ b/latest/cases/00149/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.75 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00149/output.heta b/latest/cases/00149/output.heta new file mode 100644 index 000000000..b58eb7ce1 --- /dev/null +++ b/latest/cases/00149/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case the initial value declared for parameter k1 is inconsistent +with the value calculated by the assignmentRule. The calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ 750$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 750; +k1 := 0.75; + diff --git a/latest/cases/00149/synopsis.txt b/latest/cases/00149/synopsis.txt new file mode 100644 index 000000000..1ea2a0e3b --- /dev/null +++ b/latest/cases/00149/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case the initial value declared for parameter k1 is inconsistent +with the value calculated by the assignmentRule. The calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ 750$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00150/l2v5/heta-code/output.heta b/latest/cases/00150/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2e9dd5012 --- /dev/null +++ b/latest/cases/00150/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00150/l2v5/index.heta b/latest/cases/00150/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00150/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00150/l2v5/json/output.json b/latest/cases/00150/l2v5/json/output.json new file mode 100644 index 000000000..6e1c55b0a --- /dev/null +++ b/latest/cases/00150/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00150/l3v2/heta-code/output.heta b/latest/cases/00150/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b4b1dd9f2 --- /dev/null +++ b/latest/cases/00150/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00150/l3v2/index.heta b/latest/cases/00150/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00150/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00150/l3v2/json/output.json b/latest/cases/00150/l3v2/json/output.json new file mode 100644 index 000000000..05fd4dbe2 --- /dev/null +++ b/latest/cases/00150/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00150/model-sbml-l2v5.xml b/latest/cases/00150/model-sbml-l2v5.xml new file mode 100644 index 000000000..161e48266 --- /dev/null +++ b/latest/cases/00150/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + 0.75 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00150/model-sbml-l3v2.xml b/latest/cases/00150/model-sbml-l3v2.xml new file mode 100644 index 000000000..147c90a34 --- /dev/null +++ b/latest/cases/00150/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.75 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00150/output.heta b/latest/cases/00150/output.heta new file mode 100644 index 000000000..2ac1c6724 --- /dev/null +++ b/latest/cases/00150/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00150/synopsis.txt b/latest/cases/00150/synopsis.txt new file mode 100644 index 000000000..ff599fb34 --- /dev/null +++ b/latest/cases/00150/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00151/l2v5/heta-code/output.heta b/latest/cases/00151/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1b1afc05b --- /dev/null +++ b/latest/cases/00151/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00151/l2v5/index.heta b/latest/cases/00151/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00151/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00151/l2v5/json/output.json b/latest/cases/00151/l2v5/json/output.json new file mode 100644 index 000000000..e70ac49a1 --- /dev/null +++ b/latest/cases/00151/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00151/l3v2/heta-code/output.heta b/latest/cases/00151/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9602c195d --- /dev/null +++ b/latest/cases/00151/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00151/l3v2/index.heta b/latest/cases/00151/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00151/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00151/l3v2/json/output.json b/latest/cases/00151/l3v2/json/output.json new file mode 100644 index 000000000..812a3cce4 --- /dev/null +++ b/latest/cases/00151/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00151/model-sbml-l2v5.xml b/latest/cases/00151/model-sbml-l2v5.xml new file mode 100644 index 000000000..ca7048c93 --- /dev/null +++ b/latest/cases/00151/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00151/model-sbml-l3v2.xml b/latest/cases/00151/model-sbml-l3v2.xml new file mode 100644 index 000000000..a9636f81a --- /dev/null +++ b/latest/cases/00151/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00151/output.heta b/latest/cases/00151/output.heta new file mode 100644 index 000000000..d0e822f30 --- /dev/null +++ b/latest/cases/00151/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Two reactions with four species in one 2-dimensional +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it must be considered during +simulation. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Area of compartment "compartment" |$ 1$ |rmetre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00151/synopsis.txt b/latest/cases/00151/synopsis.txt new file mode 100644 index 000000000..76cf01b32 --- /dev/null +++ b/latest/cases/00151/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Two reactions with four species in one 2-dimensional +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it must be considered during +simulation. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Area of compartment "compartment" |$ 1$ |rmetre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00152/l2v5/heta-code/output.heta b/latest/cases/00152/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3f910b6be --- /dev/null +++ b/latest/cases/00152/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00152/l2v5/index.heta b/latest/cases/00152/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00152/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00152/l2v5/json/output.json b/latest/cases/00152/l2v5/json/output.json new file mode 100644 index 000000000..9838144c7 --- /dev/null +++ b/latest/cases/00152/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "1.5e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00152/l3v2/heta-code/output.heta b/latest/cases/00152/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4cbd00141 --- /dev/null +++ b/latest/cases/00152/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00152/l3v2/index.heta b/latest/cases/00152/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00152/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00152/l3v2/json/output.json b/latest/cases/00152/l3v2/json/output.json new file mode 100644 index 000000000..75f9005f5 --- /dev/null +++ b/latest/cases/00152/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "1.5e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00152/model-sbml-l2v5.xml b/latest/cases/00152/model-sbml-l2v5.xml new file mode 100644 index 000000000..a3f825227 --- /dev/null +++ b/latest/cases/00152/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00152/model-sbml-l3v2.xml b/latest/cases/00152/model-sbml-l3v2.xml new file mode 100644 index 000000000..55d64e58b --- /dev/null +++ b/latest/cases/00152/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00152/output.heta b/latest/cases/00152/output.heta new file mode 100644 index 000000000..dcf5c7521 --- /dev/null +++ b/latest/cases/00152/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one + 2-dimensional compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it must be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto} |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00152/synopsis.txt b/latest/cases/00152/synopsis.txt new file mode 100644 index 000000000..4db9b9cb0 --- /dev/null +++ b/latest/cases/00152/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one + 2-dimensional compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it must be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto} |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00153/l2v5/heta-code/output.heta b/latest/cases/00153/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3a019741f --- /dev/null +++ b/latest/cases/00153/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 0.001 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1500; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00153/l2v5/index.heta b/latest/cases/00153/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00153/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00153/l2v5/json/output.json b/latest/cases/00153/l2v5/json/output.json new file mode 100644 index 000000000..772d6719b --- /dev/null +++ b/latest/cases/00153/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00153/l3v2/heta-code/output.heta b/latest/cases/00153/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1589595f9 --- /dev/null +++ b/latest/cases/00153/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 1500; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00153/l3v2/index.heta b/latest/cases/00153/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00153/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00153/l3v2/json/output.json b/latest/cases/00153/l3v2/json/output.json new file mode 100644 index 000000000..9f40d9512 --- /dev/null +++ b/latest/cases/00153/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00153/model-sbml-l2v5.xml b/latest/cases/00153/model-sbml-l2v5.xml new file mode 100644 index 000000000..15287e086 --- /dev/null +++ b/latest/cases/00153/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00153/model-sbml-l3v2.xml b/latest/cases/00153/model-sbml-l3v2.xml new file mode 100644 index 000000000..3bb490fd9 --- /dev/null +++ b/latest/cases/00153/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00153/output.heta b/latest/cases/00153/output.heta new file mode 100644 index 000000000..a94d78f97 --- /dev/null +++ b/latest/cases/00153/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Two reactions with four species in one 1-dimensional +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it must be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1 \x 10^-3$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^3$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 1500; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00153/synopsis.txt b/latest/cases/00153/synopsis.txt new file mode 100644 index 000000000..e0fa44c18 --- /dev/null +++ b/latest/cases/00153/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Two reactions with four species in one 1-dimensional +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it must be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1 \x 10^-3$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^3$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00154/l2v5/heta-code/output.heta b/latest/cases/00154/l2v5/heta-code/output.heta new file mode 100644 index 000000000..80be6ab4f --- /dev/null +++ b/latest/cases/00154/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00154/l2v5/index.heta b/latest/cases/00154/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00154/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00154/l2v5/json/output.json b/latest/cases/00154/l2v5/json/output.json new file mode 100644 index 000000000..cf4f2f83f --- /dev/null +++ b/latest/cases/00154/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00154/l3v2/heta-code/output.heta b/latest/cases/00154/l3v2/heta-code/output.heta new file mode 100644 index 000000000..58a9493ce --- /dev/null +++ b/latest/cases/00154/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00154/l3v2/index.heta b/latest/cases/00154/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00154/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00154/l3v2/json/output.json b/latest/cases/00154/l3v2/json/output.json new file mode 100644 index 000000000..734bea70c --- /dev/null +++ b/latest/cases/00154/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00154/model-sbml-l2v5.xml b/latest/cases/00154/model-sbml-l2v5.xml new file mode 100644 index 000000000..685751dd2 --- /dev/null +++ b/latest/cases/00154/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00154/model-sbml-l3v2.xml b/latest/cases/00154/model-sbml-l3v2.xml new file mode 100644 index 000000000..4131e9792 --- /dev/null +++ b/latest/cases/00154/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00154/output.heta b/latest/cases/00154/output.heta new file mode 100644 index 000000000..6118cee1b --- /dev/null +++ b/latest/cases/00154/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one + 1-dimensional compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00154/synopsis.txt b/latest/cases/00154/synopsis.txt new file mode 100644 index 000000000..cf63e5122 --- /dev/null +++ b/latest/cases/00154/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one + 1-dimensional compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00155/l2v5/heta-code/output.heta b/latest/cases/00155/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e606a34dc --- /dev/null +++ b/latest/cases/00155/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 1500; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00155/l2v5/index.heta b/latest/cases/00155/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00155/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00155/l2v5/json/output.json b/latest/cases/00155/l2v5/json/output.json new file mode 100644 index 000000000..9aad5ee36 --- /dev/null +++ b/latest/cases/00155/l2v5/json/output.json @@ -0,0 +1,153 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00155/l3v2/heta-code/output.heta b/latest/cases/00155/l3v2/heta-code/output.heta new file mode 100644 index 000000000..898c8766a --- /dev/null +++ b/latest/cases/00155/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 1500; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00155/l3v2/index.heta b/latest/cases/00155/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00155/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00155/l3v2/json/output.json b/latest/cases/00155/l3v2/json/output.json new file mode 100644 index 000000000..799c08ba9 --- /dev/null +++ b/latest/cases/00155/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00155/model-sbml-l2v5.xml b/latest/cases/00155/model-sbml-l2v5.xml new file mode 100644 index 000000000..435da00e8 --- /dev/null +++ b/latest/cases/00155/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00155/model-sbml-l3v2.xml b/latest/cases/00155/model-sbml-l3v2.xml new file mode 100644 index 000000000..85e786459 --- /dev/null +++ b/latest/cases/00155/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00155/output.heta b/latest/cases/00155/output.heta new file mode 100644 index 000000000..39a10bf31 --- /dev/null +++ b/latest/cases/00155/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Two reactions with four species in one 0-dimensional +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, 0D-Compartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Compartment "compartment" is 0-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +| Initial amount of S1:| $ 1 \x 10^-3$ | mole | +| Initial amount of S2:| $ 1.5 \x 10^-3$ | mole | +| Initial amount of S3:| $ 1 \x 10^-3$ | mole | +| Initial amount of S4:| $ undeclared$ | mole | +| Value of parameter k1:| $ 1.5 \x 10^3$ | litre mole^-1^ second^-1^ | +| Value of parameter k2:| $ 50$ | second^-1^ | +| Value of parameter k3:| $ 1.5$ | dimensionless |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 1500; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00155/synopsis.txt b/latest/cases/00155/synopsis.txt new file mode 100644 index 000000000..56a00b550 --- /dev/null +++ b/latest/cases/00155/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Two reactions with four species in one 0-dimensional +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, 0D-Compartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Compartment "compartment" is 0-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +| Initial amount of S1:| $ 1 \x 10^-3$ | mole | +| Initial amount of S2:| $ 1.5 \x 10^-3$ | mole | +| Initial amount of S3:| $ 1 \x 10^-3$ | mole | +| Initial amount of S4:| $ undeclared$ | mole | +| Value of parameter k1:| $ 1.5 \x 10^3$ | litre mole^-1^ second^-1^ | +| Value of parameter k2:| $ 50$ | second^-1^ | +| Value of parameter k3:| $ 1.5$ | dimensionless |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00156/l2v5/heta-code/output.heta b/latest/cases/00156/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a167ea88c --- /dev/null +++ b/latest/cases/00156/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.015; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00156/l2v5/index.heta b/latest/cases/00156/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00156/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00156/l2v5/json/output.json b/latest/cases/00156/l2v5/json/output.json new file mode 100644 index 000000000..aae2cadbd --- /dev/null +++ b/latest/cases/00156/l2v5/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00156/l3v2/heta-code/output.heta b/latest/cases/00156/l3v2/heta-code/output.heta new file mode 100644 index 000000000..784df7ff2 --- /dev/null +++ b/latest/cases/00156/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00156/l3v2/index.heta b/latest/cases/00156/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00156/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00156/l3v2/json/output.json b/latest/cases/00156/l3v2/json/output.json new file mode 100644 index 000000000..1ddef03c3 --- /dev/null +++ b/latest/cases/00156/l3v2/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00156/model-sbml-l2v5.xml b/latest/cases/00156/model-sbml-l2v5.xml new file mode 100644 index 000000000..1cd567452 --- /dev/null +++ b/latest/cases/00156/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + k2 + S1 + + + + + + + diff --git a/latest/cases/00156/model-sbml-l3v2.xml b/latest/cases/00156/model-sbml-l3v2.xml new file mode 100644 index 000000000..6719ac79e --- /dev/null +++ b/latest/cases/00156/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + k2 + S1 + + + + + + + diff --git a/latest/cases/00156/output.heta b/latest/cases/00156/output.heta new file mode 100644 index 000000000..9258b24c8 --- /dev/null +++ b/latest/cases/00156/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one + 0-dimensional compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, 0D-Compartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +| Initial amount of S1:| $ 1 \x 10^-2$ | mole | +| Initial amount of S2:| $1.5 \x 10^-2$ | mole | +| Initial amount of S3:| $ undeclared$ | mole | +| Value of parameter k1:| $ 0.75$ | dimensionless | +| Value of parameter k2:| $ 50$ | second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00156/synopsis.txt b/latest/cases/00156/synopsis.txt new file mode 100644 index 000000000..6993203f6 --- /dev/null +++ b/latest/cases/00156/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one + 0-dimensional compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, 0D-Compartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +| Initial amount of S1:| $ 1 \x 10^-2$ | mole | +| Initial amount of S2:| $1.5 \x 10^-2$ | mole | +| Initial amount of S3:| $ undeclared$ | mole | +| Value of parameter k1:| $ 0.75$ | dimensionless | +| Value of parameter k2:| $ 50$ | second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00157/l2v5/heta-code/output.heta b/latest/cases/00157/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1ec10dddd --- /dev/null +++ b/latest/cases/00157/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 0.01; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.01 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 3.25; +k2 @Record 'k2' { } .= 1.75; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00157/l2v5/index.heta b/latest/cases/00157/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00157/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00157/l2v5/json/output.json b/latest/cases/00157/l2v5/json/output.json new file mode 100644 index 000000000..febb9141a --- /dev/null +++ b/latest/cases/00157/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "0.01" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "3.25" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.75" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00157/l3v2/heta-code/output.heta b/latest/cases/00157/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d03bc16af --- /dev/null +++ b/latest/cases/00157/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.01; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 3.25; +k2 @Const 'k2' { } = 1.75; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00157/l3v2/index.heta b/latest/cases/00157/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00157/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00157/l3v2/json/output.json b/latest/cases/00157/l3v2/json/output.json new file mode 100644 index 000000000..e13b5aefa --- /dev/null +++ b/latest/cases/00157/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "0.01" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 3.25 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.75 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00157/model-sbml-l2v5.xml b/latest/cases/00157/model-sbml-l2v5.xml new file mode 100644 index 000000000..a650af778 --- /dev/null +++ b/latest/cases/00157/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00157/model-sbml-l3v2.xml b/latest/cases/00157/model-sbml-l3v2.xml new file mode 100644 index 000000000..5c11575f3 --- /dev/null +++ b/latest/cases/00157/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00157/output.heta b/latest/cases/00157/output.heta new file mode 100644 index 000000000..d59cd7b28 --- /dev/null +++ b/latest/cases/00157/output.heta @@ -0,0 +1,68 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ 1 \x 10^-2$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 3.25$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 1.75$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 0.01$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.01; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 3.25; +k2 @Const 'k2' { } = 1.75; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00157/synopsis.txt b/latest/cases/00157/synopsis.txt new file mode 100644 index 000000000..e8c60321d --- /dev/null +++ b/latest/cases/00157/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-2$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ 1 \x 10^-2$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 3.25$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 1.75$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 0.01$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00158/l2v5/heta-code/output.heta b/latest/cases/00158/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bf7318dc8 --- /dev/null +++ b/latest/cases/00158/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 0.08; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00158/l2v5/index.heta b/latest/cases/00158/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00158/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00158/l2v5/json/output.json b/latest/cases/00158/l2v5/json/output.json new file mode 100644 index 000000000..9dac02799 --- /dev/null +++ b/latest/cases/00158/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "0.08" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00158/l3v2/heta-code/output.heta b/latest/cases/00158/l3v2/heta-code/output.heta new file mode 100644 index 000000000..84e5927f8 --- /dev/null +++ b/latest/cases/00158/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.08; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00158/l3v2/index.heta b/latest/cases/00158/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00158/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00158/l3v2/json/output.json b/latest/cases/00158/l3v2/json/output.json new file mode 100644 index 000000000..388984e3f --- /dev/null +++ b/latest/cases/00158/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "0.08" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00158/model-sbml-l2v5.xml b/latest/cases/00158/model-sbml-l2v5.xml new file mode 100644 index 000000000..41fffb601 --- /dev/null +++ b/latest/cases/00158/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00158/model-sbml-l3v2.xml b/latest/cases/00158/model-sbml-l3v2.xml new file mode 100644 index 000000000..55410b1da --- /dev/null +++ b/latest/cases/00158/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00158/output.heta b/latest/cases/00158/output.heta new file mode 100644 index 000000000..b5d62e7de --- /dev/null +++ b/latest/cases/00158/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 0.08$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.08; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00158/synopsis.txt b/latest/cases/00158/synopsis.txt new file mode 100644 index 000000000..3cc1f3473 --- /dev/null +++ b/latest/cases/00158/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 0.08$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00159/l2v5/heta-code/output.heta b/latest/cases/00159/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1b14ee690 --- /dev/null +++ b/latest/cases/00159/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00159/l2v5/index.heta b/latest/cases/00159/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00159/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00159/l2v5/json/output.json b/latest/cases/00159/l2v5/json/output.json new file mode 100644 index 000000000..c5b7ab2b7 --- /dev/null +++ b/latest/cases/00159/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00159/l3v2/heta-code/output.heta b/latest/cases/00159/l3v2/heta-code/output.heta new file mode 100644 index 000000000..141062597 --- /dev/null +++ b/latest/cases/00159/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00159/l3v2/index.heta b/latest/cases/00159/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00159/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00159/l3v2/json/output.json b/latest/cases/00159/l3v2/json/output.json new file mode 100644 index 000000000..0b85e490e --- /dev/null +++ b/latest/cases/00159/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00159/model-sbml-l2v5.xml b/latest/cases/00159/model-sbml-l2v5.xml new file mode 100644 index 000000000..712a94ff6 --- /dev/null +++ b/latest/cases/00159/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00159/model-sbml-l3v2.xml b/latest/cases/00159/model-sbml-l3v2.xml new file mode 100644 index 000000000..a0e3f5d41 --- /dev/null +++ b/latest/cases/00159/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00159/output.heta b/latest/cases/00159/output.heta new file mode 100644 index 000000000..c3f4bb64a --- /dev/null +++ b/latest/cases/00159/output.heta @@ -0,0 +1,68 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00159/synopsis.txt b/latest/cases/00159/synopsis.txt new file mode 100644 index 000000000..075ae1d4f --- /dev/null +++ b/latest/cases/00159/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00160/l2v5/heta-code/output.heta b/latest/cases/00160/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4affac12f --- /dev/null +++ b/latest/cases/00160/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00160/l2v5/index.heta b/latest/cases/00160/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00160/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00160/l2v5/json/output.json b/latest/cases/00160/l2v5/json/output.json new file mode 100644 index 000000000..57bc6051f --- /dev/null +++ b/latest/cases/00160/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00160/l3v2/heta-code/output.heta b/latest/cases/00160/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ccc57bf1b --- /dev/null +++ b/latest/cases/00160/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00160/l3v2/index.heta b/latest/cases/00160/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00160/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00160/l3v2/json/output.json b/latest/cases/00160/l3v2/json/output.json new file mode 100644 index 000000000..1190943c6 --- /dev/null +++ b/latest/cases/00160/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00160/model-sbml-l2v5.xml b/latest/cases/00160/model-sbml-l2v5.xml new file mode 100644 index 000000000..5445694a2 --- /dev/null +++ b/latest/cases/00160/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00160/model-sbml-l3v2.xml b/latest/cases/00160/model-sbml-l3v2.xml new file mode 100644 index 000000000..07caf0801 --- /dev/null +++ b/latest/cases/00160/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00160/output.heta b/latest/cases/00160/output.heta new file mode 100644 index 000000000..cfe8e56da --- /dev/null +++ b/latest/cases/00160/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-15 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00160/synopsis.txt b/latest/cases/00160/synopsis.txt new file mode 100644 index 000000000..b4ec25289 --- /dev/null +++ b/latest/cases/00160/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00161/l2v5/heta-code/output.heta b/latest/cases/00161/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2969a094f --- /dev/null +++ b/latest/cases/00161/l2v5/heta-code/output.heta @@ -0,0 +1,18 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00161/l2v5/index.heta b/latest/cases/00161/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00161/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00161/l2v5/json/output.json b/latest/cases/00161/l2v5/json/output.json new file mode 100644 index 000000000..df4397e10 --- /dev/null +++ b/latest/cases/00161/l2v5/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00161/l3v2/heta-code/output.heta b/latest/cases/00161/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1d551a3fb --- /dev/null +++ b/latest/cases/00161/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00161/l3v2/index.heta b/latest/cases/00161/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00161/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00161/l3v2/json/output.json b/latest/cases/00161/l3v2/json/output.json new file mode 100644 index 000000000..f7a098618 --- /dev/null +++ b/latest/cases/00161/l3v2/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00161/model-sbml-l2v5.xml b/latest/cases/00161/model-sbml-l2v5.xml new file mode 100644 index 000000000..271139161 --- /dev/null +++ b/latest/cases/00161/model-sbml-l2v5.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + -1 + k1 + S1 + + + + + + + + k1 + S1 + + + + + + diff --git a/latest/cases/00161/model-sbml-l3v2.xml b/latest/cases/00161/model-sbml-l3v2.xml new file mode 100644 index 000000000..4e32b5f5e --- /dev/null +++ b/latest/cases/00161/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + -1 + k1 + S1 + + + + + + + + k1 + S1 + + + + + + diff --git a/latest/cases/00161/output.heta b/latest/cases/00161/output.heta new file mode 100644 index 000000000..1ed66b463 --- /dev/null +++ b/latest/cases/00161/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-S1 * k1$ | + | Rate | S2 | $S1 * k1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00161/synopsis.txt b/latest/cases/00161/synopsis.txt new file mode 100644 index 000000000..c7a690dca --- /dev/null +++ b/latest/cases/00161/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-S1 * k1$ | + | Rate | S2 | $S1 * k1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ |] + + diff --git a/latest/cases/00162/l2v5/heta-code/output.heta b/latest/cases/00162/l2v5/heta-code/output.heta new file mode 100644 index 000000000..008850bab --- /dev/null +++ b/latest/cases/00162/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0; +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0; + diff --git a/latest/cases/00162/l2v5/index.heta b/latest/cases/00162/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00162/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00162/l2v5/json/output.json b/latest/cases/00162/l2v5/json/output.json new file mode 100644 index 000000000..35d8b1bee --- /dev/null +++ b/latest/cases/00162/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00162/l3v2/heta-code/output.heta b/latest/cases/00162/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4079ed077 --- /dev/null +++ b/latest/cases/00162/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0; + diff --git a/latest/cases/00162/l3v2/index.heta b/latest/cases/00162/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00162/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00162/l3v2/json/output.json b/latest/cases/00162/l3v2/json/output.json new file mode 100644 index 000000000..ce8214ab2 --- /dev/null +++ b/latest/cases/00162/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00162/model-sbml-l2v5.xml b/latest/cases/00162/model-sbml-l2v5.xml new file mode 100644 index 000000000..a85c9f56b --- /dev/null +++ b/latest/cases/00162/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + diff --git a/latest/cases/00162/model-sbml-l3v2.xml b/latest/cases/00162/model-sbml-l3v2.xml new file mode 100644 index 000000000..b54b36e5b --- /dev/null +++ b/latest/cases/00162/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + diff --git a/latest/cases/00162/output.heta b/latest/cases/00162/output.heta new file mode 100644 index 000000000..8feb2db4c --- /dev/null +++ b/latest/cases/00162/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and +not species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $S2 * k2-S1 * k1$ | + | Rate | S2 | $S1 * k1-S2 * k2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0; + diff --git a/latest/cases/00162/synopsis.txt b/latest/cases/00162/synopsis.txt new file mode 100644 index 000000000..e9ec8c80b --- /dev/null +++ b/latest/cases/00162/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and +not species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $S2 * k2-S1 * k1$ | + | Rate | S2 | $S1 * k1-S2 * k2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0$ |second^-1^ |] + + diff --git a/latest/cases/00163/l2v5/heta-code/output.heta b/latest/cases/00163/l2v5/heta-code/output.heta new file mode 100644 index 000000000..00f2da4e5 --- /dev/null +++ b/latest/cases/00163/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0; +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 0.5; + diff --git a/latest/cases/00163/l2v5/index.heta b/latest/cases/00163/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00163/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00163/l2v5/json/output.json b/latest/cases/00163/l2v5/json/output.json new file mode 100644 index 000000000..f03d6a5a8 --- /dev/null +++ b/latest/cases/00163/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00163/l3v2/heta-code/output.heta b/latest/cases/00163/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9cbdf3e87 --- /dev/null +++ b/latest/cases/00163/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00163/l3v2/index.heta b/latest/cases/00163/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00163/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00163/l3v2/json/output.json b/latest/cases/00163/l3v2/json/output.json new file mode 100644 index 000000000..d168d46ee --- /dev/null +++ b/latest/cases/00163/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00163/model-sbml-l2v5.xml b/latest/cases/00163/model-sbml-l2v5.xml new file mode 100644 index 000000000..82c47bd52 --- /dev/null +++ b/latest/cases/00163/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + diff --git a/latest/cases/00163/model-sbml-l3v2.xml b/latest/cases/00163/model-sbml-l3v2.xml new file mode 100644 index 000000000..1c10ed158 --- /dev/null +++ b/latest/cases/00163/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + diff --git a/latest/cases/00163/output.heta b/latest/cases/00163/output.heta new file mode 100644 index 000000000..3a31b6031 --- /dev/null +++ b/latest/cases/00163/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and +not species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $S2 * k2-S1 * k1$ | + | Rate | S2 | $S1 * k1-S2 * k2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00163/synopsis.txt b/latest/cases/00163/synopsis.txt new file mode 100644 index 000000000..e13716196 --- /dev/null +++ b/latest/cases/00163/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and +not species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $S2 * k2-S1 * k1$ | + | Rate | S2 | $S1 * k1-S2 * k2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ |] + + diff --git a/latest/cases/00164/l2v5/heta-code/output.heta b/latest/cases/00164/l2v5/heta-code/output.heta new file mode 100644 index 000000000..65d61dc7d --- /dev/null +++ b/latest/cases/00164/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0.015; +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 0.5; + diff --git a/latest/cases/00164/l2v5/index.heta b/latest/cases/00164/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00164/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00164/l2v5/json/output.json b/latest/cases/00164/l2v5/json/output.json new file mode 100644 index 000000000..4ae59408d --- /dev/null +++ b/latest/cases/00164/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00164/l3v2/heta-code/output.heta b/latest/cases/00164/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b40b032fc --- /dev/null +++ b/latest/cases/00164/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0.015; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00164/l3v2/index.heta b/latest/cases/00164/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00164/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00164/l3v2/json/output.json b/latest/cases/00164/l3v2/json/output.json new file mode 100644 index 000000000..f6a794a97 --- /dev/null +++ b/latest/cases/00164/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00164/model-sbml-l2v5.xml b/latest/cases/00164/model-sbml-l2v5.xml new file mode 100644 index 000000000..ee65bb454 --- /dev/null +++ b/latest/cases/00164/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + diff --git a/latest/cases/00164/model-sbml-l3v2.xml b/latest/cases/00164/model-sbml-l3v2.xml new file mode 100644 index 000000000..42f517cd7 --- /dev/null +++ b/latest/cases/00164/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + diff --git a/latest/cases/00164/output.heta b/latest/cases/00164/output.heta new file mode 100644 index 000000000..6da3733d3 --- /dev/null +++ b/latest/cases/00164/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and +not species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $S2 * k2-S1 * k1$ | + | Rate | S2 | $S1 * k1-S2 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$1.5 \x 10^-2$ |same as S1 | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0.015; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00164/synopsis.txt b/latest/cases/00164/synopsis.txt new file mode 100644 index 000000000..7fa659607 --- /dev/null +++ b/latest/cases/00164/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and +not species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $S2 * k2-S1 * k1$ | + | Rate | S2 | $S1 * k1-S2 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$1.5 \x 10^-2$ |same as S1 | +|Value of parameter k1 |$ 0.5$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ |] + + diff --git a/latest/cases/00165/l2v5/heta-code/output.heta b/latest/cases/00165/l2v5/heta-code/output.heta new file mode 100644 index 000000000..63a9b177d --- /dev/null +++ b/latest/cases/00165/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0.02; +S3 @Record 'S3' { } .= 0.01; +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 0.5; + diff --git a/latest/cases/00165/l2v5/index.heta b/latest/cases/00165/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00165/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00165/l2v5/json/output.json b/latest/cases/00165/l2v5/json/output.json new file mode 100644 index 000000000..ee0275026 --- /dev/null +++ b/latest/cases/00165/l2v5/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00165/l3v2/heta-code/output.heta b/latest/cases/00165/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ea9e442d9 --- /dev/null +++ b/latest/cases/00165/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0.02; +S3 @Record 'S3' { } .= 0.01; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00165/l3v2/index.heta b/latest/cases/00165/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00165/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00165/l3v2/json/output.json b/latest/cases/00165/l3v2/json/output.json new file mode 100644 index 000000000..d3ee82638 --- /dev/null +++ b/latest/cases/00165/l3v2/json/output.json @@ -0,0 +1,90 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00165/model-sbml-l2v5.xml b/latest/cases/00165/model-sbml-l2v5.xml new file mode 100644 index 000000000..18bd0d7ce --- /dev/null +++ b/latest/cases/00165/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + diff --git a/latest/cases/00165/model-sbml-l3v2.xml b/latest/cases/00165/model-sbml-l3v2.xml new file mode 100644 index 000000000..82b205158 --- /dev/null +++ b/latest/cases/00165/model-sbml-l3v2.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + diff --git a/latest/cases/00165/output.heta b/latest/cases/00165/output.heta new file mode 100644 index 000000000..a878917be --- /dev/null +++ b/latest/cases/00165/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3-k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3-k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2-k2 * S3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$ 2 \x 10^-2$ |same as S1 | +|Value of parameter S3 |$ 1 \x 10^-2$ |same as S1 | +|Value of parameter k1 |$ 0.5$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0.02; +S3 @Record 'S3' { } .= 0.01; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00165/synopsis.txt b/latest/cases/00165/synopsis.txt new file mode 100644 index 000000000..9ddd4fc71 --- /dev/null +++ b/latest/cases/00165/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3-k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3-k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2-k2 * S3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$ 2 \x 10^-2$ |same as S1 | +|Value of parameter S3 |$ 1 \x 10^-2$ |same as S1 | +|Value of parameter k1 |$ 0.5$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ |] + + diff --git a/latest/cases/00166/l2v5/heta-code/output.heta b/latest/cases/00166/l2v5/heta-code/output.heta new file mode 100644 index 000000000..69501da02 --- /dev/null +++ b/latest/cases/00166/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 * S4 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 * S4 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k1 * S1 * S2 + (-1) * k2 * S3 * S4; + +S1 @Record 'S1' { } .= 0.01; +S2 @Record 'S2' { } .= 0.01; +S3 @Record 'S3' { } .= 0.02; +S4 @Record 'S4' { } .= 0.01; +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 25; + diff --git a/latest/cases/00166/l2v5/index.heta b/latest/cases/00166/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00166/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00166/l2v5/json/output.json b/latest/cases/00166/l2v5/json/output.json new file mode 100644 index 000000000..ba518902a --- /dev/null +++ b/latest/cases/00166/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 * S4 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 * S4 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule4" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00166/l3v2/heta-code/output.heta b/latest/cases/00166/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3bd42ebbd --- /dev/null +++ b/latest/cases/00166/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 * S4 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 * S4 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k1 * S1 * S2 + (-1) * k2 * S3 * S4; + +S1 @Record 'S1' { } .= 0.01; +S2 @Record 'S2' { } .= 0.01; +S3 @Record 'S3' { } .= 0.02; +S4 @Record 'S4' { } .= 0.01; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00166/l3v2/index.heta b/latest/cases/00166/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00166/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00166/l3v2/json/output.json b/latest/cases/00166/l3v2/json/output.json new file mode 100644 index 000000000..ab3b5d080 --- /dev/null +++ b/latest/cases/00166/l3v2/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 * S4 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 * S4 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule4" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00166/model-sbml-l2v5.xml b/latest/cases/00166/model-sbml-l2v5.xml new file mode 100644 index 000000000..7709e61a0 --- /dev/null +++ b/latest/cases/00166/model-sbml-l2v5.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + S4 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + S4 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00166/model-sbml-l3v2.xml b/latest/cases/00166/model-sbml-l3v2.xml new file mode 100644 index 000000000..e23604aca --- /dev/null +++ b/latest/cases/00166/model-sbml-l3v2.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + S4 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + S4 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00166/output.heta b/latest/cases/00166/output.heta new file mode 100644 index 000000000..564df10c6 --- /dev/null +++ b/latest/cases/00166/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +two constant parameters called k1 and k2. (Note +that indeed S1, S2, S3 and S4 are parameters and not species in this +model.) + +The model contains four rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 * S4-k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 * S4-k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2-k2 * S3 * S4$ | + | Rate | S4 | $k1 * S1 * S2-k2 * S3 * S4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-2$ |any | +|Value of parameter S2 |$1.0 \x 10^-2$ |same as S1 | +|Value of parameter S3 |$2.0 \x 10^-2$ |same as S1 | +|Value of parameter S4 |$1.0 \x 10^-2$ |same as S1 | +|Value of parameter k1 |$0.75 \x 10^2$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |(units of S1)^-1^ second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 * S4 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 * S4 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k1 * S1 * S2 + (-1) * k2 * S3 * S4; + +S1 @Record 'S1' { } .= 0.01; +S2 @Record 'S2' { } .= 0.01; +S3 @Record 'S3' { } .= 0.02; +S4 @Record 'S4' { } .= 0.01; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00166/synopsis.txt b/latest/cases/00166/synopsis.txt new file mode 100644 index 000000000..e1a4952a0 --- /dev/null +++ b/latest/cases/00166/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +two constant parameters called k1 and k2. (Note +that indeed S1, S2, S3 and S4 are parameters and not species in this +model.) + +The model contains four rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 * S4-k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 * S4-k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2-k2 * S3 * S4$ | + | Rate | S4 | $k1 * S1 * S2-k2 * S3 * S4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-2$ |any | +|Value of parameter S2 |$1.0 \x 10^-2$ |same as S1 | +|Value of parameter S3 |$2.0 \x 10^-2$ |same as S1 | +|Value of parameter S4 |$1.0 \x 10^-2$ |same as S1 | +|Value of parameter k1 |$0.75 \x 10^2$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |(units of S1)^-1^ second^-1^ |] + + diff --git a/latest/cases/00167/l2v5/heta-code/output.heta b/latest/cases/00167/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bce5ecad6 --- /dev/null +++ b/latest/cases/00167/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2 + (-1) * k3 * S2 + k4 * S3 * S4; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k3 * S2 + (-1) * k4 * S3 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k3 * S2 + (-1) * k4 * S3 * S4; + +S1 @Record 'S1' { } .= 0.01; +S2 @Record 'S2' { } .= 0.02; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.15; +k4 @Record 'k4' { } .= 0.1; + diff --git a/latest/cases/00167/l2v5/index.heta b/latest/cases/00167/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00167/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00167/l2v5/json/output.json b/latest/cases/00167/l2v5/json/output.json new file mode 100644 index 000000000..c9fe87652 --- /dev/null +++ b/latest/cases/00167/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2 + (-1) * k3 * S2 + k4 * S3 * S4" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k3 * S2 + (-1) * k4 * S3 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule4" + }, + "assignments": { + "ode_": "k3 * S2 + (-1) * k4 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00167/l3v2/heta-code/output.heta b/latest/cases/00167/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9275f392b --- /dev/null +++ b/latest/cases/00167/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2 + (-1) * k3 * S2 + k4 * S3 * S4; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k3 * S2 + (-1) * k4 * S3 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k3 * S2 + (-1) * k4 * S3 * S4; + +S1 @Record 'S1' { } .= 0.01; +S2 @Record 'S2' { } .= 0.02; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.15; +k4 @Const 'k4' { } = 0.1; + diff --git a/latest/cases/00167/l3v2/index.heta b/latest/cases/00167/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00167/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00167/l3v2/json/output.json b/latest/cases/00167/l3v2/json/output.json new file mode 100644 index 000000000..9b0ace052 --- /dev/null +++ b/latest/cases/00167/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.15 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.1 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2 + (-1) * k3 * S2 + k4 * S3 * S4" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k3 * S2 + (-1) * k4 * S3 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule4" + }, + "assignments": { + "ode_": "k3 * S2 + (-1) * k4 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00167/model-sbml-l2v5.xml b/latest/cases/00167/model-sbml-l2v5.xml new file mode 100644 index 000000000..8a9898fb2 --- /dev/null +++ b/latest/cases/00167/model-sbml-l2v5.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + -1 + k3 + S2 + + + + k4 + S3 + S4 + + + + + + + + + + + k3 + S2 + + + + -1 + k4 + S3 + S4 + + + + + + + + + + + k3 + S2 + + + + -1 + k4 + S3 + S4 + + + + + + + diff --git a/latest/cases/00167/model-sbml-l3v2.xml b/latest/cases/00167/model-sbml-l3v2.xml new file mode 100644 index 000000000..fc213bfc9 --- /dev/null +++ b/latest/cases/00167/model-sbml-l3v2.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + -1 + k3 + S2 + + + + k4 + S3 + S4 + + + + + + + + + + + k3 + S2 + + + + -1 + k4 + S3 + S4 + + + + + + + + + + + k3 + S2 + + + + -1 + k4 + S3 + S4 + + + + + + + diff --git a/latest/cases/00167/output.heta b/latest/cases/00167/output.heta new file mode 100644 index 000000000..eb2f368cb --- /dev/null +++ b/latest/cases/00167/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +four constant parameters called k1, k2, k3 and k4. (Note that indeed S1, +S2, S3, and S4 are parameters and not species in this model.) + +The model contains four rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S2-k1 * S1$ | + | Rate | S2 | $k1 * S1-k2 * S2-k3 * S2 + k4 * S3 * S4$ | + | Rate | S3 | $k3 * S2-k4 * S3 * S4$ | + | Rate | S4 | $k3 * S2-k4 * S3 * S4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-2$ |any | +|Value of parameter S2 |$2.0 \x 10^-2$ |same as S1 | +|Value of parameter S3 |$ 0$ |same as S1 | +|Value of parameter S4 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter k3 |$ 0.15$ |second^-1^ | +|Value of parameter k4 |$ 0.1$ |(units of S1)^-1^ second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2 + (-1) * k3 * S2 + k4 * S3 * S4; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k3 * S2 + (-1) * k4 * S3 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k3 * S2 + (-1) * k4 * S3 * S4; + +S1 @Record 'S1' { } .= 0.01; +S2 @Record 'S2' { } .= 0.02; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.15; +k4 @Const 'k4' { } = 0.1; + diff --git a/latest/cases/00167/synopsis.txt b/latest/cases/00167/synopsis.txt new file mode 100644 index 000000000..b616b5a70 --- /dev/null +++ b/latest/cases/00167/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +four constant parameters called k1, k2, k3 and k4. (Note that indeed S1, +S2, S3, and S4 are parameters and not species in this model.) + +The model contains four rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S2-k1 * S1$ | + | Rate | S2 | $k1 * S1-k2 * S2-k3 * S2 + k4 * S3 * S4$ | + | Rate | S3 | $k3 * S2-k4 * S3 * S4$ | + | Rate | S4 | $k3 * S2-k4 * S3 * S4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-2$ |any | +|Value of parameter S2 |$2.0 \x 10^-2$ |same as S1 | +|Value of parameter S3 |$ 0$ |same as S1 | +|Value of parameter S4 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter k3 |$ 0.15$ |second^-1^ | +|Value of parameter k4 |$ 0.1$ |(units of S1)^-1^ second^-1^ |] + + diff --git a/latest/cases/00168/l2v5/heta-code/output.heta b/latest/cases/00168/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bcd7b7dc5 --- /dev/null +++ b/latest/cases/00168/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1 * S2 + k2 * S3 + k3 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3 + (-1) * k3 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k3 * S3; + +S1 @Record 'S1' { } .= 0.02; +S2 @Record 'S2' { } .= 0.02; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; +k1 @Record 'k1' { } .= 100; +k2 @Record 'k2' { } .= 0.9; +k3 @Record 'k3' { } .= 0.7; + diff --git a/latest/cases/00168/l2v5/index.heta b/latest/cases/00168/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00168/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00168/l2v5/json/output.json b/latest/cases/00168/l2v5/json/output.json new file mode 100644 index 000000000..d1a821f15 --- /dev/null +++ b/latest/cases/00168/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "100" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1 * S2 + k2 * S3 + k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3 + (-1) * k3 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule4" + }, + "assignments": { + "ode_": "k3 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00168/l3v2/heta-code/output.heta b/latest/cases/00168/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2520912a9 --- /dev/null +++ b/latest/cases/00168/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1 * S2 + k2 * S3 + k3 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3 + (-1) * k3 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k3 * S3; + +S1 @Record 'S1' { } .= 0.02; +S2 @Record 'S2' { } .= 0.02; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; + +k1 @Const 'k1' { } = 100; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00168/l3v2/index.heta b/latest/cases/00168/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00168/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00168/l3v2/json/output.json b/latest/cases/00168/l3v2/json/output.json new file mode 100644 index 000000000..d87aebfdf --- /dev/null +++ b/latest/cases/00168/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 100 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.9 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.7 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1 * S2 + k2 * S3 + k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3 + (-1) * k3 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule4" + }, + "assignments": { + "ode_": "k3 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00168/model-sbml-l2v5.xml b/latest/cases/00168/model-sbml-l2v5.xml new file mode 100644 index 000000000..a1264cd4f --- /dev/null +++ b/latest/cases/00168/model-sbml-l2v5.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + -1 + k1 + S1 + S2 + + + + k2 + S3 + + + + k3 + S3 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + -1 + k3 + S3 + + + + + + + + + k3 + S3 + + + + + + diff --git a/latest/cases/00168/model-sbml-l3v2.xml b/latest/cases/00168/model-sbml-l3v2.xml new file mode 100644 index 000000000..1899cc59e --- /dev/null +++ b/latest/cases/00168/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + k1 + S1 + S2 + + + + k2 + S3 + + + + k3 + S3 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + -1 + k3 + S3 + + + + + + + + + k3 + S3 + + + + + + diff --git a/latest/cases/00168/output.heta b/latest/cases/00168/output.heta new file mode 100644 index 000000000..c93fcbde9 --- /dev/null +++ b/latest/cases/00168/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +three constant parameters called k1, k2 and k3. (Note that indeed S1, +S2, S3, and S4 are parameters and not species in this model.) + +The model contains four rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3-k1 * S1 * S2 + k3 * S3$ | + | Rate | S2 | $k2 * S3-k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2-k2 * S3-k3 * S3$ | + | Rate | S4 | $k3 * S3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$2.0 \x 10^-2$ |any | +|Value of parameter S2 |$2.0 \x 10^-2$ |same as S1 | +|Value of parameter S3 |$ 0$ |same as S1 | +|Value of parameter S4 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1.0 \x 10^2$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$ 0.9$ |second^-1^ | +|Value of parameter k3 |$ 0.7$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1 * S2 + k2 * S3 + k3 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3 + (-1) * k3 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k3 * S3; + +S1 @Record 'S1' { } .= 0.02; +S2 @Record 'S2' { } .= 0.02; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; + +k1 @Const 'k1' { } = 100; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00168/synopsis.txt b/latest/cases/00168/synopsis.txt new file mode 100644 index 000000000..d46d8652a --- /dev/null +++ b/latest/cases/00168/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +three constant parameters called k1, k2 and k3. (Note that indeed S1, +S2, S3, and S4 are parameters and not species in this model.) + +The model contains four rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3-k1 * S1 * S2 + k3 * S3$ | + | Rate | S2 | $k2 * S3-k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2-k2 * S3-k3 * S3$ | + | Rate | S4 | $k3 * S3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$2.0 \x 10^-2$ |any | +|Value of parameter S2 |$2.0 \x 10^-2$ |same as S1 | +|Value of parameter S3 |$ 0$ |same as S1 | +|Value of parameter S4 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1.0 \x 10^2$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$ 0.9$ |second^-1^ | +|Value of parameter k3 |$ 0.7$ |second^-1^ |] + + diff --git a/latest/cases/00169/l2v5/heta-code/output.heta b/latest/cases/00169/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cc1dfaeff --- /dev/null +++ b/latest/cases/00169/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k2 * S2 + (-1) * k3 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k3 * S3; + +S1 @Record 'S1' { } .= 0.01; +S2 @Record 'S2' { } .= 0; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00169/l2v5/index.heta b/latest/cases/00169/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00169/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00169/l2v5/json/output.json b/latest/cases/00169/l2v5/json/output.json new file mode 100644 index 000000000..dde9db8ca --- /dev/null +++ b/latest/cases/00169/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k3 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule4" + }, + "assignments": { + "ode_": "k3 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00169/l3v2/heta-code/output.heta b/latest/cases/00169/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9cfd076c9 --- /dev/null +++ b/latest/cases/00169/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k2 * S2 + (-1) * k3 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k3 * S3; + +S1 @Record 'S1' { } .= 0.01; +S2 @Record 'S2' { } .= 0; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00169/l3v2/index.heta b/latest/cases/00169/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00169/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00169/l3v2/json/output.json b/latest/cases/00169/l3v2/json/output.json new file mode 100644 index 000000000..32462b904 --- /dev/null +++ b/latest/cases/00169/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k3 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule4" + }, + "assignments": { + "ode_": "k3 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00169/model-sbml-l2v5.xml b/latest/cases/00169/model-sbml-l2v5.xml new file mode 100644 index 000000000..49b9391d0 --- /dev/null +++ b/latest/cases/00169/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + -1 + k1 + S1 + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + k3 + S3 + + + + + + diff --git a/latest/cases/00169/model-sbml-l3v2.xml b/latest/cases/00169/model-sbml-l3v2.xml new file mode 100644 index 000000000..03476fcb6 --- /dev/null +++ b/latest/cases/00169/model-sbml-l3v2.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + -1 + k1 + S1 + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + k3 + S3 + + + + + + diff --git a/latest/cases/00169/output.heta b/latest/cases/00169/output.heta new file mode 100644 index 000000000..622f09ccb --- /dev/null +++ b/latest/cases/00169/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +three constant parameters called k1, k2 and k3. (Note that indeed S1, +S2, S3, and S4 are parameters and not species in this model.) + +The model contains four rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-k1 * S1$ | + | Rate | S2 | $k1 * S1-k2 * S2$ | + | Rate | S3 | $k2 * S2-k3 * S3$ | + | Rate | S4 | $k3 * S3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-2$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter S3 |$ 0$ |same as S1 | +|Value of parameter S4 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 0.7$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.0$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k2 * S2 + (-1) * k3 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule4"}}, }; +S4_proc := k3 * S3; + +S1 @Record 'S1' { } .= 0.01; +S2 @Record 'S2' { } .= 0; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00169/synopsis.txt b/latest/cases/00169/synopsis.txt new file mode 100644 index 000000000..915c8b008 --- /dev/null +++ b/latest/cases/00169/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +three constant parameters called k1, k2 and k3. (Note that indeed S1, +S2, S3, and S4 are parameters and not species in this model.) + +The model contains four rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-k1 * S1$ | + | Rate | S2 | $k1 * S1-k2 * S2$ | + | Rate | S3 | $k2 * S2-k3 * S3$ | + | Rate | S4 | $k3 * S3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-2$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter S3 |$ 0$ |same as S1 | +|Value of parameter S4 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 0.7$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.0$ |second^-1^ |] + + diff --git a/latest/cases/00170/l2v5/heta-code/output.heta b/latest/cases/00170/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e3cb114e9 --- /dev/null +++ b/latest/cases/00170/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule2"}}, }; +S3_proc := k3 * S2 + (-1) * k4 * S3 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule3"}}, }; +S4_proc := k3 * S2 + (-1) * k4 * S3 * S4; + +S1 @Record 'S1' { } .= 1e-4; +S2 @Record 'S2' { } .= 2e-4; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.15; +k4 @Record 'k4' { } .= 0.1; + diff --git a/latest/cases/00170/l2v5/index.heta b/latest/cases/00170/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00170/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00170/l2v5/json/output.json b/latest/cases/00170/l2v5/json/output.json new file mode 100644 index 000000000..c100b3c16 --- /dev/null +++ b/latest/cases/00170/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1e-4" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2e-4" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k3 * S2 + (-1) * k4 * S3 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k3 * S2 + (-1) * k4 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00170/l3v2/heta-code/output.heta b/latest/cases/00170/l3v2/heta-code/output.heta new file mode 100644 index 000000000..83328dffe --- /dev/null +++ b/latest/cases/00170/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule2"}}, }; +S3_proc := k3 * S2 + (-1) * k4 * S3 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule3"}}, }; +S4_proc := k3 * S2 + (-1) * k4 * S3 * S4; + +S1 @Record 'S1' { } .= 1e-4; +S2 @Record 'S2' { } .= 2e-4; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.15; +k4 @Const 'k4' { } = 0.1; + diff --git a/latest/cases/00170/l3v2/index.heta b/latest/cases/00170/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00170/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00170/l3v2/json/output.json b/latest/cases/00170/l3v2/json/output.json new file mode 100644 index 000000000..ac3cf1a91 --- /dev/null +++ b/latest/cases/00170/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1e-4" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2e-4" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.15 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.1 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k3 * S2 + (-1) * k4 * S3 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k3 * S2 + (-1) * k4 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00170/model-sbml-l2v5.xml b/latest/cases/00170/model-sbml-l2v5.xml new file mode 100644 index 000000000..315a88fab --- /dev/null +++ b/latest/cases/00170/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k3 + S2 + + + + -1 + k4 + S3 + S4 + + + + + + + + + + + k3 + S2 + + + + -1 + k4 + S3 + S4 + + + + + + + diff --git a/latest/cases/00170/model-sbml-l3v2.xml b/latest/cases/00170/model-sbml-l3v2.xml new file mode 100644 index 000000000..207e91843 --- /dev/null +++ b/latest/cases/00170/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S2 + + + + -1 + k1 + S1 + + + + + + + + + + + k3 + S2 + + + + -1 + k4 + S3 + S4 + + + + + + + + + + + k3 + S2 + + + + -1 + k4 + S3 + S4 + + + + + + + diff --git a/latest/cases/00170/output.heta b/latest/cases/00170/output.heta new file mode 100644 index 000000000..b36aa92fe --- /dev/null +++ b/latest/cases/00170/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +four constant parameters called k1, k2, k3 and k4. (Note that indeed S1, +S2, S3, and S4 are parameters and not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S2-k1 * S1$ | + | Rate | S3 | $k3 * S2-k4 * S3 * S4$ | + | Rate | S4 | $k3 * S2-k4 * S3 * S4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-4$ |any | +|Value of parameter S2 |$2.0 \x 10^-4$ |any | +|Value of parameter S3 |$ 0$ |any | +|Value of parameter S4 |$ 0$ |same as S3 | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |(units of S1) (units of S2)^-1^ second^-1^ | +|Value of parameter k3 |$ 0.15$ |(units of S3) (units of S2)^-1^ second^-1^ | +|Value of parameter k4 |$ 0.1$ |(units of S3)^-1^ second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S2 + (-1) * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule2"}}, }; +S3_proc := k3 * S2 + (-1) * k4 * S3 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule3"}}, }; +S4_proc := k3 * S2 + (-1) * k4 * S3 * S4; + +S1 @Record 'S1' { } .= 1e-4; +S2 @Record 'S2' { } .= 2e-4; +S3 @Record 'S3' { } .= 0; +S4 @Record 'S4' { } .= 0; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.15; +k4 @Const 'k4' { } = 0.1; + diff --git a/latest/cases/00170/synopsis.txt b/latest/cases/00170/synopsis.txt new file mode 100644 index 000000000..add56ee19 --- /dev/null +++ b/latest/cases/00170/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Model using parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +four constant parameters called k1, k2, k3 and k4. (Note that indeed S1, +S2, S3, and S4 are parameters and not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S2-k1 * S1$ | + | Rate | S3 | $k3 * S2-k4 * S3 * S4$ | + | Rate | S4 | $k3 * S2-k4 * S3 * S4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-4$ |any | +|Value of parameter S2 |$2.0 \x 10^-4$ |any | +|Value of parameter S3 |$ 0$ |any | +|Value of parameter S4 |$ 0$ |same as S3 | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |(units of S1) (units of S2)^-1^ second^-1^ | +|Value of parameter k3 |$ 0.15$ |(units of S3) (units of S2)^-1^ second^-1^ | +|Value of parameter k4 |$ 0.1$ |(units of S3)^-1^ second^-1^ |] + + diff --git a/latest/cases/00171/l2v5/heta-code/output.heta b/latest/cases/00171/l2v5/heta-code/output.heta new file mode 100644 index 000000000..977e66837 --- /dev/null +++ b/latest/cases/00171/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * multiply(k1, S1); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := multiply(k1, S1); + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0.015; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00171/l2v5/index.heta b/latest/cases/00171/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00171/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00171/l2v5/json/output.json b/latest/cases/00171/l2v5/json/output.json new file mode 100644 index 000000000..54555b541 --- /dev/null +++ b/latest/cases/00171/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00171/l3v2/heta-code/output.heta b/latest/cases/00171/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4f1b27e2a --- /dev/null +++ b/latest/cases/00171/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * multiply(k1, S1); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := multiply(k1, S1); + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0.015; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00171/l3v2/index.heta b/latest/cases/00171/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00171/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00171/l3v2/json/output.json b/latest/cases/00171/l3v2/json/output.json new file mode 100644 index 000000000..160528ca9 --- /dev/null +++ b/latest/cases/00171/l3v2/json/output.json @@ -0,0 +1,69 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00171/model-sbml-l2v5.xml b/latest/cases/00171/model-sbml-l2v5.xml new file mode 100644 index 000000000..7d3bad535 --- /dev/null +++ b/latest/cases/00171/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + -1 + + multiply + k1 + S1 + + + + + + + + multiply + k1 + S1 + + + + + + diff --git a/latest/cases/00171/model-sbml-l3v2.xml b/latest/cases/00171/model-sbml-l3v2.xml new file mode 100644 index 000000000..2174f149f --- /dev/null +++ b/latest/cases/00171/model-sbml-l3v2.xml @@ -0,0 +1,60 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + -1 + + multiply + k1 + S1 + + + + + + + + multiply + k1 + S1 + + + + + + diff --git a/latest/cases/00171/output.heta b/latest/cases/00171/output.heta new file mode 100644 index 000000000..bef1cad97 --- /dev/null +++ b/latest/cases/00171/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Model using rules and parameters with a functionDefinition. +componentTags: Parameter, FunctionDefinition, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-multiply(k1, S1)$ | + | Rate | S2 | $multiply(k1, S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$1.5 \x 10^-2$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ |] + + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * multiply(k1, S1); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := multiply(k1, S1); + +S1 @Record 'S1' { } .= 0.015; +S2 @Record 'S2' { } .= 0.015; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00171/synopsis.txt b/latest/cases/00171/synopsis.txt new file mode 100644 index 000000000..2eb955a0b --- /dev/null +++ b/latest/cases/00171/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Model using rules and parameters with a functionDefinition. +componentTags: Parameter, FunctionDefinition, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-multiply(k1, S1)$ | + | Rate | S2 | $multiply(k1, S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-2$ |any | +|Value of parameter S2 |$1.5 \x 10^-2$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ |] + + diff --git a/latest/cases/00172/l2v5/heta-code/output.heta b/latest/cases/00172/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3c258d2e3 --- /dev/null +++ b/latest/cases/00172/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= 1; +S2 @Record 'S2' { } .= 0; +k1 @Record 'k1' { } .= 1; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00172/l2v5/index.heta b/latest/cases/00172/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00172/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00172/l2v5/json/output.json b/latest/cases/00172/l2v5/json/output.json new file mode 100644 index 000000000..f2b60e0ca --- /dev/null +++ b/latest/cases/00172/l2v5/json/output.json @@ -0,0 +1,93 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00172/l3v2/heta-code/output.heta b/latest/cases/00172/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0f2c0c30d --- /dev/null +++ b/latest/cases/00172/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= 1; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 1; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00172/l3v2/index.heta b/latest/cases/00172/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00172/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00172/l3v2/json/output.json b/latest/cases/00172/l3v2/json/output.json new file mode 100644 index 000000000..df68246e3 --- /dev/null +++ b/latest/cases/00172/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + } +] \ No newline at end of file diff --git a/latest/cases/00172/model-sbml-l2v5.xml b/latest/cases/00172/model-sbml-l2v5.xml new file mode 100644 index 000000000..316b7dab9 --- /dev/null +++ b/latest/cases/00172/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + -1 + k1 + S1 + + + + + + + + k1 + S1 + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00172/model-sbml-l3v2.xml b/latest/cases/00172/model-sbml-l3v2.xml new file mode 100644 index 000000000..a804d036d --- /dev/null +++ b/latest/cases/00172/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + -1 + k1 + S1 + + + + + + + + k1 + S1 + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00172/output.heta b/latest/cases/00172/output.heta new file mode 100644 index 000000000..f322d452a --- /dev/null +++ b/latest/cases/00172/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Model using rules and parameters with an event. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-k1 * S1$ | + | Rate | S2 | $k1 * S1$ |] + + +The model contains one event defined as: + +[{width:30em,margin: 1em auto}| | Trigger | Delay | Assignments | + | Event1 | $S1 < 0.1$ | $-$ | $S1 = 1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 1.0$ |any | +|Value of parameter S2 |$ 0.0$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= 1; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 1; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00172/synopsis.txt b/latest/cases/00172/synopsis.txt new file mode 100644 index 000000000..1fb7cbeac --- /dev/null +++ b/latest/cases/00172/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Model using rules and parameters with an event. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-k1 * S1$ | + | Rate | S2 | $k1 * S1$ |] + + +The model contains one event defined as: + +[{width:30em,margin: 1em auto}| | Trigger | Delay | Assignments | + | Event1 | $S1 < 0.1$ | $-$ | $S1 = 1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 1.0$ |any | +|Value of parameter S2 |$ 0.0$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ |] + + diff --git a/latest/cases/00173/l2v5/heta-code/output.heta b/latest/cases/00173/l2v5/heta-code/output.heta new file mode 100644 index 000000000..952062467 --- /dev/null +++ b/latest/cases/00173/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * factorial(ceil(p1 * S1)) * pow(p2, (-1)); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := factorial(ceil(p1 * S1)) * pow(p2, (-1)); + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 0; +p1 @Record 'p1' { } .= 4; +p2 @Record 'p2' { } .= 25; + diff --git a/latest/cases/00173/l2v5/index.heta b/latest/cases/00173/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00173/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00173/l2v5/json/output.json b/latest/cases/00173/l2v5/json/output.json new file mode 100644 index 000000000..978c44f72 --- /dev/null +++ b/latest/cases/00173/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "4" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "25" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * factorial(ceil(p1 * S1)) * pow(p2, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "factorial(ceil(p1 * S1)) * pow(p2, (-1))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00173/l3v2/heta-code/output.heta b/latest/cases/00173/l3v2/heta-code/output.heta new file mode 100644 index 000000000..276da93e6 --- /dev/null +++ b/latest/cases/00173/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * factorial(ceil(p1 * S1)) * pow(p2, (-1)); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := factorial(ceil(p1 * S1)) * pow(p2, (-1)); + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 0; + +p1 @Const 'p1' { } = 4; +p2 @Const 'p2' { } = 25; + diff --git a/latest/cases/00173/l3v2/index.heta b/latest/cases/00173/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00173/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00173/l3v2/json/output.json b/latest/cases/00173/l3v2/json/output.json new file mode 100644 index 000000000..bcecfbca2 --- /dev/null +++ b/latest/cases/00173/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 4 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 25 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * factorial(ceil(p1 * S1)) * pow(p2, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "factorial(ceil(p1 * S1)) * pow(p2, (-1))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00173/model-sbml-l2v5.xml b/latest/cases/00173/model-sbml-l2v5.xml new file mode 100644 index 000000000..bf16a417c --- /dev/null +++ b/latest/cases/00173/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + -1 + + + + + + + p1 + S1 + + + + + + p2 + -1 + + + + + + + + + + + + + + + p1 + S1 + + + + + + p2 + -1 + + + + + + + diff --git a/latest/cases/00173/model-sbml-l3v2.xml b/latest/cases/00173/model-sbml-l3v2.xml new file mode 100644 index 000000000..a33a658d7 --- /dev/null +++ b/latest/cases/00173/model-sbml-l3v2.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + + p1 + S1 + + + + + + p2 + -1 + + + + + + + + + + + + + + + p1 + S1 + + + + + + p2 + -1 + + + + + + + diff --git a/latest/cases/00173/output.heta b/latest/cases/00173/output.heta new file mode 100644 index 000000000..2e5a4263d --- /dev/null +++ b/latest/cases/00173/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: Model using rules and parameters with a rate that causes a discontinuity + in the output. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called p1 and p2. (Note that indeed S1 and S2 are parameters and +not species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-Ceiling(S1 * p1)! / p2$ | + | Rate | S2 | $Ceiling(S1 * p1)! / p2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 1.0$ |any | +|Value of parameter S2 |$ 0.0$ |same as S1 | +|Value of parameter p1 |$ $ |(units of S1)^-1^ | +|Value of parameter p2 |$ 2$ |second (units of S1)^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * factorial(ceil(p1 * S1)) * pow(p2, (-1)); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := factorial(ceil(p1 * S1)) * pow(p2, (-1)); + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 0; + +p1 @Const 'p1' { } = 4; +p2 @Const 'p2' { } = 25; + diff --git a/latest/cases/00173/synopsis.txt b/latest/cases/00173/synopsis.txt new file mode 100644 index 000000000..66361efa9 --- /dev/null +++ b/latest/cases/00173/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Model using rules and parameters with a rate that causes a discontinuity + in the output. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called p1 and p2. (Note that indeed S1 and S2 are parameters and +not species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-Ceiling(S1 * p1)! / p2$ | + | Rate | S2 | $Ceiling(S1 * p1)! / p2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 1.0$ |any | +|Value of parameter S2 |$ 0.0$ |same as S1 | +|Value of parameter p1 |$ $ |(units of S1)^-1^ | +|Value of parameter p2 |$ 2$ |second (units of S1)^-1^ |] + + diff --git a/latest/cases/00174/l2v5/heta-code/output.heta b/latest/cases/00174/l2v5/heta-code/output.heta new file mode 100644 index 000000000..df93f11a5 --- /dev/null +++ b/latest/cases/00174/l2v5/heta-code/output.heta @@ -0,0 +1,12 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1 @Record 'S1' { } .= 0; +S1 := 7; + diff --git a/latest/cases/00174/l2v5/index.heta b/latest/cases/00174/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00174/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00174/l2v5/json/output.json b/latest/cases/00174/l2v5/json/output.json new file mode 100644 index 000000000..0bd2984e1 --- /dev/null +++ b/latest/cases/00174/l2v5/json/output.json @@ -0,0 +1,39 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0", + "ode_": "7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00174/l3v2/heta-code/output.heta b/latest/cases/00174/l3v2/heta-code/output.heta new file mode 100644 index 000000000..031b4839d --- /dev/null +++ b/latest/cases/00174/l3v2/heta-code/output.heta @@ -0,0 +1,7 @@ + + +t @TimeScale { units: second, }; + +S1 @Record 'S1' { } .= 0; +S1 := 7; + diff --git a/latest/cases/00174/l3v2/index.heta b/latest/cases/00174/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00174/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00174/l3v2/json/output.json b/latest/cases/00174/l3v2/json/output.json new file mode 100644 index 000000000..a92fd9876 --- /dev/null +++ b/latest/cases/00174/l3v2/json/output.json @@ -0,0 +1,15 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0", + "ode_": "7" + } + } +] \ No newline at end of file diff --git a/latest/cases/00174/model-sbml-l2v5.xml b/latest/cases/00174/model-sbml-l2v5.xml new file mode 100644 index 000000000..97effcdd4 --- /dev/null +++ b/latest/cases/00174/model-sbml-l2v5.xml @@ -0,0 +1,15 @@ + + + + + + + + + + 7 + + + + + diff --git a/latest/cases/00174/model-sbml-l3v2.xml b/latest/cases/00174/model-sbml-l3v2.xml new file mode 100644 index 000000000..77487300b --- /dev/null +++ b/latest/cases/00174/model-sbml-l3v2.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + 7 + + + + + diff --git a/latest/cases/00174/output.heta b/latest/cases/00174/output.heta new file mode 100644 index 000000000..0c285c81f --- /dev/null +++ b/latest/cases/00174/output.heta @@ -0,0 +1,33 @@ +/* +category: Test +synopsis: Model using rules and parameters only. +componentTags: Parameter, AssignmentRule +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying parameter called S1. (Note that indeed +S1 is a parameter and not species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S1 | $3 + 4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 0.0$ |any |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1 @Record 'S1' { } .= 0; +S1 := 7; + diff --git a/latest/cases/00174/synopsis.txt b/latest/cases/00174/synopsis.txt new file mode 100644 index 000000000..d7c186ab1 --- /dev/null +++ b/latest/cases/00174/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Model using rules and parameters only. +componentTags: Parameter, AssignmentRule +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying parameter called S1. (Note that indeed +S1 is a parameter and not species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S1 | $3 + 4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 0.0$ |any |] + + diff --git a/latest/cases/00175/l2v5/heta-code/output.heta b/latest/cases/00175/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3beef85f6 --- /dev/null +++ b/latest/cases/00175/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := 7; + +S1 @Record 'S1' { } .= 0; + diff --git a/latest/cases/00175/l2v5/index.heta b/latest/cases/00175/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00175/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00175/l2v5/json/output.json b/latest/cases/00175/l2v5/json/output.json new file mode 100644 index 000000000..65733b611 --- /dev/null +++ b/latest/cases/00175/l2v5/json/output.json @@ -0,0 +1,54 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "7" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00175/l3v2/heta-code/output.heta b/latest/cases/00175/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5da4284af --- /dev/null +++ b/latest/cases/00175/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := 7; + +S1 @Record 'S1' { } .= 0; + diff --git a/latest/cases/00175/l3v2/index.heta b/latest/cases/00175/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00175/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00175/l3v2/json/output.json b/latest/cases/00175/l3v2/json/output.json new file mode 100644 index 000000000..27891c047 --- /dev/null +++ b/latest/cases/00175/l3v2/json/output.json @@ -0,0 +1,30 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "7" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00175/model-sbml-l2v5.xml b/latest/cases/00175/model-sbml-l2v5.xml new file mode 100644 index 000000000..e03bb11e6 --- /dev/null +++ b/latest/cases/00175/model-sbml-l2v5.xml @@ -0,0 +1,15 @@ + + + + + + + + + + 7 + + + + + diff --git a/latest/cases/00175/model-sbml-l3v2.xml b/latest/cases/00175/model-sbml-l3v2.xml new file mode 100644 index 000000000..71b9227d6 --- /dev/null +++ b/latest/cases/00175/model-sbml-l3v2.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + 7 + + + + + diff --git a/latest/cases/00175/output.heta b/latest/cases/00175/output.heta new file mode 100644 index 000000000..db8448c8f --- /dev/null +++ b/latest/cases/00175/output.heta @@ -0,0 +1,35 @@ +/* +category: Test +synopsis: Model using rules and parameters only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying parameter called S1. (Note that indeed +S1 is a parameter and not species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 0.0$ |any |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := 7; + +S1 @Record 'S1' { } .= 0; + diff --git a/latest/cases/00175/synopsis.txt b/latest/cases/00175/synopsis.txt new file mode 100644 index 000000000..787861466 --- /dev/null +++ b/latest/cases/00175/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Model using rules and parameters only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying parameter called S1. (Note that indeed +S1 is a parameter and not species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 0.0$ |any |] + + diff --git a/latest/cases/00176/l2v5/heta-code/output.heta b/latest/cases/00176/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2d9fba8e0 --- /dev/null +++ b/latest/cases/00176/l2v5/heta-code/output.heta @@ -0,0 +1,18 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 0.15; +S2 @Record 'S2' { } .= 0; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00176/l2v5/index.heta b/latest/cases/00176/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00176/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00176/l2v5/json/output.json b/latest/cases/00176/l2v5/json/output.json new file mode 100644 index 000000000..8db4fc9a6 --- /dev/null +++ b/latest/cases/00176/l2v5/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00176/l3v2/heta-code/output.heta b/latest/cases/00176/l3v2/heta-code/output.heta new file mode 100644 index 000000000..40922c8db --- /dev/null +++ b/latest/cases/00176/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 0.15; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00176/l3v2/index.heta b/latest/cases/00176/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00176/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00176/l3v2/json/output.json b/latest/cases/00176/l3v2/json/output.json new file mode 100644 index 000000000..e41c86490 --- /dev/null +++ b/latest/cases/00176/l3v2/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00176/model-sbml-l2v5.xml b/latest/cases/00176/model-sbml-l2v5.xml new file mode 100644 index 000000000..a81c282f3 --- /dev/null +++ b/latest/cases/00176/model-sbml-l2v5.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + -1 + k1 + S1 + + + + + + + + k1 + S1 + + + + + + diff --git a/latest/cases/00176/model-sbml-l3v2.xml b/latest/cases/00176/model-sbml-l3v2.xml new file mode 100644 index 000000000..34a6990a9 --- /dev/null +++ b/latest/cases/00176/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + -1 + k1 + S1 + + + + + + + + k1 + S1 + + + + + + diff --git a/latest/cases/00176/output.heta b/latest/cases/00176/output.heta new file mode 100644 index 000000000..6d76a4d24 --- /dev/null +++ b/latest/cases/00176/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Model with parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-(k1 * S1)$ | + | Rate | S2 | $k1 * S1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-1$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 0.15; +S2 @Record 'S2' { } .= 0; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00176/synopsis.txt b/latest/cases/00176/synopsis.txt new file mode 100644 index 000000000..acd3a0a0a --- /dev/null +++ b/latest/cases/00176/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Model with parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-(k1 * S1)$ | + | Rate | S2 | $k1 * S1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-1$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1$ |second^-1^ |] + + diff --git a/latest/cases/00177/l2v5/heta-code/output.heta b/latest/cases/00177/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e549202ec --- /dev/null +++ b/latest/cases/00177/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := 0.5; +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 0.15; +S2 @Record 'S2' { } .= 0; +k1 @Record 'k1' { } .= 0.1; + diff --git a/latest/cases/00177/l2v5/index.heta b/latest/cases/00177/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00177/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00177/l2v5/json/output.json b/latest/cases/00177/l2v5/json/output.json new file mode 100644 index 000000000..24a14fdf2 --- /dev/null +++ b/latest/cases/00177/l2v5/json/output.json @@ -0,0 +1,102 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00177/l3v2/heta-code/output.heta b/latest/cases/00177/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f7421e8d6 --- /dev/null +++ b/latest/cases/00177/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := 0.5; +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 0.15; +S2 @Record 'S2' { } .= 0; +k1 @Record 'k1' { } .= 0.1; + diff --git a/latest/cases/00177/l3v2/index.heta b/latest/cases/00177/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00177/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00177/l3v2/json/output.json b/latest/cases/00177/l3v2/json/output.json new file mode 100644 index 000000000..43d5d63c4 --- /dev/null +++ b/latest/cases/00177/l3v2/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00177/model-sbml-l2v5.xml b/latest/cases/00177/model-sbml-l2v5.xml new file mode 100644 index 000000000..38d2b6b81 --- /dev/null +++ b/latest/cases/00177/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + 0.5 + + + + + + + -1 + k1 + S1 + + + + + + + + k1 + S1 + + + + + + diff --git a/latest/cases/00177/model-sbml-l3v2.xml b/latest/cases/00177/model-sbml-l3v2.xml new file mode 100644 index 000000000..8aeffbf23 --- /dev/null +++ b/latest/cases/00177/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + + 0.5 + + + + + + + -1 + k1 + S1 + + + + + + + + k1 + S1 + + + + + + diff --git a/latest/cases/00177/output.heta b/latest/cases/00177/output.heta new file mode 100644 index 000000000..b7c6dd9ca --- /dev/null +++ b/latest/cases/00177/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Model with parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $0.5$ | + | Rate | S1 | $-(k1 * S1)$ | + | Rate | S2 | $k1 * S1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-1$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1 \x 10^-1$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := 0.5; +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k1 * S1; + +S1 @Record 'S1' { } .= 0.15; +S2 @Record 'S2' { } .= 0; +k1 @Record 'k1' { } .= 0.1; + diff --git a/latest/cases/00177/synopsis.txt b/latest/cases/00177/synopsis.txt new file mode 100644 index 000000000..125c9cca5 --- /dev/null +++ b/latest/cases/00177/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Model with parameters and rules only. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and one constant +parameter called k1. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $0.5$ | + | Rate | S1 | $-(k1 * S1)$ | + | Rate | S2 | $k1 * S1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.5 \x 10^-1$ |any | +|Value of parameter S2 |$ 0$ |same as S1 | +|Value of parameter k1 |$ 1 \x 10^-1$ |second^-1^ |] + + diff --git a/latest/cases/00178/l2v5/heta-code/output.heta b/latest/cases/00178/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b5bc11cc5 --- /dev/null +++ b/latest/cases/00178/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { }; + +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := multiply(k1, S1, S2) + (-1) * k2 * S3; +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := k2 * S3 + (-1) * multiply(k1, S1, S2); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S3 + (-1) * multiply(k1, S1, S2); + +S1 @Record 'S1' { } .= 0.1; +S2 @Record 'S2' { } .= 0.2; +S3 @Record 'S3' { } .= 0.1; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00178/l2v5/index.heta b/latest/cases/00178/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00178/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00178/l2v5/json/output.json b/latest/cases/00178/l2v5/json/output.json new file mode 100644 index 000000000..bcf1a0de1 --- /dev/null +++ b/latest/cases/00178/l2v5/json/output.json @@ -0,0 +1,128 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(k1, S1, S2) + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00178/l3v2/heta-code/output.heta b/latest/cases/00178/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e240f514f --- /dev/null +++ b/latest/cases/00178/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := multiply(k1, S1, S2) + (-1) * k2 * S3; +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := k2 * S3 + (-1) * multiply(k1, S1, S2); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S3 + (-1) * multiply(k1, S1, S2); + +S1 @Record 'S1' { } .= 0.1; +S2 @Record 'S2' { } .= 0.2; +S3 @Record 'S3' { } .= 0.1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00178/l3v2/index.heta b/latest/cases/00178/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00178/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00178/l3v2/json/output.json b/latest/cases/00178/l3v2/json/output.json new file mode 100644 index 000000000..b629291a3 --- /dev/null +++ b/latest/cases/00178/l3v2/json/output.json @@ -0,0 +1,100 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(k1, S1, S2) + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00178/model-sbml-l2v5.xml b/latest/cases/00178/model-sbml-l2v5.xml new file mode 100644 index 000000000..daac38973 --- /dev/null +++ b/latest/cases/00178/model-sbml-l2v5.xml @@ -0,0 +1,100 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + multiply + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + k2 + S3 + + + + -1 + + multiply + k1 + S1 + S2 + + + + + + + + + + + + k2 + S3 + + + + -1 + + multiply + k1 + S1 + S2 + + + + + + + + diff --git a/latest/cases/00178/model-sbml-l3v2.xml b/latest/cases/00178/model-sbml-l3v2.xml new file mode 100644 index 000000000..180c663b8 --- /dev/null +++ b/latest/cases/00178/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + k2 + S3 + + + + -1 + + multiply + k1 + S1 + S2 + + + + + + + + + + + + k2 + S3 + + + + -1 + + multiply + k1 + S1 + S2 + + + + + + + + diff --git a/latest/cases/00178/output.heta b/latest/cases/00178/output.heta new file mode 100644 index 000000000..7755aad5b --- /dev/null +++ b/latest/cases/00178/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Model with parameters and rules with a functionDefinition. +componentTags: Parameter, FunctionDefinition, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $multiply(k1, S1, S2)$ | + | Rate | S1 | $k2 * S3 - multiply(k1, S1, S2)$ | + | Rate | S2 | $k2 * S3 - multiply(k1, S1, S2)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-1$ |any | +|Value of parameter S2 |$2.0 \x 10^-1$ |same as S1 | +|Value of parameter S3 |$1.0 \x 10^-1$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + + +*/ + + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := multiply(k1, S1, S2) + (-1) * k2 * S3; +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := k2 * S3 + (-1) * multiply(k1, S1, S2); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S3 + (-1) * multiply(k1, S1, S2); + +S1 @Record 'S1' { } .= 0.1; +S2 @Record 'S2' { } .= 0.2; +S3 @Record 'S3' { } .= 0.1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00178/synopsis.txt b/latest/cases/00178/synopsis.txt new file mode 100644 index 000000000..c834ad932 --- /dev/null +++ b/latest/cases/00178/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Model with parameters and rules with a functionDefinition. +componentTags: Parameter, FunctionDefinition, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $multiply(k1, S1, S2)$ | + | Rate | S1 | $k2 * S3 - multiply(k1, S1, S2)$ | + | Rate | S2 | $k2 * S3 - multiply(k1, S1, S2)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-1$ |any | +|Value of parameter S2 |$2.0 \x 10^-1$ |same as S1 | +|Value of parameter S3 |$1.0 \x 10^-1$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + + diff --git a/latest/cases/00179/l2v5/heta-code/output.heta b/latest/cases/00179/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cf5efcf10 --- /dev/null +++ b/latest/cases/00179/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := multiply(k1, S1 * S2) + (-1) * k2 * S3 * S4; +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2)); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2)); + +S1 @Record 'S1' { } .= 0.1; +S2 @Record 'S2' { } .= 0.2; +S3 @Record 'S3' { } .= 0.1; +S4 @Record 'S4' { } .= 0.1; +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 2.5; + diff --git a/latest/cases/00179/l2v5/index.heta b/latest/cases/00179/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00179/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00179/l2v5/json/output.json b/latest/cases/00179/l2v5/json/output.json new file mode 100644 index 000000000..ca207039b --- /dev/null +++ b/latest/cases/00179/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(k1, S1 * S2) + (-1) * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00179/l3v2/heta-code/output.heta b/latest/cases/00179/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5a4b336d7 --- /dev/null +++ b/latest/cases/00179/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := multiply(k1, S1 * S2) + (-1) * k2 * S3 * S4; +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2)); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2)); + +S1 @Record 'S1' { } .= 0.1; +S2 @Record 'S2' { } .= 0.2; +S3 @Record 'S3' { } .= 0.1; +S4 @Record 'S4' { } .= 0.1; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00179/l3v2/index.heta b/latest/cases/00179/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00179/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00179/l3v2/json/output.json b/latest/cases/00179/l3v2/json/output.json new file mode 100644 index 000000000..b4ce59c69 --- /dev/null +++ b/latest/cases/00179/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(k1, S1 * S2) + (-1) * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00179/model-sbml-l2v5.xml b/latest/cases/00179/model-sbml-l2v5.xml new file mode 100644 index 000000000..1c5aca4ff --- /dev/null +++ b/latest/cases/00179/model-sbml-l2v5.xml @@ -0,0 +1,109 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + multiply + k1 + + + S1 + S2 + + + + + -1 + k2 + S3 + S4 + + + + + + + + + + + k2 + S3 + S4 + + + + -1 + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + k2 + S3 + S4 + + + + -1 + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + diff --git a/latest/cases/00179/model-sbml-l3v2.xml b/latest/cases/00179/model-sbml-l3v2.xml new file mode 100644 index 000000000..7c201d6b6 --- /dev/null +++ b/latest/cases/00179/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + + + S1 + S2 + + + + + -1 + k2 + S3 + S4 + + + + + + + + + + + k2 + S3 + S4 + + + + -1 + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + k2 + S3 + S4 + + + + -1 + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + diff --git a/latest/cases/00179/output.heta b/latest/cases/00179/output.heta new file mode 100644 index 000000000..e5eab57dd --- /dev/null +++ b/latest/cases/00179/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Model with parameters and rules with a functionDefinition. +componentTags: Parameter, FunctionDefinition, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +two constant parameters called k1 and k2. (Note +that indeed S1, S2, S3 and S4 are parameters and not species in this +model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $multiply(k1, (S1 * S2))$ | + | Rate | S1 | $k2 * S3 * S4 - multiply(k1, multiply(S1, S2))$ | + | Rate | S2 | $k2 * S3 * S4 - multiply(k1, multiply(S1, S2))$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-1$ |any | +|Value of parameter S2 |$2.0 \x 10^-1$ |same as S1 | +|Value of parameter S3 |$1.0 \x 10^-1$ |same as S1 | +|Value of parameter S4 |$1.0 \x 10^-1$ |any | +|Value of parameter k1 |$0.75 \x 10^1$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |(units of S4)^-1^ second^-1^ |] + + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := multiply(k1, S1 * S2) + (-1) * k2 * S3 * S4; +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2)); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2)); + +S1 @Record 'S1' { } .= 0.1; +S2 @Record 'S2' { } .= 0.2; +S3 @Record 'S3' { } .= 0.1; +S4 @Record 'S4' { } .= 0.1; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00179/synopsis.txt b/latest/cases/00179/synopsis.txt new file mode 100644 index 000000000..13e2fa0c3 --- /dev/null +++ b/latest/cases/00179/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Model with parameters and rules with a functionDefinition. +componentTags: Parameter, FunctionDefinition, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four varying parameters called S1, S2, S3 and S4 and +two constant parameters called k1 and k2. (Note +that indeed S1, S2, S3 and S4 are parameters and not species in this +model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $multiply(k1, (S1 * S2))$ | + | Rate | S1 | $k2 * S3 * S4 - multiply(k1, multiply(S1, S2))$ | + | Rate | S2 | $k2 * S3 * S4 - multiply(k1, multiply(S1, S2))$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$1.0 \x 10^-1$ |any | +|Value of parameter S2 |$2.0 \x 10^-1$ |same as S1 | +|Value of parameter S3 |$1.0 \x 10^-1$ |same as S1 | +|Value of parameter S4 |$1.0 \x 10^-1$ |any | +|Value of parameter k1 |$0.75 \x 10^1$ |(units of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |(units of S4)^-1^ second^-1^ |] + + diff --git a/latest/cases/00180/l2v5/heta-code/output.heta b/latest/cases/00180/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a39bc9993 --- /dev/null +++ b/latest/cases/00180/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k2 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= k1 * S2; +S2 @Record 'S2' { } .= 0.2; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00180/l2v5/index.heta b/latest/cases/00180/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00180/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00180/l2v5/json/output.json b/latest/cases/00180/l2v5/json/output.json new file mode 100644 index 000000000..cfdb14866 --- /dev/null +++ b/latest/cases/00180/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "k1 * S2" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k2 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00180/l3v2/heta-code/output.heta b/latest/cases/00180/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2cde7ada1 --- /dev/null +++ b/latest/cases/00180/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k2 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= k1 * S2; +S2 @Record 'S2' { } .= 0.2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00180/l3v2/index.heta b/latest/cases/00180/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00180/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00180/l3v2/json/output.json b/latest/cases/00180/l3v2/json/output.json new file mode 100644 index 000000000..6ff0fe396 --- /dev/null +++ b/latest/cases/00180/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "k1 * S2" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k2 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00180/model-sbml-l2v5.xml b/latest/cases/00180/model-sbml-l2v5.xml new file mode 100644 index 000000000..31eb9a235 --- /dev/null +++ b/latest/cases/00180/model-sbml-l2v5.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + -1 + k2 + S1 + + + + + + + + k2 + S1 + + + + + + diff --git a/latest/cases/00180/model-sbml-l3v2.xml b/latest/cases/00180/model-sbml-l3v2.xml new file mode 100644 index 000000000..9064f1c23 --- /dev/null +++ b/latest/cases/00180/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + -1 + k2 + S1 + + + + + + + + k2 + S1 + + + + + + diff --git a/latest/cases/00180/output.heta b/latest/cases/00180/output.heta new file mode 100644 index 000000000..0a94495d4 --- /dev/null +++ b/latest/cases/00180/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Model with parameters and rules with an initialAssignment. +componentTags: Parameter, InitialAssignment, RateRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-k2 * S1 $ | + | Rate | S2 | $k2 * S1 $ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: InitialAssignments override any declared initial values. In this +case, the initial value of S1 has not been explicitly declared and must be +calculated using the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ undeclared$ |any | +|Value of parameter S2 |$2.0 \x 10^-1$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := (-1) * k2 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= k1 * S2; +S2 @Record 'S2' { } .= 0.2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00180/synopsis.txt b/latest/cases/00180/synopsis.txt new file mode 100644 index 000000000..49990b3b4 --- /dev/null +++ b/latest/cases/00180/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Model with parameters and rules with an initialAssignment. +componentTags: Parameter, InitialAssignment, RateRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $-k2 * S1 $ | + | Rate | S2 | $k2 * S1 $ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: InitialAssignments override any declared initial values. In this +case, the initial value of S1 has not been explicitly declared and must be +calculated using the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ undeclared$ |any | +|Value of parameter S2 |$2.0 \x 10^-1$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + + diff --git a/latest/cases/00181/l2v5/heta-code/output.heta b/latest/cases/00181/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ce3ab9563 --- /dev/null +++ b/latest/cases/00181/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * k2 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 1.5e-15; +S3 @Record 'S3' { }; +S3 := k1 * S2; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00181/l2v5/index.heta b/latest/cases/00181/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00181/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00181/l2v5/json/output.json b/latest/cases/00181/l2v5/json/output.json new file mode 100644 index 000000000..9b47a4454 --- /dev/null +++ b/latest/cases/00181/l2v5/json/output.json @@ -0,0 +1,102 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "1.5e-15" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "ode_": "k1 * S2" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00181/l3v2/heta-code/output.heta b/latest/cases/00181/l3v2/heta-code/output.heta new file mode 100644 index 000000000..343bf3535 --- /dev/null +++ b/latest/cases/00181/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * k2 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 1.5e-15; +S3 @Record 'S3' { }; +S3 := k1 * S2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00181/l3v2/index.heta b/latest/cases/00181/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00181/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00181/l3v2/json/output.json b/latest/cases/00181/l3v2/json/output.json new file mode 100644 index 000000000..d58bc9c02 --- /dev/null +++ b/latest/cases/00181/l3v2/json/output.json @@ -0,0 +1,74 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "1.5e-15" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "ode_": "k1 * S2" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00181/model-sbml-l2v5.xml b/latest/cases/00181/model-sbml-l2v5.xml new file mode 100644 index 000000000..f10b6eaae --- /dev/null +++ b/latest/cases/00181/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + -1 + k2 + S1 + + + + + + + + k2 + S1 + + + + + + diff --git a/latest/cases/00181/model-sbml-l3v2.xml b/latest/cases/00181/model-sbml-l3v2.xml new file mode 100644 index 000000000..62ba0d0ba --- /dev/null +++ b/latest/cases/00181/model-sbml-l3v2.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + -1 + k2 + S1 + + + + + + + + k2 + S1 + + + + + + diff --git a/latest/cases/00181/output.heta b/latest/cases/00181/output.heta new file mode 100644 index 000000000..fca7f5965 --- /dev/null +++ b/latest/cases/00181/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Model using parameters and both rate and assignment rules. +componentTags: Parameter, RateRule, AssignmentRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ | + | Rate | S1 | $-k2 * S1 $ | + | Rate | S2 | $k2 * S1 $ |] + +Note the initial value for parameter S3 is undeclared and must be +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 1$ |any | +|Value of parameter S2 |$1.5 \x 10^-15$ |same as S1 | +|Value of parameter S3 |$ undeclared$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * k2 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 1.5e-15; +S3 @Record 'S3' { }; +S3 := k1 * S2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00181/synopsis.txt b/latest/cases/00181/synopsis.txt new file mode 100644 index 000000000..9d6ff08df --- /dev/null +++ b/latest/cases/00181/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Model using parameters and both rate and assignment rules. +componentTags: Parameter, RateRule, AssignmentRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ | + | Rate | S1 | $-k2 * S1 $ | + | Rate | S2 | $k2 * S1 $ |] + +Note the initial value for parameter S3 is undeclared and must be +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 1$ |any | +|Value of parameter S2 |$1.5 \x 10^-15$ |same as S1 | +|Value of parameter S3 |$ undeclared$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ |] + + diff --git a/latest/cases/00182/l2v5/build.log b/latest/cases/00182/l2v5/build.log new file mode 100644 index 000000000..cc9df7e0d --- /dev/null +++ b/latest/cases/00182/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00182/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00182/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00182/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00182/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00182/l2v5/index.heta b/latest/cases/00182/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00182/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00182/l3v2/build.log b/latest/cases/00182/l3v2/build.log new file mode 100644 index 000000000..01867664f --- /dev/null +++ b/latest/cases/00182/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00182/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00182/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00182/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00182/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00182/l3v2/index.heta b/latest/cases/00182/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00182/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00182/model-sbml-l2v5.xml b/latest/cases/00182/model-sbml-l2v5.xml new file mode 100644 index 000000000..3213bd3f3 --- /dev/null +++ b/latest/cases/00182/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + -1 + k1 + + S1 + S2 + + + + + + + + k2 + S2 + + + + + + diff --git a/latest/cases/00182/model-sbml-l3v2.xml b/latest/cases/00182/model-sbml-l3v2.xml new file mode 100644 index 000000000..3074bd556 --- /dev/null +++ b/latest/cases/00182/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + + + + + + + -1 + k1 + + S1 + S2 + + + + + + + + k2 + S2 + + + + + + diff --git a/latest/cases/00182/synopsis.txt b/latest/cases/00182/synopsis.txt new file mode 100644 index 000000000..911eb1f9d --- /dev/null +++ b/latest/cases/00182/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Model using parameters and both rate and algebraic rules. +componentTags: Parameter, RateRule, AlgebraicRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | | $S1 + S2-k1$ | + | Rate | S1 | $k2 * S2 $ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 0.5$ |any | +|Value of parameter S2 |$ 0.5$ |same as S1 | +|Value of parameter k1 |$ 1.0$ |same as S1 | +|Value of parameter k2 |$ 0.8$ |second^-1^ |] + + diff --git a/latest/cases/00183/l2v5/heta-code/output.heta b/latest/cases/00183/l2v5/heta-code/output.heta new file mode 100644 index 000000000..102a01297 --- /dev/null +++ b/latest/cases/00183/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * multiply(k2, S1); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 0.5; +S3 @Record 'S3' { }; +S3 := multiply(k1, S2); +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 40; + diff --git a/latest/cases/00183/l2v5/index.heta b/latest/cases/00183/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00183/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00183/l2v5/json/output.json b/latest/cases/00183/l2v5/json/output.json new file mode 100644 index 000000000..2344bf9a5 --- /dev/null +++ b/latest/cases/00183/l2v5/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "ode_": "multiply(k1, S2)" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "40" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * multiply(k2, S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00183/l3v2/heta-code/output.heta b/latest/cases/00183/l3v2/heta-code/output.heta new file mode 100644 index 000000000..050a34581 --- /dev/null +++ b/latest/cases/00183/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * multiply(k2, S1); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 0.5; +S3 @Record 'S3' { }; +S3 := multiply(k1, S2); + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 40; + diff --git a/latest/cases/00183/l3v2/index.heta b/latest/cases/00183/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00183/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00183/l3v2/json/output.json b/latest/cases/00183/l3v2/json/output.json new file mode 100644 index 000000000..6766c7dcb --- /dev/null +++ b/latest/cases/00183/l3v2/json/output.json @@ -0,0 +1,83 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "ode_": "multiply(k1, S2)" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 40 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * multiply(k2, S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00183/model-sbml-l2v5.xml b/latest/cases/00183/model-sbml-l2v5.xml new file mode 100644 index 000000000..fbbce3226 --- /dev/null +++ b/latest/cases/00183/model-sbml-l2v5.xml @@ -0,0 +1,64 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + -1 + + multiply + k2 + S1 + + + + + + + + + k2 + S1 + + + + + + diff --git a/latest/cases/00183/model-sbml-l3v2.xml b/latest/cases/00183/model-sbml-l3v2.xml new file mode 100644 index 000000000..bc2febee1 --- /dev/null +++ b/latest/cases/00183/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + -1 + + multiply + k2 + S1 + + + + + + + + + k2 + S1 + + + + + + diff --git a/latest/cases/00183/output.heta b/latest/cases/00183/output.heta new file mode 100644 index 000000000..e54dd8e1e --- /dev/null +++ b/latest/cases/00183/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Model using parameters and both rate and assignment rules + with a functionDefinition. +componentTags: Parameter, FunctionDefinition, RateRule, AssignmentRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ | + | Rate | S1 | $-multiply(k2, S1)$ | + | Rate | S2 | $k2 * S1 $ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note the initial value for parameter S3 is undeclared and must be +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 1$ |any | +|Value of parameter S2 |$ 0.5$ |same as S1 | +|Value of parameter S3 |$ undeclared$ |any | +|Value of parameter k1 |$ 0.7$ |(units of S3) (units of S1)^-1^ | +|Value of parameter k2 |$ 40$ |second^-1^ |] + + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * multiply(k2, S1); +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 0.5; +S3 @Record 'S3' { }; +S3 := multiply(k1, S2); + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 40; + diff --git a/latest/cases/00183/synopsis.txt b/latest/cases/00183/synopsis.txt new file mode 100644 index 000000000..b9313f6e2 --- /dev/null +++ b/latest/cases/00183/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Model using parameters and both rate and assignment rules + with a functionDefinition. +componentTags: Parameter, FunctionDefinition, RateRule, AssignmentRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ | + | Rate | S1 | $-multiply(k2, S1)$ | + | Rate | S2 | $k2 * S1 $ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note the initial value for parameter S3 is undeclared and must be +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 1$ |any | +|Value of parameter S2 |$ 0.5$ |same as S1 | +|Value of parameter S3 |$ undeclared$ |any | +|Value of parameter k1 |$ 0.7$ |(units of S3) (units of S1)^-1^ | +|Value of parameter k2 |$ 40$ |second^-1^ |] + + diff --git a/latest/cases/00184/l2v5/build.log b/latest/cases/00184/l2v5/build.log new file mode 100644 index 000000000..b688b02d5 --- /dev/null +++ b/latest/cases/00184/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00184/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00184/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00184/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00184/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00184/l2v5/index.heta b/latest/cases/00184/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00184/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00184/l3v2/build.log b/latest/cases/00184/l3v2/build.log new file mode 100644 index 000000000..c5adf4013 --- /dev/null +++ b/latest/cases/00184/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00184/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00184/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00184/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00184/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00184/l3v2/index.heta b/latest/cases/00184/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00184/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00184/model-sbml-l2v5.xml b/latest/cases/00184/model-sbml-l2v5.xml new file mode 100644 index 000000000..dfdc26825 --- /dev/null +++ b/latest/cases/00184/model-sbml-l2v5.xml @@ -0,0 +1,75 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + add + S1 + + add + S2 + + + -1 + k1 + + + + + + + + + multiply + k2 + S2 + + + + + + diff --git a/latest/cases/00184/model-sbml-l3v2.xml b/latest/cases/00184/model-sbml-l3v2.xml new file mode 100644 index 000000000..0d841ffa4 --- /dev/null +++ b/latest/cases/00184/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + add + S1 + + add + S2 + + + -1 + k1 + + + + + + + + + multiply + k2 + S2 + + + + + + diff --git a/latest/cases/00184/synopsis.txt b/latest/cases/00184/synopsis.txt new file mode 100644 index 000000000..5eef31027 --- /dev/null +++ b/latest/cases/00184/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Model using parameters and both rate and algebraic rules + with functionDefinitions. +componentTags: Parameter, FunctionDefinition, RateRule, AlgebraicRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called S1 and S2 and two constant +parameters called k1 and k2. (Note that indeed S1 and S2 are parameters and not +species in this model.) + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | | $add(S1, add(S2, -k1))$ | + | Rate | S1 | $multiply(k2, S2)$ |] + + +The model contains two functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ 0.5$ |any | +|Value of parameter S2 |$ 0.5$ |same as S1 | +|Value of parameter k1 |$ 1.0$ |same as S1 | +|Value of parameter k2 |$ 0.8$ |second^-1^ |] + + diff --git a/latest/cases/00185/l2v5/heta-code/output.heta b/latest/cases/00185/l2v5/heta-code/output.heta new file mode 100644 index 000000000..67e96e7e4 --- /dev/null +++ b/latest/cases/00185/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * k2 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= 1.33333333333333 * k1; +S2 @Record 'S2' { } .= k2 * (3e-17); +S3 @Record 'S3' { }; +S3 := k1 * S2; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00185/l2v5/index.heta b/latest/cases/00185/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00185/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00185/l2v5/json/output.json b/latest/cases/00185/l2v5/json/output.json new file mode 100644 index 000000000..cb74b7245 --- /dev/null +++ b/latest/cases/00185/l2v5/json/output.json @@ -0,0 +1,102 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1.33333333333333 * k1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "k2 * (3e-17)" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "ode_": "k1 * S2" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00185/l3v2/heta-code/output.heta b/latest/cases/00185/l3v2/heta-code/output.heta new file mode 100644 index 000000000..39d22fe5a --- /dev/null +++ b/latest/cases/00185/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * k2 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= 1.33333333333333 * k1; +S2 @Record 'S2' { } .= k2 * (3e-17); +S3 @Record 'S3' { }; +S3 := k1 * S2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00185/l3v2/index.heta b/latest/cases/00185/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00185/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00185/l3v2/json/output.json b/latest/cases/00185/l3v2/json/output.json new file mode 100644 index 000000000..4853921d3 --- /dev/null +++ b/latest/cases/00185/l3v2/json/output.json @@ -0,0 +1,74 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1.33333333333333 * k1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "k2 * (3e-17)" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "ode_": "k1 * S2" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00185/model-sbml-l2v5.xml b/latest/cases/00185/model-sbml-l2v5.xml new file mode 100644 index 000000000..9d57238d9 --- /dev/null +++ b/latest/cases/00185/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + 1.33333333333333 + k1 + + + + + + + + k2 + 3 -17 + + + + + + + + + + k1 + S2 + + + + + + + + -1 + k2 + S1 + + + + + + + + k2 + S1 + + + + + + diff --git a/latest/cases/00185/model-sbml-l3v2.xml b/latest/cases/00185/model-sbml-l3v2.xml new file mode 100644 index 000000000..29c33bf83 --- /dev/null +++ b/latest/cases/00185/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + 1.33333333333333 + k1 + + + + + + + + k2 + 3 -17 + + + + + + + + + + k1 + S2 + + + + + + + + -1 + k2 + S1 + + + + + + + + k2 + S1 + + + + + + diff --git a/latest/cases/00185/output.heta b/latest/cases/00185/output.heta new file mode 100644 index 000000000..d8394e9c7 --- /dev/null +++ b/latest/cases/00185/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Model using parameters and both rate and assignment rules + including initialAssignments. +componentTags: Parameter, InitialAssignment, RateRule, AssignmentRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ | + | Rate | S1 | $-k2 * S1 $ | + | Rate | S2 | $k2 * S1 $ |] + +The model contains two initialAssignments: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 0.75$ | + | S2 | $k2 * 3 \x 10^-17$ |] + +Note: InitialAssignments override any declared initial values. The initial +values of parameters S1, S2 and S3 are undeclared and so must be calculated +by the initialAssignments. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ undeclared$ |any | +|Value of parameter S2 |$ undeclared$ |same as S1 | +|Value of parameter S3 |$ undeclared$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ |] + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule2"}}, }; +S1_proc := (-1) * k2 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule3"}}, }; +S2_proc := k2 * S1; + +S1 @Record 'S1' { } .= 1.33333333333333 * k1; +S2 @Record 'S2' { } .= k2 * (3e-17); +S3 @Record 'S3' { }; +S3 := k1 * S2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00185/synopsis.txt b/latest/cases/00185/synopsis.txt new file mode 100644 index 000000000..929d85f2c --- /dev/null +++ b/latest/cases/00185/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Model using parameters and both rate and assignment rules + including initialAssignments. +componentTags: Parameter, InitialAssignment, RateRule, AssignmentRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ | + | Rate | S1 | $-k2 * S1 $ | + | Rate | S2 | $k2 * S1 $ |] + +The model contains two initialAssignments: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 0.75$ | + | S2 | $k2 * 3 \x 10^-17$ |] + +Note: InitialAssignments override any declared initial values. The initial +values of parameters S1, S2 and S3 are undeclared and so must be calculated +by the initialAssignments. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter S1 |$ undeclared$ |any | +|Value of parameter S2 |$ undeclared$ |same as S1 | +|Value of parameter S3 |$ undeclared$ |same as S1 | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ |] + diff --git a/latest/cases/00186/l2v5/heta-code/output.heta b/latest/cases/00186/l2v5/heta-code/output.heta new file mode 100644 index 000000000..178011fcd --- /dev/null +++ b/latest/cases/00186/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.1e-4 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 0; + diff --git a/latest/cases/00186/l2v5/index.heta b/latest/cases/00186/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00186/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00186/l2v5/json/output.json b/latest/cases/00186/l2v5/json/output.json new file mode 100644 index 000000000..055396181 --- /dev/null +++ b/latest/cases/00186/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00186/l3v2/heta-code/output.heta b/latest/cases/00186/l3v2/heta-code/output.heta new file mode 100644 index 000000000..054ba9b2b --- /dev/null +++ b/latest/cases/00186/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.1e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0; + diff --git a/latest/cases/00186/l3v2/index.heta b/latest/cases/00186/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00186/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00186/l3v2/json/output.json b/latest/cases/00186/l3v2/json/output.json new file mode 100644 index 000000000..4151b9458 --- /dev/null +++ b/latest/cases/00186/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0 + } +] \ No newline at end of file diff --git a/latest/cases/00186/model-sbml-l2v5.xml b/latest/cases/00186/model-sbml-l2v5.xml new file mode 100644 index 000000000..d0faa790b --- /dev/null +++ b/latest/cases/00186/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00186/model-sbml-l3v2.xml b/latest/cases/00186/model-sbml-l3v2.xml new file mode 100644 index 000000000..9c19091dd --- /dev/null +++ b/latest/cases/00186/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00186/output.heta b/latest/cases/00186/output.heta new file mode 100644 index 000000000..d096e81bc --- /dev/null +++ b/latest/cases/00186/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic reactions with three species in a one compartment, + with one reaction having a rate of zero. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The value of k2 is zero, which means the +reverse reaction should occur at zero rate (i.e. not at all). + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.1 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.1e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0; + diff --git a/latest/cases/00186/synopsis.txt b/latest/cases/00186/synopsis.txt new file mode 100644 index 000000000..612a787c4 --- /dev/null +++ b/latest/cases/00186/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic reactions with three species in a one compartment, + with one reaction having a rate of zero. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The value of k2 is zero, which means the +reverse reaction should occur at zero rate (i.e. not at all). + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.1 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00187/l2v5/heta-code/output.heta b/latest/cases/00187/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bd4de84be --- /dev/null +++ b/latest/cases/00187/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.1e-4 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 0; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00187/l2v5/index.heta b/latest/cases/00187/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00187/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00187/l2v5/json/output.json b/latest/cases/00187/l2v5/json/output.json new file mode 100644 index 000000000..9866eab94 --- /dev/null +++ b/latest/cases/00187/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00187/l3v2/heta-code/output.heta b/latest/cases/00187/l3v2/heta-code/output.heta new file mode 100644 index 000000000..97e3cd50b --- /dev/null +++ b/latest/cases/00187/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.1e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00187/l3v2/index.heta b/latest/cases/00187/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00187/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00187/l3v2/json/output.json b/latest/cases/00187/l3v2/json/output.json new file mode 100644 index 000000000..ae6eb1966 --- /dev/null +++ b/latest/cases/00187/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00187/model-sbml-l2v5.xml b/latest/cases/00187/model-sbml-l2v5.xml new file mode 100644 index 000000000..f83c318d7 --- /dev/null +++ b/latest/cases/00187/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00187/model-sbml-l3v2.xml b/latest/cases/00187/model-sbml-l3v2.xml new file mode 100644 index 000000000..0431965ef --- /dev/null +++ b/latest/cases/00187/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00187/output.heta b/latest/cases/00187/output.heta new file mode 100644 index 000000000..9bc32b687 --- /dev/null +++ b/latest/cases/00187/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic reactions with three species in a one compartment, + with one reaction having a rate of zero. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The value of k1 is zero, which means the first reaction should occur at +zero rate (i.e. not at all). + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.1 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 0$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.1e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00187/synopsis.txt b/latest/cases/00187/synopsis.txt new file mode 100644 index 000000000..b367cf9f6 --- /dev/null +++ b/latest/cases/00187/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic reactions with three species in a one compartment, + with one reaction having a rate of zero. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The value of k1 is zero, which means the first reaction should occur at +zero rate (i.e. not at all). + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.1 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 0$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00188/l2v5/heta-code/output.heta b/latest/cases/00188/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4a60d0de2 --- /dev/null +++ b/latest/cases/00188/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 0; + diff --git a/latest/cases/00188/l2v5/index.heta b/latest/cases/00188/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00188/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00188/l2v5/json/output.json b/latest/cases/00188/l2v5/json/output.json new file mode 100644 index 000000000..bee41f470 --- /dev/null +++ b/latest/cases/00188/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00188/l3v2/heta-code/output.heta b/latest/cases/00188/l3v2/heta-code/output.heta new file mode 100644 index 000000000..151564251 --- /dev/null +++ b/latest/cases/00188/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0; + diff --git a/latest/cases/00188/l3v2/index.heta b/latest/cases/00188/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00188/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00188/l3v2/json/output.json b/latest/cases/00188/l3v2/json/output.json new file mode 100644 index 000000000..bd5c461c9 --- /dev/null +++ b/latest/cases/00188/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0 + } +] \ No newline at end of file diff --git a/latest/cases/00188/model-sbml-l2v5.xml b/latest/cases/00188/model-sbml-l2v5.xml new file mode 100644 index 000000000..377e97637 --- /dev/null +++ b/latest/cases/00188/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00188/model-sbml-l3v2.xml b/latest/cases/00188/model-sbml-l3v2.xml new file mode 100644 index 000000000..d576173f9 --- /dev/null +++ b/latest/cases/00188/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00188/output.heta b/latest/cases/00188/output.heta new file mode 100644 index 000000000..0fb19d557 --- /dev/null +++ b/latest/cases/00188/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment, + with one reaction having a rate of zero. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The value of k2 is zero, which means the reverse reaction should occur at +zero rate (i.e. not at all). + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0; + diff --git a/latest/cases/00188/synopsis.txt b/latest/cases/00188/synopsis.txt new file mode 100644 index 000000000..3d2e260f1 --- /dev/null +++ b/latest/cases/00188/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment, + with one reaction having a rate of zero. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The value of k2 is zero, which means the reverse reaction should occur at +zero rate (i.e. not at all). + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00189/l2v5/heta-code/output.heta b/latest/cases/00189/l2v5/heta-code/output.heta new file mode 100644 index 000000000..041c01464 --- /dev/null +++ b/latest/cases/00189/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 0; +k2 @Record 'k2' { } .= 7500; + diff --git a/latest/cases/00189/l2v5/index.heta b/latest/cases/00189/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00189/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00189/l2v5/json/output.json b/latest/cases/00189/l2v5/json/output.json new file mode 100644 index 000000000..ba62b3dcf --- /dev/null +++ b/latest/cases/00189/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "7500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00189/l3v2/heta-code/output.heta b/latest/cases/00189/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6c3f6b608 --- /dev/null +++ b/latest/cases/00189/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 0; +k2 @Const 'k2' { } = 7500; + diff --git a/latest/cases/00189/l3v2/index.heta b/latest/cases/00189/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00189/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00189/l3v2/json/output.json b/latest/cases/00189/l3v2/json/output.json new file mode 100644 index 000000000..ad5609257 --- /dev/null +++ b/latest/cases/00189/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 7500 + } +] \ No newline at end of file diff --git a/latest/cases/00189/model-sbml-l2v5.xml b/latest/cases/00189/model-sbml-l2v5.xml new file mode 100644 index 000000000..55c076ce9 --- /dev/null +++ b/latest/cases/00189/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00189/model-sbml-l3v2.xml b/latest/cases/00189/model-sbml-l3v2.xml new file mode 100644 index 000000000..e11cd418d --- /dev/null +++ b/latest/cases/00189/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00189/output.heta b/latest/cases/00189/output.heta new file mode 100644 index 000000000..6b341ef3f --- /dev/null +++ b/latest/cases/00189/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment, + with one reaction having a rate of zero. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The value of k1 is zero, which means the +first reaction should occur at zero rate (i.e. not at all). + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 0$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 0; +k2 @Const 'k2' { } = 7500; + diff --git a/latest/cases/00189/synopsis.txt b/latest/cases/00189/synopsis.txt new file mode 100644 index 000000000..7f9e87a0e --- /dev/null +++ b/latest/cases/00189/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment, + with one reaction having a rate of zero. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The value of k1 is zero, which means the +first reaction should occur at zero rate (i.e. not at all). + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 0$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00190/l2v5/heta-code/output.heta b/latest/cases/00190/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5dac4b853 --- /dev/null +++ b/latest/cases/00190/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := (false ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; + diff --git a/latest/cases/00190/l2v5/index.heta b/latest/cases/00190/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00190/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00190/l2v5/json/output.json b/latest/cases/00190/l2v5/json/output.json new file mode 100644 index 000000000..f228da379 --- /dev/null +++ b/latest/cases/00190/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(false ? p1 : p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00190/l3v2/heta-code/output.heta b/latest/cases/00190/l3v2/heta-code/output.heta new file mode 100644 index 000000000..310d6b21b --- /dev/null +++ b/latest/cases/00190/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := (false ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; + diff --git a/latest/cases/00190/l3v2/index.heta b/latest/cases/00190/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00190/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00190/l3v2/json/output.json b/latest/cases/00190/l3v2/json/output.json new file mode 100644 index 000000000..b73bcb6e1 --- /dev/null +++ b/latest/cases/00190/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(false ? p1 : p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + } +] \ No newline at end of file diff --git a/latest/cases/00190/model-sbml-l2v5.xml b/latest/cases/00190/model-sbml-l2v5.xml new file mode 100644 index 000000000..14a564559 --- /dev/null +++ b/latest/cases/00190/model-sbml-l2v5.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + + + p2 + + + + + + + + diff --git a/latest/cases/00190/model-sbml-l3v2.xml b/latest/cases/00190/model-sbml-l3v2.xml new file mode 100644 index 000000000..3056b1309 --- /dev/null +++ b/latest/cases/00190/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + + + p2 + + + + + + + + diff --git a/latest/cases/00190/output.heta b/latest/cases/00190/output.heta new file mode 100644 index 000000000..0419dafa7 --- /dev/null +++ b/latest/cases/00190/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using MathML in the rate equation. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $Piecewise({{p1, False}}, p2)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := (false ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; + diff --git a/latest/cases/00190/synopsis.txt b/latest/cases/00190/synopsis.txt new file mode 100644 index 000000000..9d95e2648 --- /dev/null +++ b/latest/cases/00190/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using MathML in the rate equation. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $Piecewise({{p1, False}}, p2)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00191/l2v5/heta-code/output.heta b/latest/cases/00191/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4601c2a3a --- /dev/null +++ b/latest/cases/00191/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 >= 4) ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00191/l2v5/index.heta b/latest/cases/00191/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00191/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00191/l2v5/json/output.json b/latest/cases/00191/l2v5/json/output.json new file mode 100644 index 000000000..257f7fdb3 --- /dev/null +++ b/latest/cases/00191/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 >= 4) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00191/l3v2/heta-code/output.heta b/latest/cases/00191/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8b0d6d846 --- /dev/null +++ b/latest/cases/00191/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 >= 4) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00191/l3v2/index.heta b/latest/cases/00191/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00191/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00191/l3v2/json/output.json b/latest/cases/00191/l3v2/json/output.json new file mode 100644 index 000000000..8dee276b6 --- /dev/null +++ b/latest/cases/00191/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 >= 4) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00191/model-sbml-l2v5.xml b/latest/cases/00191/model-sbml-l2v5.xml new file mode 100644 index 000000000..313d20055 --- /dev/null +++ b/latest/cases/00191/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S2 + 4 + + + + p2 + + + + + + + + diff --git a/latest/cases/00191/model-sbml-l3v2.xml b/latest/cases/00191/model-sbml-l3v2.xml new file mode 100644 index 000000000..f57de7f44 --- /dev/null +++ b/latest/cases/00191/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S2 + 4 + + + + p2 + + + + + + + + diff --git a/latest/cases/00191/output.heta b/latest/cases/00191/output.heta new file mode 100644 index 000000000..f2b24091b --- /dev/null +++ b/latest/cases/00191/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, S2 >= 4}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 >= 4) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00191/synopsis.txt b/latest/cases/00191/synopsis.txt new file mode 100644 index 000000000..388caf757 --- /dev/null +++ b/latest/cases/00191/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, S2 >= 4}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00192/l2v5/heta-code/output.heta b/latest/cases/00192/l2v5/heta-code/output.heta new file mode 100644 index 000000000..dac327ad8 --- /dev/null +++ b/latest/cases/00192/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 > 7) ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00192/l2v5/index.heta b/latest/cases/00192/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00192/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00192/l2v5/json/output.json b/latest/cases/00192/l2v5/json/output.json new file mode 100644 index 000000000..95f873f66 --- /dev/null +++ b/latest/cases/00192/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 > 7) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00192/l3v2/heta-code/output.heta b/latest/cases/00192/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a194e930f --- /dev/null +++ b/latest/cases/00192/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 > 7) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00192/l3v2/index.heta b/latest/cases/00192/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00192/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00192/l3v2/json/output.json b/latest/cases/00192/l3v2/json/output.json new file mode 100644 index 000000000..529cb0290 --- /dev/null +++ b/latest/cases/00192/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 > 7) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00192/model-sbml-l2v5.xml b/latest/cases/00192/model-sbml-l2v5.xml new file mode 100644 index 000000000..4a16b7476 --- /dev/null +++ b/latest/cases/00192/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S2 + 7 + + + + p2 + + + + + + + + diff --git a/latest/cases/00192/model-sbml-l3v2.xml b/latest/cases/00192/model-sbml-l3v2.xml new file mode 100644 index 000000000..2fd012749 --- /dev/null +++ b/latest/cases/00192/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S2 + 7 + + + + p2 + + + + + + + + diff --git a/latest/cases/00192/output.heta b/latest/cases/00192/output.heta new file mode 100644 index 000000000..bb188110a --- /dev/null +++ b/latest/cases/00192/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, S2 > 7}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 > 7) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00192/synopsis.txt b/latest/cases/00192/synopsis.txt new file mode 100644 index 000000000..8540f7978 --- /dev/null +++ b/latest/cases/00192/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, S2 > 7}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00193/l2v5/heta-code/output.heta b/latest/cases/00193/l2v5/heta-code/output.heta new file mode 100644 index 000000000..db03124ea --- /dev/null +++ b/latest/cases/00193/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := ((S1 <= 4) ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00193/l2v5/index.heta b/latest/cases/00193/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00193/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00193/l2v5/json/output.json b/latest/cases/00193/l2v5/json/output.json new file mode 100644 index 000000000..29f9d369a --- /dev/null +++ b/latest/cases/00193/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S1 <= 4) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00193/l3v2/heta-code/output.heta b/latest/cases/00193/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f371c789b --- /dev/null +++ b/latest/cases/00193/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := ((S1 <= 4) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00193/l3v2/index.heta b/latest/cases/00193/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00193/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00193/l3v2/json/output.json b/latest/cases/00193/l3v2/json/output.json new file mode 100644 index 000000000..d91bddfe2 --- /dev/null +++ b/latest/cases/00193/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S1 <= 4) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00193/model-sbml-l2v5.xml b/latest/cases/00193/model-sbml-l2v5.xml new file mode 100644 index 000000000..92aaa118c --- /dev/null +++ b/latest/cases/00193/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S1 + 4 + + + + p2 + + + + + + + + diff --git a/latest/cases/00193/model-sbml-l3v2.xml b/latest/cases/00193/model-sbml-l3v2.xml new file mode 100644 index 000000000..bd8883ea9 --- /dev/null +++ b/latest/cases/00193/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S1 + 4 + + + + p2 + + + + + + + + diff --git a/latest/cases/00193/output.heta b/latest/cases/00193/output.heta new file mode 100644 index 000000000..bb71082cf --- /dev/null +++ b/latest/cases/00193/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, S1 <= 4}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 5$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := ((S1 <= 4) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00193/synopsis.txt b/latest/cases/00193/synopsis.txt new file mode 100644 index 000000000..867bde73e --- /dev/null +++ b/latest/cases/00193/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, S1 <= 4}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 5$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00194/l2v5/heta-code/output.heta b/latest/cases/00194/l2v5/heta-code/output.heta new file mode 100644 index 000000000..db9c00934 --- /dev/null +++ b/latest/cases/00194/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := ((S1 < 2.5) ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00194/l2v5/index.heta b/latest/cases/00194/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00194/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00194/l2v5/json/output.json b/latest/cases/00194/l2v5/json/output.json new file mode 100644 index 000000000..516af3607 --- /dev/null +++ b/latest/cases/00194/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S1 < 2.5) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00194/l3v2/heta-code/output.heta b/latest/cases/00194/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dec9f8c7c --- /dev/null +++ b/latest/cases/00194/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := ((S1 < 2.5) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00194/l3v2/index.heta b/latest/cases/00194/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00194/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00194/l3v2/json/output.json b/latest/cases/00194/l3v2/json/output.json new file mode 100644 index 000000000..c2865dcac --- /dev/null +++ b/latest/cases/00194/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S1 < 2.5) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00194/model-sbml-l2v5.xml b/latest/cases/00194/model-sbml-l2v5.xml new file mode 100644 index 000000000..7097f1e0c --- /dev/null +++ b/latest/cases/00194/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S1 + 2.5 + + + + p2 + + + + + + + + diff --git a/latest/cases/00194/model-sbml-l3v2.xml b/latest/cases/00194/model-sbml-l3v2.xml new file mode 100644 index 000000000..7ab2bba4a --- /dev/null +++ b/latest/cases/00194/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S1 + 2.5 + + + + p2 + + + + + + + + diff --git a/latest/cases/00194/output.heta b/latest/cases/00194/output.heta new file mode 100644 index 000000000..48a659dd8 --- /dev/null +++ b/latest/cases/00194/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, S1 < 2.5}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 5$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := ((S1 < 2.5) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00194/synopsis.txt b/latest/cases/00194/synopsis.txt new file mode 100644 index 000000000..65184ca66 --- /dev/null +++ b/latest/cases/00194/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, S1 < 2.5}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 5$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00195/l2v5/heta-code/output.heta b/latest/cases/00195/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0fae5bfb5 --- /dev/null +++ b/latest/cases/00195/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := S1 * compartment * (true ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; + diff --git a/latest/cases/00195/l2v5/index.heta b/latest/cases/00195/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00195/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00195/l2v5/json/output.json b/latest/cases/00195/l2v5/json/output.json new file mode 100644 index 000000000..77309073f --- /dev/null +++ b/latest/cases/00195/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "S1 * compartment * (true ? p1 : p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00195/l3v2/heta-code/output.heta b/latest/cases/00195/l3v2/heta-code/output.heta new file mode 100644 index 000000000..870bed98c --- /dev/null +++ b/latest/cases/00195/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := S1 * compartment * (true ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; + diff --git a/latest/cases/00195/l3v2/index.heta b/latest/cases/00195/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00195/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00195/l3v2/json/output.json b/latest/cases/00195/l3v2/json/output.json new file mode 100644 index 000000000..740e012e3 --- /dev/null +++ b/latest/cases/00195/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "S1 * compartment * (true ? p1 : p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + } +] \ No newline at end of file diff --git a/latest/cases/00195/model-sbml-l2v5.xml b/latest/cases/00195/model-sbml-l2v5.xml new file mode 100644 index 000000000..5cef391f3 --- /dev/null +++ b/latest/cases/00195/model-sbml-l2v5.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + compartment + + + p1 + + + + p2 + + + + + + + + + diff --git a/latest/cases/00195/model-sbml-l3v2.xml b/latest/cases/00195/model-sbml-l3v2.xml new file mode 100644 index 000000000..b90bed4bf --- /dev/null +++ b/latest/cases/00195/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + compartment + + + p1 + + + + p2 + + + + + + + + + diff --git a/latest/cases/00195/output.heta b/latest/cases/00195/output.heta new file mode 100644 index 000000000..f477b8883 --- /dev/null +++ b/latest/cases/00195/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using MathML in the rate equation. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * S1 * Piecewise({{p1, True}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |second^-1^ | +|Value of parameter p2 |$ 0.05$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := S1 * compartment * (true ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; + diff --git a/latest/cases/00195/synopsis.txt b/latest/cases/00195/synopsis.txt new file mode 100644 index 000000000..10a4e2882 --- /dev/null +++ b/latest/cases/00195/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using MathML in the rate equation. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * S1 * Piecewise({{p1, True}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |second^-1^ | +|Value of parameter p2 |$ 0.05$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00196/l2v5/heta-code/output.heta b/latest/cases/00196/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0f7cc75d6 --- /dev/null +++ b/latest/cases/00196/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := floor(p1 * S1) * pow(p2, (-1)); + +p1 @Record 'p1' { } .= 10.5; +p2 @Record 'p2' { } .= 10; + diff --git a/latest/cases/00196/l2v5/index.heta b/latest/cases/00196/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00196/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00196/l2v5/json/output.json b/latest/cases/00196/l2v5/json/output.json new file mode 100644 index 000000000..e6e56da69 --- /dev/null +++ b/latest/cases/00196/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "floor(p1 * S1) * pow(p2, (-1))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "10.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "10" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00196/l3v2/heta-code/output.heta b/latest/cases/00196/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7611085e6 --- /dev/null +++ b/latest/cases/00196/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := floor(p1 * S1) * pow(p2, (-1)); + +p1 @Const 'p1' { } = 10.5; +p2 @Const 'p2' { } = 10; + diff --git a/latest/cases/00196/l3v2/index.heta b/latest/cases/00196/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00196/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00196/l3v2/json/output.json b/latest/cases/00196/l3v2/json/output.json new file mode 100644 index 000000000..ccb1b53b3 --- /dev/null +++ b/latest/cases/00196/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "floor(p1 * S1) * pow(p2, (-1))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 10.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 10 + } +] \ No newline at end of file diff --git a/latest/cases/00196/model-sbml-l2v5.xml b/latest/cases/00196/model-sbml-l2v5.xml new file mode 100644 index 000000000..35f1a5617 --- /dev/null +++ b/latest/cases/00196/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + S1 + + + + + p2 + -1 + + + + + + + + diff --git a/latest/cases/00196/model-sbml-l3v2.xml b/latest/cases/00196/model-sbml-l3v2.xml new file mode 100644 index 000000000..9931ac052 --- /dev/null +++ b/latest/cases/00196/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + S1 + + + + + p2 + -1 + + + + + + + + diff --git a/latest/cases/00196/output.heta b/latest/cases/00196/output.heta new file mode 100644 index 000000000..892d358ff --- /dev/null +++ b/latest/cases/00196/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $Floor(S1 * p1) / p2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 0.0$ |mole | +|Value of parameter p1 |$ 10.5$ |litre | +|Value of parameter p2 |$ 10$ |second | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := floor(p1 * S1) * pow(p2, (-1)); + +p1 @Const 'p1' { } = 10.5; +p2 @Const 'p2' { } = 10; + diff --git a/latest/cases/00196/synopsis.txt b/latest/cases/00196/synopsis.txt new file mode 100644 index 000000000..5f4f4802f --- /dev/null +++ b/latest/cases/00196/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $Floor(S1 * p1) / p2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 0.0$ |mole | +|Value of parameter p1 |$ 10.5$ |litre | +|Value of parameter p2 |$ 10$ |second | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00197/l2v5/heta-code/output.heta b/latest/cases/00197/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c51a8c1b0 --- /dev/null +++ b/latest/cases/00197/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := ceil(p1 * S1) * pow(p2, (-1)); + +p1 @Record 'p1' { } .= 10.5; +p2 @Record 'p2' { } .= 10; + diff --git a/latest/cases/00197/l2v5/index.heta b/latest/cases/00197/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00197/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00197/l2v5/json/output.json b/latest/cases/00197/l2v5/json/output.json new file mode 100644 index 000000000..d9828b3ce --- /dev/null +++ b/latest/cases/00197/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "ceil(p1 * S1) * pow(p2, (-1))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "10.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "10" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00197/l3v2/heta-code/output.heta b/latest/cases/00197/l3v2/heta-code/output.heta new file mode 100644 index 000000000..55d39d8e8 --- /dev/null +++ b/latest/cases/00197/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := ceil(p1 * S1) * pow(p2, (-1)); + +p1 @Const 'p1' { } = 10.5; +p2 @Const 'p2' { } = 10; + diff --git a/latest/cases/00197/l3v2/index.heta b/latest/cases/00197/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00197/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00197/l3v2/json/output.json b/latest/cases/00197/l3v2/json/output.json new file mode 100644 index 000000000..68336b057 --- /dev/null +++ b/latest/cases/00197/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "ceil(p1 * S1) * pow(p2, (-1))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 10.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 10 + } +] \ No newline at end of file diff --git a/latest/cases/00197/model-sbml-l2v5.xml b/latest/cases/00197/model-sbml-l2v5.xml new file mode 100644 index 000000000..dd19106dc --- /dev/null +++ b/latest/cases/00197/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + S1 + + + + + p2 + -1 + + + + + + + + diff --git a/latest/cases/00197/model-sbml-l3v2.xml b/latest/cases/00197/model-sbml-l3v2.xml new file mode 100644 index 000000000..a265b7be7 --- /dev/null +++ b/latest/cases/00197/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + S1 + + + + + p2 + -1 + + + + + + + + diff --git a/latest/cases/00197/output.heta b/latest/cases/00197/output.heta new file mode 100644 index 000000000..3569338af --- /dev/null +++ b/latest/cases/00197/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $Ceiling(S1 * p1)/p2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 0.0$ |mole | +|Value of parameter p1 |$ 10.5$ |litre | +|Value of parameter p2 |$ 10$ |second | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := ceil(p1 * S1) * pow(p2, (-1)); + +p1 @Const 'p1' { } = 10.5; +p2 @Const 'p2' { } = 10; + diff --git a/latest/cases/00197/synopsis.txt b/latest/cases/00197/synopsis.txt new file mode 100644 index 000000000..f2e2cb27f --- /dev/null +++ b/latest/cases/00197/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $Ceiling(S1 * p1)/p2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 0.0$ |mole | +|Value of parameter p1 |$ 10.5$ |litre | +|Value of parameter p2 |$ 10$ |second | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00198/l2v5/heta-code/output.heta b/latest/cases/00198/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6b3575d41 --- /dev/null +++ b/latest/cases/00198/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1, S2], reversible: false, }; +reaction2 := ((S2 > 4 and S1 < 5 and S2 < 8) ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00198/l2v5/index.heta b/latest/cases/00198/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00198/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00198/l2v5/json/output.json b/latest/cases/00198/l2v5/json/output.json new file mode 100644 index 000000000..4b428dc06 --- /dev/null +++ b/latest/cases/00198/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 > 4 and S1 < 5 and S2 < 8) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + }, + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00198/l3v2/heta-code/output.heta b/latest/cases/00198/l3v2/heta-code/output.heta new file mode 100644 index 000000000..276e8cbd7 --- /dev/null +++ b/latest/cases/00198/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1, S2], reversible: false, }; +reaction2 := ((S2 > 4 and S1 < 5 and S2 < 8) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00198/l3v2/index.heta b/latest/cases/00198/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00198/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00198/l3v2/json/output.json b/latest/cases/00198/l3v2/json/output.json new file mode 100644 index 000000000..e3610e491 --- /dev/null +++ b/latest/cases/00198/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 > 4 and S1 < 5 and S2 < 8) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + }, + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00198/model-sbml-l2v5.xml b/latest/cases/00198/model-sbml-l2v5.xml new file mode 100644 index 000000000..b988077fa --- /dev/null +++ b/latest/cases/00198/model-sbml-l2v5.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + + p1 + + + + + S2 + 4 + + + + S1 + 5 + + + + S2 + 8 + + + + + p2 + + + + + + + + diff --git a/latest/cases/00198/model-sbml-l3v2.xml b/latest/cases/00198/model-sbml-l3v2.xml new file mode 100644 index 000000000..27365e060 --- /dev/null +++ b/latest/cases/00198/model-sbml-l3v2.xml @@ -0,0 +1,98 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + + p1 + + + + + S2 + 4 + + + + S1 + 5 + + + + S2 + 8 + + + + + p2 + + + + + + + + diff --git a/latest/cases/00198/output.heta b/latest/cases/00198/output.heta new file mode 100644 index 000000000..2563fa3c0 --- /dev/null +++ b/latest/cases/00198/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, And(S2 > 4, S1 < 5, S2 < 8)}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1, S2], reversible: false, }; +reaction2 := ((S2 > 4 and S1 < 5 and S2 < 8) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00198/synopsis.txt b/latest/cases/00198/synopsis.txt new file mode 100644 index 000000000..7619977d5 --- /dev/null +++ b/latest/cases/00198/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, And(S2 > 4, S1 < 5, S2 < 8)}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00199/l2v5/heta-code/output.heta b/latest/cases/00199/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4601c2a3a --- /dev/null +++ b/latest/cases/00199/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 >= 4) ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00199/l2v5/index.heta b/latest/cases/00199/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00199/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00199/l2v5/json/output.json b/latest/cases/00199/l2v5/json/output.json new file mode 100644 index 000000000..257f7fdb3 --- /dev/null +++ b/latest/cases/00199/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 >= 4) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00199/l3v2/heta-code/output.heta b/latest/cases/00199/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8b0d6d846 --- /dev/null +++ b/latest/cases/00199/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 >= 4) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00199/l3v2/index.heta b/latest/cases/00199/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00199/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00199/l3v2/json/output.json b/latest/cases/00199/l3v2/json/output.json new file mode 100644 index 000000000..8dee276b6 --- /dev/null +++ b/latest/cases/00199/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 >= 4) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00199/model-sbml-l2v5.xml b/latest/cases/00199/model-sbml-l2v5.xml new file mode 100644 index 000000000..5c92c6f9c --- /dev/null +++ b/latest/cases/00199/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S2 + 4 + + + + p2 + + + + + + + + diff --git a/latest/cases/00199/model-sbml-l3v2.xml b/latest/cases/00199/model-sbml-l3v2.xml new file mode 100644 index 000000000..e92199cf9 --- /dev/null +++ b/latest/cases/00199/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + S2 + 4 + + + + p2 + + + + + + + + diff --git a/latest/cases/00199/output.heta b/latest/cases/00199/output.heta new file mode 100644 index 000000000..c83e6088c --- /dev/null +++ b/latest/cases/00199/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, Not(S2 < 4)}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 >= 4) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00199/synopsis.txt b/latest/cases/00199/synopsis.txt new file mode 100644 index 000000000..8975aa65a --- /dev/null +++ b/latest/cases/00199/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, Not(S2 < 4)}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00200/l2v5/heta-code/output.heta b/latest/cases/00200/l2v5/heta-code/output.heta new file mode 100644 index 000000000..99985dd61 --- /dev/null +++ b/latest/cases/00200/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 < 2 or S2 > 4 or S2 < 1) ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00200/l2v5/index.heta b/latest/cases/00200/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00200/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00200/l2v5/json/output.json b/latest/cases/00200/l2v5/json/output.json new file mode 100644 index 000000000..e50257d64 --- /dev/null +++ b/latest/cases/00200/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 < 2 or S2 > 4 or S2 < 1) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00200/l3v2/heta-code/output.heta b/latest/cases/00200/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d2a7c1995 --- /dev/null +++ b/latest/cases/00200/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 < 2 or S2 > 4 or S2 < 1) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00200/l3v2/index.heta b/latest/cases/00200/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00200/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00200/l3v2/json/output.json b/latest/cases/00200/l3v2/json/output.json new file mode 100644 index 000000000..5cb60e1a2 --- /dev/null +++ b/latest/cases/00200/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 < 2 or S2 > 4 or S2 < 1) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00200/model-sbml-l2v5.xml b/latest/cases/00200/model-sbml-l2v5.xml new file mode 100644 index 000000000..4dd94b8d2 --- /dev/null +++ b/latest/cases/00200/model-sbml-l2v5.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + + + S2 + 2 + + + + S2 + 4 + + + + S2 + 1 + + + + + p2 + + + + + + + + diff --git a/latest/cases/00200/model-sbml-l3v2.xml b/latest/cases/00200/model-sbml-l3v2.xml new file mode 100644 index 000000000..44b38b222 --- /dev/null +++ b/latest/cases/00200/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + + + S2 + 2 + + + + S2 + 4 + + + + S2 + 1 + + + + + p2 + + + + + + + + diff --git a/latest/cases/00200/output.heta b/latest/cases/00200/output.heta new file mode 100644 index 000000000..43c79b53c --- /dev/null +++ b/latest/cases/00200/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, Or(S2 < 2, S2 > 4, S2 < 1)}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 4$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 < 2 or S2 > 4 or S2 < 1) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00200/synopsis.txt b/latest/cases/00200/synopsis.txt new file mode 100644 index 000000000..a7a5b674d --- /dev/null +++ b/latest/cases/00200/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, Or(S2 < 2, S2 > 4, S2 < 1)}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 4$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00201/l2v5/heta-code/output.heta b/latest/cases/00201/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9878ff40b --- /dev/null +++ b/latest/cases/00201/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 > 4 xor S2 < 1 xor S2 < 2) ? p1 : p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00201/l2v5/index.heta b/latest/cases/00201/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00201/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00201/l2v5/json/output.json b/latest/cases/00201/l2v5/json/output.json new file mode 100644 index 000000000..ca109a881 --- /dev/null +++ b/latest/cases/00201/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 > 4 xor S2 < 1 xor S2 < 2) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00201/l3v2/heta-code/output.heta b/latest/cases/00201/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e4abc689f --- /dev/null +++ b/latest/cases/00201/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 > 4 xor S2 < 1 xor S2 < 2) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00201/l3v2/index.heta b/latest/cases/00201/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00201/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00201/l3v2/json/output.json b/latest/cases/00201/l3v2/json/output.json new file mode 100644 index 000000000..47a947f0f --- /dev/null +++ b/latest/cases/00201/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "((S2 > 4 xor S2 < 1 xor S2 < 2) ? p1 : p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00201/model-sbml-l2v5.xml b/latest/cases/00201/model-sbml-l2v5.xml new file mode 100644 index 000000000..69fbfd0b9 --- /dev/null +++ b/latest/cases/00201/model-sbml-l2v5.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + + + S2 + 4 + + + + S2 + 1 + + + + S2 + 2 + + + + + p2 + + + + + + + + diff --git a/latest/cases/00201/model-sbml-l3v2.xml b/latest/cases/00201/model-sbml-l3v2.xml new file mode 100644 index 000000000..cb78ded3e --- /dev/null +++ b/latest/cases/00201/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + p1 + + + + + S2 + 4 + + + + S2 + 1 + + + + S2 + 2 + + + + + p2 + + + + + + + + diff --git a/latest/cases/00201/output.heta b/latest/cases/00201/output.heta new file mode 100644 index 000000000..6cedd9c25 --- /dev/null +++ b/latest/cases/00201/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, Xor(S2 < 2, S2 > 4, S2 < 1)}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 4$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := ((S2 > 4 xor S2 < 1 xor S2 < 2) ? p1 : p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00201/synopsis.txt b/latest/cases/00201/synopsis.txt new file mode 100644 index 000000000..201b1f3c4 --- /dev/null +++ b/latest/cases/00201/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $Piecewise({{p1, Xor(S2 < 2, S2 > 4, S2 < 1)}}, p2)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 4$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00202/l2v5/heta-code/output.heta b/latest/cases/00202/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e5e984d6a --- /dev/null +++ b/latest/cases/00202/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 0.6; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 1.1; + diff --git a/latest/cases/00202/l2v5/index.heta b/latest/cases/00202/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00202/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00202/l2v5/json/output.json b/latest/cases/00202/l2v5/json/output.json new file mode 100644 index 000000000..3821f8594 --- /dev/null +++ b/latest/cases/00202/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "0.6" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00202/l3v2/heta-code/output.heta b/latest/cases/00202/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d117dcb1e --- /dev/null +++ b/latest/cases/00202/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 0.6; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1.1; + diff --git a/latest/cases/00202/l3v2/index.heta b/latest/cases/00202/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00202/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00202/l3v2/json/output.json b/latest/cases/00202/l3v2/json/output.json new file mode 100644 index 000000000..941e2d08e --- /dev/null +++ b/latest/cases/00202/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "0.6" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.1 + } +] \ No newline at end of file diff --git a/latest/cases/00202/model-sbml-l2v5.xml b/latest/cases/00202/model-sbml-l2v5.xml new file mode 100644 index 000000000..2aa29275f --- /dev/null +++ b/latest/cases/00202/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00202/model-sbml-l3v2.xml b/latest/cases/00202/model-sbml-l3v2.xml new file mode 100644 index 000000000..e7f0c38b3 --- /dev/null +++ b/latest/cases/00202/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00202/output.heta b/latest/cases/00202/output.heta new file mode 100644 index 000000000..ac8207b99 --- /dev/null +++ b/latest/cases/00202/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 2-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.1$ |second^-1^ | +|Area of compartment "compartment" |$ 0.6$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 0.6; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1.1; + diff --git a/latest/cases/00202/synopsis.txt b/latest/cases/00202/synopsis.txt new file mode 100644 index 000000000..f12927be4 --- /dev/null +++ b/latest/cases/00202/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 2-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.1$ |second^-1^ | +|Area of compartment "compartment" |$ 0.6$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00203/l2v5/heta-code/output.heta b/latest/cases/00203/l2v5/heta-code/output.heta new file mode 100644 index 000000000..261ac90a6 --- /dev/null +++ b/latest/cases/00203/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 3.7; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 25; + diff --git a/latest/cases/00203/l2v5/index.heta b/latest/cases/00203/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00203/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00203/l2v5/json/output.json b/latest/cases/00203/l2v5/json/output.json new file mode 100644 index 000000000..fd9d23589 --- /dev/null +++ b/latest/cases/00203/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "3.7" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00203/l3v2/heta-code/output.heta b/latest/cases/00203/l3v2/heta-code/output.heta new file mode 100644 index 000000000..381077712 --- /dev/null +++ b/latest/cases/00203/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 3.7; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00203/l3v2/index.heta b/latest/cases/00203/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00203/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00203/l3v2/json/output.json b/latest/cases/00203/l3v2/json/output.json new file mode 100644 index 000000000..1124bf112 --- /dev/null +++ b/latest/cases/00203/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "3.7" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + } +] \ No newline at end of file diff --git a/latest/cases/00203/model-sbml-l2v5.xml b/latest/cases/00203/model-sbml-l2v5.xml new file mode 100644 index 000000000..0b0005c48 --- /dev/null +++ b/latest/cases/00203/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00203/model-sbml-l3v2.xml b/latest/cases/00203/model-sbml-l3v2.xml new file mode 100644 index 000000000..f981be548 --- /dev/null +++ b/latest/cases/00203/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00203/output.heta b/latest/cases/00203/output.heta new file mode 100644 index 000000000..9b292f750 --- /dev/null +++ b/latest/cases/00203/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 2-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 25$ |second^-1^ | +|Area of compartment "compartment" |$ 3.7$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 3.7; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00203/synopsis.txt b/latest/cases/00203/synopsis.txt new file mode 100644 index 000000000..fc012b297 --- /dev/null +++ b/latest/cases/00203/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic reactions with three species in a 2-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 25$ |second^-1^ | +|Area of compartment "compartment" |$ 3.7$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00204/l2v5/heta-code/output.heta b/latest/cases/00204/l2v5/heta-code/output.heta new file mode 100644 index 000000000..daa9d5986 --- /dev/null +++ b/latest/cases/00204/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 0.01; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7.5e+6; +k2 @Record 'k2' { } .= 25000; + diff --git a/latest/cases/00204/l2v5/index.heta b/latest/cases/00204/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00204/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00204/l2v5/json/output.json b/latest/cases/00204/l2v5/json/output.json new file mode 100644 index 000000000..a7108bda5 --- /dev/null +++ b/latest/cases/00204/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "0.01" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25000" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00204/l3v2/heta-code/output.heta b/latest/cases/00204/l3v2/heta-code/output.heta new file mode 100644 index 000000000..026fdb063 --- /dev/null +++ b/latest/cases/00204/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 0.01; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500000; +k2 @Const 'k2' { } = 25000; + diff --git a/latest/cases/00204/l3v2/index.heta b/latest/cases/00204/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00204/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00204/l3v2/json/output.json b/latest/cases/00204/l3v2/json/output.json new file mode 100644 index 000000000..fc3e84c2d --- /dev/null +++ b/latest/cases/00204/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "0.01" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25000 + } +] \ No newline at end of file diff --git a/latest/cases/00204/model-sbml-l2v5.xml b/latest/cases/00204/model-sbml-l2v5.xml new file mode 100644 index 000000000..25e283e5d --- /dev/null +++ b/latest/cases/00204/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00204/model-sbml-l3v2.xml b/latest/cases/00204/model-sbml-l3v2.xml new file mode 100644 index 000000000..dffcd03ea --- /dev/null +++ b/latest/cases/00204/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00204/output.heta b/latest/cases/00204/output.heta new file mode 100644 index 000000000..db7aaf34d --- /dev/null +++ b/latest/cases/00204/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic reactions with four species in a 2-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 0.75 \x 10^7$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25 \x 10^5$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 0.01$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 0.01; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500000; +k2 @Const 'k2' { } = 25000; + diff --git a/latest/cases/00204/synopsis.txt b/latest/cases/00204/synopsis.txt new file mode 100644 index 000000000..06a5a8c6c --- /dev/null +++ b/latest/cases/00204/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in a 2-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 0.75 \x 10^7$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25 \x 10^5$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 0.01$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00205/l2v5/heta-code/output.heta b/latest/cases/00205/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a2b45c657 --- /dev/null +++ b/latest/cases/00205/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 0.3; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1.5e-5 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 0.9; + diff --git a/latest/cases/00205/l2v5/index.heta b/latest/cases/00205/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00205/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00205/l2v5/json/output.json b/latest/cases/00205/l2v5/json/output.json new file mode 100644 index 000000000..386e725ed --- /dev/null +++ b/latest/cases/00205/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "0.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.9" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00205/l3v2/heta-code/output.heta b/latest/cases/00205/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9d123617c --- /dev/null +++ b/latest/cases/00205/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 0.3; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 0.9; + diff --git a/latest/cases/00205/l3v2/index.heta b/latest/cases/00205/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00205/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00205/l3v2/json/output.json b/latest/cases/00205/l3v2/json/output.json new file mode 100644 index 000000000..d5d093f0e --- /dev/null +++ b/latest/cases/00205/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "0.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.9 + } +] \ No newline at end of file diff --git a/latest/cases/00205/model-sbml-l2v5.xml b/latest/cases/00205/model-sbml-l2v5.xml new file mode 100644 index 000000000..1e3436eb0 --- /dev/null +++ b/latest/cases/00205/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00205/model-sbml-l3v2.xml b/latest/cases/00205/model-sbml-l3v2.xml new file mode 100644 index 000000000..355f2763f --- /dev/null +++ b/latest/cases/00205/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00205/output.heta b/latest/cases/00205/output.heta new file mode 100644 index 000000000..3adf6eab8 --- /dev/null +++ b/latest/cases/00205/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 1-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 0.3$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 0.3; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 0.9; + diff --git a/latest/cases/00205/synopsis.txt b/latest/cases/00205/synopsis.txt new file mode 100644 index 000000000..de9dad3e5 --- /dev/null +++ b/latest/cases/00205/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 1-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 0.3$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00206/l2v5/heta-code/output.heta b/latest/cases/00206/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9fca565a4 --- /dev/null +++ b/latest/cases/00206/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 9.8; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 3.4; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00206/l2v5/index.heta b/latest/cases/00206/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00206/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00206/l2v5/json/output.json b/latest/cases/00206/l2v5/json/output.json new file mode 100644 index 000000000..95a17a4f7 --- /dev/null +++ b/latest/cases/00206/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "9.8" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "3.4" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00206/l3v2/heta-code/output.heta b/latest/cases/00206/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d9883b21e --- /dev/null +++ b/latest/cases/00206/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 9.8; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 3.4; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00206/l3v2/index.heta b/latest/cases/00206/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00206/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00206/l3v2/json/output.json b/latest/cases/00206/l3v2/json/output.json new file mode 100644 index 000000000..152535d79 --- /dev/null +++ b/latest/cases/00206/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "9.8" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 3.4 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00206/model-sbml-l2v5.xml b/latest/cases/00206/model-sbml-l2v5.xml new file mode 100644 index 000000000..d4b5a9568 --- /dev/null +++ b/latest/cases/00206/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00206/model-sbml-l3v2.xml b/latest/cases/00206/model-sbml-l3v2.xml new file mode 100644 index 000000000..948dd8772 --- /dev/null +++ b/latest/cases/00206/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00206/output.heta b/latest/cases/00206/output.heta new file mode 100644 index 000000000..f711a7ce4 --- /dev/null +++ b/latest/cases/00206/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 1-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$ 1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 3.4$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Length of compartment "compartment" |$ 9.8$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 9.8; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 3.4; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00206/synopsis.txt b/latest/cases/00206/synopsis.txt new file mode 100644 index 000000000..062bad06c --- /dev/null +++ b/latest/cases/00206/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic reactions with three species in a 1-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$ 1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 3.4$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Length of compartment "compartment" |$ 9.8$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00207/l2v5/heta-code/output.heta b/latest/cases/00207/l2v5/heta-code/output.heta new file mode 100644 index 000000000..03fdeba6b --- /dev/null +++ b/latest/cases/00207/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 4; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 2 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 1 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 9; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00207/l2v5/index.heta b/latest/cases/00207/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00207/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00207/l2v5/json/output.json b/latest/cases/00207/l2v5/json/output.json new file mode 100644 index 000000000..e307a5de1 --- /dev/null +++ b/latest/cases/00207/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "4" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "9" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00207/l3v2/heta-code/output.heta b/latest/cases/00207/l3v2/heta-code/output.heta new file mode 100644 index 000000000..63ea4c77c --- /dev/null +++ b/latest/cases/00207/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 4; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 9; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00207/l3v2/index.heta b/latest/cases/00207/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00207/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00207/l3v2/json/output.json b/latest/cases/00207/l3v2/json/output.json new file mode 100644 index 000000000..b6f457bcd --- /dev/null +++ b/latest/cases/00207/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "4" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 9 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00207/model-sbml-l2v5.xml b/latest/cases/00207/model-sbml-l2v5.xml new file mode 100644 index 000000000..a3d9cd5bc --- /dev/null +++ b/latest/cases/00207/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00207/model-sbml-l3v2.xml b/latest/cases/00207/model-sbml-l3v2.xml new file mode 100644 index 000000000..1bb3491f2 --- /dev/null +++ b/latest/cases/00207/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00207/output.heta b/latest/cases/00207/output.heta new file mode 100644 index 000000000..13430f194 --- /dev/null +++ b/latest/cases/00207/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic reactions with four species in a 1-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 9$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 4$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 4; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 9; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00207/synopsis.txt b/latest/cases/00207/synopsis.txt new file mode 100644 index 000000000..38254a34e --- /dev/null +++ b/latest/cases/00207/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with four species in a 1-dimensional + non-unity compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 9$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 4$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00208/l2v5/heta-code/output.heta b/latest/cases/00208/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c6c1e05ef --- /dev/null +++ b/latest/cases/00208/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-4; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00208/l2v5/index.heta b/latest/cases/00208/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00208/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00208/l2v5/json/output.json b/latest/cases/00208/l2v5/json/output.json new file mode 100644 index 000000000..353e3cd73 --- /dev/null +++ b/latest/cases/00208/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00208/l3v2/heta-code/output.heta b/latest/cases/00208/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9319280f8 --- /dev/null +++ b/latest/cases/00208/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-4; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00208/l3v2/index.heta b/latest/cases/00208/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00208/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00208/l3v2/json/output.json b/latest/cases/00208/l3v2/json/output.json new file mode 100644 index 000000000..f209862fd --- /dev/null +++ b/latest/cases/00208/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00208/model-sbml-l2v5.xml b/latest/cases/00208/model-sbml-l2v5.xml new file mode 100644 index 000000000..31ac23890 --- /dev/null +++ b/latest/cases/00208/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00208/model-sbml-l3v2.xml b/latest/cases/00208/model-sbml-l3v2.xml new file mode 100644 index 000000000..14af0287b --- /dev/null +++ b/latest/cases/00208/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00208/output.heta b/latest/cases/00208/output.heta new file mode 100644 index 000000000..d451989e9 --- /dev/null +++ b/latest/cases/00208/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Species S1 and S2 are declared to have +only substance units. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$ 1 \x 10^-4$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-4; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00208/synopsis.txt b/latest/cases/00208/synopsis.txt new file mode 100644 index 000000000..1a0925cb8 --- /dev/null +++ b/latest/cases/00208/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Species S1 and S2 are declared to have +only substance units. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$ 1 \x 10^-4$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00209/l2v5/heta-code/output.heta b/latest/cases/00209/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0253be1e8 --- /dev/null +++ b/latest/cases/00209/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.2; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 25; + diff --git a/latest/cases/00209/l2v5/index.heta b/latest/cases/00209/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00209/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00209/l2v5/json/output.json b/latest/cases/00209/l2v5/json/output.json new file mode 100644 index 000000000..0f582cc7a --- /dev/null +++ b/latest/cases/00209/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00209/l3v2/heta-code/output.heta b/latest/cases/00209/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b348b97ea --- /dev/null +++ b/latest/cases/00209/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00209/l3v2/index.heta b/latest/cases/00209/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00209/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00209/l3v2/json/output.json b/latest/cases/00209/l3v2/json/output.json new file mode 100644 index 000000000..f70b080e1 --- /dev/null +++ b/latest/cases/00209/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + } +] \ No newline at end of file diff --git a/latest/cases/00209/model-sbml-l2v5.xml b/latest/cases/00209/model-sbml-l2v5.xml new file mode 100644 index 000000000..8081f7504 --- /dev/null +++ b/latest/cases/00209/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00209/model-sbml-l3v2.xml b/latest/cases/00209/model-sbml-l3v2.xml new file mode 100644 index 000000000..93b84fd73 --- /dev/null +++ b/latest/cases/00209/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00209/output.heta b/latest/cases/00209/output.heta new file mode 100644 index 000000000..9cc8a1f93 --- /dev/null +++ b/latest/cases/00209/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic reaction with two species in a 2-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S1, S2 and S3 are +declared to have only substance units. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00209/synopsis.txt b/latest/cases/00209/synopsis.txt new file mode 100644 index 000000000..b6392c58d --- /dev/null +++ b/latest/cases/00209/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic reaction with two species in a 2-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S1, S2 and S3 are +declared to have only substance units. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00210/l2v5/heta-code/output.heta b/latest/cases/00210/l2v5/heta-code/output.heta new file mode 100644 index 000000000..12e5e7530 --- /dev/null +++ b/latest/cases/00210/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.002; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 250; + diff --git a/latest/cases/00210/l2v5/index.heta b/latest/cases/00210/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00210/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00210/l2v5/json/output.json b/latest/cases/00210/l2v5/json/output.json new file mode 100644 index 000000000..1d79772d7 --- /dev/null +++ b/latest/cases/00210/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "250" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00210/l3v2/heta-code/output.heta b/latest/cases/00210/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d5238ab4c --- /dev/null +++ b/latest/cases/00210/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00210/l3v2/index.heta b/latest/cases/00210/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00210/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00210/l3v2/json/output.json b/latest/cases/00210/l3v2/json/output.json new file mode 100644 index 000000000..13425c267 --- /dev/null +++ b/latest/cases/00210/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 250 + } +] \ No newline at end of file diff --git a/latest/cases/00210/model-sbml-l2v5.xml b/latest/cases/00210/model-sbml-l2v5.xml new file mode 100644 index 000000000..de7847b53 --- /dev/null +++ b/latest/cases/00210/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00210/model-sbml-l3v2.xml b/latest/cases/00210/model-sbml-l3v2.xml new file mode 100644 index 000000000..0b3a52fd2 --- /dev/null +++ b/latest/cases/00210/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00210/output.heta b/latest/cases/00210/output.heta new file mode 100644 index 000000000..901e0afbf --- /dev/null +++ b/latest/cases/00210/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. All four species are declared +to have only substance units. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 7.5 \x 10^3$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00210/synopsis.txt b/latest/cases/00210/synopsis.txt new file mode 100644 index 000000000..f06c25333 --- /dev/null +++ b/latest/cases/00210/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. All four species are declared +to have only substance units. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 7.5 \x 10^3$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00211/l2v5/heta-code/output.heta b/latest/cases/00211/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9de2f69e7 --- /dev/null +++ b/latest/cases/00211/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00211/l2v5/index.heta b/latest/cases/00211/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00211/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00211/l2v5/json/output.json b/latest/cases/00211/l2v5/json/output.json new file mode 100644 index 000000000..4be66d461 --- /dev/null +++ b/latest/cases/00211/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00211/l3v2/heta-code/output.heta b/latest/cases/00211/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cf950f7d4 --- /dev/null +++ b/latest/cases/00211/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00211/l3v2/index.heta b/latest/cases/00211/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00211/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00211/l3v2/json/output.json b/latest/cases/00211/l3v2/json/output.json new file mode 100644 index 000000000..3acf8f90f --- /dev/null +++ b/latest/cases/00211/l3v2/json/output.json @@ -0,0 +1,62 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00211/model-sbml-l2v5.xml b/latest/cases/00211/model-sbml-l2v5.xml new file mode 100644 index 000000000..a053c2a94 --- /dev/null +++ b/latest/cases/00211/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00211/model-sbml-l3v2.xml b/latest/cases/00211/model-sbml-l3v2.xml new file mode 100644 index 000000000..97853897d --- /dev/null +++ b/latest/cases/00211/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00211/output.heta b/latest/cases/00211/output.heta new file mode 100644 index 000000000..4cc405a38 --- /dev/null +++ b/latest/cases/00211/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Species S1 is labeled as an SBML +boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00211/synopsis.txt b/latest/cases/00211/synopsis.txt new file mode 100644 index 000000000..c1914b659 --- /dev/null +++ b/latest/cases/00211/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Species S1 is labeled as an SBML +boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00212/l2v5/heta-code/output.heta b/latest/cases/00212/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1c7afbaa4 --- /dev/null +++ b/latest/cases/00212/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/area, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00212/l2v5/index.heta b/latest/cases/00212/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00212/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00212/l2v5/json/output.json b/latest/cases/00212/l2v5/json/output.json new file mode 100644 index 000000000..748ad8dbc --- /dev/null +++ b/latest/cases/00212/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00212/l3v2/heta-code/output.heta b/latest/cases/00212/l3v2/heta-code/output.heta new file mode 100644 index 000000000..75a4cd5c3 --- /dev/null +++ b/latest/cases/00212/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00212/l3v2/index.heta b/latest/cases/00212/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00212/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00212/l3v2/json/output.json b/latest/cases/00212/l3v2/json/output.json new file mode 100644 index 000000000..6878a3a3e --- /dev/null +++ b/latest/cases/00212/l3v2/json/output.json @@ -0,0 +1,62 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00212/model-sbml-l2v5.xml b/latest/cases/00212/model-sbml-l2v5.xml new file mode 100644 index 000000000..4b7a87d60 --- /dev/null +++ b/latest/cases/00212/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00212/model-sbml-l3v2.xml b/latest/cases/00212/model-sbml-l3v2.xml new file mode 100644 index 000000000..daae3c8d6 --- /dev/null +++ b/latest/cases/00212/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00212/output.heta b/latest/cases/00212/output.heta new file mode 100644 index 000000000..17769c5d9 --- /dev/null +++ b/latest/cases/00212/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Species S2 is labeled as an SBML +boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00212/synopsis.txt b/latest/cases/00212/synopsis.txt new file mode 100644 index 000000000..92ad4fedd --- /dev/null +++ b/latest/cases/00212/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Species S2 is labeled as an SBML +boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00213/l2v5/heta-code/output.heta b/latest/cases/00213/l2v5/heta-code/output.heta new file mode 100644 index 000000000..557cfcfea --- /dev/null +++ b/latest/cases/00213/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/area, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00213/l2v5/index.heta b/latest/cases/00213/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00213/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00213/l2v5/json/output.json b/latest/cases/00213/l2v5/json/output.json new file mode 100644 index 000000000..74538ae6e --- /dev/null +++ b/latest/cases/00213/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00213/l3v2/heta-code/output.heta b/latest/cases/00213/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9202703b --- /dev/null +++ b/latest/cases/00213/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00213/l3v2/index.heta b/latest/cases/00213/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00213/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00213/l3v2/json/output.json b/latest/cases/00213/l3v2/json/output.json new file mode 100644 index 000000000..0920ebd63 --- /dev/null +++ b/latest/cases/00213/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00213/model-sbml-l2v5.xml b/latest/cases/00213/model-sbml-l2v5.xml new file mode 100644 index 000000000..bfef24fe6 --- /dev/null +++ b/latest/cases/00213/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00213/model-sbml-l3v2.xml b/latest/cases/00213/model-sbml-l3v2.xml new file mode 100644 index 000000000..c1a3c100c --- /dev/null +++ b/latest/cases/00213/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00213/output.heta b/latest/cases/00213/output.heta new file mode 100644 index 000000000..a48e81052 --- /dev/null +++ b/latest/cases/00213/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment, with both species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Both species S1 and S2 are labeled as an +SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +!!!|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00213/synopsis.txt b/latest/cases/00213/synopsis.txt new file mode 100644 index 000000000..ac6f37ad3 --- /dev/null +++ b/latest/cases/00213/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment, with both species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Both species S1 and S2 are labeled as an +SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +!!!|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00214/l2v5/heta-code/output.heta b/latest/cases/00214/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3bbd8098a --- /dev/null +++ b/latest/cases/00214/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, boundary: true, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00214/l2v5/index.heta b/latest/cases/00214/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00214/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00214/l2v5/json/output.json b/latest/cases/00214/l2v5/json/output.json new file mode 100644 index 000000000..2732e63ba --- /dev/null +++ b/latest/cases/00214/l2v5/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00214/l3v2/heta-code/output.heta b/latest/cases/00214/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dbe079612 --- /dev/null +++ b/latest/cases/00214/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00214/l3v2/index.heta b/latest/cases/00214/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00214/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00214/l3v2/json/output.json b/latest/cases/00214/l3v2/json/output.json new file mode 100644 index 000000000..633fe28c1 --- /dev/null +++ b/latest/cases/00214/l3v2/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00214/model-sbml-l2v5.xml b/latest/cases/00214/model-sbml-l2v5.xml new file mode 100644 index 000000000..91c038e37 --- /dev/null +++ b/latest/cases/00214/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00214/model-sbml-l3v2.xml b/latest/cases/00214/model-sbml-l3v2.xml new file mode 100644 index 000000000..04e0ff55e --- /dev/null +++ b/latest/cases/00214/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00214/output.heta b/latest/cases/00214/output.heta new file mode 100644 index 000000000..64a4c3ed3 --- /dev/null +++ b/latest/cases/00214/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 2-dimensional compartment. +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S1 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00214/synopsis.txt b/latest/cases/00214/synopsis.txt new file mode 100644 index 000000000..f5d03c636 --- /dev/null +++ b/latest/cases/00214/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic reactions with three species in a 2-dimensional compartment. +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S1 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00215/l2v5/heta-code/output.heta b/latest/cases/00215/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1b5ec6c06 --- /dev/null +++ b/latest/cases/00215/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: substance/area, boundary: true, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00215/l2v5/index.heta b/latest/cases/00215/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00215/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00215/l2v5/json/output.json b/latest/cases/00215/l2v5/json/output.json new file mode 100644 index 000000000..754b14be3 --- /dev/null +++ b/latest/cases/00215/l2v5/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00215/l3v2/heta-code/output.heta b/latest/cases/00215/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f5898fe2b --- /dev/null +++ b/latest/cases/00215/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00215/l3v2/index.heta b/latest/cases/00215/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00215/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00215/l3v2/json/output.json b/latest/cases/00215/l3v2/json/output.json new file mode 100644 index 000000000..0b01b198c --- /dev/null +++ b/latest/cases/00215/l3v2/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00215/model-sbml-l2v5.xml b/latest/cases/00215/model-sbml-l2v5.xml new file mode 100644 index 000000000..ca9fa03a0 --- /dev/null +++ b/latest/cases/00215/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00215/model-sbml-l3v2.xml b/latest/cases/00215/model-sbml-l3v2.xml new file mode 100644 index 000000000..e0686f93c --- /dev/null +++ b/latest/cases/00215/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00215/output.heta b/latest/cases/00215/output.heta new file mode 100644 index 000000000..4e2d8e243 --- /dev/null +++ b/latest/cases/00215/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 2-dimensional compartment. +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S3 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00215/synopsis.txt b/latest/cases/00215/synopsis.txt new file mode 100644 index 000000000..bcad1ff22 --- /dev/null +++ b/latest/cases/00215/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic reactions with three species in a 2-dimensional compartment. +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S3 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00216/l2v5/heta-code/output.heta b/latest/cases/00216/l2v5/heta-code/output.heta new file mode 100644 index 000000000..48173f24c --- /dev/null +++ b/latest/cases/00216/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/area, boundary: true, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00216/l2v5/index.heta b/latest/cases/00216/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00216/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00216/l2v5/json/output.json b/latest/cases/00216/l2v5/json/output.json new file mode 100644 index 000000000..10b7a10ed --- /dev/null +++ b/latest/cases/00216/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.02 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00216/l3v2/heta-code/output.heta b/latest/cases/00216/l3v2/heta-code/output.heta new file mode 100644 index 000000000..aea60dc7a --- /dev/null +++ b/latest/cases/00216/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00216/l3v2/index.heta b/latest/cases/00216/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00216/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00216/l3v2/json/output.json b/latest/cases/00216/l3v2/json/output.json new file mode 100644 index 000000000..e29bcd227 --- /dev/null +++ b/latest/cases/00216/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.02 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00216/model-sbml-l2v5.xml b/latest/cases/00216/model-sbml-l2v5.xml new file mode 100644 index 000000000..ea1712d8c --- /dev/null +++ b/latest/cases/00216/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00216/model-sbml-l3v2.xml b/latest/cases/00216/model-sbml-l3v2.xml new file mode 100644 index 000000000..5c6a7733a --- /dev/null +++ b/latest/cases/00216/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00216/output.heta b/latest/cases/00216/output.heta new file mode 100644 index 000000000..ca674490b --- /dev/null +++ b/latest/cases/00216/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 2-dimensional compartment. +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00216/synopsis.txt b/latest/cases/00216/synopsis.txt new file mode 100644 index 000000000..29013d99a --- /dev/null +++ b/latest/cases/00216/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic reactions with three species in a 2-dimensional compartment. +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00217/l2v5/heta-code/output.heta b/latest/cases/00217/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9205369d3 --- /dev/null +++ b/latest/cases/00217/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: substance/area, boundary: true, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00217/l2v5/index.heta b/latest/cases/00217/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00217/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00217/l2v5/json/output.json b/latest/cases/00217/l2v5/json/output.json new file mode 100644 index 000000000..dc470dc01 --- /dev/null +++ b/latest/cases/00217/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00217/l3v2/heta-code/output.heta b/latest/cases/00217/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7f20d901c --- /dev/null +++ b/latest/cases/00217/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00217/l3v2/index.heta b/latest/cases/00217/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00217/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00217/l3v2/json/output.json b/latest/cases/00217/l3v2/json/output.json new file mode 100644 index 000000000..4e7c5db61 --- /dev/null +++ b/latest/cases/00217/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00217/model-sbml-l2v5.xml b/latest/cases/00217/model-sbml-l2v5.xml new file mode 100644 index 000000000..86183812f --- /dev/null +++ b/latest/cases/00217/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00217/model-sbml-l3v2.xml b/latest/cases/00217/model-sbml-l3v2.xml new file mode 100644 index 000000000..0e04a6c04 --- /dev/null +++ b/latest/cases/00217/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00217/output.heta b/latest/cases/00217/output.heta new file mode 100644 index 000000000..54cbdf76c --- /dev/null +++ b/latest/cases/00217/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 2-dimensional compartment. +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S1 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00217/synopsis.txt b/latest/cases/00217/synopsis.txt new file mode 100644 index 000000000..40cac3751 --- /dev/null +++ b/latest/cases/00217/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with three species in a 2-dimensional compartment. +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S1 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00218/l2v5/heta-code/output.heta b/latest/cases/00218/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9beeeefa6 --- /dev/null +++ b/latest/cases/00218/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.01 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 0.02 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 25; + diff --git a/latest/cases/00218/l2v5/index.heta b/latest/cases/00218/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00218/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00218/l2v5/json/output.json b/latest/cases/00218/l2v5/json/output.json new file mode 100644 index 000000000..895207695 --- /dev/null +++ b/latest/cases/00218/l2v5/json/output.json @@ -0,0 +1,151 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00218/l3v2/heta-code/output.heta b/latest/cases/00218/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6cd924ef6 --- /dev/null +++ b/latest/cases/00218/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00218/l3v2/index.heta b/latest/cases/00218/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00218/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00218/l3v2/json/output.json b/latest/cases/00218/l3v2/json/output.json new file mode 100644 index 000000000..37f7d3180 --- /dev/null +++ b/latest/cases/00218/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + } +] \ No newline at end of file diff --git a/latest/cases/00218/model-sbml-l2v5.xml b/latest/cases/00218/model-sbml-l2v5.xml new file mode 100644 index 000000000..df5ffcf4d --- /dev/null +++ b/latest/cases/00218/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00218/model-sbml-l3v2.xml b/latest/cases/00218/model-sbml-l3v2.xml new file mode 100644 index 000000000..d849a8bd6 --- /dev/null +++ b/latest/cases/00218/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00218/output.heta b/latest/cases/00218/output.heta new file mode 100644 index 000000000..48c3b33fb --- /dev/null +++ b/latest/cases/00218/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S1 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00218/synopsis.txt b/latest/cases/00218/synopsis.txt new file mode 100644 index 000000000..e9852d35d --- /dev/null +++ b/latest/cases/00218/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S1 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00219/l2v5/heta-code/output.heta b/latest/cases/00219/l2v5/heta-code/output.heta new file mode 100644 index 000000000..81ef1a11c --- /dev/null +++ b/latest/cases/00219/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/area, boundary: true, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00219/l2v5/index.heta b/latest/cases/00219/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00219/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00219/l2v5/json/output.json b/latest/cases/00219/l2v5/json/output.json new file mode 100644 index 000000000..544984599 --- /dev/null +++ b/latest/cases/00219/l2v5/json/output.json @@ -0,0 +1,151 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00219/l3v2/heta-code/output.heta b/latest/cases/00219/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f55d51302 --- /dev/null +++ b/latest/cases/00219/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00219/l3v2/index.heta b/latest/cases/00219/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00219/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00219/l3v2/json/output.json b/latest/cases/00219/l3v2/json/output.json new file mode 100644 index 000000000..b54c3d91d --- /dev/null +++ b/latest/cases/00219/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + } +] \ No newline at end of file diff --git a/latest/cases/00219/model-sbml-l2v5.xml b/latest/cases/00219/model-sbml-l2v5.xml new file mode 100644 index 000000000..2cc8a3e22 --- /dev/null +++ b/latest/cases/00219/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00219/model-sbml-l3v2.xml b/latest/cases/00219/model-sbml-l3v2.xml new file mode 100644 index 000000000..893ad7d47 --- /dev/null +++ b/latest/cases/00219/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00219/output.heta b/latest/cases/00219/output.heta new file mode 100644 index 000000000..a64e82eaa --- /dev/null +++ b/latest/cases/00219/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S4 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00219/synopsis.txt b/latest/cases/00219/synopsis.txt new file mode 100644 index 000000000..0d501fbf9 --- /dev/null +++ b/latest/cases/00219/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S4 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00220/l2v5/heta-code/output.heta b/latest/cases/00220/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e9b8fa363 --- /dev/null +++ b/latest/cases/00220/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/area, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00220/l2v5/index.heta b/latest/cases/00220/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00220/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00220/l2v5/json/output.json b/latest/cases/00220/l2v5/json/output.json new file mode 100644 index 000000000..fc3b0c86b --- /dev/null +++ b/latest/cases/00220/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00220/l3v2/heta-code/output.heta b/latest/cases/00220/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6c4086657 --- /dev/null +++ b/latest/cases/00220/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00220/l3v2/index.heta b/latest/cases/00220/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00220/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00220/l3v2/json/output.json b/latest/cases/00220/l3v2/json/output.json new file mode 100644 index 000000000..e17572d4e --- /dev/null +++ b/latest/cases/00220/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + } +] \ No newline at end of file diff --git a/latest/cases/00220/model-sbml-l2v5.xml b/latest/cases/00220/model-sbml-l2v5.xml new file mode 100644 index 000000000..4a8ec1495 --- /dev/null +++ b/latest/cases/00220/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00220/model-sbml-l3v2.xml b/latest/cases/00220/model-sbml-l3v2.xml new file mode 100644 index 000000000..dfdd6c2e3 --- /dev/null +++ b/latest/cases/00220/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00220/output.heta b/latest/cases/00220/output.heta new file mode 100644 index 000000000..2d9b45b4d --- /dev/null +++ b/latest/cases/00220/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00220/synopsis.txt b/latest/cases/00220/synopsis.txt new file mode 100644 index 000000000..b8eae24b7 --- /dev/null +++ b/latest/cases/00220/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00221/l2v5/heta-code/output.heta b/latest/cases/00221/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6db529e64 --- /dev/null +++ b/latest/cases/00221/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/area, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: substance/area, boundary: true, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00221/l2v5/index.heta b/latest/cases/00221/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00221/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00221/l2v5/json/output.json b/latest/cases/00221/l2v5/json/output.json new file mode 100644 index 000000000..660c9c780 --- /dev/null +++ b/latest/cases/00221/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "2e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00221/l3v2/heta-code/output.heta b/latest/cases/00221/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e3629f4c3 --- /dev/null +++ b/latest/cases/00221/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00221/l3v2/index.heta b/latest/cases/00221/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00221/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00221/l3v2/json/output.json b/latest/cases/00221/l3v2/json/output.json new file mode 100644 index 000000000..1cde2d734 --- /dev/null +++ b/latest/cases/00221/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + } +] \ No newline at end of file diff --git a/latest/cases/00221/model-sbml-l2v5.xml b/latest/cases/00221/model-sbml-l2v5.xml new file mode 100644 index 000000000..6bc999a02 --- /dev/null +++ b/latest/cases/00221/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00221/model-sbml-l3v2.xml b/latest/cases/00221/model-sbml-l3v2.xml new file mode 100644 index 000000000..390b86a98 --- /dev/null +++ b/latest/cases/00221/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00221/output.heta b/latest/cases/00221/output.heta new file mode 100644 index 000000000..4871ab442 --- /dev/null +++ b/latest/cases/00221/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S2 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00221/synopsis.txt b/latest/cases/00221/synopsis.txt new file mode 100644 index 000000000..e4b281966 --- /dev/null +++ b/latest/cases/00221/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S2 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00222/l2v5/heta-code/output.heta b/latest/cases/00222/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8e57b33e2 --- /dev/null +++ b/latest/cases/00222/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: substance/area, boundary: true, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/area, boundary: true, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00222/l2v5/index.heta b/latest/cases/00222/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00222/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00222/l2v5/json/output.json b/latest/cases/00222/l2v5/json/output.json new file mode 100644 index 000000000..52106491e --- /dev/null +++ b/latest/cases/00222/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "2e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00222/l3v2/heta-code/output.heta b/latest/cases/00222/l3v2/heta-code/output.heta new file mode 100644 index 000000000..40d9db190 --- /dev/null +++ b/latest/cases/00222/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00222/l3v2/index.heta b/latest/cases/00222/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00222/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00222/l3v2/json/output.json b/latest/cases/00222/l3v2/json/output.json new file mode 100644 index 000000000..b769973d2 --- /dev/null +++ b/latest/cases/00222/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + } +] \ No newline at end of file diff --git a/latest/cases/00222/model-sbml-l2v5.xml b/latest/cases/00222/model-sbml-l2v5.xml new file mode 100644 index 000000000..62ae6b1be --- /dev/null +++ b/latest/cases/00222/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00222/model-sbml-l3v2.xml b/latest/cases/00222/model-sbml-l3v2.xml new file mode 100644 index 000000000..aaa974726 --- /dev/null +++ b/latest/cases/00222/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00222/output.heta b/latest/cases/00222/output.heta new file mode 100644 index 000000000..23a577caf --- /dev/null +++ b/latest/cases/00222/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S3 and S4 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00222/synopsis.txt b/latest/cases/00222/synopsis.txt new file mode 100644 index 000000000..f574466a9 --- /dev/null +++ b/latest/cases/00222/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Both species S3 and S4 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00223/l2v5/heta-code/output.heta b/latest/cases/00223/l2v5/heta-code/output.heta new file mode 100644 index 000000000..212066d56 --- /dev/null +++ b/latest/cases/00223/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00223/l2v5/index.heta b/latest/cases/00223/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00223/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00223/l2v5/json/output.json b/latest/cases/00223/l2v5/json/output.json new file mode 100644 index 000000000..55322916d --- /dev/null +++ b/latest/cases/00223/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00223/l3v2/heta-code/output.heta b/latest/cases/00223/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0fa942354 --- /dev/null +++ b/latest/cases/00223/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00223/l3v2/index.heta b/latest/cases/00223/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00223/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00223/l3v2/json/output.json b/latest/cases/00223/l3v2/json/output.json new file mode 100644 index 000000000..7c5e3efa3 --- /dev/null +++ b/latest/cases/00223/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00223/model-sbml-l2v5.xml b/latest/cases/00223/model-sbml-l2v5.xml new file mode 100644 index 000000000..a993d8f2e --- /dev/null +++ b/latest/cases/00223/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00223/model-sbml-l3v2.xml b/latest/cases/00223/model-sbml-l3v2.xml new file mode 100644 index 000000000..b6c295266 --- /dev/null +++ b/latest/cases/00223/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00223/output.heta b/latest/cases/00223/output.heta new file mode 100644 index 000000000..9ff6a640d --- /dev/null +++ b/latest/cases/00223/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Species S1 and S2 are declared to have +only substance units. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00223/synopsis.txt b/latest/cases/00223/synopsis.txt new file mode 100644 index 000000000..447960e1c --- /dev/null +++ b/latest/cases/00223/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Species S1 and S2 are declared to have +only substance units. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00224/l2v5/heta-code/output.heta b/latest/cases/00224/l2v5/heta-code/output.heta new file mode 100644 index 000000000..21ef38e68 --- /dev/null +++ b/latest/cases/00224/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 2; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00224/l2v5/index.heta b/latest/cases/00224/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00224/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00224/l2v5/json/output.json b/latest/cases/00224/l2v5/json/output.json new file mode 100644 index 000000000..7e182db13 --- /dev/null +++ b/latest/cases/00224/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00224/l3v2/heta-code/output.heta b/latest/cases/00224/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c44330233 --- /dev/null +++ b/latest/cases/00224/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00224/l3v2/index.heta b/latest/cases/00224/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00224/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00224/l3v2/json/output.json b/latest/cases/00224/l3v2/json/output.json new file mode 100644 index 000000000..d584ccd93 --- /dev/null +++ b/latest/cases/00224/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00224/model-sbml-l2v5.xml b/latest/cases/00224/model-sbml-l2v5.xml new file mode 100644 index 000000000..9c40ab5fc --- /dev/null +++ b/latest/cases/00224/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00224/model-sbml-l3v2.xml b/latest/cases/00224/model-sbml-l3v2.xml new file mode 100644 index 000000000..3ae6594e0 --- /dev/null +++ b/latest/cases/00224/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00224/output.heta b/latest/cases/00224/output.heta new file mode 100644 index 000000000..eac0bcfed --- /dev/null +++ b/latest/cases/00224/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic reaction with two species in a 1-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S1, S2 and S3 are +declared to have only substance units. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00224/synopsis.txt b/latest/cases/00224/synopsis.txt new file mode 100644 index 000000000..3e67e567e --- /dev/null +++ b/latest/cases/00224/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic reaction with two species in a 1-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S1, S2 and S3 are +declared to have only substance units. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00225/l2v5/heta-code/output.heta b/latest/cases/00225/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5cc48c0c9 --- /dev/null +++ b/latest/cases/00225/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.015; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.02; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 620; +k2 @Record 'k2' { } .= 500; + diff --git a/latest/cases/00225/l2v5/index.heta b/latest/cases/00225/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00225/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00225/l2v5/json/output.json b/latest/cases/00225/l2v5/json/output.json new file mode 100644 index 000000000..253b218e7 --- /dev/null +++ b/latest/cases/00225/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "620" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00225/l3v2/heta-code/output.heta b/latest/cases/00225/l3v2/heta-code/output.heta new file mode 100644 index 000000000..64da8d2be --- /dev/null +++ b/latest/cases/00225/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 620; +k2 @Const 'k2' { } = 500; + diff --git a/latest/cases/00225/l3v2/index.heta b/latest/cases/00225/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00225/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00225/l3v2/json/output.json b/latest/cases/00225/l3v2/json/output.json new file mode 100644 index 000000000..b6682d842 --- /dev/null +++ b/latest/cases/00225/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 620 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 500 + } +] \ No newline at end of file diff --git a/latest/cases/00225/model-sbml-l2v5.xml b/latest/cases/00225/model-sbml-l2v5.xml new file mode 100644 index 000000000..9f9eb2062 --- /dev/null +++ b/latest/cases/00225/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00225/model-sbml-l3v2.xml b/latest/cases/00225/model-sbml-l3v2.xml new file mode 100644 index 000000000..f9a80466b --- /dev/null +++ b/latest/cases/00225/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00225/output.heta b/latest/cases/00225/output.heta new file mode 100644 index 000000000..d5cc840eb --- /dev/null +++ b/latest/cases/00225/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. All four species are declared +to have only substance units. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^2$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 620; +k2 @Const 'k2' { } = 500; + diff --git a/latest/cases/00225/synopsis.txt b/latest/cases/00225/synopsis.txt new file mode 100644 index 000000000..926ada351 --- /dev/null +++ b/latest/cases/00225/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. All four species are declared +to have only substance units. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^2$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00226/l2v5/heta-code/output.heta b/latest/cases/00226/l2v5/heta-code/output.heta new file mode 100644 index 000000000..01abd25d5 --- /dev/null +++ b/latest/cases/00226/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00226/l2v5/index.heta b/latest/cases/00226/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00226/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00226/l2v5/json/output.json b/latest/cases/00226/l2v5/json/output.json new file mode 100644 index 000000000..f4b17bf3c --- /dev/null +++ b/latest/cases/00226/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00226/l3v2/heta-code/output.heta b/latest/cases/00226/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cb6f593aa --- /dev/null +++ b/latest/cases/00226/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00226/l3v2/index.heta b/latest/cases/00226/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00226/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00226/l3v2/json/output.json b/latest/cases/00226/l3v2/json/output.json new file mode 100644 index 000000000..4419808d3 --- /dev/null +++ b/latest/cases/00226/l3v2/json/output.json @@ -0,0 +1,62 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00226/model-sbml-l2v5.xml b/latest/cases/00226/model-sbml-l2v5.xml new file mode 100644 index 000000000..612841426 --- /dev/null +++ b/latest/cases/00226/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00226/model-sbml-l3v2.xml b/latest/cases/00226/model-sbml-l3v2.xml new file mode 100644 index 000000000..023da3cce --- /dev/null +++ b/latest/cases/00226/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00226/output.heta b/latest/cases/00226/output.heta new file mode 100644 index 000000000..33409f677 --- /dev/null +++ b/latest/cases/00226/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Species S1 is labeled as an SBML +boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00226/synopsis.txt b/latest/cases/00226/synopsis.txt new file mode 100644 index 000000000..d76ecf776 --- /dev/null +++ b/latest/cases/00226/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Species S1 is labeled as an SBML +boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00227/l2v5/heta-code/output.heta b/latest/cases/00227/l2v5/heta-code/output.heta new file mode 100644 index 000000000..db8838855 --- /dev/null +++ b/latest/cases/00227/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: substance/length, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00227/l2v5/index.heta b/latest/cases/00227/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00227/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00227/l2v5/json/output.json b/latest/cases/00227/l2v5/json/output.json new file mode 100644 index 000000000..4eb25d890 --- /dev/null +++ b/latest/cases/00227/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00227/l3v2/heta-code/output.heta b/latest/cases/00227/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3de4d24c7 --- /dev/null +++ b/latest/cases/00227/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00227/l3v2/index.heta b/latest/cases/00227/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00227/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00227/l3v2/json/output.json b/latest/cases/00227/l3v2/json/output.json new file mode 100644 index 000000000..53e7eb92d --- /dev/null +++ b/latest/cases/00227/l3v2/json/output.json @@ -0,0 +1,62 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00227/model-sbml-l2v5.xml b/latest/cases/00227/model-sbml-l2v5.xml new file mode 100644 index 000000000..18f183813 --- /dev/null +++ b/latest/cases/00227/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00227/model-sbml-l3v2.xml b/latest/cases/00227/model-sbml-l3v2.xml new file mode 100644 index 000000000..71c94c06f --- /dev/null +++ b/latest/cases/00227/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00227/output.heta b/latest/cases/00227/output.heta new file mode 100644 index 000000000..7d75759f0 --- /dev/null +++ b/latest/cases/00227/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Species S2 is labeled as an SBML +boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00227/synopsis.txt b/latest/cases/00227/synopsis.txt new file mode 100644 index 000000000..12831f730 --- /dev/null +++ b/latest/cases/00227/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Species S2 is labeled as an SBML +boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00228/l2v5/heta-code/output.heta b/latest/cases/00228/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cfc6c9d1b --- /dev/null +++ b/latest/cases/00228/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: substance/length, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00228/l2v5/index.heta b/latest/cases/00228/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00228/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00228/l2v5/json/output.json b/latest/cases/00228/l2v5/json/output.json new file mode 100644 index 000000000..91c1db1e9 --- /dev/null +++ b/latest/cases/00228/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00228/l3v2/heta-code/output.heta b/latest/cases/00228/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0d05b1477 --- /dev/null +++ b/latest/cases/00228/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00228/l3v2/index.heta b/latest/cases/00228/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00228/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00228/l3v2/json/output.json b/latest/cases/00228/l3v2/json/output.json new file mode 100644 index 000000000..476998e3f --- /dev/null +++ b/latest/cases/00228/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00228/model-sbml-l2v5.xml b/latest/cases/00228/model-sbml-l2v5.xml new file mode 100644 index 000000000..9820f5d16 --- /dev/null +++ b/latest/cases/00228/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00228/model-sbml-l3v2.xml b/latest/cases/00228/model-sbml-l3v2.xml new file mode 100644 index 000000000..433c2813c --- /dev/null +++ b/latest/cases/00228/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00228/output.heta b/latest/cases/00228/output.heta new file mode 100644 index 000000000..efda1dbd0 --- /dev/null +++ b/latest/cases/00228/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment, with both species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Both species S1 and S2 are labeled as an +SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00228/synopsis.txt b/latest/cases/00228/synopsis.txt new file mode 100644 index 000000000..97cd35f42 --- /dev/null +++ b/latest/cases/00228/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment, with both species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Both species S1 and S2 are labeled as an +SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00229/l2v5/heta-code/output.heta b/latest/cases/00229/l2v5/heta-code/output.heta new file mode 100644 index 000000000..34f945ebc --- /dev/null +++ b/latest/cases/00229/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/length, boundary: true, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00229/l2v5/index.heta b/latest/cases/00229/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00229/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00229/l2v5/json/output.json b/latest/cases/00229/l2v5/json/output.json new file mode 100644 index 000000000..e4f3d50a4 --- /dev/null +++ b/latest/cases/00229/l2v5/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00229/l3v2/heta-code/output.heta b/latest/cases/00229/l3v2/heta-code/output.heta new file mode 100644 index 000000000..011394a60 --- /dev/null +++ b/latest/cases/00229/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00229/l3v2/index.heta b/latest/cases/00229/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00229/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00229/l3v2/json/output.json b/latest/cases/00229/l3v2/json/output.json new file mode 100644 index 000000000..eb5ffd0e5 --- /dev/null +++ b/latest/cases/00229/l3v2/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00229/model-sbml-l2v5.xml b/latest/cases/00229/model-sbml-l2v5.xml new file mode 100644 index 000000000..54bccb30c --- /dev/null +++ b/latest/cases/00229/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00229/model-sbml-l3v2.xml b/latest/cases/00229/model-sbml-l3v2.xml new file mode 100644 index 000000000..ee6a51d91 --- /dev/null +++ b/latest/cases/00229/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00229/output.heta b/latest/cases/00229/output.heta new file mode 100644 index 000000000..a1c3dbcf3 --- /dev/null +++ b/latest/cases/00229/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S2 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00229/synopsis.txt b/latest/cases/00229/synopsis.txt new file mode 100644 index 000000000..747df3a10 --- /dev/null +++ b/latest/cases/00229/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic reactions with three species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S2 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00230/l2v5/heta-code/output.heta b/latest/cases/00230/l2v5/heta-code/output.heta new file mode 100644 index 000000000..74584e06b --- /dev/null +++ b/latest/cases/00230/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: substance/length, boundary: true, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00230/l2v5/index.heta b/latest/cases/00230/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00230/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00230/l2v5/json/output.json b/latest/cases/00230/l2v5/json/output.json new file mode 100644 index 000000000..eda18ed16 --- /dev/null +++ b/latest/cases/00230/l2v5/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1.5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00230/l3v2/heta-code/output.heta b/latest/cases/00230/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c3cb68355 --- /dev/null +++ b/latest/cases/00230/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00230/l3v2/index.heta b/latest/cases/00230/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00230/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00230/l3v2/json/output.json b/latest/cases/00230/l3v2/json/output.json new file mode 100644 index 000000000..bb9cdde42 --- /dev/null +++ b/latest/cases/00230/l3v2/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1.5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00230/model-sbml-l2v5.xml b/latest/cases/00230/model-sbml-l2v5.xml new file mode 100644 index 000000000..0736010cb --- /dev/null +++ b/latest/cases/00230/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00230/model-sbml-l3v2.xml b/latest/cases/00230/model-sbml-l3v2.xml new file mode 100644 index 000000000..983311b72 --- /dev/null +++ b/latest/cases/00230/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00230/output.heta b/latest/cases/00230/output.heta new file mode 100644 index 000000000..7f0fb9b94 --- /dev/null +++ b/latest/cases/00230/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S3 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00230/synopsis.txt b/latest/cases/00230/synopsis.txt new file mode 100644 index 000000000..dc142b8dd --- /dev/null +++ b/latest/cases/00230/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic reactions with three species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S3 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00231/l2v5/heta-code/output.heta b/latest/cases/00231/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2aaa3af29 --- /dev/null +++ b/latest/cases/00231/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, boundary: true, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/length, boundary: true, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00231/l2v5/index.heta b/latest/cases/00231/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00231/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00231/l2v5/json/output.json b/latest/cases/00231/l2v5/json/output.json new file mode 100644 index 000000000..c284256e9 --- /dev/null +++ b/latest/cases/00231/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00231/l3v2/heta-code/output.heta b/latest/cases/00231/l3v2/heta-code/output.heta new file mode 100644 index 000000000..06b4a6130 --- /dev/null +++ b/latest/cases/00231/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00231/l3v2/index.heta b/latest/cases/00231/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00231/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00231/l3v2/json/output.json b/latest/cases/00231/l3v2/json/output.json new file mode 100644 index 000000000..1bce157fd --- /dev/null +++ b/latest/cases/00231/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00231/model-sbml-l2v5.xml b/latest/cases/00231/model-sbml-l2v5.xml new file mode 100644 index 000000000..f5fdbc11e --- /dev/null +++ b/latest/cases/00231/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00231/model-sbml-l3v2.xml b/latest/cases/00231/model-sbml-l3v2.xml new file mode 100644 index 000000000..0d98dc766 --- /dev/null +++ b/latest/cases/00231/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00231/output.heta b/latest/cases/00231/output.heta new file mode 100644 index 000000000..ec24f86b2 --- /dev/null +++ b/latest/cases/00231/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00231/synopsis.txt b/latest/cases/00231/synopsis.txt new file mode 100644 index 000000000..2626a10c9 --- /dev/null +++ b/latest/cases/00231/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic reactions with three species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00232/l2v5/heta-code/output.heta b/latest/cases/00232/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2c629f332 --- /dev/null +++ b/latest/cases/00232/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, boundary: true, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: substance/length, boundary: true, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00232/l2v5/index.heta b/latest/cases/00232/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00232/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00232/l2v5/json/output.json b/latest/cases/00232/l2v5/json/output.json new file mode 100644 index 000000000..b6d4cd206 --- /dev/null +++ b/latest/cases/00232/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1.5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00232/l3v2/heta-code/output.heta b/latest/cases/00232/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e0c8dc089 --- /dev/null +++ b/latest/cases/00232/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00232/l3v2/index.heta b/latest/cases/00232/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00232/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00232/l3v2/json/output.json b/latest/cases/00232/l3v2/json/output.json new file mode 100644 index 000000000..a5c61f81e --- /dev/null +++ b/latest/cases/00232/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1.5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00232/model-sbml-l2v5.xml b/latest/cases/00232/model-sbml-l2v5.xml new file mode 100644 index 000000000..fe54ff418 --- /dev/null +++ b/latest/cases/00232/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00232/model-sbml-l3v2.xml b/latest/cases/00232/model-sbml-l3v2.xml new file mode 100644 index 000000000..1b3aa509a --- /dev/null +++ b/latest/cases/00232/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00232/output.heta b/latest/cases/00232/output.heta new file mode 100644 index 000000000..49ccce19f --- /dev/null +++ b/latest/cases/00232/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S1 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00232/synopsis.txt b/latest/cases/00232/synopsis.txt new file mode 100644 index 000000000..65f08fbee --- /dev/null +++ b/latest/cases/00232/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic reactions with three species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S1 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00233/l2v5/heta-code/output.heta b/latest/cases/00233/l2v5/heta-code/output.heta new file mode 100644 index 000000000..21469a06c --- /dev/null +++ b/latest/cases/00233/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/length, boundary: true, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 62000; +k2 @Record 'k2' { } .= 50000; + diff --git a/latest/cases/00233/l2v5/index.heta b/latest/cases/00233/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00233/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00233/l2v5/json/output.json b/latest/cases/00233/l2v5/json/output.json new file mode 100644 index 000000000..88e8c098b --- /dev/null +++ b/latest/cases/00233/l2v5/json/output.json @@ -0,0 +1,151 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "62000" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50000" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00233/l3v2/heta-code/output.heta b/latest/cases/00233/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2d7e56a34 --- /dev/null +++ b/latest/cases/00233/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 62000; +k2 @Const 'k2' { } = 50000; + diff --git a/latest/cases/00233/l3v2/index.heta b/latest/cases/00233/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00233/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00233/l3v2/json/output.json b/latest/cases/00233/l3v2/json/output.json new file mode 100644 index 000000000..bc09d726d --- /dev/null +++ b/latest/cases/00233/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 62000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50000 + } +] \ No newline at end of file diff --git a/latest/cases/00233/model-sbml-l2v5.xml b/latest/cases/00233/model-sbml-l2v5.xml new file mode 100644 index 000000000..1f52577d7 --- /dev/null +++ b/latest/cases/00233/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00233/model-sbml-l3v2.xml b/latest/cases/00233/model-sbml-l3v2.xml new file mode 100644 index 000000000..a7d4cbc0d --- /dev/null +++ b/latest/cases/00233/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00233/output.heta b/latest/cases/00233/output.heta new file mode 100644 index 000000000..25cefd355 --- /dev/null +++ b/latest/cases/00233/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S2 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-5$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^4$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^4$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 62000; +k2 @Const 'k2' { } = 50000; + diff --git a/latest/cases/00233/synopsis.txt b/latest/cases/00233/synopsis.txt new file mode 100644 index 000000000..383d80b9a --- /dev/null +++ b/latest/cases/00233/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S2 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-5$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^4$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^4$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00234/l2v5/heta-code/output.heta b/latest/cases/00234/l2v5/heta-code/output.heta new file mode 100644 index 000000000..673e524d7 --- /dev/null +++ b/latest/cases/00234/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: substance/length, boundary: true, compartment: compartment, } .= 0.002 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 6200; +k2 @Record 'k2' { } .= 5000; + diff --git a/latest/cases/00234/l2v5/index.heta b/latest/cases/00234/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00234/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00234/l2v5/json/output.json b/latest/cases/00234/l2v5/json/output.json new file mode 100644 index 000000000..b84a8a384 --- /dev/null +++ b/latest/cases/00234/l2v5/json/output.json @@ -0,0 +1,151 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "0.002 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "6200" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5000" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00234/l3v2/heta-code/output.heta b/latest/cases/00234/l3v2/heta-code/output.heta new file mode 100644 index 000000000..669398b03 --- /dev/null +++ b/latest/cases/00234/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.002 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 6200; +k2 @Const 'k2' { } = 5000; + diff --git a/latest/cases/00234/l3v2/index.heta b/latest/cases/00234/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00234/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00234/l3v2/json/output.json b/latest/cases/00234/l3v2/json/output.json new file mode 100644 index 000000000..e9531697f --- /dev/null +++ b/latest/cases/00234/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "0.002 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 6200 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5000 + } +] \ No newline at end of file diff --git a/latest/cases/00234/model-sbml-l2v5.xml b/latest/cases/00234/model-sbml-l2v5.xml new file mode 100644 index 000000000..0c7a26070 --- /dev/null +++ b/latest/cases/00234/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00234/model-sbml-l3v2.xml b/latest/cases/00234/model-sbml-l3v2.xml new file mode 100644 index 000000000..da86444c7 --- /dev/null +++ b/latest/cases/00234/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00234/output.heta b/latest/cases/00234/output.heta new file mode 100644 index 000000000..ee426b671 --- /dev/null +++ b/latest/cases/00234/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S3 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^3$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^3$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.002 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 6200; +k2 @Const 'k2' { } = 5000; + diff --git a/latest/cases/00234/synopsis.txt b/latest/cases/00234/synopsis.txt new file mode 100644 index 000000000..7bf2fbf85 --- /dev/null +++ b/latest/cases/00234/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S3 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^3$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^3$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00235/l2v5/heta-code/output.heta b/latest/cases/00235/l2v5/heta-code/output.heta new file mode 100644 index 000000000..fc3e29b32 --- /dev/null +++ b/latest/cases/00235/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, boundary: true, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: substance/length, boundary: true, compartment: compartment, } .= 0.15 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 0.2 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 62; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00235/l2v5/index.heta b/latest/cases/00235/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00235/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00235/l2v5/json/output.json b/latest/cases/00235/l2v5/json/output.json new file mode 100644 index 000000000..d66f7e3a6 --- /dev/null +++ b/latest/cases/00235/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0.15 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "0.2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "62" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00235/l3v2/heta-code/output.heta b/latest/cases/00235/l3v2/heta-code/output.heta new file mode 100644 index 000000000..78f988248 --- /dev/null +++ b/latest/cases/00235/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.15 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.2 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 62; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00235/l3v2/index.heta b/latest/cases/00235/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00235/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00235/l3v2/json/output.json b/latest/cases/00235/l3v2/json/output.json new file mode 100644 index 000000000..3296f629c --- /dev/null +++ b/latest/cases/00235/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0.15 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "0.2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 62 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00235/model-sbml-l2v5.xml b/latest/cases/00235/model-sbml-l2v5.xml new file mode 100644 index 000000000..932df3ca4 --- /dev/null +++ b/latest/cases/00235/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00235/model-sbml-l3v2.xml b/latest/cases/00235/model-sbml-l3v2.xml new file mode 100644 index 000000000..0b2504e0e --- /dev/null +++ b/latest/cases/00235/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00235/output.heta b/latest/cases/00235/output.heta new file mode 100644 index 000000000..1d3ab913d --- /dev/null +++ b/latest/cases/00235/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^1$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^1$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.15 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.2 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 62; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00235/synopsis.txt b/latest/cases/00235/synopsis.txt new file mode 100644 index 000000000..5010801c7 --- /dev/null +++ b/latest/cases/00235/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^1$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^1$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00236/l2v5/heta-code/output.heta b/latest/cases/00236/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7a98b90bb --- /dev/null +++ b/latest/cases/00236/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: substance/length, boundary: true, compartment: compartment, } .= 0.02 / compartment; +S4 @Species 'S4' { units: substance/length, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 620; +k2 @Record 'k2' { } .= 500; + diff --git a/latest/cases/00236/l2v5/index.heta b/latest/cases/00236/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00236/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00236/l2v5/json/output.json b/latest/cases/00236/l2v5/json/output.json new file mode 100644 index 000000000..25e43a368 --- /dev/null +++ b/latest/cases/00236/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "0.02 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "620" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00236/l3v2/heta-code/output.heta b/latest/cases/00236/l3v2/heta-code/output.heta new file mode 100644 index 000000000..400f2a8bf --- /dev/null +++ b/latest/cases/00236/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.02 / compartment; +S4 @Species 'S4' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 620; +k2 @Const 'k2' { } = 500; + diff --git a/latest/cases/00236/l3v2/index.heta b/latest/cases/00236/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00236/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00236/l3v2/json/output.json b/latest/cases/00236/l3v2/json/output.json new file mode 100644 index 000000000..35238327b --- /dev/null +++ b/latest/cases/00236/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "0.02 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "0.001 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 620 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 500 + } +] \ No newline at end of file diff --git a/latest/cases/00236/model-sbml-l2v5.xml b/latest/cases/00236/model-sbml-l2v5.xml new file mode 100644 index 000000000..5c2d998a5 --- /dev/null +++ b/latest/cases/00236/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00236/model-sbml-l3v2.xml b/latest/cases/00236/model-sbml-l3v2.xml new file mode 100644 index 000000000..4f5ea3b90 --- /dev/null +++ b/latest/cases/00236/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00236/output.heta b/latest/cases/00236/output.heta new file mode 100644 index 000000000..1c043a2b9 --- /dev/null +++ b/latest/cases/00236/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S3 and S4 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^2$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.02 / compartment; +S4 @Species 'S4' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 620; +k2 @Const 'k2' { } = 500; + diff --git a/latest/cases/00236/synopsis.txt b/latest/cases/00236/synopsis.txt new file mode 100644 index 000000000..d83a51ef5 --- /dev/null +++ b/latest/cases/00236/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S3 and S4 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^2$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00237/l2v5/heta-code/output.heta b/latest/cases/00237/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1d8dc031d --- /dev/null +++ b/latest/cases/00237/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/length, boundary: true, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: substance/length, boundary: true, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 62000; +k2 @Record 'k2' { } .= 50000; + diff --git a/latest/cases/00237/l2v5/index.heta b/latest/cases/00237/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00237/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00237/l2v5/json/output.json b/latest/cases/00237/l2v5/json/output.json new file mode 100644 index 000000000..92662684a --- /dev/null +++ b/latest/cases/00237/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "62000" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50000" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00237/l3v2/heta-code/output.heta b/latest/cases/00237/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8c9e15001 --- /dev/null +++ b/latest/cases/00237/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 62000; +k2 @Const 'k2' { } = 50000; + diff --git a/latest/cases/00237/l3v2/index.heta b/latest/cases/00237/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00237/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00237/l3v2/json/output.json b/latest/cases/00237/l3v2/json/output.json new file mode 100644 index 000000000..31ae87774 --- /dev/null +++ b/latest/cases/00237/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 62000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50000 + } +] \ No newline at end of file diff --git a/latest/cases/00237/model-sbml-l2v5.xml b/latest/cases/00237/model-sbml-l2v5.xml new file mode 100644 index 000000000..15425749a --- /dev/null +++ b/latest/cases/00237/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00237/model-sbml-l3v2.xml b/latest/cases/00237/model-sbml-l3v2.xml new file mode 100644 index 000000000..265e272ef --- /dev/null +++ b/latest/cases/00237/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00237/output.heta b/latest/cases/00237/output.heta new file mode 100644 index 000000000..15c966c67 --- /dev/null +++ b/latest/cases/00237/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S2 and S4 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-5$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^4$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^4$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 62000; +k2 @Const 'k2' { } = 50000; + diff --git a/latest/cases/00237/synopsis.txt b/latest/cases/00237/synopsis.txt new file mode 100644 index 000000000..2a1284eaf --- /dev/null +++ b/latest/cases/00237/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Both species S2 and S4 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-5$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^4$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^4$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00238/l2v5/heta-code/output.heta b/latest/cases/00238/l2v5/heta-code/output.heta new file mode 100644 index 000000000..afc218bb2 --- /dev/null +++ b/latest/cases/00238/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Record 'k1' { } .= 1.023; + diff --git a/latest/cases/00238/l2v5/index.heta b/latest/cases/00238/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00238/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00238/l2v5/json/output.json b/latest/cases/00238/l2v5/json/output.json new file mode 100644 index 000000000..c86f6fc04 --- /dev/null +++ b/latest/cases/00238/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.15" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.023" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00238/l3v2/heta-code/output.heta b/latest/cases/00238/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3471e022a --- /dev/null +++ b/latest/cases/00238/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.023; + diff --git a/latest/cases/00238/l3v2/index.heta b/latest/cases/00238/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00238/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00238/l3v2/json/output.json b/latest/cases/00238/l3v2/json/output.json new file mode 100644 index 000000000..c67ebfd72 --- /dev/null +++ b/latest/cases/00238/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.15" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.023 + } +] \ No newline at end of file diff --git a/latest/cases/00238/model-sbml-l2v5.xml b/latest/cases/00238/model-sbml-l2v5.xml new file mode 100644 index 000000000..9f7fbac36 --- /dev/null +++ b/latest/cases/00238/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00238/model-sbml-l3v2.xml b/latest/cases/00238/model-sbml-l3v2.xml new file mode 100644 index 000000000..efada110b --- /dev/null +++ b/latest/cases/00238/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00238/output.heta b/latest/cases/00238/output.heta new file mode 100644 index 000000000..b8ed77f2d --- /dev/null +++ b/latest/cases/00238/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 0-dimensional. Species S1 is labeled as an SBML boundary +species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.023$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.023; + diff --git a/latest/cases/00238/synopsis.txt b/latest/cases/00238/synopsis.txt new file mode 100644 index 000000000..0909e3b95 --- /dev/null +++ b/latest/cases/00238/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 0-dimensional. Species S1 is labeled as an SBML boundary +species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.023$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00239/l2v5/heta-code/output.heta b/latest/cases/00239/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8a4c6cf02 --- /dev/null +++ b/latest/cases/00239/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Record 'k1' { } .= 1.023; + diff --git a/latest/cases/00239/l2v5/index.heta b/latest/cases/00239/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00239/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00239/l2v5/json/output.json b/latest/cases/00239/l2v5/json/output.json new file mode 100644 index 000000000..f40371c85 --- /dev/null +++ b/latest/cases/00239/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.023" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00239/l3v2/heta-code/output.heta b/latest/cases/00239/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b65cea86e --- /dev/null +++ b/latest/cases/00239/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.023; + diff --git a/latest/cases/00239/l3v2/index.heta b/latest/cases/00239/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00239/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00239/l3v2/json/output.json b/latest/cases/00239/l3v2/json/output.json new file mode 100644 index 000000000..4a82f6605 --- /dev/null +++ b/latest/cases/00239/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.023 + } +] \ No newline at end of file diff --git a/latest/cases/00239/model-sbml-l2v5.xml b/latest/cases/00239/model-sbml-l2v5.xml new file mode 100644 index 000000000..4ea224738 --- /dev/null +++ b/latest/cases/00239/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00239/model-sbml-l3v2.xml b/latest/cases/00239/model-sbml-l3v2.xml new file mode 100644 index 000000000..5cf1855c0 --- /dev/null +++ b/latest/cases/00239/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00239/output.heta b/latest/cases/00239/output.heta new file mode 100644 index 000000000..d01a3b6fc --- /dev/null +++ b/latest/cases/00239/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 0-dimensional. Species S2 is labeled as an SBML boundary +species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.023$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.023; + diff --git a/latest/cases/00239/synopsis.txt b/latest/cases/00239/synopsis.txt new file mode 100644 index 000000000..2cc38fccd --- /dev/null +++ b/latest/cases/00239/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 0-dimensional. Species S2 is labeled as an SBML boundary +species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.023$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00240/l2v5/heta-code/output.heta b/latest/cases/00240/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d63a30b4b --- /dev/null +++ b/latest/cases/00240/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 9.8; +k2 @Record 'k2' { } .= 0.57; + diff --git a/latest/cases/00240/l2v5/index.heta b/latest/cases/00240/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00240/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00240/l2v5/json/output.json b/latest/cases/00240/l2v5/json/output.json new file mode 100644 index 000000000..ca6f4c3dd --- /dev/null +++ b/latest/cases/00240/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "9.8" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.57" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00240/l3v2/heta-code/output.heta b/latest/cases/00240/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c6fe19849 --- /dev/null +++ b/latest/cases/00240/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 9.8; +k2 @Const 'k2' { } = 0.57; + diff --git a/latest/cases/00240/l3v2/index.heta b/latest/cases/00240/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00240/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00240/l3v2/json/output.json b/latest/cases/00240/l3v2/json/output.json new file mode 100644 index 000000000..b69d3c47f --- /dev/null +++ b/latest/cases/00240/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 9.8 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.57 + } +] \ No newline at end of file diff --git a/latest/cases/00240/model-sbml-l2v5.xml b/latest/cases/00240/model-sbml-l2v5.xml new file mode 100644 index 000000000..ab76bd9bc --- /dev/null +++ b/latest/cases/00240/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00240/model-sbml-l3v2.xml b/latest/cases/00240/model-sbml-l3v2.xml new file mode 100644 index 000000000..d2727013b --- /dev/null +++ b/latest/cases/00240/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00240/output.heta b/latest/cases/00240/output.heta new file mode 100644 index 000000000..96f15c802 --- /dev/null +++ b/latest/cases/00240/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S2 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-15$ |mole | +|Initial amount of S2 |$2.0 \x 10^-15$ |mole | +|Initial amount of S3 |$1.0 \x 10^-15$ |mole | +|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 9.8; +k2 @Const 'k2' { } = 0.57; + diff --git a/latest/cases/00240/synopsis.txt b/latest/cases/00240/synopsis.txt new file mode 100644 index 000000000..317d533e7 --- /dev/null +++ b/latest/cases/00240/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reactions with three species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S2 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-15$ |mole | +|Initial amount of S2 |$2.0 \x 10^-15$ |mole | +|Initial amount of S3 |$1.0 \x 10^-15$ |mole | +|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00241/l2v5/heta-code/output.heta b/latest/cases/00241/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9db341099 --- /dev/null +++ b/latest/cases/00241/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 9.8; +k2 @Record 'k2' { } .= 0.57; + diff --git a/latest/cases/00241/l2v5/index.heta b/latest/cases/00241/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00241/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00241/l2v5/json/output.json b/latest/cases/00241/l2v5/json/output.json new file mode 100644 index 000000000..6733ad3cb --- /dev/null +++ b/latest/cases/00241/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "9.8" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.57" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00241/l3v2/heta-code/output.heta b/latest/cases/00241/l3v2/heta-code/output.heta new file mode 100644 index 000000000..40ed6acda --- /dev/null +++ b/latest/cases/00241/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 9.8; +k2 @Const 'k2' { } = 0.57; + diff --git a/latest/cases/00241/l3v2/index.heta b/latest/cases/00241/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00241/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00241/l3v2/json/output.json b/latest/cases/00241/l3v2/json/output.json new file mode 100644 index 000000000..d03d8aada --- /dev/null +++ b/latest/cases/00241/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 9.8 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.57 + } +] \ No newline at end of file diff --git a/latest/cases/00241/model-sbml-l2v5.xml b/latest/cases/00241/model-sbml-l2v5.xml new file mode 100644 index 000000000..583baf86f --- /dev/null +++ b/latest/cases/00241/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00241/model-sbml-l3v2.xml b/latest/cases/00241/model-sbml-l3v2.xml new file mode 100644 index 000000000..13a9585f0 --- /dev/null +++ b/latest/cases/00241/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00241/output.heta b/latest/cases/00241/output.heta new file mode 100644 index 000000000..0c0f68517 --- /dev/null +++ b/latest/cases/00241/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S3 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-15$ |mole | +|Initial amount of S2 |$2.0 \x 10^-15$ |mole | +|Initial amount of S3 |$1.0 \x 10^-15$ |mole | +|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 9.8; +k2 @Const 'k2' { } = 0.57; + diff --git a/latest/cases/00241/synopsis.txt b/latest/cases/00241/synopsis.txt new file mode 100644 index 000000000..9cc58d44a --- /dev/null +++ b/latest/cases/00241/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Basic reactions with three species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S3 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-15$ |mole | +|Initial amount of S2 |$2.0 \x 10^-15$ |mole | +|Initial amount of S3 |$1.0 \x 10^-15$ |mole | +|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00242/l2v5/heta-code/output.heta b/latest/cases/00242/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4c2ee1e26 --- /dev/null +++ b/latest/cases/00242/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 9.8; +k2 @Record 'k2' { } .= 0.57; + diff --git a/latest/cases/00242/l2v5/index.heta b/latest/cases/00242/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00242/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00242/l2v5/json/output.json b/latest/cases/00242/l2v5/json/output.json new file mode 100644 index 000000000..e7287fe16 --- /dev/null +++ b/latest/cases/00242/l2v5/json/output.json @@ -0,0 +1,136 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "9.8" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.57" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00242/l3v2/heta-code/output.heta b/latest/cases/00242/l3v2/heta-code/output.heta new file mode 100644 index 000000000..363b1c72b --- /dev/null +++ b/latest/cases/00242/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 9.8; +k2 @Const 'k2' { } = 0.57; + diff --git a/latest/cases/00242/l3v2/index.heta b/latest/cases/00242/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00242/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00242/l3v2/json/output.json b/latest/cases/00242/l3v2/json/output.json new file mode 100644 index 000000000..c1e2fbce1 --- /dev/null +++ b/latest/cases/00242/l3v2/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 9.8 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.57 + } +] \ No newline at end of file diff --git a/latest/cases/00242/model-sbml-l2v5.xml b/latest/cases/00242/model-sbml-l2v5.xml new file mode 100644 index 000000000..3dff3dd84 --- /dev/null +++ b/latest/cases/00242/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00242/model-sbml-l3v2.xml b/latest/cases/00242/model-sbml-l3v2.xml new file mode 100644 index 000000000..5a107c552 --- /dev/null +++ b/latest/cases/00242/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00242/output.heta b/latest/cases/00242/output.heta new file mode 100644 index 000000000..4b2b6474b --- /dev/null +++ b/latest/cases/00242/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic reactions with three species in a 0-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Both species S2 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-15$ |mole | +|Initial amount of S2 |$2.0 \x 10^-15$ |mole | +|Initial amount of S3 |$1.0 \x 10^-15$ |mole | +|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 9.8; +k2 @Const 'k2' { } = 0.57; + diff --git a/latest/cases/00242/synopsis.txt b/latest/cases/00242/synopsis.txt new file mode 100644 index 000000000..8cb71a7fd --- /dev/null +++ b/latest/cases/00242/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic reactions with three species in a 0-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Both species S2 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-15$ |mole | +|Initial amount of S2 |$2.0 \x 10^-15$ |mole | +|Initial amount of S3 |$1.0 \x 10^-15$ |mole | +|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00243/l2v5/heta-code/output.heta b/latest/cases/00243/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e85ae2dcc --- /dev/null +++ b/latest/cases/00243/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 0.6; +k2 @Record 'k2' { } .= 0.13; + diff --git a/latest/cases/00243/l2v5/index.heta b/latest/cases/00243/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00243/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00243/l2v5/json/output.json b/latest/cases/00243/l2v5/json/output.json new file mode 100644 index 000000000..734d830d4 --- /dev/null +++ b/latest/cases/00243/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.13" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00243/l3v2/heta-code/output.heta b/latest/cases/00243/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9d182659a --- /dev/null +++ b/latest/cases/00243/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00243/l3v2/index.heta b/latest/cases/00243/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00243/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00243/l3v2/json/output.json b/latest/cases/00243/l3v2/json/output.json new file mode 100644 index 000000000..01923816f --- /dev/null +++ b/latest/cases/00243/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.6 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.13 + } +] \ No newline at end of file diff --git a/latest/cases/00243/model-sbml-l2v5.xml b/latest/cases/00243/model-sbml-l2v5.xml new file mode 100644 index 000000000..d3768cf03 --- /dev/null +++ b/latest/cases/00243/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00243/model-sbml-l3v2.xml b/latest/cases/00243/model-sbml-l3v2.xml new file mode 100644 index 000000000..389a46c71 --- /dev/null +++ b/latest/cases/00243/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00243/output.heta b/latest/cases/00243/output.heta new file mode 100644 index 000000000..8f69cc66c --- /dev/null +++ b/latest/cases/00243/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S1 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00243/synopsis.txt b/latest/cases/00243/synopsis.txt new file mode 100644 index 000000000..747f7ff7b --- /dev/null +++ b/latest/cases/00243/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S1 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00244/l2v5/heta-code/output.heta b/latest/cases/00244/l2v5/heta-code/output.heta new file mode 100644 index 000000000..980a31374 --- /dev/null +++ b/latest/cases/00244/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 0.6; +k2 @Record 'k2' { } .= 0.13; + diff --git a/latest/cases/00244/l2v5/index.heta b/latest/cases/00244/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00244/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00244/l2v5/json/output.json b/latest/cases/00244/l2v5/json/output.json new file mode 100644 index 000000000..e649985b2 --- /dev/null +++ b/latest/cases/00244/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.5" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.13" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00244/l3v2/heta-code/output.heta b/latest/cases/00244/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cdb483065 --- /dev/null +++ b/latest/cases/00244/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00244/l3v2/index.heta b/latest/cases/00244/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00244/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00244/l3v2/json/output.json b/latest/cases/00244/l3v2/json/output.json new file mode 100644 index 000000000..8c29971fa --- /dev/null +++ b/latest/cases/00244/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.5" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.6 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.13 + } +] \ No newline at end of file diff --git a/latest/cases/00244/model-sbml-l2v5.xml b/latest/cases/00244/model-sbml-l2v5.xml new file mode 100644 index 000000000..5318a5c0e --- /dev/null +++ b/latest/cases/00244/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00244/model-sbml-l3v2.xml b/latest/cases/00244/model-sbml-l3v2.xml new file mode 100644 index 000000000..ebd96c5c6 --- /dev/null +++ b/latest/cases/00244/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00244/output.heta b/latest/cases/00244/output.heta new file mode 100644 index 000000000..4032236c2 --- /dev/null +++ b/latest/cases/00244/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S4 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00244/synopsis.txt b/latest/cases/00244/synopsis.txt new file mode 100644 index 000000000..059fa1a01 --- /dev/null +++ b/latest/cases/00244/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with a species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S4 is labeled as an +SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00245/l2v5/heta-code/output.heta b/latest/cases/00245/l2v5/heta-code/output.heta new file mode 100644 index 000000000..51cf75f82 --- /dev/null +++ b/latest/cases/00245/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 0.6; +k2 @Record 'k2' { } .= 0.13; + diff --git a/latest/cases/00245/l2v5/index.heta b/latest/cases/00245/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00245/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00245/l2v5/json/output.json b/latest/cases/00245/l2v5/json/output.json new file mode 100644 index 000000000..ebf27b32c --- /dev/null +++ b/latest/cases/00245/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.13" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00245/l3v2/heta-code/output.heta b/latest/cases/00245/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a17252dc4 --- /dev/null +++ b/latest/cases/00245/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00245/l3v2/index.heta b/latest/cases/00245/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00245/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00245/l3v2/json/output.json b/latest/cases/00245/l3v2/json/output.json new file mode 100644 index 000000000..826fbc0b3 --- /dev/null +++ b/latest/cases/00245/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.6 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.13 + } +] \ No newline at end of file diff --git a/latest/cases/00245/model-sbml-l2v5.xml b/latest/cases/00245/model-sbml-l2v5.xml new file mode 100644 index 000000000..f8d992c04 --- /dev/null +++ b/latest/cases/00245/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00245/model-sbml-l3v2.xml b/latest/cases/00245/model-sbml-l3v2.xml new file mode 100644 index 000000000..0c665f1e9 --- /dev/null +++ b/latest/cases/00245/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00245/output.heta b/latest/cases/00245/output.heta new file mode 100644 index 000000000..ff5c05360 --- /dev/null +++ b/latest/cases/00245/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00245/synopsis.txt b/latest/cases/00245/synopsis.txt new file mode 100644 index 000000000..dfdcf53c2 --- /dev/null +++ b/latest/cases/00245/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Both species S1 and S2 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00246/l2v5/heta-code/output.heta b/latest/cases/00246/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c9544eb6a --- /dev/null +++ b/latest/cases/00246/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 0.6; +k2 @Record 'k2' { } .= 0.13; + diff --git a/latest/cases/00246/l2v5/index.heta b/latest/cases/00246/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00246/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00246/l2v5/json/output.json b/latest/cases/00246/l2v5/json/output.json new file mode 100644 index 000000000..5390abd05 --- /dev/null +++ b/latest/cases/00246/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.13" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00246/l3v2/heta-code/output.heta b/latest/cases/00246/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b42b60289 --- /dev/null +++ b/latest/cases/00246/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00246/l3v2/index.heta b/latest/cases/00246/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00246/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00246/l3v2/json/output.json b/latest/cases/00246/l3v2/json/output.json new file mode 100644 index 000000000..748ad683c --- /dev/null +++ b/latest/cases/00246/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.6 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.13 + } +] \ No newline at end of file diff --git a/latest/cases/00246/model-sbml-l2v5.xml b/latest/cases/00246/model-sbml-l2v5.xml new file mode 100644 index 000000000..394bf7dd7 --- /dev/null +++ b/latest/cases/00246/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00246/model-sbml-l3v2.xml b/latest/cases/00246/model-sbml-l3v2.xml new file mode 100644 index 000000000..ecdb7299a --- /dev/null +++ b/latest/cases/00246/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00246/output.heta b/latest/cases/00246/output.heta new file mode 100644 index 000000000..dc0973f62 --- /dev/null +++ b/latest/cases/00246/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Both species S1 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00246/synopsis.txt b/latest/cases/00246/synopsis.txt new file mode 100644 index 000000000..b15ea9dc2 --- /dev/null +++ b/latest/cases/00246/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Both species S1 and S3 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00247/l2v5/heta-code/output.heta b/latest/cases/00247/l2v5/heta-code/output.heta new file mode 100644 index 000000000..edecc7631 --- /dev/null +++ b/latest/cases/00247/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 0.6; +k2 @Record 'k2' { } .= 0.13; + diff --git a/latest/cases/00247/l2v5/index.heta b/latest/cases/00247/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00247/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00247/l2v5/json/output.json b/latest/cases/00247/l2v5/json/output.json new file mode 100644 index 000000000..55180eb14 --- /dev/null +++ b/latest/cases/00247/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.5" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.13" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00247/l3v2/heta-code/output.heta b/latest/cases/00247/l3v2/heta-code/output.heta new file mode 100644 index 000000000..614c57cd9 --- /dev/null +++ b/latest/cases/00247/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00247/l3v2/index.heta b/latest/cases/00247/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00247/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00247/l3v2/json/output.json b/latest/cases/00247/l3v2/json/output.json new file mode 100644 index 000000000..84a3a848e --- /dev/null +++ b/latest/cases/00247/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.5" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.6 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.13 + } +] \ No newline at end of file diff --git a/latest/cases/00247/model-sbml-l2v5.xml b/latest/cases/00247/model-sbml-l2v5.xml new file mode 100644 index 000000000..a4b2e819b --- /dev/null +++ b/latest/cases/00247/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00247/model-sbml-l3v2.xml b/latest/cases/00247/model-sbml-l3v2.xml new file mode 100644 index 000000000..df763afe3 --- /dev/null +++ b/latest/cases/00247/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00247/output.heta b/latest/cases/00247/output.heta new file mode 100644 index 000000000..f6e73e24a --- /dev/null +++ b/latest/cases/00247/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Both species S3 and S4 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2; +S4 @Species 'S4' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.13; + diff --git a/latest/cases/00247/synopsis.txt b/latest/cases/00247/synopsis.txt new file mode 100644 index 000000000..1ad99964d --- /dev/null +++ b/latest/cases/00247/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with four species in a 0-dimensional +compartment, with two species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, 0D-Compartment, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Both species S3 and S4 are +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 2.0$ |mole | +|Initial amount of S4 |$ 0.5$ |mole | +|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00248/l2v5/heta-code/output.heta b/latest/cases/00248/l2v5/heta-code/output.heta new file mode 100644 index 000000000..01823cdc9 --- /dev/null +++ b/latest/cases/00248/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1.34; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.5 / compartment; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: compartment, } .= 1.2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * S1 * S3; + +k1 @Record 'k1' { } .= 1.78; + diff --git a/latest/cases/00248/l2v5/index.heta b/latest/cases/00248/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00248/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00248/l2v5/json/output.json b/latest/cases/00248/l2v5/json/output.json new file mode 100644 index 000000000..20118f373 --- /dev/null +++ b/latest/cases/00248/l2v5/json/output.json @@ -0,0 +1,103 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1.34" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.78" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00248/l3v2/heta-code/output.heta b/latest/cases/00248/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a1d21590e --- /dev/null +++ b/latest/cases/00248/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1.34; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.5 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.78; + diff --git a/latest/cases/00248/l3v2/index.heta b/latest/cases/00248/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00248/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00248/l3v2/json/output.json b/latest/cases/00248/l3v2/json/output.json new file mode 100644 index 000000000..a4d09c584 --- /dev/null +++ b/latest/cases/00248/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1.34" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.78 + } +] \ No newline at end of file diff --git a/latest/cases/00248/model-sbml-l2v5.xml b/latest/cases/00248/model-sbml-l2v5.xml new file mode 100644 index 000000000..c6e4f1a80 --- /dev/null +++ b/latest/cases/00248/model-sbml-l2v5.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00248/model-sbml-l3v2.xml b/latest/cases/00248/model-sbml-l3v2.xml new file mode 100644 index 000000000..0f1e275bc --- /dev/null +++ b/latest/cases/00248/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00248/output.heta b/latest/cases/00248/output.heta new file mode 100644 index 000000000..2869b08f2 --- /dev/null +++ b/latest/cases/00248/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Species S3 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 1.2$ |mole | +|Value of parameter k1 |$ 1.78$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1.34$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1.34; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.5 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.78; + diff --git a/latest/cases/00248/synopsis.txt b/latest/cases/00248/synopsis.txt new file mode 100644 index 000000000..17a25ddd6 --- /dev/null +++ b/latest/cases/00248/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic single forward reaction with three species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Species S3 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 1.2$ |mole | +|Value of parameter k1 |$ 1.78$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1.34$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00249/l2v5/heta-code/output.heta b/latest/cases/00249/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1838d9d34 --- /dev/null +++ b/latest/cases/00249/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1.2; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 7.5e-4 / compartment; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.00125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 1680; +k2 @Record 'k2' { } .= 270; + diff --git a/latest/cases/00249/l2v5/index.heta b/latest/cases/00249/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00249/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00249/l2v5/json/output.json b/latest/cases/00249/l2v5/json/output.json new file mode 100644 index 000000000..842fc11b4 --- /dev/null +++ b/latest/cases/00249/l2v5/json/output.json @@ -0,0 +1,148 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1.2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "7.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.00125 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1680" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "270" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00249/l3v2/heta-code/output.heta b/latest/cases/00249/l3v2/heta-code/output.heta new file mode 100644 index 000000000..92bb04a4c --- /dev/null +++ b/latest/cases/00249/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1.2; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 7.5e-4 / compartment; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.00125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 1680; +k2 @Const 'k2' { } = 270; + diff --git a/latest/cases/00249/l3v2/index.heta b/latest/cases/00249/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00249/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00249/l3v2/json/output.json b/latest/cases/00249/l3v2/json/output.json new file mode 100644 index 000000000..035510e0c --- /dev/null +++ b/latest/cases/00249/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1.2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "7.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.00125 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1680 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 270 + } +] \ No newline at end of file diff --git a/latest/cases/00249/model-sbml-l2v5.xml b/latest/cases/00249/model-sbml-l2v5.xml new file mode 100644 index 000000000..7458cc0d7 --- /dev/null +++ b/latest/cases/00249/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00249/model-sbml-l3v2.xml b/latest/cases/00249/model-sbml-l3v2.xml new file mode 100644 index 000000000..0f9cf465f --- /dev/null +++ b/latest/cases/00249/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00249/output.heta b/latest/cases/00249/output.heta new file mode 100644 index 000000000..192c51fd0 --- /dev/null +++ b/latest/cases/00249/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reactions with four species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S4 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$0.75 \x 10^-3$ |mole | +|Initial amount of S4 |$1.25 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.68 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.27 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1.2$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1.2; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 7.5e-4 / compartment; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.00125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 1680; +k2 @Const 'k2' { } = 270; + diff --git a/latest/cases/00249/synopsis.txt b/latest/cases/00249/synopsis.txt new file mode 100644 index 000000000..58964333b --- /dev/null +++ b/latest/cases/00249/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic reactions with four species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S4 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$0.75 \x 10^-3$ |mole | +|Initial amount of S4 |$1.25 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.68 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.27 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 1.2$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00250/l2v5/heta-code/output.heta b/latest/cases/00250/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1e0f6a5cb --- /dev/null +++ b/latest/cases/00250/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 0.2; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: substance/volume, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Record 'k1' { } .= 1300; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00250/l2v5/index.heta b/latest/cases/00250/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00250/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00250/l2v5/json/output.json b/latest/cases/00250/l2v5/json/output.json new file mode 100644 index 000000000..fb1b989ad --- /dev/null +++ b/latest/cases/00250/l2v5/json/output.json @@ -0,0 +1,166 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "0.2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1300" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00250/l3v2/heta-code/output.heta b/latest/cases/00250/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7d15d9831 --- /dev/null +++ b/latest/cases/00250/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.2; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00250/l3v2/index.heta b/latest/cases/00250/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00250/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00250/l3v2/json/output.json b/latest/cases/00250/l3v2/json/output.json new file mode 100644 index 000000000..6d7d7613d --- /dev/null +++ b/latest/cases/00250/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "0.2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1300 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00250/model-sbml-l2v5.xml b/latest/cases/00250/model-sbml-l2v5.xml new file mode 100644 index 000000000..c178d5714 --- /dev/null +++ b/latest/cases/00250/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00250/model-sbml-l3v2.xml b/latest/cases/00250/model-sbml-l3v2.xml new file mode 100644 index 000000000..06da4a534 --- /dev/null +++ b/latest/cases/00250/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00250/output.heta b/latest/cases/00250/output.heta new file mode 100644 index 000000000..b6298acad --- /dev/null +++ b/latest/cases/00250/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions with five species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Species S5 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 0.2$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.2; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00250/synopsis.txt b/latest/cases/00250/synopsis.txt new file mode 100644 index 000000000..b797c2ff4 --- /dev/null +++ b/latest/cases/00250/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic two reactions with five species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Species S5 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 0.2$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00251/l2v5/heta-code/output.heta b/latest/cases/00251/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a36bbd66c --- /dev/null +++ b/latest/cases/00251/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.5 / compartment; +S3 @Species 'S3' { units: substance/area, boundary: true, compartment: compartment, } .= 1.2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * S1 * S3; + +k1 @Record 'k1' { } .= 1.78; + diff --git a/latest/cases/00251/l2v5/index.heta b/latest/cases/00251/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00251/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00251/l2v5/json/output.json b/latest/cases/00251/l2v5/json/output.json new file mode 100644 index 000000000..56dc9e0d9 --- /dev/null +++ b/latest/cases/00251/l2v5/json/output.json @@ -0,0 +1,103 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1.2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.78" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00251/l3v2/heta-code/output.heta b/latest/cases/00251/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2812de7f5 --- /dev/null +++ b/latest/cases/00251/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.5 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1.2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.78; + diff --git a/latest/cases/00251/l3v2/index.heta b/latest/cases/00251/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00251/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00251/l3v2/json/output.json b/latest/cases/00251/l3v2/json/output.json new file mode 100644 index 000000000..89662504e --- /dev/null +++ b/latest/cases/00251/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1.2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.78 + } +] \ No newline at end of file diff --git a/latest/cases/00251/model-sbml-l2v5.xml b/latest/cases/00251/model-sbml-l2v5.xml new file mode 100644 index 000000000..efa1f9b8e --- /dev/null +++ b/latest/cases/00251/model-sbml-l2v5.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00251/model-sbml-l3v2.xml b/latest/cases/00251/model-sbml-l3v2.xml new file mode 100644 index 000000000..e7b0bc56c --- /dev/null +++ b/latest/cases/00251/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00251/output.heta b/latest/cases/00251/output.heta new file mode 100644 index 000000000..ebcd90b69 --- /dev/null +++ b/latest/cases/00251/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in a + 2 dimensional compartment, where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 2-dimensional. Species S3 is labeled as constant and +therefore cannot be changed by rules or reactions. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 1.2$ |mole | +|Value of parameter k1 |$ 1.78$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.5 / compartment; +S3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1.2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.78; + diff --git a/latest/cases/00251/synopsis.txt b/latest/cases/00251/synopsis.txt new file mode 100644 index 000000000..84a2ae5b0 --- /dev/null +++ b/latest/cases/00251/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with three species in a + 2 dimensional compartment, where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 2-dimensional. Species S3 is labeled as constant and +therefore cannot be changed by rules or reactions. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 1.2$ |mole | +|Value of parameter k1 |$ 1.78$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00252/l2v5/heta-code/output.heta b/latest/cases/00252/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d5579f8ad --- /dev/null +++ b/latest/cases/00252/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 7.5e-4 / compartment; +S4 @Species 'S4' { units: substance/area, boundary: true, compartment: compartment, } .= 0.00125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 1680; +k2 @Record 'k2' { } .= 270; + diff --git a/latest/cases/00252/l2v5/index.heta b/latest/cases/00252/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00252/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00252/l2v5/json/output.json b/latest/cases/00252/l2v5/json/output.json new file mode 100644 index 000000000..22bb8f2e3 --- /dev/null +++ b/latest/cases/00252/l2v5/json/output.json @@ -0,0 +1,148 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "7.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "0.00125 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1680" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "270" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00252/l3v2/heta-code/output.heta b/latest/cases/00252/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7b90d7a6d --- /dev/null +++ b/latest/cases/00252/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 7.5e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.00125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 1680; +k2 @Const 'k2' { } = 270; + diff --git a/latest/cases/00252/l3v2/index.heta b/latest/cases/00252/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00252/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00252/l3v2/json/output.json b/latest/cases/00252/l3v2/json/output.json new file mode 100644 index 000000000..324b19571 --- /dev/null +++ b/latest/cases/00252/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "7.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "0.00125 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1680 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 270 + } +] \ No newline at end of file diff --git a/latest/cases/00252/model-sbml-l2v5.xml b/latest/cases/00252/model-sbml-l2v5.xml new file mode 100644 index 000000000..4cb15f061 --- /dev/null +++ b/latest/cases/00252/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00252/model-sbml-l3v2.xml b/latest/cases/00252/model-sbml-l3v2.xml new file mode 100644 index 000000000..1f2b07ea5 --- /dev/null +++ b/latest/cases/00252/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00252/output.heta b/latest/cases/00252/output.heta new file mode 100644 index 000000000..2090fc006 --- /dev/null +++ b/latest/cases/00252/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic reactions with four species in a 2 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S4 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$0.75 \x 10^-3$ |mole | +|Initial amount of S4 |$1.25 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.68 \x 10^3$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.27 \x 10^3$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 7.5e-4 / compartment; +S4 @Species 'S4' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.00125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 1680; +k2 @Const 'k2' { } = 270; + diff --git a/latest/cases/00252/synopsis.txt b/latest/cases/00252/synopsis.txt new file mode 100644 index 000000000..f44f06787 --- /dev/null +++ b/latest/cases/00252/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic reactions with four species in a 2 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S4 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$0.75 \x 10^-3$ |mole | +|Initial amount of S4 |$1.25 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.68 \x 10^3$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.27 \x 10^3$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00253/l2v5/heta-code/output.heta b/latest/cases/00253/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0e1dc84de --- /dev/null +++ b/latest/cases/00253/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: substance/area, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Record 'k1' { } .= 1.3e+6; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00253/l2v5/index.heta b/latest/cases/00253/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00253/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00253/l2v5/json/output.json b/latest/cases/00253/l2v5/json/output.json new file mode 100644 index 000000000..68357806f --- /dev/null +++ b/latest/cases/00253/l2v5/json/output.json @@ -0,0 +1,166 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/area", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.3e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00253/l3v2/heta-code/output.heta b/latest/cases/00253/l3v2/heta-code/output.heta new file mode 100644 index 000000000..93f869b4b --- /dev/null +++ b/latest/cases/00253/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00253/l3v2/index.heta b/latest/cases/00253/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00253/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00253/l3v2/json/output.json b/latest/cases/00253/l3v2/json/output.json new file mode 100644 index 000000000..406645249 --- /dev/null +++ b/latest/cases/00253/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1300000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00253/model-sbml-l2v5.xml b/latest/cases/00253/model-sbml-l2v5.xml new file mode 100644 index 000000000..bb5c39560 --- /dev/null +++ b/latest/cases/00253/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00253/model-sbml-l3v2.xml b/latest/cases/00253/model-sbml-l3v2.xml new file mode 100644 index 000000000..a2a6bf4f9 --- /dev/null +++ b/latest/cases/00253/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00253/output.heta b/latest/cases/00253/output.heta new file mode 100644 index 000000000..c51620e3b --- /dev/null +++ b/latest/cases/00253/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic two reactions with five species in a 2 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S5 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00253/synopsis.txt b/latest/cases/00253/synopsis.txt new file mode 100644 index 000000000..4bd8f8845 --- /dev/null +++ b/latest/cases/00253/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with five species in a 2 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S5 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00254/l2v5/heta-code/output.heta b/latest/cases/00254/l2v5/heta-code/output.heta new file mode 100644 index 000000000..349710065 --- /dev/null +++ b/latest/cases/00254/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0.5 / compartment; +S3 @Species 'S3' { units: substance/length, boundary: true, compartment: compartment, } .= 1.2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * S1 * S3; + +k1 @Record 'k1' { } .= 1.78; + diff --git a/latest/cases/00254/l2v5/index.heta b/latest/cases/00254/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00254/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00254/l2v5/json/output.json b/latest/cases/00254/l2v5/json/output.json new file mode 100644 index 000000000..133751d15 --- /dev/null +++ b/latest/cases/00254/l2v5/json/output.json @@ -0,0 +1,103 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1.2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.78" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00254/l3v2/heta-code/output.heta b/latest/cases/00254/l3v2/heta-code/output.heta new file mode 100644 index 000000000..edbae623c --- /dev/null +++ b/latest/cases/00254/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.5 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.78; + diff --git a/latest/cases/00254/l3v2/index.heta b/latest/cases/00254/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00254/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00254/l3v2/json/output.json b/latest/cases/00254/l3v2/json/output.json new file mode 100644 index 000000000..6aaa558ed --- /dev/null +++ b/latest/cases/00254/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1.2 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.78 + } +] \ No newline at end of file diff --git a/latest/cases/00254/model-sbml-l2v5.xml b/latest/cases/00254/model-sbml-l2v5.xml new file mode 100644 index 000000000..a317abcb1 --- /dev/null +++ b/latest/cases/00254/model-sbml-l2v5.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00254/model-sbml-l3v2.xml b/latest/cases/00254/model-sbml-l3v2.xml new file mode 100644 index 000000000..c9e31a2a0 --- /dev/null +++ b/latest/cases/00254/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00254/output.heta b/latest/cases/00254/output.heta new file mode 100644 index 000000000..568d3efcf --- /dev/null +++ b/latest/cases/00254/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in a + 1 dimensional compartment, where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 1-dimensional. Species S3 is labeled as constant and +therefore cannot be changed by rules or reactions. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 1.2$ |mole | +|Value of parameter k1 |$ 1.78$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.5 / compartment; +S3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.2 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := compartment * k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.78; + diff --git a/latest/cases/00254/synopsis.txt b/latest/cases/00254/synopsis.txt new file mode 100644 index 000000000..33b061621 --- /dev/null +++ b/latest/cases/00254/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with three species in a + 1 dimensional compartment, where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 1-dimensional. Species S3 is labeled as constant and +therefore cannot be changed by rules or reactions. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 1.2$ |mole | +|Value of parameter k1 |$ 1.78$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00255/l2v5/heta-code/output.heta b/latest/cases/00255/l2v5/heta-code/output.heta new file mode 100644 index 000000000..df470182c --- /dev/null +++ b/latest/cases/00255/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 7.5e-4 / compartment; +S4 @Species 'S4' { units: substance/length, boundary: true, compartment: compartment, } .= 0.00125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 1680; +k2 @Record 'k2' { } .= 270; + diff --git a/latest/cases/00255/l2v5/index.heta b/latest/cases/00255/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00255/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00255/l2v5/json/output.json b/latest/cases/00255/l2v5/json/output.json new file mode 100644 index 000000000..24982bfbd --- /dev/null +++ b/latest/cases/00255/l2v5/json/output.json @@ -0,0 +1,148 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "7.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "0.00125 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1680" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "270" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00255/l3v2/heta-code/output.heta b/latest/cases/00255/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a8ab219e3 --- /dev/null +++ b/latest/cases/00255/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 7.5e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.00125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 1680; +k2 @Const 'k2' { } = 270; + diff --git a/latest/cases/00255/l3v2/index.heta b/latest/cases/00255/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00255/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00255/l3v2/json/output.json b/latest/cases/00255/l3v2/json/output.json new file mode 100644 index 000000000..15a97a9c8 --- /dev/null +++ b/latest/cases/00255/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "7.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "0.00125 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1680 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 270 + } +] \ No newline at end of file diff --git a/latest/cases/00255/model-sbml-l2v5.xml b/latest/cases/00255/model-sbml-l2v5.xml new file mode 100644 index 000000000..4dc67e40a --- /dev/null +++ b/latest/cases/00255/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00255/model-sbml-l3v2.xml b/latest/cases/00255/model-sbml-l3v2.xml new file mode 100644 index 000000000..86cbedb64 --- /dev/null +++ b/latest/cases/00255/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00255/output.heta b/latest/cases/00255/output.heta new file mode 100644 index 000000000..32f322da3 --- /dev/null +++ b/latest/cases/00255/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic reactions with four species in a 1 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S4 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$0.75 \x 10^-3$ |mole | +|Initial amount of S4 |$1.25 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.68 \x 10^3$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.27 \x 10^3$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 7.5e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.00125 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 1680; +k2 @Const 'k2' { } = 270; + diff --git a/latest/cases/00255/synopsis.txt b/latest/cases/00255/synopsis.txt new file mode 100644 index 000000000..7b68b46ff --- /dev/null +++ b/latest/cases/00255/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic reactions with four species in a 1 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S4 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$0.75 \x 10^-3$ |mole | +|Initial amount of S4 |$1.25 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.68 \x 10^3$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.27 \x 10^3$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00256/l2v5/heta-code/output.heta b/latest/cases/00256/l2v5/heta-code/output.heta new file mode 100644 index 000000000..74b05a1fb --- /dev/null +++ b/latest/cases/00256/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: substance/length, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Record 'k1' { } .= 1.3e+6; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00256/l2v5/index.heta b/latest/cases/00256/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00256/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00256/l2v5/json/output.json b/latest/cases/00256/l2v5/json/output.json new file mode 100644 index 000000000..a3a7cbaf1 --- /dev/null +++ b/latest/cases/00256/l2v5/json/output.json @@ -0,0 +1,166 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/length", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.3e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00256/l3v2/heta-code/output.heta b/latest/cases/00256/l3v2/heta-code/output.heta new file mode 100644 index 000000000..58811d47d --- /dev/null +++ b/latest/cases/00256/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00256/l3v2/index.heta b/latest/cases/00256/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00256/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00256/l3v2/json/output.json b/latest/cases/00256/l3v2/json/output.json new file mode 100644 index 000000000..bd0be6d76 --- /dev/null +++ b/latest/cases/00256/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/metre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1300000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00256/model-sbml-l2v5.xml b/latest/cases/00256/model-sbml-l2v5.xml new file mode 100644 index 000000000..06c2e1c4c --- /dev/null +++ b/latest/cases/00256/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00256/model-sbml-l3v2.xml b/latest/cases/00256/model-sbml-l3v2.xml new file mode 100644 index 000000000..d0095a0fb --- /dev/null +++ b/latest/cases/00256/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00256/output.heta b/latest/cases/00256/output.heta new file mode 100644 index 000000000..66d371e6c --- /dev/null +++ b/latest/cases/00256/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic two reactions with five species in a 1 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S5 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.5e-6 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 5e-7 / compartment; +S5 @Species 'S5' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00256/synopsis.txt b/latest/cases/00256/synopsis.txt new file mode 100644 index 000000000..b98419921 --- /dev/null +++ b/latest/cases/00256/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with five species in a 1 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S5 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00257/l2v5/heta-code/output.heta b/latest/cases/00257/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7545690d1 --- /dev/null +++ b/latest/cases/00257/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.5; +S3 @Species 'S3' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 1.2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := k1 * S1 * S3; + +k1 @Record 'k1' { } .= 1.78; + diff --git a/latest/cases/00257/l2v5/index.heta b/latest/cases/00257/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00257/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00257/l2v5/json/output.json b/latest/cases/00257/l2v5/json/output.json new file mode 100644 index 000000000..ab76ba877 --- /dev/null +++ b/latest/cases/00257/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1.2" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.78" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00257/l3v2/heta-code/output.heta b/latest/cases/00257/l3v2/heta-code/output.heta new file mode 100644 index 000000000..602714f3c --- /dev/null +++ b/latest/cases/00257/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.5; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1.2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.78; + diff --git a/latest/cases/00257/l3v2/index.heta b/latest/cases/00257/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00257/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00257/l3v2/json/output.json b/latest/cases/00257/l3v2/json/output.json new file mode 100644 index 000000000..3738b61fb --- /dev/null +++ b/latest/cases/00257/l3v2/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1.2" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.78 + } +] \ No newline at end of file diff --git a/latest/cases/00257/model-sbml-l2v5.xml b/latest/cases/00257/model-sbml-l2v5.xml new file mode 100644 index 000000000..976d15967 --- /dev/null +++ b/latest/cases/00257/model-sbml-l2v5.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00257/model-sbml-l3v2.xml b/latest/cases/00257/model-sbml-l3v2.xml new file mode 100644 index 000000000..b6b04a8d2 --- /dev/null +++ b/latest/cases/00257/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00257/output.heta b/latest/cases/00257/output.heta new file mode 100644 index 000000000..c3fc03230 --- /dev/null +++ b/latest/cases/00257/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in a + 0 dimensional compartment, where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 0-dimensional. Species S3 is labeled as constant and +therefore cannot be changed by rules or reactions. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 1.2$ |mole | +|Value of parameter k1 |$ 1.78$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.5; +S3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1.2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.78; + diff --git a/latest/cases/00257/synopsis.txt b/latest/cases/00257/synopsis.txt new file mode 100644 index 000000000..f82c267de --- /dev/null +++ b/latest/cases/00257/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Basic single forward reaction with three species in a + 0 dimensional compartment, where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 0-dimensional. Species S3 is labeled as constant and +therefore cannot be changed by rules or reactions. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 1.2$ |mole | +|Value of parameter k1 |$ 1.78$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00258/l2v5/heta-code/output.heta b/latest/cases/00258/l2v5/heta-code/output.heta new file mode 100644 index 000000000..69c407c53 --- /dev/null +++ b/latest/cases/00258/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 7.5e-4; +S4 @Species 'S4' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 0.00125; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 1680; +k2 @Record 'k2' { } .= 270; + diff --git a/latest/cases/00258/l2v5/index.heta b/latest/cases/00258/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00258/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00258/l2v5/json/output.json b/latest/cases/00258/l2v5/json/output.json new file mode 100644 index 000000000..e9124b70f --- /dev/null +++ b/latest/cases/00258/l2v5/json/output.json @@ -0,0 +1,151 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "7.5e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.00125" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1680" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "270" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00258/l3v2/heta-code/output.heta b/latest/cases/00258/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d054980de --- /dev/null +++ b/latest/cases/00258/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 7.5e-4; +S4 @Species 'S4' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.00125; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 1680; +k2 @Const 'k2' { } = 270; + diff --git a/latest/cases/00258/l3v2/index.heta b/latest/cases/00258/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00258/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00258/l3v2/json/output.json b/latest/cases/00258/l3v2/json/output.json new file mode 100644 index 000000000..325434c59 --- /dev/null +++ b/latest/cases/00258/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "7.5e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.00125" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1680 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 270 + } +] \ No newline at end of file diff --git a/latest/cases/00258/model-sbml-l2v5.xml b/latest/cases/00258/model-sbml-l2v5.xml new file mode 100644 index 000000000..fe85ce249 --- /dev/null +++ b/latest/cases/00258/model-sbml-l2v5.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00258/model-sbml-l3v2.xml b/latest/cases/00258/model-sbml-l3v2.xml new file mode 100644 index 000000000..c8e6cbaee --- /dev/null +++ b/latest/cases/00258/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00258/output.heta b/latest/cases/00258/output.heta new file mode 100644 index 000000000..48b9b8324 --- /dev/null +++ b/latest/cases/00258/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic reactions with four species in a 0 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S4 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$0.75 \x 10^-3$ |mole | +|Initial amount of S4 |$1.25 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.68 \x 10^3$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.27 \x 10^3$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 7.5e-4; +S4 @Species 'S4' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.00125; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 1680; +k2 @Const 'k2' { } = 270; + diff --git a/latest/cases/00258/synopsis.txt b/latest/cases/00258/synopsis.txt new file mode 100644 index 000000000..44f386602 --- /dev/null +++ b/latest/cases/00258/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic reactions with four species in a 0 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S4 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$0.75 \x 10^-3$ |mole | +|Initial amount of S4 |$1.25 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.68 \x 10^3$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.27 \x 10^3$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00259/l2v5/heta-code/output.heta b/latest/cases/00259/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1530e8cdf --- /dev/null +++ b/latest/cases/00259/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 5e-7; +S5 @Species 'S5' { units: substance, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Record 'k1' { } .= 1.3e+6; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00259/l2v5/index.heta b/latest/cases/00259/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00259/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00259/l2v5/json/output.json b/latest/cases/00259/l2v5/json/output.json new file mode 100644 index 000000000..1bb1fd882 --- /dev/null +++ b/latest/cases/00259/l2v5/json/output.json @@ -0,0 +1,170 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.3e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00259/l3v2/heta-code/output.heta b/latest/cases/00259/l3v2/heta-code/output.heta new file mode 100644 index 000000000..57a75c772 --- /dev/null +++ b/latest/cases/00259/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; +S5 @Species 'S5' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00259/l3v2/index.heta b/latest/cases/00259/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00259/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00259/l3v2/json/output.json b/latest/cases/00259/l3v2/json/output.json new file mode 100644 index 000000000..f6e43876c --- /dev/null +++ b/latest/cases/00259/l3v2/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "boundary": true, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1300000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00259/model-sbml-l2v5.xml b/latest/cases/00259/model-sbml-l2v5.xml new file mode 100644 index 000000000..cd9f7a593 --- /dev/null +++ b/latest/cases/00259/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00259/model-sbml-l3v2.xml b/latest/cases/00259/model-sbml-l3v2.xml new file mode 100644 index 000000000..5a877fb68 --- /dev/null +++ b/latest/cases/00259/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00259/output.heta b/latest/cases/00259/output.heta new file mode 100644 index 000000000..22c449796 --- /dev/null +++ b/latest/cases/00259/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic two reactions with five species in a 0 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S5 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 / S5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; +S5 @Species 'S5' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00259/synopsis.txt b/latest/cases/00259/synopsis.txt new file mode 100644 index 000000000..266f2aebf --- /dev/null +++ b/latest/cases/00259/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic two reactions with five species in a 0 dimensional compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ConstantSpecies, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are five +species named S1, S2, S3, S4 and S5 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. Species S5 is labeled as +constant and therefore cannot be changed by rules or reactions. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 / S5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S5 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00260/l2v5/heta-code/output.heta b/latest/cases/00260/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5c9b2121c --- /dev/null +++ b/latest/cases/00260/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * pow(S2, 2); + +k1 @Record 'k1' { } .= 0.35; +k2 @Record 'k2' { } .= 180; + diff --git a/latest/cases/00260/l2v5/index.heta b/latest/cases/00260/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00260/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00260/l2v5/json/output.json b/latest/cases/00260/l2v5/json/output.json new file mode 100644 index 000000000..23f64d3e0 --- /dev/null +++ b/latest/cases/00260/l2v5/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * pow(S2, 2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.35" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "180" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00260/l3v2/heta-code/output.heta b/latest/cases/00260/l3v2/heta-code/output.heta new file mode 100644 index 000000000..87e8dd089 --- /dev/null +++ b/latest/cases/00260/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * pow(S2, 2); + +k1 @Const 'k1' { } = 0.35; +k2 @Const 'k2' { } = 180; + diff --git a/latest/cases/00260/l3v2/index.heta b/latest/cases/00260/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00260/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00260/l3v2/json/output.json b/latest/cases/00260/l3v2/json/output.json new file mode 100644 index 000000000..14a51c07a --- /dev/null +++ b/latest/cases/00260/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * pow(S2, 2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.35 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 180 + } +] \ No newline at end of file diff --git a/latest/cases/00260/model-sbml-l2v5.xml b/latest/cases/00260/model-sbml-l2v5.xml new file mode 100644 index 000000000..f482c385a --- /dev/null +++ b/latest/cases/00260/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment + k2 + + + S2 + 2 + + + + + + + + diff --git a/latest/cases/00260/model-sbml-l3v2.xml b/latest/cases/00260/model-sbml-l3v2.xml new file mode 100644 index 000000000..764568f75 --- /dev/null +++ b/latest/cases/00260/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment + k2 + + + S2 + 2 + + + + + + + + diff --git a/latest/cases/00260/output.heta b/latest/cases/00260/output.heta new file mode 100644 index 000000000..7734d51d7 --- /dev/null +++ b/latest/cases/00260/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions involving two species in one + 2 dimensional compartment, with non-unity stoichiometries. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. Compartment +"compartment" is 2-dimensional. The model contains two reactions defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $k1 * S1 * compartment$ | +| 2 S2 -> S1 | $k2 * S2 * S2 * compartment$ |] + +Note the stoichiometry of S2 is 2 in both reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.35$ |second^-1^ | +|Value of parameter k2 |$ 180$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * pow(S2, 2); + +k1 @Const 'k1' { } = 0.35; +k2 @Const 'k2' { } = 180; + diff --git a/latest/cases/00260/synopsis.txt b/latest/cases/00260/synopsis.txt new file mode 100644 index 000000000..071d1976a --- /dev/null +++ b/latest/cases/00260/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions involving two species in one + 2 dimensional compartment, with non-unity stoichiometries. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. Compartment +"compartment" is 2-dimensional. The model contains two reactions defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $k1 * S1 * compartment$ | +| 2 S2 -> S1 | $k2 * S2 * S2 * compartment$ |] + +Note the stoichiometry of S2 is 2 in both reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.35$ |second^-1^ | +|Value of parameter k2 |$ 180$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00261/l2v5/heta-code/output.heta b/latest/cases/00261/l2v5/heta-code/output.heta new file mode 100644 index 000000000..21d121366 --- /dev/null +++ b/latest/cases/00261/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * pow(S2, 2); + +k1 @Record 'k1' { } .= 0.35; +k2 @Record 'k2' { } .= 180; + diff --git a/latest/cases/00261/l2v5/index.heta b/latest/cases/00261/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00261/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00261/l2v5/json/output.json b/latest/cases/00261/l2v5/json/output.json new file mode 100644 index 000000000..f525c7873 --- /dev/null +++ b/latest/cases/00261/l2v5/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * pow(S2, 2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.35" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "180" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00261/l3v2/heta-code/output.heta b/latest/cases/00261/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4a339af38 --- /dev/null +++ b/latest/cases/00261/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * pow(S2, 2); + +k1 @Const 'k1' { } = 0.35; +k2 @Const 'k2' { } = 180; + diff --git a/latest/cases/00261/l3v2/index.heta b/latest/cases/00261/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00261/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00261/l3v2/json/output.json b/latest/cases/00261/l3v2/json/output.json new file mode 100644 index 000000000..a3d2149c4 --- /dev/null +++ b/latest/cases/00261/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * pow(S2, 2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.35 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 180 + } +] \ No newline at end of file diff --git a/latest/cases/00261/model-sbml-l2v5.xml b/latest/cases/00261/model-sbml-l2v5.xml new file mode 100644 index 000000000..1ed4bcee8 --- /dev/null +++ b/latest/cases/00261/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment + k2 + + + S2 + 2 + + + + + + + + diff --git a/latest/cases/00261/model-sbml-l3v2.xml b/latest/cases/00261/model-sbml-l3v2.xml new file mode 100644 index 000000000..4aa0894cf --- /dev/null +++ b/latest/cases/00261/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment + k2 + + + S2 + 2 + + + + + + + + diff --git a/latest/cases/00261/output.heta b/latest/cases/00261/output.heta new file mode 100644 index 000000000..8e05be0df --- /dev/null +++ b/latest/cases/00261/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions involving two species in one + 1 dimensional compartment, with non-unity stoichiometries. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. Compartment +"compartment" is 1-dimensional. The model contains two reactions defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $k1 * S1 * compartment$ | +| 2 S2 -> S1 | $k2 * S2 * S2 * compartment$ |] + +Note the stoichiometry of S2 is 2 in both reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.35$ |second^-1^ | +|Value of parameter k2 |$ 180$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := compartment * k2 * pow(S2, 2); + +k1 @Const 'k1' { } = 0.35; +k2 @Const 'k2' { } = 180; + diff --git a/latest/cases/00261/synopsis.txt b/latest/cases/00261/synopsis.txt new file mode 100644 index 000000000..94e3b9639 --- /dev/null +++ b/latest/cases/00261/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions involving two species in one + 1 dimensional compartment, with non-unity stoichiometries. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. Compartment +"compartment" is 1-dimensional. The model contains two reactions defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $k1 * S1 * compartment$ | +| 2 S2 -> S1 | $k2 * S2 * S2 * compartment$ |] + +Note the stoichiometry of S2 is 2 in both reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.35$ |second^-1^ | +|Value of parameter k2 |$ 180$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00262/l2v5/heta-code/output.heta b/latest/cases/00262/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a705bdb3f --- /dev/null +++ b/latest/cases/00262/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-4; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := k1 * S1; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := k2 * pow(S2, 2); + +k1 @Record 'k1' { } .= 0.35; +k2 @Record 'k2' { } .= 180; + diff --git a/latest/cases/00262/l2v5/index.heta b/latest/cases/00262/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00262/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00262/l2v5/json/output.json b/latest/cases/00262/l2v5/json/output.json new file mode 100644 index 000000000..4201ffaae --- /dev/null +++ b/latest/cases/00262/l2v5/json/output.json @@ -0,0 +1,115 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * pow(S2, 2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.35" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "180" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00262/l3v2/heta-code/output.heta b/latest/cases/00262/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7029b809a --- /dev/null +++ b/latest/cases/00262/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-4; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := k1 * S1; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := k2 * pow(S2, 2); + +k1 @Const 'k1' { } = 0.35; +k2 @Const 'k2' { } = 180; + diff --git a/latest/cases/00262/l3v2/index.heta b/latest/cases/00262/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00262/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00262/l3v2/json/output.json b/latest/cases/00262/l3v2/json/output.json new file mode 100644 index 000000000..7e1890f5f --- /dev/null +++ b/latest/cases/00262/l3v2/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * pow(S2, 2)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.35 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 180 + } +] \ No newline at end of file diff --git a/latest/cases/00262/model-sbml-l2v5.xml b/latest/cases/00262/model-sbml-l2v5.xml new file mode 100644 index 000000000..fd7a0537d --- /dev/null +++ b/latest/cases/00262/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + + + + + + + + + + k2 + + + S2 + 2 + + + + + + + + diff --git a/latest/cases/00262/model-sbml-l3v2.xml b/latest/cases/00262/model-sbml-l3v2.xml new file mode 100644 index 000000000..36d4820c3 --- /dev/null +++ b/latest/cases/00262/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + + + + + + + + + + k2 + + + S2 + 2 + + + + + + + + diff --git a/latest/cases/00262/output.heta b/latest/cases/00262/output.heta new file mode 100644 index 000000000..65ad09df3 --- /dev/null +++ b/latest/cases/00262/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Basic two reactions involving two species in one + 0 dimensional compartment, with non-unity stoichiometries. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. Compartment +"compartment" is 0-dimensional. The model contains two reactions defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $k1 * S1$ | +| 2 S2 -> S1 | $k2 * S2 * S2$ |] + +Note the stoichiometry of S2 is 2 in both reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.35$ |second^-1^ | +|Value of parameter k2 |$ 180$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-4; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := k1 * S1; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, }; +reaction2 := k2 * pow(S2, 2); + +k1 @Const 'k1' { } = 0.35; +k2 @Const 'k2' { } = 180; + diff --git a/latest/cases/00262/synopsis.txt b/latest/cases/00262/synopsis.txt new file mode 100644 index 000000000..3935b2c23 --- /dev/null +++ b/latest/cases/00262/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic two reactions involving two species in one + 0 dimensional compartment, with non-unity stoichiometries. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and k2. Compartment +"compartment" is 0-dimensional. The model contains two reactions defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2 S2 | $k1 * S1$ | +| 2 S2 -> S1 | $k2 * S2 * S2$ |] + +Note the stoichiometry of S2 is 2 in both reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.35$ |second^-1^ | +|Value of parameter k2 |$ 180$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00263/l2v5/heta-code/output.heta b/latest/cases/00263/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4c6509dc0 --- /dev/null +++ b/latest/cases/00263/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 5e-5 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 16000; +k2 @Record 'k2' { } .= 0.7; + diff --git a/latest/cases/00263/l2v5/index.heta b/latest/cases/00263/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00263/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00263/l2v5/json/output.json b/latest/cases/00263/l2v5/json/output.json new file mode 100644 index 000000000..87e74f934 --- /dev/null +++ b/latest/cases/00263/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "16000" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00263/l3v2/heta-code/output.heta b/latest/cases/00263/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1dffdae86 --- /dev/null +++ b/latest/cases/00263/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 5e-5 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 16000; +k2 @Const 'k2' { } = 0.7; + diff --git a/latest/cases/00263/l3v2/index.heta b/latest/cases/00263/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00263/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00263/l3v2/json/output.json b/latest/cases/00263/l3v2/json/output.json new file mode 100644 index 000000000..df0a0981a --- /dev/null +++ b/latest/cases/00263/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 16000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00263/model-sbml-l2v5.xml b/latest/cases/00263/model-sbml-l2v5.xml new file mode 100644 index 000000000..f93f1d511 --- /dev/null +++ b/latest/cases/00263/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + + S1 + 2 + + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00263/model-sbml-l3v2.xml b/latest/cases/00263/model-sbml-l3v2.xml new file mode 100644 index 000000000..eeb5e4c9c --- /dev/null +++ b/latest/cases/00263/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + + S1 + 2 + + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00263/output.heta b/latest/cases/00263/output.heta new file mode 100644 index 000000000..e9c7f6f06 --- /dev/null +++ b/latest/cases/00263/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 2D compartment, + with one species having a stoichiometry of 2. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2 * compartment$ | +| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$0.5 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 1.6 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.7$ |second^-1^ | +|Area of compartment "compartment" |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 5e-5 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 16000; +k2 @Const 'k2' { } = 0.7; + diff --git a/latest/cases/00263/synopsis.txt b/latest/cases/00263/synopsis.txt new file mode 100644 index 000000000..0df4e31ae --- /dev/null +++ b/latest/cases/00263/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with three species in one 2D compartment, + with one species having a stoichiometry of 2. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2 * compartment$ | +| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$0.5 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 1.6 \x 10^4$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.7$ |second^-1^ | +|Area of compartment "compartment" |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00264/l2v5/heta-code/output.heta b/latest/cases/00264/l2v5/heta-code/output.heta new file mode 100644 index 000000000..696d85b98 --- /dev/null +++ b/latest/cases/00264/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 5e-4 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1600; +k2 @Record 'k2' { } .= 0.7; + diff --git a/latest/cases/00264/l2v5/index.heta b/latest/cases/00264/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00264/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00264/l2v5/json/output.json b/latest/cases/00264/l2v5/json/output.json new file mode 100644 index 000000000..9c3fcaf74 --- /dev/null +++ b/latest/cases/00264/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1600" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00264/l3v2/heta-code/output.heta b/latest/cases/00264/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5bd808f52 --- /dev/null +++ b/latest/cases/00264/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 5e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 1600; +k2 @Const 'k2' { } = 0.7; + diff --git a/latest/cases/00264/l3v2/index.heta b/latest/cases/00264/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00264/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00264/l3v2/json/output.json b/latest/cases/00264/l3v2/json/output.json new file mode 100644 index 000000000..d96490f5d --- /dev/null +++ b/latest/cases/00264/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1600 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00264/model-sbml-l2v5.xml b/latest/cases/00264/model-sbml-l2v5.xml new file mode 100644 index 000000000..c56735a80 --- /dev/null +++ b/latest/cases/00264/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + + S1 + 2 + + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00264/model-sbml-l3v2.xml b/latest/cases/00264/model-sbml-l3v2.xml new file mode 100644 index 000000000..23905cbb9 --- /dev/null +++ b/latest/cases/00264/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + + + S1 + 2 + + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00264/output.heta b/latest/cases/00264/output.heta new file mode 100644 index 000000000..b027b32c6 --- /dev/null +++ b/latest/cases/00264/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 1D compartment, + with one species having a stoichiometry of 2. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2 * compartment$ | +| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$0.5 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.6 \x 10^3$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.7$ |second^-1^ | +|Length of compartment "compartment" |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 5e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 1600; +k2 @Const 'k2' { } = 0.7; + diff --git a/latest/cases/00264/synopsis.txt b/latest/cases/00264/synopsis.txt new file mode 100644 index 000000000..8496aa278 --- /dev/null +++ b/latest/cases/00264/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with three species in one 1D compartment, + with one species having a stoichiometry of 2. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2 * compartment$ | +| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$0.5 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.6 \x 10^3$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.7$ |second^-1^ | +|Length of compartment "compartment" |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00265/l2v5/heta-code/output.heta b/latest/cases/00265/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8bbbe3ce1 --- /dev/null +++ b/latest/cases/00265/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.005; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 160; +k2 @Record 'k2' { } .= 0.7; + diff --git a/latest/cases/00265/l2v5/index.heta b/latest/cases/00265/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00265/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00265/l2v5/json/output.json b/latest/cases/00265/l2v5/json/output.json new file mode 100644 index 000000000..d985b0f7c --- /dev/null +++ b/latest/cases/00265/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.005" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "160" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00265/l3v2/heta-code/output.heta b/latest/cases/00265/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2daf63101 --- /dev/null +++ b/latest/cases/00265/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.005; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 160; +k2 @Const 'k2' { } = 0.7; + diff --git a/latest/cases/00265/l3v2/index.heta b/latest/cases/00265/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00265/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00265/l3v2/json/output.json b/latest/cases/00265/l3v2/json/output.json new file mode 100644 index 000000000..85baf21da --- /dev/null +++ b/latest/cases/00265/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.005" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 160 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00265/model-sbml-l2v5.xml b/latest/cases/00265/model-sbml-l2v5.xml new file mode 100644 index 000000000..750ae583c --- /dev/null +++ b/latest/cases/00265/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + + S1 + 2 + + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00265/model-sbml-l3v2.xml b/latest/cases/00265/model-sbml-l3v2.xml new file mode 100644 index 000000000..9b9e4b385 --- /dev/null +++ b/latest/cases/00265/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + + S1 + 2 + + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00265/output.heta b/latest/cases/00265/output.heta new file mode 100644 index 000000000..577f116f3 --- /dev/null +++ b/latest/cases/00265/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 0D compartment, + with one species having a stoichiometry of 2. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2$ | +| S3 -> 2S1 + S2 | $k2 * S3t$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0.5 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.6 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.7$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.005; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 160; +k2 @Const 'k2' { } = 0.7; + diff --git a/latest/cases/00265/synopsis.txt b/latest/cases/00265/synopsis.txt new file mode 100644 index 000000000..4b6046a05 --- /dev/null +++ b/latest/cases/00265/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Basic two reactions with three species in one 0D compartment, + with one species having a stoichiometry of 2. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2$ | +| S3 -> 2S1 + S2 | $k2 * S3t$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0.5 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.6 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.7$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00266/l2v5/heta-code/output.heta b/latest/cases/00266/l2v5/heta-code/output.heta new file mode 100644 index 000000000..16adb1ba4 --- /dev/null +++ b/latest/cases/00266/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 5e-7 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 9e+5; +k2 @Record 'k2' { } .= 1.5e+5; + diff --git a/latest/cases/00266/l2v5/index.heta b/latest/cases/00266/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00266/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00266/l2v5/json/output.json b/latest/cases/00266/l2v5/json/output.json new file mode 100644 index 000000000..3ad43036c --- /dev/null +++ b/latest/cases/00266/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "9e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00266/l3v2/heta-code/output.heta b/latest/cases/00266/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cff9f1b67 --- /dev/null +++ b/latest/cases/00266/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 5e-7 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 900000; +k2 @Const 'k2' { } = 150000; + diff --git a/latest/cases/00266/l3v2/index.heta b/latest/cases/00266/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00266/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00266/l3v2/json/output.json b/latest/cases/00266/l3v2/json/output.json new file mode 100644 index 000000000..d99b0b2dc --- /dev/null +++ b/latest/cases/00266/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 900000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 150000 + } +] \ No newline at end of file diff --git a/latest/cases/00266/model-sbml-l2v5.xml b/latest/cases/00266/model-sbml-l2v5.xml new file mode 100644 index 000000000..3cbdebca9 --- /dev/null +++ b/latest/cases/00266/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00266/model-sbml-l3v2.xml b/latest/cases/00266/model-sbml-l3v2.xml new file mode 100644 index 000000000..8982de514 --- /dev/null +++ b/latest/cases/00266/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00266/output.heta b/latest/cases/00266/output.heta new file mode 100644 index 000000000..08b773dc1 --- /dev/null +++ b/latest/cases/00266/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one 2D compartment, + with non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9 \x 10^6$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.15 \x 10^6$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 5e-7 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 900000; +k2 @Const 'k2' { } = 150000; + diff --git a/latest/cases/00266/synopsis.txt b/latest/cases/00266/synopsis.txt new file mode 100644 index 000000000..be4a3cd72 --- /dev/null +++ b/latest/cases/00266/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in one 2D compartment, + with non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9 \x 10^6$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.15 \x 10^6$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00267/l2v5/heta-code/output.heta b/latest/cases/00267/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a0b92ba55 --- /dev/null +++ b/latest/cases/00267/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 5e-7 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 9e+5; +k2 @Record 'k2' { } .= 1.5e+5; + diff --git a/latest/cases/00267/l2v5/index.heta b/latest/cases/00267/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00267/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00267/l2v5/json/output.json b/latest/cases/00267/l2v5/json/output.json new file mode 100644 index 000000000..fea33c9b9 --- /dev/null +++ b/latest/cases/00267/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "9e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00267/l3v2/heta-code/output.heta b/latest/cases/00267/l3v2/heta-code/output.heta new file mode 100644 index 000000000..134f71fab --- /dev/null +++ b/latest/cases/00267/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 5e-7 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 900000; +k2 @Const 'k2' { } = 150000; + diff --git a/latest/cases/00267/l3v2/index.heta b/latest/cases/00267/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00267/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00267/l3v2/json/output.json b/latest/cases/00267/l3v2/json/output.json new file mode 100644 index 000000000..501580de3 --- /dev/null +++ b/latest/cases/00267/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "5e-7 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 900000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 150000 + } +] \ No newline at end of file diff --git a/latest/cases/00267/model-sbml-l2v5.xml b/latest/cases/00267/model-sbml-l2v5.xml new file mode 100644 index 000000000..0fe0f9247 --- /dev/null +++ b/latest/cases/00267/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00267/model-sbml-l3v2.xml b/latest/cases/00267/model-sbml-l3v2.xml new file mode 100644 index 000000000..391702175 --- /dev/null +++ b/latest/cases/00267/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00267/output.heta b/latest/cases/00267/output.heta new file mode 100644 index 000000000..28e3795c1 --- /dev/null +++ b/latest/cases/00267/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one 1D compartment, + with non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9 \x 10^6$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.15 \x 10^6$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 5e-7 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-6 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 900000; +k2 @Const 'k2' { } = 150000; + diff --git a/latest/cases/00267/synopsis.txt b/latest/cases/00267/synopsis.txt new file mode 100644 index 000000000..ab6d11280 --- /dev/null +++ b/latest/cases/00267/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in one 1D compartment, + with non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2 * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9 \x 10^6$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.15 \x 10^6$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00268/l2v5/heta-code/output.heta b/latest/cases/00268/l2v5/heta-code/output.heta new file mode 100644 index 000000000..171bc2a40 --- /dev/null +++ b/latest/cases/00268/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 5e-7; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 9e+5; +k2 @Record 'k2' { } .= 1.5e+5; + diff --git a/latest/cases/00268/l2v5/index.heta b/latest/cases/00268/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00268/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00268/l2v5/json/output.json b/latest/cases/00268/l2v5/json/output.json new file mode 100644 index 000000000..352f32c22 --- /dev/null +++ b/latest/cases/00268/l2v5/json/output.json @@ -0,0 +1,153 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "9e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00268/l3v2/heta-code/output.heta b/latest/cases/00268/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f95753c63 --- /dev/null +++ b/latest/cases/00268/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 900000; +k2 @Const 'k2' { } = 150000; + diff --git a/latest/cases/00268/l3v2/index.heta b/latest/cases/00268/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00268/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00268/l3v2/json/output.json b/latest/cases/00268/l3v2/json/output.json new file mode 100644 index 000000000..68fb9bdec --- /dev/null +++ b/latest/cases/00268/l3v2/json/output.json @@ -0,0 +1,125 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 900000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 150000 + } +] \ No newline at end of file diff --git a/latest/cases/00268/model-sbml-l2v5.xml b/latest/cases/00268/model-sbml-l2v5.xml new file mode 100644 index 000000000..8f86be9b0 --- /dev/null +++ b/latest/cases/00268/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00268/model-sbml-l3v2.xml b/latest/cases/00268/model-sbml-l3v2.xml new file mode 100644 index 000000000..e999e5c08 --- /dev/null +++ b/latest/cases/00268/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00268/output.heta b/latest/cases/00268/output.heta new file mode 100644 index 000000000..beb9b2038 --- /dev/null +++ b/latest/cases/00268/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one 0D compartment, + with non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.15 \x 10^6$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 900000; +k2 @Const 'k2' { } = 150000; + diff --git a/latest/cases/00268/synopsis.txt b/latest/cases/00268/synopsis.txt new file mode 100644 index 000000000..f0f6f5e6b --- /dev/null +++ b/latest/cases/00268/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic two reactions with four species in one 0D compartment, + with non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 0.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.15 \x 10^6$ |mole^-1^ second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00269/l2v5/heta-code/output.heta b/latest/cases/00269/l2v5/heta-code/output.heta new file mode 100644 index 000000000..acc8bb081 --- /dev/null +++ b/latest/cases/00269/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y, z], math: factorial(ceil(x * y)) * pow(z, (-1)), }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := calculate(S1, p1, p2); + +p1 @Record 'p1' { } .= 4; +p2 @Record 'p2' { } .= 25; + diff --git a/latest/cases/00269/l2v5/index.heta b/latest/cases/00269/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00269/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00269/l2v5/json/output.json b/latest/cases/00269/l2v5/json/output.json new file mode 100644 index 000000000..e74ff48ce --- /dev/null +++ b/latest/cases/00269/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "calculate(S1, p1, p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "4" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "factorial(ceil(x * y)) * pow(z, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00269/l3v2/heta-code/output.heta b/latest/cases/00269/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5570b9dab --- /dev/null +++ b/latest/cases/00269/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + +calculate #defineFunction { arguments: [x, y, z], math: factorial(ceil(x * y)) * pow(z, (-1)), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := calculate(S1, p1, p2); + +p1 @Const 'p1' { } = 4; +p2 @Const 'p2' { } = 25; + diff --git a/latest/cases/00269/l3v2/index.heta b/latest/cases/00269/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00269/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00269/l3v2/json/output.json b/latest/cases/00269/l3v2/json/output.json new file mode 100644 index 000000000..c353cae00 --- /dev/null +++ b/latest/cases/00269/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "calculate(S1, p1, p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 4 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 25 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "factorial(ceil(x * y)) * pow(z, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00269/model-sbml-l2v5.xml b/latest/cases/00269/model-sbml-l2v5.xml new file mode 100644 index 000000000..4d7aa2380 --- /dev/null +++ b/latest/cases/00269/model-sbml-l2v5.xml @@ -0,0 +1,72 @@ + + + + + + + + + x + + + y + + + z + + + + + + + + + + x + y + + + + + + z + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + calculate + S1 + p1 + p2 + + + + + + + diff --git a/latest/cases/00269/model-sbml-l3v2.xml b/latest/cases/00269/model-sbml-l3v2.xml new file mode 100644 index 000000000..7ca44f4f8 --- /dev/null +++ b/latest/cases/00269/model-sbml-l3v2.xml @@ -0,0 +1,89 @@ + + + + + + + + + x + + + y + + + z + + + + + + + + + + x + y + + + + + + z + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + calculate + S1 + p1 + p2 + + + + + + + diff --git a/latest/cases/00269/output.heta b/latest/cases/00269/output.heta new file mode 100644 index 000000000..1394279e5 --- /dev/null +++ b/latest/cases/00269/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $calculate(S1,p1,p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Ceiling(x * y)! / z$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 0.0$ |mole | +|Value of parameter p1 |$ 4$ |litre mole^-1^ | +|Value of parameter p2 |$ 25$ |second mole^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +calculate #defineFunction { arguments: [x, y, z], math: factorial(ceil(x * y)) * pow(z, (-1)), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := calculate(S1, p1, p2); + +p1 @Const 'p1' { } = 4; +p2 @Const 'p2' { } = 25; + diff --git a/latest/cases/00269/synopsis.txt b/latest/cases/00269/synopsis.txt new file mode 100644 index 000000000..77d07ab34 --- /dev/null +++ b/latest/cases/00269/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $calculate(S1,p1,p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Ceiling(x * y)! / z$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 0.0$ |mole | +|Value of parameter p1 |$ 4$ |litre mole^-1^ | +|Value of parameter p2 |$ 25$ |second mole^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00270/l2v5/heta-code/output.heta b/latest/cases/00270/l2v5/heta-code/output.heta new file mode 100644 index 000000000..305a09718 --- /dev/null +++ b/latest/cases/00270/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y, z], math: ((x > 7) ? y : z), }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00270/l2v5/index.heta b/latest/cases/00270/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00270/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00270/l2v5/json/output.json b/latest/cases/00270/l2v5/json/output.json new file mode 100644 index 000000000..aa0b611bb --- /dev/null +++ b/latest/cases/00270/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x > 7) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00270/l3v2/heta-code/output.heta b/latest/cases/00270/l3v2/heta-code/output.heta new file mode 100644 index 000000000..73d99ab02 --- /dev/null +++ b/latest/cases/00270/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +calculate #defineFunction { arguments: [x, y, z], math: ((x > 7) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00270/l3v2/index.heta b/latest/cases/00270/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00270/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00270/l3v2/json/output.json b/latest/cases/00270/l3v2/json/output.json new file mode 100644 index 000000000..68d742b83 --- /dev/null +++ b/latest/cases/00270/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x > 7) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00270/model-sbml-l2v5.xml b/latest/cases/00270/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef393d6f3 --- /dev/null +++ b/latest/cases/00270/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 7 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00270/model-sbml-l3v2.xml b/latest/cases/00270/model-sbml-l3v2.xml new file mode 100644 index 000000000..2abdd959a --- /dev/null +++ b/latest/cases/00270/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 7 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00270/output.heta b/latest/cases/00270/output.heta new file mode 100644 index 000000000..417eecc4e --- /dev/null +++ b/latest/cases/00270/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, x > 7}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +calculate #defineFunction { arguments: [x, y, z], math: ((x > 7) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00270/synopsis.txt b/latest/cases/00270/synopsis.txt new file mode 100644 index 000000000..1f1a03779 --- /dev/null +++ b/latest/cases/00270/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, x > 7}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00271/l2v5/heta-code/output.heta b/latest/cases/00271/l2v5/heta-code/output.heta new file mode 100644 index 000000000..68c6431e5 --- /dev/null +++ b/latest/cases/00271/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y], math: y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := calculate(p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; + diff --git a/latest/cases/00271/l2v5/index.heta b/latest/cases/00271/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00271/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00271/l2v5/json/output.json b/latest/cases/00271/l2v5/json/output.json new file mode 100644 index 000000000..ebcfce23e --- /dev/null +++ b/latest/cases/00271/l2v5/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "calculate(p1, p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y" + ], + "math": "y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00271/l3v2/heta-code/output.heta b/latest/cases/00271/l3v2/heta-code/output.heta new file mode 100644 index 000000000..41237e6b0 --- /dev/null +++ b/latest/cases/00271/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + +calculate #defineFunction { arguments: [x, y], math: y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := calculate(p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; + diff --git a/latest/cases/00271/l3v2/index.heta b/latest/cases/00271/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00271/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00271/l3v2/json/output.json b/latest/cases/00271/l3v2/json/output.json new file mode 100644 index 000000000..41fae92d0 --- /dev/null +++ b/latest/cases/00271/l3v2/json/output.json @@ -0,0 +1,76 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "calculate(p1, p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y" + ], + "math": "y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00271/model-sbml-l2v5.xml b/latest/cases/00271/model-sbml-l2v5.xml new file mode 100644 index 000000000..26aac62a7 --- /dev/null +++ b/latest/cases/00271/model-sbml-l2v5.xml @@ -0,0 +1,50 @@ + + + + + + + + + x + + + y + + y + + + + + + + + + + + + + + + + + + + + + + + + + + + calculate + p1 + p2 + + + + + + + diff --git a/latest/cases/00271/model-sbml-l3v2.xml b/latest/cases/00271/model-sbml-l3v2.xml new file mode 100644 index 000000000..033cffdc0 --- /dev/null +++ b/latest/cases/00271/model-sbml-l3v2.xml @@ -0,0 +1,67 @@ + + + + + + + + + x + + + y + + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + calculate + p1 + p2 + + + + + + + diff --git a/latest/cases/00271/output.heta b/latest/cases/00271/output.heta new file mode 100644 index 000000000..7cd0e07b6 --- /dev/null +++ b/latest/cases/00271/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using MathML in the rate equation. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $calculate(p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y | $Piecewise({{x, False}}, y)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +calculate #defineFunction { arguments: [x, y], math: y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := calculate(p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; + diff --git a/latest/cases/00271/synopsis.txt b/latest/cases/00271/synopsis.txt new file mode 100644 index 000000000..9dbce9f76 --- /dev/null +++ b/latest/cases/00271/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using MathML in the rate equation. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $calculate(p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y | $Piecewise({{x, False}}, y)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00272/l2v5/heta-code/output.heta b/latest/cases/00272/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0a181e707 --- /dev/null +++ b/latest/cases/00272/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y, z], math: ((x >= 4) ? y : z), }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00272/l2v5/index.heta b/latest/cases/00272/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00272/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00272/l2v5/json/output.json b/latest/cases/00272/l2v5/json/output.json new file mode 100644 index 000000000..a39352d7f --- /dev/null +++ b/latest/cases/00272/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x >= 4) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00272/l3v2/heta-code/output.heta b/latest/cases/00272/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6e5378129 --- /dev/null +++ b/latest/cases/00272/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +calculate #defineFunction { arguments: [x, y, z], math: ((x >= 4) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00272/l3v2/index.heta b/latest/cases/00272/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00272/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00272/l3v2/json/output.json b/latest/cases/00272/l3v2/json/output.json new file mode 100644 index 000000000..fee10d22b --- /dev/null +++ b/latest/cases/00272/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x >= 4) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00272/model-sbml-l2v5.xml b/latest/cases/00272/model-sbml-l2v5.xml new file mode 100644 index 000000000..2e5c32403 --- /dev/null +++ b/latest/cases/00272/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 4 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00272/model-sbml-l3v2.xml b/latest/cases/00272/model-sbml-l3v2.xml new file mode 100644 index 000000000..52fef081e --- /dev/null +++ b/latest/cases/00272/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 4 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00272/output.heta b/latest/cases/00272/output.heta new file mode 100644 index 000000000..b8501e7b2 --- /dev/null +++ b/latest/cases/00272/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, x >= 4}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +calculate #defineFunction { arguments: [x, y, z], math: ((x >= 4) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00272/synopsis.txt b/latest/cases/00272/synopsis.txt new file mode 100644 index 000000000..046c84fd6 --- /dev/null +++ b/latest/cases/00272/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, x >= 4}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00273/l2v5/heta-code/output.heta b/latest/cases/00273/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ef884bd51 --- /dev/null +++ b/latest/cases/00273/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y, z], math: ((x <= 4) ? y : z), }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := calculate(S1, p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00273/l2v5/index.heta b/latest/cases/00273/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00273/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00273/l2v5/json/output.json b/latest/cases/00273/l2v5/json/output.json new file mode 100644 index 000000000..75c77ecfb --- /dev/null +++ b/latest/cases/00273/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S1, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x <= 4) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00273/l3v2/heta-code/output.heta b/latest/cases/00273/l3v2/heta-code/output.heta new file mode 100644 index 000000000..49bfdf799 --- /dev/null +++ b/latest/cases/00273/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +calculate #defineFunction { arguments: [x, y, z], math: ((x <= 4) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := calculate(S1, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00273/l3v2/index.heta b/latest/cases/00273/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00273/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00273/l3v2/json/output.json b/latest/cases/00273/l3v2/json/output.json new file mode 100644 index 000000000..1e64ca52a --- /dev/null +++ b/latest/cases/00273/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S1, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x <= 4) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00273/model-sbml-l2v5.xml b/latest/cases/00273/model-sbml-l2v5.xml new file mode 100644 index 000000000..649ba0680 --- /dev/null +++ b/latest/cases/00273/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 4 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S1 + p1 + p2 + + + + + + + diff --git a/latest/cases/00273/model-sbml-l3v2.xml b/latest/cases/00273/model-sbml-l3v2.xml new file mode 100644 index 000000000..2a89d587a --- /dev/null +++ b/latest/cases/00273/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 4 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S1 + p1 + p2 + + + + + + + diff --git a/latest/cases/00273/output.heta b/latest/cases/00273/output.heta new file mode 100644 index 000000000..47be7800f --- /dev/null +++ b/latest/cases/00273/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S1, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, x <= 4}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 5$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +calculate #defineFunction { arguments: [x, y, z], math: ((x <= 4) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := calculate(S1, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00273/synopsis.txt b/latest/cases/00273/synopsis.txt new file mode 100644 index 000000000..c471e3831 --- /dev/null +++ b/latest/cases/00273/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S1, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, x <= 4}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 5$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00274/l2v5/heta-code/output.heta b/latest/cases/00274/l2v5/heta-code/output.heta new file mode 100644 index 000000000..715f29001 --- /dev/null +++ b/latest/cases/00274/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y, z], math: ((x < 2.5) ? y : z), }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := calculate(S1, p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00274/l2v5/index.heta b/latest/cases/00274/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00274/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00274/l2v5/json/output.json b/latest/cases/00274/l2v5/json/output.json new file mode 100644 index 000000000..f796a94c6 --- /dev/null +++ b/latest/cases/00274/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S1, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x < 2.5) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00274/l3v2/heta-code/output.heta b/latest/cases/00274/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c077d70fc --- /dev/null +++ b/latest/cases/00274/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +calculate #defineFunction { arguments: [x, y, z], math: ((x < 2.5) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := calculate(S1, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00274/l3v2/index.heta b/latest/cases/00274/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00274/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00274/l3v2/json/output.json b/latest/cases/00274/l3v2/json/output.json new file mode 100644 index 000000000..441751a95 --- /dev/null +++ b/latest/cases/00274/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S1, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x < 2.5) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00274/model-sbml-l2v5.xml b/latest/cases/00274/model-sbml-l2v5.xml new file mode 100644 index 000000000..163c65487 --- /dev/null +++ b/latest/cases/00274/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 2.5 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S1 + p1 + p2 + + + + + + + diff --git a/latest/cases/00274/model-sbml-l3v2.xml b/latest/cases/00274/model-sbml-l3v2.xml new file mode 100644 index 000000000..f965362d6 --- /dev/null +++ b/latest/cases/00274/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 2.5 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S1 + p1 + p2 + + + + + + + diff --git a/latest/cases/00274/output.heta b/latest/cases/00274/output.heta new file mode 100644 index 000000000..b55451919 --- /dev/null +++ b/latest/cases/00274/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S1, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, x < 2.5}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 5$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +calculate #defineFunction { arguments: [x, y, z], math: ((x < 2.5) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, }; +reaction2 := calculate(S1, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00274/synopsis.txt b/latest/cases/00274/synopsis.txt new file mode 100644 index 000000000..328662f24 --- /dev/null +++ b/latest/cases/00274/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S1, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, x < 2.5}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 5$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00275/l2v5/heta-code/output.heta b/latest/cases/00275/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0a7504a7c --- /dev/null +++ b/latest/cases/00275/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y], math: x, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * S1 * calculate(p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; + diff --git a/latest/cases/00275/l2v5/index.heta b/latest/cases/00275/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00275/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00275/l2v5/json/output.json b/latest/cases/00275/l2v5/json/output.json new file mode 100644 index 000000000..75c702c43 --- /dev/null +++ b/latest/cases/00275/l2v5/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * S1 * calculate(p1, p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y" + ], + "math": "x", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00275/l3v2/heta-code/output.heta b/latest/cases/00275/l3v2/heta-code/output.heta new file mode 100644 index 000000000..192b7fa29 --- /dev/null +++ b/latest/cases/00275/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + +calculate #defineFunction { arguments: [x, y], math: x, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * S1 * calculate(p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; + diff --git a/latest/cases/00275/l3v2/index.heta b/latest/cases/00275/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00275/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00275/l3v2/json/output.json b/latest/cases/00275/l3v2/json/output.json new file mode 100644 index 000000000..9db2c0d8f --- /dev/null +++ b/latest/cases/00275/l3v2/json/output.json @@ -0,0 +1,76 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * S1 * calculate(p1, p2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y" + ], + "math": "x", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00275/model-sbml-l2v5.xml b/latest/cases/00275/model-sbml-l2v5.xml new file mode 100644 index 000000000..a8c41d464 --- /dev/null +++ b/latest/cases/00275/model-sbml-l2v5.xml @@ -0,0 +1,55 @@ + + + + + + + + + x + + + y + + x + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + S1 + + calculate + p1 + p2 + + + + + + + + diff --git a/latest/cases/00275/model-sbml-l3v2.xml b/latest/cases/00275/model-sbml-l3v2.xml new file mode 100644 index 000000000..a9d2685d8 --- /dev/null +++ b/latest/cases/00275/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + x + + + y + + x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + S1 + + calculate + p1 + p2 + + + + + + + + diff --git a/latest/cases/00275/output.heta b/latest/cases/00275/output.heta new file mode 100644 index 000000000..26502159d --- /dev/null +++ b/latest/cases/00275/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using MathML in the rate equation. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * S1 * calculate(p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y | $Piecewise({{x, True}}, y)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |second^-1^ | +|Value of parameter p2 |$ 0.05$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +calculate #defineFunction { arguments: [x, y], math: x, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * S1 * calculate(p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; + diff --git a/latest/cases/00275/synopsis.txt b/latest/cases/00275/synopsis.txt new file mode 100644 index 000000000..882f1a6bd --- /dev/null +++ b/latest/cases/00275/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using MathML in the rate equation. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * S1 * calculate(p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y | $Piecewise({{x, True}}, y)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |second^-1^ | +|Value of parameter p2 |$ 0.05$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00276/l2v5/heta-code/output.heta b/latest/cases/00276/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4409a1a1e --- /dev/null +++ b/latest/cases/00276/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [w, x, y, z], math: ((x > 4 and w < 5 and x < 8) ? y : z), }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1, S2], reversible: false, }; +reaction2 := calculate(S1, S2, p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00276/l2v5/index.heta b/latest/cases/00276/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00276/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00276/l2v5/json/output.json b/latest/cases/00276/l2v5/json/output.json new file mode 100644 index 000000000..ef0bcd25f --- /dev/null +++ b/latest/cases/00276/l2v5/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S1, S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + }, + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "w", + "x", + "y", + "z" + ], + "math": "((x > 4 and w < 5 and x < 8) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00276/l3v2/heta-code/output.heta b/latest/cases/00276/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2a0289bd6 --- /dev/null +++ b/latest/cases/00276/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +calculate #defineFunction { arguments: [w, x, y, z], math: ((x > 4 and w < 5 and x < 8) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1, S2], reversible: false, }; +reaction2 := calculate(S1, S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00276/l3v2/index.heta b/latest/cases/00276/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00276/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00276/l3v2/json/output.json b/latest/cases/00276/l3v2/json/output.json new file mode 100644 index 000000000..cd485afd3 --- /dev/null +++ b/latest/cases/00276/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S1, S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + }, + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "calculate", + "arguments": [ + "w", + "x", + "y", + "z" + ], + "math": "((x > 4 and w < 5 and x < 8) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00276/model-sbml-l2v5.xml b/latest/cases/00276/model-sbml-l2v5.xml new file mode 100644 index 000000000..354d4d74d --- /dev/null +++ b/latest/cases/00276/model-sbml-l2v5.xml @@ -0,0 +1,108 @@ + + + + + + + + + w + + + x + + + y + + + z + + + + y + + + + + x + 4 + + + + w + 5 + + + + x + 8 + + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + calculate + S1 + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00276/model-sbml-l3v2.xml b/latest/cases/00276/model-sbml-l3v2.xml new file mode 100644 index 000000000..2daba4df2 --- /dev/null +++ b/latest/cases/00276/model-sbml-l3v2.xml @@ -0,0 +1,125 @@ + + + + + + + + + w + + + x + + + y + + + z + + + + y + + + + + x + 4 + + + + w + 5 + + + + x + 8 + + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + + calculate + S1 + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00276/output.heta b/latest/cases/00276/output.heta new file mode 100644 index 000000000..4711a6c6e --- /dev/null +++ b/latest/cases/00276/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S1, S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | w, x, y, z | $Piecewise({{y, And(x > 4, w < 5, x < 8)}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +calculate #defineFunction { arguments: [w, x, y, z], math: ((x > 4 and w < 5 and x < 8) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1, S2], reversible: false, }; +reaction2 := calculate(S1, S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00276/synopsis.txt b/latest/cases/00276/synopsis.txt new file mode 100644 index 000000000..418efb6ae --- /dev/null +++ b/latest/cases/00276/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S1, S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | w, x, y, z | $Piecewise({{y, And(x > 4, w < 5, x < 8)}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00277/l2v5/heta-code/output.heta b/latest/cases/00277/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0a181e707 --- /dev/null +++ b/latest/cases/00277/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y, z], math: ((x >= 4) ? y : z), }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00277/l2v5/index.heta b/latest/cases/00277/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00277/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00277/l2v5/json/output.json b/latest/cases/00277/l2v5/json/output.json new file mode 100644 index 000000000..a39352d7f --- /dev/null +++ b/latest/cases/00277/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x >= 4) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00277/l3v2/heta-code/output.heta b/latest/cases/00277/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6e5378129 --- /dev/null +++ b/latest/cases/00277/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +calculate #defineFunction { arguments: [x, y, z], math: ((x >= 4) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00277/l3v2/index.heta b/latest/cases/00277/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00277/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00277/l3v2/json/output.json b/latest/cases/00277/l3v2/json/output.json new file mode 100644 index 000000000..fee10d22b --- /dev/null +++ b/latest/cases/00277/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "10 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x >= 4) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00277/model-sbml-l2v5.xml b/latest/cases/00277/model-sbml-l2v5.xml new file mode 100644 index 000000000..008f3d890 --- /dev/null +++ b/latest/cases/00277/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 4 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00277/model-sbml-l3v2.xml b/latest/cases/00277/model-sbml-l3v2.xml new file mode 100644 index 000000000..317270324 --- /dev/null +++ b/latest/cases/00277/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + x + 4 + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00277/output.heta b/latest/cases/00277/output.heta new file mode 100644 index 000000000..efc697534 --- /dev/null +++ b/latest/cases/00277/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the +reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, Not(x < 4)}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +calculate #defineFunction { arguments: [x, y, z], math: ((x >= 4) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00277/synopsis.txt b/latest/cases/00277/synopsis.txt new file mode 100644 index 000000000..a01a0bde3 --- /dev/null +++ b/latest/cases/00277/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the +reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, Not(x < 4)}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 10$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 10$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00278/l2v5/heta-code/output.heta b/latest/cases/00278/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2d55df1c9 --- /dev/null +++ b/latest/cases/00278/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y, z], math: ((x < 2 or x > 4 or x < 1) ? y : z), }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00278/l2v5/index.heta b/latest/cases/00278/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00278/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00278/l2v5/json/output.json b/latest/cases/00278/l2v5/json/output.json new file mode 100644 index 000000000..b816eb033 --- /dev/null +++ b/latest/cases/00278/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x < 2 or x > 4 or x < 1) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00278/l3v2/heta-code/output.heta b/latest/cases/00278/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9e144e5d8 --- /dev/null +++ b/latest/cases/00278/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +calculate #defineFunction { arguments: [x, y, z], math: ((x < 2 or x > 4 or x < 1) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00278/l3v2/index.heta b/latest/cases/00278/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00278/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00278/l3v2/json/output.json b/latest/cases/00278/l3v2/json/output.json new file mode 100644 index 000000000..2e09a257c --- /dev/null +++ b/latest/cases/00278/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x < 2 or x > 4 or x < 1) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00278/model-sbml-l2v5.xml b/latest/cases/00278/model-sbml-l2v5.xml new file mode 100644 index 000000000..d0b4ba1c3 --- /dev/null +++ b/latest/cases/00278/model-sbml-l2v5.xml @@ -0,0 +1,103 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + + + x + 2 + + + + x + 4 + + + + x + 1 + + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00278/model-sbml-l3v2.xml b/latest/cases/00278/model-sbml-l3v2.xml new file mode 100644 index 000000000..6c182683f --- /dev/null +++ b/latest/cases/00278/model-sbml-l3v2.xml @@ -0,0 +1,120 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + + + x + 2 + + + + x + 4 + + + + x + 1 + + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00278/output.heta b/latest/cases/00278/output.heta new file mode 100644 index 000000000..2e33a1c22 --- /dev/null +++ b/latest/cases/00278/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the +reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, Or(x < 2, x > 4, x < 1)}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 4$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +calculate #defineFunction { arguments: [x, y, z], math: ((x < 2 or x > 4 or x < 1) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00278/synopsis.txt b/latest/cases/00278/synopsis.txt new file mode 100644 index 000000000..cf3d254de --- /dev/null +++ b/latest/cases/00278/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the +reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, Or(x < 2, x > 4, x < 1)}}, z)$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 4$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00279/l2v5/heta-code/output.heta b/latest/cases/00279/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a19d01697 --- /dev/null +++ b/latest/cases/00279/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +calculate #defineFunction { arguments: [x, y, z], math: ((x > 4 xor x < 1 xor x < 2) ? y : z), }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Record 'p1' { } .= 1.5; +p2 @Record 'p2' { } .= 0.05; +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00279/l2v5/index.heta b/latest/cases/00279/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00279/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00279/l2v5/json/output.json b/latest/cases/00279/l2v5/json/output.json new file mode 100644 index 000000000..79d0385c3 --- /dev/null +++ b/latest/cases/00279/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x > 4 xor x < 1 xor x < 2) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00279/l3v2/heta-code/output.heta b/latest/cases/00279/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4c816d2ee --- /dev/null +++ b/latest/cases/00279/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +calculate #defineFunction { arguments: [x, y, z], math: ((x > 4 xor x < 1 xor x < 2) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00279/l3v2/index.heta b/latest/cases/00279/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00279/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00279/l3v2/json/output.json b/latest/cases/00279/l3v2/json/output.json new file mode 100644 index 000000000..f113bae23 --- /dev/null +++ b/latest/cases/00279/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "calculate(S2, p1, p2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S2" + } + ] + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1.5 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.05 + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "calculate", + "arguments": [ + "x", + "y", + "z" + ], + "math": "((x > 4 xor x < 1 xor x < 2) ? y : z)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00279/model-sbml-l2v5.xml b/latest/cases/00279/model-sbml-l2v5.xml new file mode 100644 index 000000000..04273a05e --- /dev/null +++ b/latest/cases/00279/model-sbml-l2v5.xml @@ -0,0 +1,103 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + + + x + 4 + + + + x + 1 + + + + x + 2 + + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00279/model-sbml-l3v2.xml b/latest/cases/00279/model-sbml-l3v2.xml new file mode 100644 index 000000000..7e84d6edb --- /dev/null +++ b/latest/cases/00279/model-sbml-l3v2.xml @@ -0,0 +1,120 @@ + + + + + + + + + x + + + y + + + z + + + + y + + + + + x + 4 + + + + x + 1 + + + + x + 2 + + + + + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + + + calculate + S2 + p1 + p2 + + + + + + + diff --git a/latest/cases/00279/output.heta b/latest/cases/00279/output.heta new file mode 100644 index 000000000..9ec51a26f --- /dev/null +++ b/latest/cases/00279/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the +reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, Xor(x < 2, x > 4, x < 1)}}, z)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 4$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +calculate #defineFunction { arguments: [x, y, z], math: ((x > 4 xor x < 1 xor x < 2) ? y : z), }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, }; +reaction2 := calculate(S2, p1, p2); + +p1 @Const 'p1' { } = 1.5; +p2 @Const 'p2' { } = 0.05; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00279/synopsis.txt b/latest/cases/00279/synopsis.txt new file mode 100644 index 000000000..b13127253 --- /dev/null +++ b/latest/cases/00279/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reactions with four species in one +compartment using a rate that causes a discontinuity in the output. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named p1, p2 and k1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k1 * S1$ | +| S3 -> S4 | $calculate(S2, p1, p2)$ |] + +The model contains one functionDefinition, which is used within the +reaction, defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | calculate | x, y, z | $Piecewise({{y, Xor(x < 2, x > 4, x < 1)}}, z)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 4$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Value of parameter p1 |$ 1.5$ |mole second^-1^ | +|Value of parameter p2 |$ 0.05$ |mole second^-1^ | +|Value of parameter k1 |$ 1.0$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00280/l2v5/heta-code/output.heta b/latest/cases/00280/l2v5/heta-code/output.heta new file mode 100644 index 000000000..022e843d7 --- /dev/null +++ b/latest/cases/00280/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 3.5; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 0.15 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.05 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Record 'k1' { } .= 1.75; + diff --git a/latest/cases/00280/l2v5/index.heta b/latest/cases/00280/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00280/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00280/l2v5/json/output.json b/latest/cases/00280/l2v5/json/output.json new file mode 100644 index 000000000..301dcde3e --- /dev/null +++ b/latest/cases/00280/l2v5/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "3.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.05 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00280/l3v2/heta-code/output.heta b/latest/cases/00280/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c41a53ac9 --- /dev/null +++ b/latest/cases/00280/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 3.5; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.15 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.05 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Const 'k1' { } = 1.75; + diff --git a/latest/cases/00280/l3v2/index.heta b/latest/cases/00280/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00280/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00280/l3v2/json/output.json b/latest/cases/00280/l3v2/json/output.json new file mode 100644 index 000000000..0dafd6ee2 --- /dev/null +++ b/latest/cases/00280/l3v2/json/output.json @@ -0,0 +1,70 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "3.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.05 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.75 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00280/model-sbml-l2v5.xml b/latest/cases/00280/model-sbml-l2v5.xml new file mode 100644 index 000000000..d4e73f52e --- /dev/null +++ b/latest/cases/00280/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00280/model-sbml-l3v2.xml b/latest/cases/00280/model-sbml-l3v2.xml new file mode 100644 index 000000000..91195d6c4 --- /dev/null +++ b/latest/cases/00280/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00280/output.heta b/latest/cases/00280/output.heta new file mode 100644 index 000000000..974e6d985 --- /dev/null +++ b/latest/cases/00280/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 2D +compartment and nonzero initial amounts using a function to apply +the kinetic law. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 2-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * multiply(k1,S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$0.5 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Area of compartment "compartment" |$ 3.5$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 3.5; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.15 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.05 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Const 'k1' { } = 1.75; + diff --git a/latest/cases/00280/synopsis.txt b/latest/cases/00280/synopsis.txt new file mode 100644 index 000000000..53f1e9258 --- /dev/null +++ b/latest/cases/00280/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 2D +compartment and nonzero initial amounts using a function to apply +the kinetic law. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 2-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * multiply(k1,S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$0.5 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Area of compartment "compartment" |$ 3.5$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00281/l2v5/heta-code/output.heta b/latest/cases/00281/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4792e0873 --- /dev/null +++ b/latest/cases/00281/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 0.07; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1.5e-4 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 1.5e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Record 'k1' { } .= 0.00263; + diff --git a/latest/cases/00281/l2v5/index.heta b/latest/cases/00281/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00281/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00281/l2v5/json/output.json b/latest/cases/00281/l2v5/json/output.json new file mode 100644 index 000000000..2b11afbc2 --- /dev/null +++ b/latest/cases/00281/l2v5/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "0.07" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.00263" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00281/l3v2/heta-code/output.heta b/latest/cases/00281/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3a1bdefc1 --- /dev/null +++ b/latest/cases/00281/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 0.07; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.5e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Const 'k1' { } = 0.00263; + diff --git a/latest/cases/00281/l3v2/index.heta b/latest/cases/00281/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00281/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00281/l3v2/json/output.json b/latest/cases/00281/l3v2/json/output.json new file mode 100644 index 000000000..8e2c01821 --- /dev/null +++ b/latest/cases/00281/l3v2/json/output.json @@ -0,0 +1,70 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "0.07" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.00263 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00281/model-sbml-l2v5.xml b/latest/cases/00281/model-sbml-l2v5.xml new file mode 100644 index 000000000..e82864efc --- /dev/null +++ b/latest/cases/00281/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00281/model-sbml-l3v2.xml b/latest/cases/00281/model-sbml-l3v2.xml new file mode 100644 index 000000000..5d6860df1 --- /dev/null +++ b/latest/cases/00281/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00281/output.heta b/latest/cases/00281/output.heta new file mode 100644 index 000000000..208e56549 --- /dev/null +++ b/latest/cases/00281/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 1D +compartment and nonzero initial amounts using a function to apply +the kinetic law. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 1-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Value of parameter k1 |$2.63 \x 10^-3$ |second^-1^ | +|Length of compartment "compartment" |$ 0.07$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 0.07; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.5e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * multiply(k1, S1); + +k1 @Const 'k1' { } = 0.00263; + diff --git a/latest/cases/00281/synopsis.txt b/latest/cases/00281/synopsis.txt new file mode 100644 index 000000000..a136f931d --- /dev/null +++ b/latest/cases/00281/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 1D +compartment and nonzero initial amounts using a function to apply +the kinetic law. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is 1-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Value of parameter k1 |$2.63 \x 10^-3$ |second^-1^ | +|Length of compartment "compartment" |$ 0.07$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00282/l2v5/heta-code/output.heta b/latest/cases/00282/l2v5/heta-code/output.heta new file mode 100644 index 000000000..382e9c7f1 --- /dev/null +++ b/latest/cases/00282/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 6.8; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 3.24; +k2 @Record 'k2' { } .= 0.125; + diff --git a/latest/cases/00282/l2v5/index.heta b/latest/cases/00282/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00282/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00282/l2v5/json/output.json b/latest/cases/00282/l2v5/json/output.json new file mode 100644 index 000000000..28c6c35ca --- /dev/null +++ b/latest/cases/00282/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "6.8" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "3.24" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00282/l3v2/heta-code/output.heta b/latest/cases/00282/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ff8bc6dd0 --- /dev/null +++ b/latest/cases/00282/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 6.8; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 3.24; +k2 @Const 'k2' { } = 0.125; + diff --git a/latest/cases/00282/l3v2/index.heta b/latest/cases/00282/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00282/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00282/l3v2/json/output.json b/latest/cases/00282/l3v2/json/output.json new file mode 100644 index 000000000..9b05dec3a --- /dev/null +++ b/latest/cases/00282/l3v2/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "6.8" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 3.24 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.125 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00282/model-sbml-l2v5.xml b/latest/cases/00282/model-sbml-l2v5.xml new file mode 100644 index 000000000..0e405391d --- /dev/null +++ b/latest/cases/00282/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00282/model-sbml-l3v2.xml b/latest/cases/00282/model-sbml-l3v2.xml new file mode 100644 index 000000000..83ce9207b --- /dev/null +++ b/latest/cases/00282/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00282/output.heta b/latest/cases/00282/output.heta new file mode 100644 index 000000000..dfe86fb1b --- /dev/null +++ b/latest/cases/00282/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 3.24$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.125$ |second^-1^ | +|Area of compartment "compartment" |$ 6.8$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 6.8; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 3.24; +k2 @Const 'k2' { } = 0.125; + diff --git a/latest/cases/00282/synopsis.txt b/latest/cases/00282/synopsis.txt new file mode 100644 index 000000000..840a78627 --- /dev/null +++ b/latest/cases/00282/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 3.24$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.125$ |second^-1^ | +|Area of compartment "compartment" |$ 6.8$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00283/l2v5/heta-code/output.heta b/latest/cases/00283/l2v5/heta-code/output.heta new file mode 100644 index 000000000..dd54f9a0e --- /dev/null +++ b/latest/cases/00283/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 6.8; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 3.24; +k2 @Record 'k2' { } .= 0.125; + diff --git a/latest/cases/00283/l2v5/index.heta b/latest/cases/00283/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00283/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00283/l2v5/json/output.json b/latest/cases/00283/l2v5/json/output.json new file mode 100644 index 000000000..e468e2733 --- /dev/null +++ b/latest/cases/00283/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "6.8" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "3.24" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00283/l3v2/heta-code/output.heta b/latest/cases/00283/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a7aa87c09 --- /dev/null +++ b/latest/cases/00283/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 6.8; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 3.24; +k2 @Const 'k2' { } = 0.125; + diff --git a/latest/cases/00283/l3v2/index.heta b/latest/cases/00283/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00283/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00283/l3v2/json/output.json b/latest/cases/00283/l3v2/json/output.json new file mode 100644 index 000000000..25e8216fb --- /dev/null +++ b/latest/cases/00283/l3v2/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "6.8" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 3.24 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.125 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00283/model-sbml-l2v5.xml b/latest/cases/00283/model-sbml-l2v5.xml new file mode 100644 index 000000000..7e75be878 --- /dev/null +++ b/latest/cases/00283/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00283/model-sbml-l3v2.xml b/latest/cases/00283/model-sbml-l3v2.xml new file mode 100644 index 000000000..77028308c --- /dev/null +++ b/latest/cases/00283/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00283/output.heta b/latest/cases/00283/output.heta new file mode 100644 index 000000000..155372835 --- /dev/null +++ b/latest/cases/00283/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 3.24$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.125$ |second^-1^ | +|Length of compartment "compartment" |$ 6.8$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 6.8; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 3.24; +k2 @Const 'k2' { } = 0.125; + diff --git a/latest/cases/00283/synopsis.txt b/latest/cases/00283/synopsis.txt new file mode 100644 index 000000000..04d0a76c1 --- /dev/null +++ b/latest/cases/00283/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.0 \x 10^-6$ |mole | +|Value of parameter k1 |$ 3.24$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.125$ |second^-1^ | +|Length of compartment "compartment" |$ 6.8$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00284/l2v5/heta-code/output.heta b/latest/cases/00284/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d2f58b549 --- /dev/null +++ b/latest/cases/00284/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1.98; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 0.009 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.011 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 0.012 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 127.5; +k2 @Record 'k2' { } .= 2.5; + diff --git a/latest/cases/00284/l2v5/index.heta b/latest/cases/00284/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00284/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00284/l2v5/json/output.json b/latest/cases/00284/l2v5/json/output.json new file mode 100644 index 000000000..1e4a026cf --- /dev/null +++ b/latest/cases/00284/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1.98" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.009 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.011 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.012 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "127.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00284/l3v2/heta-code/output.heta b/latest/cases/00284/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f0bf42417 --- /dev/null +++ b/latest/cases/00284/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1.98; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.009 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.011 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.012 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 127.5; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00284/l3v2/index.heta b/latest/cases/00284/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00284/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00284/l3v2/json/output.json b/latest/cases/00284/l3v2/json/output.json new file mode 100644 index 000000000..77ec31d3c --- /dev/null +++ b/latest/cases/00284/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1.98" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.009 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.011 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.012 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 127.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00284/model-sbml-l2v5.xml b/latest/cases/00284/model-sbml-l2v5.xml new file mode 100644 index 000000000..41364542d --- /dev/null +++ b/latest/cases/00284/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00284/model-sbml-l3v2.xml b/latest/cases/00284/model-sbml-l3v2.xml new file mode 100644 index 000000000..0b0ab6374 --- /dev/null +++ b/latest/cases/00284/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00284/output.heta b/latest/cases/00284/output.heta new file mode 100644 index 000000000..038f4f2ce --- /dev/null +++ b/latest/cases/00284/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one 2D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.9 \x 10^-2$ |mole | +|Initial amount of S2 |$1.1 \x 10^-2$ |mole | +|Initial amount of S3 |$1.2 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$12.75 \x 10^1$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1.98$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1.98; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.009 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.011 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.012 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 127.5; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00284/synopsis.txt b/latest/cases/00284/synopsis.txt new file mode 100644 index 000000000..f2c32ae96 --- /dev/null +++ b/latest/cases/00284/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with four species in one 2D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.9 \x 10^-2$ |mole | +|Initial amount of S2 |$1.1 \x 10^-2$ |mole | +|Initial amount of S3 |$1.2 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$12.75 \x 10^1$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 1.98$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00285/l2v5/heta-code/output.heta b/latest/cases/00285/l2v5/heta-code/output.heta new file mode 100644 index 000000000..24ae5aca0 --- /dev/null +++ b/latest/cases/00285/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1.98; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 9e-5 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 1.1e-4 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 1.2e-4 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00285/l2v5/index.heta b/latest/cases/00285/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00285/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00285/l2v5/json/output.json b/latest/cases/00285/l2v5/json/output.json new file mode 100644 index 000000000..bf8125a8b --- /dev/null +++ b/latest/cases/00285/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1.98" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "9e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1.1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1.2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00285/l3v2/heta-code/output.heta b/latest/cases/00285/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95b91ddab --- /dev/null +++ b/latest/cases/00285/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1.98; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 9e-5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00285/l3v2/index.heta b/latest/cases/00285/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00285/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00285/l3v2/json/output.json b/latest/cases/00285/l3v2/json/output.json new file mode 100644 index 000000000..11a5172cc --- /dev/null +++ b/latest/cases/00285/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1.98" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "9e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1.1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1.2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00285/model-sbml-l2v5.xml b/latest/cases/00285/model-sbml-l2v5.xml new file mode 100644 index 000000000..29be7cd9b --- /dev/null +++ b/latest/cases/00285/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00285/model-sbml-l3v2.xml b/latest/cases/00285/model-sbml-l3v2.xml new file mode 100644 index 000000000..9b395d405 --- /dev/null +++ b/latest/cases/00285/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + compartment + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00285/output.heta b/latest/cases/00285/output.heta new file mode 100644 index 000000000..46a24504d --- /dev/null +++ b/latest/cases/00285/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one 1D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.9 \x 10^-4$ |mole | +|Initial amount of S2 |$1.1 \x 10^-4$ |mole | +|Initial amount of S3 |$1.2 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1.98$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1.98; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 9e-5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.1e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.2e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := compartment * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00285/synopsis.txt b/latest/cases/00285/synopsis.txt new file mode 100644 index 000000000..5139bf41b --- /dev/null +++ b/latest/cases/00285/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with four species in one 1D compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.9 \x 10^-4$ |mole | +|Initial amount of S2 |$1.1 \x 10^-4$ |mole | +|Initial amount of S3 |$1.2 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 1.98$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00286/l2v5/heta-code/output.heta b/latest/cases/00286/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7e31e3bac --- /dev/null +++ b/latest/cases/00286/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S4 := k3 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.25; + diff --git a/latest/cases/00286/l2v5/index.heta b/latest/cases/00286/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00286/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00286/l2v5/json/output.json b/latest/cases/00286/l2v5/json/output.json new file mode 100644 index 000000000..9135ced62 --- /dev/null +++ b/latest/cases/00286/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1", + "ode_": "k3 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00286/l3v2/heta-code/output.heta b/latest/cases/00286/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c8a09f098 --- /dev/null +++ b/latest/cases/00286/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 := k3 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.25; + diff --git a/latest/cases/00286/l3v2/index.heta b/latest/cases/00286/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00286/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00286/l3v2/json/output.json b/latest/cases/00286/l3v2/json/output.json new file mode 100644 index 000000000..9ffbc5cf8 --- /dev/null +++ b/latest/cases/00286/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1", + "ode_": "k3 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00286/model-sbml-l2v5.xml b/latest/cases/00286/model-sbml-l2v5.xml new file mode 100644 index 000000000..a1c74102a --- /dev/null +++ b/latest/cases/00286/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + diff --git a/latest/cases/00286/model-sbml-l3v2.xml b/latest/cases/00286/model-sbml-l3v2.xml new file mode 100644 index 000000000..d70990737 --- /dev/null +++ b/latest/cases/00286/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + diff --git a/latest/cases/00286/output.heta b/latest/cases/00286/output.heta new file mode 100644 index 000000000..138971d04 --- /dev/null +++ b/latest/cases/00286/output.heta @@ -0,0 +1,80 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are four species named S1, S2, S3 and S4 and three parameters named +k1, k2 and k3. Compartment "compartment" contains species S1 and S2. +Compartment "compartment1" contains species S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 3 parameters (k1, k2, k3) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |] + +The first reaction occurs entirely in compartment "compartment", whereas +the second reaction occurs between a species in "compartment" and a species +in "compartment1". + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S4 | $k3 * S3$ |] + +In this case the initial value declared for species S4 is consistent with +that calculated by the assignmentRule. Note that since this assignmentRule +must always remain true, it should be considered during simulation. +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S4 | $k3 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k3 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 := k3 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.25; + diff --git a/latest/cases/00286/synopsis.txt b/latest/cases/00286/synopsis.txt new file mode 100644 index 000000000..11fb67b47 --- /dev/null +++ b/latest/cases/00286/synopsis.txt @@ -0,0 +1,56 @@ + +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are four species named S1, S2, S3 and S4 and three parameters named +k1, k2 and k3. Compartment "compartment" contains species S1 and S2. +Compartment "compartment1" contains species S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 3 parameters (k1, k2, k3) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |] + +The first reaction occurs entirely in compartment "compartment", whereas +the second reaction occurs between a species in "compartment" and a species +in "compartment1". + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S4 | $k3 * S3$ |] + +In this case the initial value declared for species S4 is consistent with +that calculated by the assignmentRule. Note that since this assignmentRule +must always remain true, it should be considered during simulation. +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S4 | $k3 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k3 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00287/l2v5/heta-code/output.heta b/latest/cases/00287/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8b985d964 --- /dev/null +++ b/latest/cases/00287/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: substance/volume, compartment: compartment1, } .= 0.1 / compartment1; +S5 @Species 'S5' { units: substance/volume, compartment: compartment1, } .= 0.1 / compartment1; +S5 := k4 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 7.5; +k3 @Record 'k3' { } .= 0.75; +k4 @Record 'k4' { } .= 0.5; + diff --git a/latest/cases/00287/l2v5/index.heta b/latest/cases/00287/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00287/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00287/l2v5/json/output.json b/latest/cases/00287/l2v5/json/output.json new file mode 100644 index 000000000..2d95e4c50 --- /dev/null +++ b/latest/cases/00287/l2v5/json/output.json @@ -0,0 +1,198 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment1", + "ode_": "k4 * S2" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "compartment * k3 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00287/l3v2/heta-code/output.heta b/latest/cases/00287/l3v2/heta-code/output.heta new file mode 100644 index 000000000..137e2af22 --- /dev/null +++ b/latest/cases/00287/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; +S5 := k4 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 7.5; +k3 @Const 'k3' { } = 0.75; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00287/l3v2/index.heta b/latest/cases/00287/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00287/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00287/l3v2/json/output.json b/latest/cases/00287/l3v2/json/output.json new file mode 100644 index 000000000..38839913c --- /dev/null +++ b/latest/cases/00287/l3v2/json/output.json @@ -0,0 +1,166 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment1", + "ode_": "k4 * S2" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "compartment * k3 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 7.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.75 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00287/model-sbml-l2v5.xml b/latest/cases/00287/model-sbml-l2v5.xml new file mode 100644 index 000000000..cb241eb22 --- /dev/null +++ b/latest/cases/00287/model-sbml-l2v5.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k4 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + + + + + + + + + + + compartment + k3 + S3 + S4 + + + + + + + diff --git a/latest/cases/00287/model-sbml-l3v2.xml b/latest/cases/00287/model-sbml-l3v2.xml new file mode 100644 index 000000000..41fc196be --- /dev/null +++ b/latest/cases/00287/model-sbml-l3v2.xml @@ -0,0 +1,118 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k4 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + + + + + + + + + + + compartment + k3 + S3 + S4 + + + + + + + diff --git a/latest/cases/00287/output.heta b/latest/cases/00287/output.heta new file mode 100644 index 000000000..b0d07e08e --- /dev/null +++ b/latest/cases/00287/output.heta @@ -0,0 +1,90 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are five species named S1, S2, S3, S4 and S5 and four parameters +named k1, k2, k3 and k4. Compartment "compartment" contains species S1 and +S2. Compartment "compartment1" contains species S3, S4 and S5. + +The model contains: +* 5 species (S1, S2, S3, S4, S5) +* 4 parameters (k1, k2, k3, k4) +* 2 compartments (compartment, compartment1) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ | +| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |] + +The first reaction occurs entirely within compartment "compartment", the +second reaction occurs between a species in compartment "compartment" and a +species in "compartment1" and the third reaction occurs entirely within +"compartment1". + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S2$ |] + +In this case the initial value declared for species S5 is inconsistent with +that calculated by the assignmentRule; the calculated value should be used. +Note that since this assignmentRule must always remain true, it should be +considered during simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial amount of species S4 | $0.1$ | variable | +| Initial concentration of species S5 | $k4 * S2$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $7.5$ | constant | +| Initial value of parameter k3 | $0.75$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; +S5 := k4 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 7.5; +k3 @Const 'k3' { } = 0.75; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00287/synopsis.txt b/latest/cases/00287/synopsis.txt new file mode 100644 index 000000000..47bec872d --- /dev/null +++ b/latest/cases/00287/synopsis.txt @@ -0,0 +1,62 @@ + +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are five species named S1, S2, S3, S4 and S5 and four parameters +named k1, k2, k3 and k4. Compartment "compartment" contains species S1 and +S2. Compartment "compartment1" contains species S3, S4 and S5. + +The model contains: +* 5 species (S1, S2, S3, S4, S5) +* 4 parameters (k1, k2, k3, k4) +* 2 compartments (compartment, compartment1) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ | +| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |] + +The first reaction occurs entirely within compartment "compartment", the +second reaction occurs between a species in compartment "compartment" and a +species in "compartment1" and the third reaction occurs entirely within +"compartment1". + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S2$ |] + +In this case the initial value declared for species S5 is inconsistent with +that calculated by the assignmentRule; the calculated value should be used. +Note that since this assignmentRule must always remain true, it should be +considered during simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial amount of species S4 | $0.1$ | variable | +| Initial concentration of species S5 | $k4 * S2$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $7.5$ | constant | +| Initial value of parameter k3 | $0.75$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00288/l2v5/heta-code/output.heta b/latest/cases/00288/l2v5/heta-code/output.heta new file mode 100644 index 000000000..12dd7fa72 --- /dev/null +++ b/latest/cases/00288/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S5 @Species 'S5' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S5 := k4 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k4 @Record 'k4' { } .= 0.5; + diff --git a/latest/cases/00288/l2v5/index.heta b/latest/cases/00288/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00288/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00288/l2v5/json/output.json b/latest/cases/00288/l2v5/json/output.json new file mode 100644 index 000000000..1b51c851b --- /dev/null +++ b/latest/cases/00288/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1", + "ode_": "k4 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S3 + (-1) * S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00288/l3v2/heta-code/output.heta b/latest/cases/00288/l3v2/heta-code/output.heta new file mode 100644 index 000000000..63e33f8ec --- /dev/null +++ b/latest/cases/00288/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S5 := k4 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00288/l3v2/index.heta b/latest/cases/00288/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00288/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00288/l3v2/json/output.json b/latest/cases/00288/l3v2/json/output.json new file mode 100644 index 000000000..40b41c677 --- /dev/null +++ b/latest/cases/00288/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1", + "ode_": "k4 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S3 + (-1) * S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00288/model-sbml-l2v5.xml b/latest/cases/00288/model-sbml-l2v5.xml new file mode 100644 index 000000000..2a7e7545c --- /dev/null +++ b/latest/cases/00288/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + k4 + S3 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S3 + + + -1 + S1 + + + + + + + + + diff --git a/latest/cases/00288/model-sbml-l3v2.xml b/latest/cases/00288/model-sbml-l3v2.xml new file mode 100644 index 000000000..b490d9f96 --- /dev/null +++ b/latest/cases/00288/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k4 + S3 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S3 + + + -1 + S1 + + + + + + + + + diff --git a/latest/cases/00288/output.heta b/latest/cases/00288/output.heta new file mode 100644 index 000000000..cb8b2c2eb --- /dev/null +++ b/latest/cases/00288/output.heta @@ -0,0 +1,77 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are three species named S1, S3 and S5 and three parameters named k1, +k2 and k4. Compartment "compartment" contains species S1. Compartment +"compartment1" contains species S3 and S5. + +The model contains: +* 3 species (S1, S3, S5) +* 3 parameters (k1, k2, k4) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 -> S3 | $compartment * k1 * S1$ | +| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |] + +Both reactions occur between species within different compartments. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S3$ |] + +In this case the initial value declared for species S5 is consistent with +that calculated by the assignmentRule. Note that since this assignmentRule +must always remain true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S5 | $k4 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S5 := k4 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00288/synopsis.txt b/latest/cases/00288/synopsis.txt new file mode 100644 index 000000000..b9c7471e3 --- /dev/null +++ b/latest/cases/00288/synopsis.txt @@ -0,0 +1,54 @@ + +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are three species named S1, S3 and S5 and three parameters named k1, +k2 and k4. Compartment "compartment" contains species S1. Compartment +"compartment1" contains species S3 and S5. + +The model contains: +* 3 species (S1, S3, S5) +* 3 parameters (k1, k2, k4) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 -> S3 | $compartment * k1 * S1$ | +| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |] + +Both reactions occur between species within different compartments. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S3$ |] + +In this case the initial value declared for species S5 is consistent with +that calculated by the assignmentRule. Note that since this assignmentRule +must always remain true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S5 | $k4 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00289/l2v5/heta-code/output.heta b/latest/cases/00289/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9946b42c5 --- /dev/null +++ b/latest/cases/00289/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: substance/volume, compartment: compartment1, } .= 1 / compartment1; +S4 := k3 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.25; + diff --git a/latest/cases/00289/l2v5/index.heta b/latest/cases/00289/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00289/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00289/l2v5/json/output.json b/latest/cases/00289/l2v5/json/output.json new file mode 100644 index 000000000..7b4b63dbc --- /dev/null +++ b/latest/cases/00289/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment1", + "ode_": "k3 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00289/l3v2/heta-code/output.heta b/latest/cases/00289/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ad1fec83d --- /dev/null +++ b/latest/cases/00289/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 1 / compartment1; +S4 := k3 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.25; + diff --git a/latest/cases/00289/l3v2/index.heta b/latest/cases/00289/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00289/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00289/l3v2/json/output.json b/latest/cases/00289/l3v2/json/output.json new file mode 100644 index 000000000..34ce7d781 --- /dev/null +++ b/latest/cases/00289/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment1", + "ode_": "k3 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00289/model-sbml-l2v5.xml b/latest/cases/00289/model-sbml-l2v5.xml new file mode 100644 index 000000000..f57d3b3ef --- /dev/null +++ b/latest/cases/00289/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + diff --git a/latest/cases/00289/model-sbml-l3v2.xml b/latest/cases/00289/model-sbml-l3v2.xml new file mode 100644 index 000000000..49d1b80bf --- /dev/null +++ b/latest/cases/00289/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + diff --git a/latest/cases/00289/output.heta b/latest/cases/00289/output.heta new file mode 100644 index 000000000..896f09edc --- /dev/null +++ b/latest/cases/00289/output.heta @@ -0,0 +1,81 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are four species named S1, S2, S3 and S4 and three parameters named +k1, k2 and k3. Compartment "compartment" contains species S1 and S2. +Compartment "compartment1" contains species S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 3 parameters (k1, k2, k3) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |] + +The first reaction occurs entirely in compartment, whereas the second reaction +occurs between a species in compartment and a species in compartment1. + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S4 | $k3 * S3$ |] + +In this case the initial value declared for species S4 is inconsistent with +that calculated by the assignmentRule; the calculated value should be used. +Note that since this assignmentRule must always remain true, it should be +considered during simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S4 | $k3 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k3 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 1 / compartment1; +S4 := k3 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.25; + diff --git a/latest/cases/00289/synopsis.txt b/latest/cases/00289/synopsis.txt new file mode 100644 index 000000000..6ad8532e5 --- /dev/null +++ b/latest/cases/00289/synopsis.txt @@ -0,0 +1,57 @@ + +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are four species named S1, S2, S3 and S4 and three parameters named +k1, k2 and k3. Compartment "compartment" contains species S1 and S2. +Compartment "compartment1" contains species S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 3 parameters (k1, k2, k3) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |] + +The first reaction occurs entirely in compartment, whereas the second reaction +occurs between a species in compartment and a species in compartment1. + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S4 | $k3 * S3$ |] + +In this case the initial value declared for species S4 is inconsistent with +that calculated by the assignmentRule; the calculated value should be used. +Note that since this assignmentRule must always remain true, it should be +considered during simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S4 | $k3 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k3 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00290/l2v5/heta-code/output.heta b/latest/cases/00290/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9f91fbcc1 --- /dev/null +++ b/latest/cases/00290/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: substance/volume, compartment: compartment1, }; +S4 := k3 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.25; + diff --git a/latest/cases/00290/l2v5/index.heta b/latest/cases/00290/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00290/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00290/l2v5/json/output.json b/latest/cases/00290/l2v5/json/output.json new file mode 100644 index 000000000..25a32704e --- /dev/null +++ b/latest/cases/00290/l2v5/json/output.json @@ -0,0 +1,156 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k3 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00290/l3v2/heta-code/output.heta b/latest/cases/00290/l3v2/heta-code/output.heta new file mode 100644 index 000000000..12741bbeb --- /dev/null +++ b/latest/cases/00290/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, }; +S4 := k3 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.25; + diff --git a/latest/cases/00290/l3v2/index.heta b/latest/cases/00290/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00290/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00290/l3v2/json/output.json b/latest/cases/00290/l3v2/json/output.json new file mode 100644 index 000000000..f1469f368 --- /dev/null +++ b/latest/cases/00290/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k3 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00290/model-sbml-l2v5.xml b/latest/cases/00290/model-sbml-l2v5.xml new file mode 100644 index 000000000..4b5032ce1 --- /dev/null +++ b/latest/cases/00290/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + diff --git a/latest/cases/00290/model-sbml-l3v2.xml b/latest/cases/00290/model-sbml-l3v2.xml new file mode 100644 index 000000000..1d725cf55 --- /dev/null +++ b/latest/cases/00290/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + diff --git a/latest/cases/00290/output.heta b/latest/cases/00290/output.heta new file mode 100644 index 000000000..4b8cb8b73 --- /dev/null +++ b/latest/cases/00290/output.heta @@ -0,0 +1,81 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are four species named S1, S2, S3 and S4 and three parameters named +k1, k2 and k3. Compartment "compartment" contains species S1 and S2. +Compartment "compartment1" contains species S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 3 parameters (k1, k2, k3) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |] + +The first reaction occurs entirely in compartment, whereas the second reaction +occurs between a species in compartment and a species in compartment1. + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S4 | $k3 * S3$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S4 | $k3 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k3 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, }; +S4 := k3 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.25; + diff --git a/latest/cases/00290/synopsis.txt b/latest/cases/00290/synopsis.txt new file mode 100644 index 000000000..a912081d3 --- /dev/null +++ b/latest/cases/00290/synopsis.txt @@ -0,0 +1,57 @@ + +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are four species named S1, S2, S3 and S4 and three parameters named +k1, k2 and k3. Compartment "compartment" contains species S1 and S2. +Compartment "compartment1" contains species S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 3 parameters (k1, k2, k3) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |] + +The first reaction occurs entirely in compartment, whereas the second reaction +occurs between a species in compartment and a species in compartment1. + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S4 | $k3 * S3$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S4 | $k3 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k3 | $0.25$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00291/l2v5/heta-code/output.heta b/latest/cases/00291/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c2c01e6ff --- /dev/null +++ b/latest/cases/00291/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: substance/volume, compartment: compartment1, } .= 0.1 / compartment1; +S5 @Species 'S5' { units: substance/volume, compartment: compartment1, } .= 0.5 / compartment1; +S5 := k4 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 7.5; +k3 @Record 'k3' { } .= 0.75; +k4 @Record 'k4' { } .= 0.5; + diff --git a/latest/cases/00291/l2v5/index.heta b/latest/cases/00291/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00291/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00291/l2v5/json/output.json b/latest/cases/00291/l2v5/json/output.json new file mode 100644 index 000000000..ac594d159 --- /dev/null +++ b/latest/cases/00291/l2v5/json/output.json @@ -0,0 +1,198 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / compartment1", + "ode_": "k4 * S2" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "compartment * k3 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00291/l3v2/heta-code/output.heta b/latest/cases/00291/l3v2/heta-code/output.heta new file mode 100644 index 000000000..60d55de92 --- /dev/null +++ b/latest/cases/00291/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 0.5 / compartment1; +S5 := k4 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 7.5; +k3 @Const 'k3' { } = 0.75; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00291/l3v2/index.heta b/latest/cases/00291/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00291/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00291/l3v2/json/output.json b/latest/cases/00291/l3v2/json/output.json new file mode 100644 index 000000000..91cb66461 --- /dev/null +++ b/latest/cases/00291/l3v2/json/output.json @@ -0,0 +1,166 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / compartment1", + "ode_": "k4 * S2" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "compartment * k3 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 7.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.75 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00291/model-sbml-l2v5.xml b/latest/cases/00291/model-sbml-l2v5.xml new file mode 100644 index 000000000..ae00ca5af --- /dev/null +++ b/latest/cases/00291/model-sbml-l2v5.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k4 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + + + + + + + + + + + compartment + k3 + S3 + S4 + + + + + + + diff --git a/latest/cases/00291/model-sbml-l3v2.xml b/latest/cases/00291/model-sbml-l3v2.xml new file mode 100644 index 000000000..185aeb7d0 --- /dev/null +++ b/latest/cases/00291/model-sbml-l3v2.xml @@ -0,0 +1,118 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k4 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + + + + + + + + + + + compartment + k3 + S3 + S4 + + + + + + + diff --git a/latest/cases/00291/output.heta b/latest/cases/00291/output.heta new file mode 100644 index 000000000..e5a69e773 --- /dev/null +++ b/latest/cases/00291/output.heta @@ -0,0 +1,89 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are five species named S1, S2, S3, S4 and S5 and four parameters +named k1, k2, k3 and k4. Compartment "compartment" contains species S1 and +S2. Compartment "compartment1" contains species S3, S4 and S5. + +The model contains: +* 5 species (S1, S2, S3, S4, S5) +* 4 parameters (k1, k2, k3, k4) +* 2 compartments (compartment, compartment1) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ | +| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |] + +The first reaction occurs entirely within compartment, the second reaction +occurs between a species in compartment and a species in compartment1 and the +third reaction occurs entirely within compartment1. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S2$ |] + +In this case the initial value declared for species S5 is consistent with that calculated +by the assignmentRule. Note that since this assignmentRule +must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial amount of species S4 | $0.1$ | variable | +| Initial concentration of species S5 | $k4 * S2$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $7.5$ | constant | +| Initial value of parameter k3 | $0.75$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 0.5 / compartment1; +S5 := k4 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 7.5; +k3 @Const 'k3' { } = 0.75; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00291/synopsis.txt b/latest/cases/00291/synopsis.txt new file mode 100644 index 000000000..68a0d7918 --- /dev/null +++ b/latest/cases/00291/synopsis.txt @@ -0,0 +1,61 @@ + +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are five species named S1, S2, S3, S4 and S5 and four parameters +named k1, k2, k3 and k4. Compartment "compartment" contains species S1 and +S2. Compartment "compartment1" contains species S3, S4 and S5. + +The model contains: +* 5 species (S1, S2, S3, S4, S5) +* 4 parameters (k1, k2, k3, k4) +* 2 compartments (compartment, compartment1) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ | +| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |] + +The first reaction occurs entirely within compartment, the second reaction +occurs between a species in compartment and a species in compartment1 and the +third reaction occurs entirely within compartment1. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S2$ |] + +In this case the initial value declared for species S5 is consistent with that calculated +by the assignmentRule. Note that since this assignmentRule +must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial amount of species S4 | $0.1$ | variable | +| Initial concentration of species S5 | $k4 * S2$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $7.5$ | constant | +| Initial value of parameter k3 | $0.75$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00292/l2v5/heta-code/output.heta b/latest/cases/00292/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d1db11ef1 --- /dev/null +++ b/latest/cases/00292/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: substance/volume, compartment: compartment1, } .= 0.1 / compartment1; +S5 @Species 'S5' { units: substance/volume, compartment: compartment1, }; +S5 := k4 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 7.5; +k3 @Record 'k3' { } .= 0.75; +k4 @Record 'k4' { } .= 0.5; + diff --git a/latest/cases/00292/l2v5/index.heta b/latest/cases/00292/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00292/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00292/l2v5/json/output.json b/latest/cases/00292/l2v5/json/output.json new file mode 100644 index 000000000..a5e834620 --- /dev/null +++ b/latest/cases/00292/l2v5/json/output.json @@ -0,0 +1,197 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "ode_": "k4 * S2" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "compartment * k3 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00292/l3v2/heta-code/output.heta b/latest/cases/00292/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a0ab54025 --- /dev/null +++ b/latest/cases/00292/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, }; +S5 := k4 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 7.5; +k3 @Const 'k3' { } = 0.75; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00292/l3v2/index.heta b/latest/cases/00292/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00292/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00292/l3v2/json/output.json b/latest/cases/00292/l3v2/json/output.json new file mode 100644 index 000000000..56beb9da1 --- /dev/null +++ b/latest/cases/00292/l3v2/json/output.json @@ -0,0 +1,165 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "ode_": "k4 * S2" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S2 + (-1) * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "compartment * k3 * S3 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 7.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.75 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00292/model-sbml-l2v5.xml b/latest/cases/00292/model-sbml-l2v5.xml new file mode 100644 index 000000000..7267533f9 --- /dev/null +++ b/latest/cases/00292/model-sbml-l2v5.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k4 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + + + + + + + + + + + compartment + k3 + S3 + S4 + + + + + + + diff --git a/latest/cases/00292/model-sbml-l3v2.xml b/latest/cases/00292/model-sbml-l3v2.xml new file mode 100644 index 000000000..a754cc185 --- /dev/null +++ b/latest/cases/00292/model-sbml-l3v2.xml @@ -0,0 +1,118 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k4 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S2 + + + -1 + S3 + + + + + + + + + + + + + + + + + + + compartment + k3 + S3 + S4 + + + + + + + diff --git a/latest/cases/00292/output.heta b/latest/cases/00292/output.heta new file mode 100644 index 000000000..5b4cf82e5 --- /dev/null +++ b/latest/cases/00292/output.heta @@ -0,0 +1,89 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are five species named S1, S2, S3, S4 and S5 and four parameters +named k1, k2, k3 and k4. Compartment "compartment" contains species S1 and +S2. Compartment "compartment1" contains species S3, S4 and S5. + +The model contains: +* 5 species (S1, S2, S3, S4, S5) +* 4 parameters (k1, k2, k3, k4) +* 2 compartments (compartment, compartment1) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ | +| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |] + +The first reaction occurs entirely within compartment, the second reaction +occurs between a species in compartment and a species in compartment1 and the +third reaction occurs entirely within compartment1. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial amount of species S4 | $0.1$ | variable | +| Initial concentration of species S5 | $k4 * S2$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $7.5$ | constant | +| Initial value of parameter k3 | $0.75$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, }; +S5 := k4 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := compartment1 * k2 * (S2 + (-1) * S3); +reaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, }; +reaction3 := compartment * k3 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 7.5; +k3 @Const 'k3' { } = 0.75; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00292/synopsis.txt b/latest/cases/00292/synopsis.txt new file mode 100644 index 000000000..7a7c49397 --- /dev/null +++ b/latest/cases/00292/synopsis.txt @@ -0,0 +1,61 @@ + +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are five species named S1, S2, S3, S4 and S5 and four parameters +named k1, k2, k3 and k4. Compartment "compartment" contains species S1 and +S2. Compartment "compartment1" contains species S3, S4 and S5. + +The model contains: +* 5 species (S1, S2, S3, S4, S5) +* 4 parameters (k1, k2, k3, k4) +* 2 compartments (compartment, compartment1) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ | +| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ | +| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |] + +The first reaction occurs entirely within compartment, the second reaction +occurs between a species in compartment and a species in compartment1 and the +third reaction occurs entirely within compartment1. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial amount of species S4 | $0.1$ | variable | +| Initial concentration of species S5 | $k4 * S2$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $7.5$ | constant | +| Initial value of parameter k3 | $0.75$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00293/l2v5/heta-code/output.heta b/latest/cases/00293/l2v5/heta-code/output.heta new file mode 100644 index 000000000..855702d74 --- /dev/null +++ b/latest/cases/00293/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S5 @Species 'S5' { units: substance/volume, compartment: compartment1, } .= 1 / compartment1; +S5 := k4 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k4 @Record 'k4' { } .= 0.5; + diff --git a/latest/cases/00293/l2v5/index.heta b/latest/cases/00293/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00293/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00293/l2v5/json/output.json b/latest/cases/00293/l2v5/json/output.json new file mode 100644 index 000000000..50be577a7 --- /dev/null +++ b/latest/cases/00293/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment1", + "ode_": "k4 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S3 + (-1) * S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00293/l3v2/heta-code/output.heta b/latest/cases/00293/l3v2/heta-code/output.heta new file mode 100644 index 000000000..544e1b696 --- /dev/null +++ b/latest/cases/00293/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 1 / compartment1; +S5 := k4 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00293/l3v2/index.heta b/latest/cases/00293/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00293/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00293/l3v2/json/output.json b/latest/cases/00293/l3v2/json/output.json new file mode 100644 index 000000000..590862904 --- /dev/null +++ b/latest/cases/00293/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment1", + "ode_": "k4 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S3 + (-1) * S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00293/model-sbml-l2v5.xml b/latest/cases/00293/model-sbml-l2v5.xml new file mode 100644 index 000000000..699e41f88 --- /dev/null +++ b/latest/cases/00293/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + k4 + S3 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S3 + + + -1 + S1 + + + + + + + + + diff --git a/latest/cases/00293/model-sbml-l3v2.xml b/latest/cases/00293/model-sbml-l3v2.xml new file mode 100644 index 000000000..3818b3cff --- /dev/null +++ b/latest/cases/00293/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k4 + S3 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S3 + + + -1 + S1 + + + + + + + + + diff --git a/latest/cases/00293/output.heta b/latest/cases/00293/output.heta new file mode 100644 index 000000000..46c0b5554 --- /dev/null +++ b/latest/cases/00293/output.heta @@ -0,0 +1,78 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are three species named S1, S3 and S5 and three parameters named k1, +k2 and k4. Compartment "compartment" contains species S1. Compartment +"compartment1" contains species S3 and S5. + +The model contains: +* 3 species (S1, S3, S5) +* 3 parameters (k1, k2, k4) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 -> S3 | $compartment * k1 * S1$ | +| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |] + +Both reactions occur between species within different compartments. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S3$ |] + +In this case the initial value declared for species S5 is inconsistent with +that calculated by the assignmentRule; the calculated value should be used. +Note that since this assignmentRule must always remain true, it should be +considered during simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S5 | $k4 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 1 / compartment1; +S5 := k4 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00293/synopsis.txt b/latest/cases/00293/synopsis.txt new file mode 100644 index 000000000..7a5264df8 --- /dev/null +++ b/latest/cases/00293/synopsis.txt @@ -0,0 +1,55 @@ + +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are three species named S1, S3 and S5 and three parameters named k1, +k2 and k4. Compartment "compartment" contains species S1. Compartment +"compartment1" contains species S3 and S5. + +The model contains: +* 3 species (S1, S3, S5) +* 3 parameters (k1, k2, k4) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 -> S3 | $compartment * k1 * S1$ | +| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |] + +Both reactions occur between species within different compartments. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S3$ |] + +In this case the initial value declared for species S5 is inconsistent with +that calculated by the assignmentRule; the calculated value should be used. +Note that since this assignmentRule must always remain true, it should be +considered during simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S5 | $k4 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00294/l2v5/heta-code/output.heta b/latest/cases/00294/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0336b1ea4 --- /dev/null +++ b/latest/cases/00294/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment1, } .= 0 / compartment1; +S5 @Species 'S5' { units: substance/volume, compartment: compartment1, }; +S5 := k4 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k4 @Record 'k4' { } .= 0.5; + diff --git a/latest/cases/00294/l2v5/index.heta b/latest/cases/00294/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00294/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00294/l2v5/json/output.json b/latest/cases/00294/l2v5/json/output.json new file mode 100644 index 000000000..fcd193233 --- /dev/null +++ b/latest/cases/00294/l2v5/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "ode_": "k4 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S3 + (-1) * S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00294/l3v2/heta-code/output.heta b/latest/cases/00294/l3v2/heta-code/output.heta new file mode 100644 index 000000000..63ca9379c --- /dev/null +++ b/latest/cases/00294/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, }; +S5 := k4 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00294/l3v2/index.heta b/latest/cases/00294/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00294/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00294/l3v2/json/output.json b/latest/cases/00294/l3v2/json/output.json new file mode 100644 index 000000000..648d22c26 --- /dev/null +++ b/latest/cases/00294/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "compartment1", + "title": "compartment1", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment1" + }, + "compartment": "compartment1" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "ode_": "k4 * S3" + }, + "compartment": "compartment1" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment1 * k2 * (S3 + (-1) * S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00294/model-sbml-l2v5.xml b/latest/cases/00294/model-sbml-l2v5.xml new file mode 100644 index 000000000..ca4e23043 --- /dev/null +++ b/latest/cases/00294/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + k4 + S3 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S3 + + + -1 + S1 + + + + + + + + + diff --git a/latest/cases/00294/model-sbml-l3v2.xml b/latest/cases/00294/model-sbml-l3v2.xml new file mode 100644 index 000000000..37c784f49 --- /dev/null +++ b/latest/cases/00294/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k4 + S3 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + + + + + + + + + + compartment1 + k2 + + + S3 + + + -1 + S1 + + + + + + + + + diff --git a/latest/cases/00294/output.heta b/latest/cases/00294/output.heta new file mode 100644 index 000000000..8997b98cf --- /dev/null +++ b/latest/cases/00294/output.heta @@ -0,0 +1,78 @@ +/* +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are three species named S1, S3 and S5 and three parameters named k1, +k2 and k4. Compartment "compartment" contains species S1. Compartment +"compartment1" contains species S3 and S5. + +The model contains: +* 3 species (S1, S3, S5) +* 3 parameters (k1, k2, k4) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 -> S3 | $compartment * k1 * S1$ | +| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |] + +Both reactions occur between species within different compartments. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S3$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S5 | $k4 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; +compartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1; +S5 @Species 'S5' { units: mole/litre, compartment: compartment1, }; +S5 := k4 * S3; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, }; +reaction2 := compartment1 * k2 * (S3 + (-1) * S1); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k4 @Const 'k4' { } = 0.5; + diff --git a/latest/cases/00294/synopsis.txt b/latest/cases/00294/synopsis.txt new file mode 100644 index 000000000..3b1904f0e --- /dev/null +++ b/latest/cases/00294/synopsis.txt @@ -0,0 +1,55 @@ + +category: Test +synopsis: Reactions occurring between two compartments. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, MultiCompartment, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +The model contains two compartments named compartment and compartment1. +There are three species named S1, S3 and S5 and three parameters named k1, +k2 and k4. Compartment "compartment" contains species S1. Compartment +"compartment1" contains species S3 and S5. + +The model contains: +* 3 species (S1, S3, S5) +* 3 parameters (k1, k2, k4) +* 2 compartments (compartment, compartment1) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| reaction1: S1 -> S3 | $compartment * k1 * S1$ | +| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |] + +Both reactions occur between species within different compartments. + +The model contains one rule which assigns value to species S5: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S5 | $k4 * S3$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $0$ | variable | +| Initial concentration of species S5 | $k4 * S3$ | variable | +| Initial value of parameter k1 | $0.75$ | constant | +| Initial value of parameter k2 | $0.25$ | constant | +| Initial value of parameter k4 | $0.5$ | constant | +| Initial volume of compartment 'compartment' | $1$ | constant | +| Initial volume of compartment 'compartment1' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00295/l2v5/heta-code/output.heta b/latest/cases/00295/l2v5/heta-code/output.heta new file mode 100644 index 000000000..41c48fa9f --- /dev/null +++ b/latest/cases/00295/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.15; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k2 * S1; + +k1 @Record 'k1' { } .= 1.05; +k2 @Record 'k2' { } .= 1.15; + diff --git a/latest/cases/00295/l2v5/index.heta b/latest/cases/00295/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00295/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00295/l2v5/json/output.json b/latest/cases/00295/l2v5/json/output.json new file mode 100644 index 000000000..4a38ac321 --- /dev/null +++ b/latest/cases/00295/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.05" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.15" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00295/l3v2/heta-code/output.heta b/latest/cases/00295/l3v2/heta-code/output.heta new file mode 100644 index 000000000..67c87ab96 --- /dev/null +++ b/latest/cases/00295/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00295/l3v2/index.heta b/latest/cases/00295/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00295/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00295/l3v2/json/output.json b/latest/cases/00295/l3v2/json/output.json new file mode 100644 index 000000000..feb9456a9 --- /dev/null +++ b/latest/cases/00295/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.05 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.15 + } +] \ No newline at end of file diff --git a/latest/cases/00295/model-sbml-l2v5.xml b/latest/cases/00295/model-sbml-l2v5.xml new file mode 100644 index 000000000..beddfc599 --- /dev/null +++ b/latest/cases/00295/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + k2 + S1 + + + + + + + diff --git a/latest/cases/00295/model-sbml-l3v2.xml b/latest/cases/00295/model-sbml-l3v2.xml new file mode 100644 index 000000000..3cf4594de --- /dev/null +++ b/latest/cases/00295/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + k2 + S1 + + + + + + + diff --git a/latest/cases/00295/output.heta b/latest/cases/00295/output.heta new file mode 100644 index 000000000..cc89f48d4 --- /dev/null +++ b/latest/cases/00295/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00295/synopsis.txt b/latest/cases/00295/synopsis.txt new file mode 100644 index 000000000..107c703ed --- /dev/null +++ b/latest/cases/00295/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00296/l2v5/heta-code/output.heta b/latest/cases/00296/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7a420e289 --- /dev/null +++ b/latest/cases/00296/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-5; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-5; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 1e-5; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 2.25e-5; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00296/l2v5/index.heta b/latest/cases/00296/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00296/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00296/l2v5/json/output.json b/latest/cases/00296/l2v5/json/output.json new file mode 100644 index 000000000..0c885203e --- /dev/null +++ b/latest/cases/00296/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "2.25e-5", + "ode_": "k3 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00296/l3v2/heta-code/output.heta b/latest/cases/00296/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e386e6346 --- /dev/null +++ b/latest/cases/00296/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 2.25e-5; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00296/l3v2/index.heta b/latest/cases/00296/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00296/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00296/l3v2/json/output.json b/latest/cases/00296/l3v2/json/output.json new file mode 100644 index 000000000..41a616c1d --- /dev/null +++ b/latest/cases/00296/l3v2/json/output.json @@ -0,0 +1,125 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "2.25e-5", + "ode_": "k3 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00296/model-sbml-l2v5.xml b/latest/cases/00296/model-sbml-l2v5.xml new file mode 100644 index 000000000..5e7abeb3d --- /dev/null +++ b/latest/cases/00296/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00296/model-sbml-l3v2.xml b/latest/cases/00296/model-sbml-l3v2.xml new file mode 100644 index 000000000..edc111571 --- /dev/null +++ b/latest/cases/00296/model-sbml-l3v2.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00296/output.heta b/latest/cases/00296/output.heta new file mode 100644 index 000000000..09d4a24cc --- /dev/null +++ b/latest/cases/00296/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 2.25e-5; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00296/synopsis.txt b/latest/cases/00296/synopsis.txt new file mode 100644 index 000000000..cc34bcfaa --- /dev/null +++ b/latest/cases/00296/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00297/l2v5/heta-code/output.heta b/latest/cases/00297/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c9637619b --- /dev/null +++ b/latest/cases/00297/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 1.05; +k2 @Record 'k2' { } .= 1.15; + diff --git a/latest/cases/00297/l2v5/index.heta b/latest/cases/00297/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00297/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00297/l2v5/json/output.json b/latest/cases/00297/l2v5/json/output.json new file mode 100644 index 000000000..0fe8fabab --- /dev/null +++ b/latest/cases/00297/l2v5/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.05" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.15" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00297/l3v2/heta-code/output.heta b/latest/cases/00297/l3v2/heta-code/output.heta new file mode 100644 index 000000000..275b976f5 --- /dev/null +++ b/latest/cases/00297/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00297/l3v2/index.heta b/latest/cases/00297/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00297/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00297/l3v2/json/output.json b/latest/cases/00297/l3v2/json/output.json new file mode 100644 index 000000000..9b164fb5f --- /dev/null +++ b/latest/cases/00297/l3v2/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.05 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.15 + } +] \ No newline at end of file diff --git a/latest/cases/00297/model-sbml-l2v5.xml b/latest/cases/00297/model-sbml-l2v5.xml new file mode 100644 index 000000000..906516715 --- /dev/null +++ b/latest/cases/00297/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00297/model-sbml-l3v2.xml b/latest/cases/00297/model-sbml-l3v2.xml new file mode 100644 index 000000000..91a3c055d --- /dev/null +++ b/latest/cases/00297/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00297/output.heta b/latest/cases/00297/output.heta new file mode 100644 index 000000000..2b33756ed --- /dev/null +++ b/latest/cases/00297/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S3 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00297/synopsis.txt b/latest/cases/00297/synopsis.txt new file mode 100644 index 000000000..3a378fdb9 --- /dev/null +++ b/latest/cases/00297/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S3 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00298/l2v5/heta-code/output.heta b/latest/cases/00298/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b376cba7c --- /dev/null +++ b/latest/cases/00298/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 1.05; +k2 @Record 'k2' { } .= 1.15; + diff --git a/latest/cases/00298/l2v5/index.heta b/latest/cases/00298/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00298/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00298/l2v5/json/output.json b/latest/cases/00298/l2v5/json/output.json new file mode 100644 index 000000000..f8593c180 --- /dev/null +++ b/latest/cases/00298/l2v5/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.05" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.15" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00298/l3v2/heta-code/output.heta b/latest/cases/00298/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d9d1319ce --- /dev/null +++ b/latest/cases/00298/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00298/l3v2/index.heta b/latest/cases/00298/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00298/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00298/l3v2/json/output.json b/latest/cases/00298/l3v2/json/output.json new file mode 100644 index 000000000..6519a03c9 --- /dev/null +++ b/latest/cases/00298/l3v2/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.05 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.15 + } +] \ No newline at end of file diff --git a/latest/cases/00298/model-sbml-l2v5.xml b/latest/cases/00298/model-sbml-l2v5.xml new file mode 100644 index 000000000..9acebb33a --- /dev/null +++ b/latest/cases/00298/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00298/model-sbml-l3v2.xml b/latest/cases/00298/model-sbml-l3v2.xml new file mode 100644 index 000000000..9457a3dc7 --- /dev/null +++ b/latest/cases/00298/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00298/output.heta b/latest/cases/00298/output.heta new file mode 100644 index 000000000..f5906417f --- /dev/null +++ b/latest/cases/00298/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S1 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00298/synopsis.txt b/latest/cases/00298/synopsis.txt new file mode 100644 index 000000000..bccb8945c --- /dev/null +++ b/latest/cases/00298/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S1 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00299/l2v5/heta-code/output.heta b/latest/cases/00299/l2v5/heta-code/output.heta new file mode 100644 index 000000000..08fe8a438 --- /dev/null +++ b/latest/cases/00299/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00299/l2v5/index.heta b/latest/cases/00299/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00299/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00299/l2v5/json/output.json b/latest/cases/00299/l2v5/json/output.json new file mode 100644 index 000000000..81d4383e1 --- /dev/null +++ b/latest/cases/00299/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00299/l3v2/heta-code/output.heta b/latest/cases/00299/l3v2/heta-code/output.heta new file mode 100644 index 000000000..849462bee --- /dev/null +++ b/latest/cases/00299/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00299/l3v2/index.heta b/latest/cases/00299/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00299/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00299/l3v2/json/output.json b/latest/cases/00299/l3v2/json/output.json new file mode 100644 index 000000000..c2ebe1735 --- /dev/null +++ b/latest/cases/00299/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00299/model-sbml-l2v5.xml b/latest/cases/00299/model-sbml-l2v5.xml new file mode 100644 index 000000000..278b6108c --- /dev/null +++ b/latest/cases/00299/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00299/model-sbml-l3v2.xml b/latest/cases/00299/model-sbml-l3v2.xml new file mode 100644 index 000000000..2d9a52f8f --- /dev/null +++ b/latest/cases/00299/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00299/output.heta b/latest/cases/00299/output.heta new file mode 100644 index 000000000..f24667e07 --- /dev/null +++ b/latest/cases/00299/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S4 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00299/synopsis.txt b/latest/cases/00299/synopsis.txt new file mode 100644 index 000000000..50c1c851f --- /dev/null +++ b/latest/cases/00299/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S4 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00300/l2v5/heta-code/output.heta b/latest/cases/00300/l2v5/heta-code/output.heta new file mode 100644 index 000000000..02c81187f --- /dev/null +++ b/latest/cases/00300/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00300/l2v5/index.heta b/latest/cases/00300/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00300/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00300/l2v5/json/output.json b/latest/cases/00300/l2v5/json/output.json new file mode 100644 index 000000000..98057007b --- /dev/null +++ b/latest/cases/00300/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00300/l3v2/heta-code/output.heta b/latest/cases/00300/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7e2e5685d --- /dev/null +++ b/latest/cases/00300/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00300/l3v2/index.heta b/latest/cases/00300/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00300/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00300/l3v2/json/output.json b/latest/cases/00300/l3v2/json/output.json new file mode 100644 index 000000000..9f2f07799 --- /dev/null +++ b/latest/cases/00300/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00300/model-sbml-l2v5.xml b/latest/cases/00300/model-sbml-l2v5.xml new file mode 100644 index 000000000..0b40a0587 --- /dev/null +++ b/latest/cases/00300/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00300/model-sbml-l3v2.xml b/latest/cases/00300/model-sbml-l3v2.xml new file mode 100644 index 000000000..5f9090f80 --- /dev/null +++ b/latest/cases/00300/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00300/output.heta b/latest/cases/00300/output.heta new file mode 100644 index 000000000..2f2a85d1b --- /dev/null +++ b/latest/cases/00300/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00300/synopsis.txt b/latest/cases/00300/synopsis.txt new file mode 100644 index 000000000..fcc293100 --- /dev/null +++ b/latest/cases/00300/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00301/l2v5/heta-code/output.heta b/latest/cases/00301/l2v5/heta-code/output.heta new file mode 100644 index 000000000..23344084f --- /dev/null +++ b/latest/cases/00301/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00301/l2v5/index.heta b/latest/cases/00301/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00301/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00301/l2v5/json/output.json b/latest/cases/00301/l2v5/json/output.json new file mode 100644 index 000000000..c74ba390a --- /dev/null +++ b/latest/cases/00301/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00301/l3v2/heta-code/output.heta b/latest/cases/00301/l3v2/heta-code/output.heta new file mode 100644 index 000000000..640d6dc1f --- /dev/null +++ b/latest/cases/00301/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00301/l3v2/index.heta b/latest/cases/00301/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00301/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00301/l3v2/json/output.json b/latest/cases/00301/l3v2/json/output.json new file mode 100644 index 000000000..4d4276d1f --- /dev/null +++ b/latest/cases/00301/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00301/model-sbml-l2v5.xml b/latest/cases/00301/model-sbml-l2v5.xml new file mode 100644 index 000000000..5a724e8b8 --- /dev/null +++ b/latest/cases/00301/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00301/model-sbml-l3v2.xml b/latest/cases/00301/model-sbml-l3v2.xml new file mode 100644 index 000000000..ea937e6e0 --- /dev/null +++ b/latest/cases/00301/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00301/output.heta b/latest/cases/00301/output.heta new file mode 100644 index 000000000..0169feb74 --- /dev/null +++ b/latest/cases/00301/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S3 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +!!!|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00301/synopsis.txt b/latest/cases/00301/synopsis.txt new file mode 100644 index 000000000..c3a059306 --- /dev/null +++ b/latest/cases/00301/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S3 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +!!!|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00302/l2v5/heta-code/output.heta b/latest/cases/00302/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a271d5de1 --- /dev/null +++ b/latest/cases/00302/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00302/l2v5/index.heta b/latest/cases/00302/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00302/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00302/l2v5/json/output.json b/latest/cases/00302/l2v5/json/output.json new file mode 100644 index 000000000..f807c4a62 --- /dev/null +++ b/latest/cases/00302/l2v5/json/output.json @@ -0,0 +1,153 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00302/l3v2/heta-code/output.heta b/latest/cases/00302/l3v2/heta-code/output.heta new file mode 100644 index 000000000..474da1963 --- /dev/null +++ b/latest/cases/00302/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00302/l3v2/index.heta b/latest/cases/00302/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00302/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00302/l3v2/json/output.json b/latest/cases/00302/l3v2/json/output.json new file mode 100644 index 000000000..02a1353cf --- /dev/null +++ b/latest/cases/00302/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00302/model-sbml-l2v5.xml b/latest/cases/00302/model-sbml-l2v5.xml new file mode 100644 index 000000000..e3836e206 --- /dev/null +++ b/latest/cases/00302/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00302/model-sbml-l3v2.xml b/latest/cases/00302/model-sbml-l3v2.xml new file mode 100644 index 000000000..e7b407f54 --- /dev/null +++ b/latest/cases/00302/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00302/output.heta b/latest/cases/00302/output.heta new file mode 100644 index 000000000..b368a07ef --- /dev/null +++ b/latest/cases/00302/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Both species S3 and S4 are labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00302/synopsis.txt b/latest/cases/00302/synopsis.txt new file mode 100644 index 000000000..e9b44e7f8 --- /dev/null +++ b/latest/cases/00302/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Both species S3 and S4 are labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00303/l2v5/heta-code/output.heta b/latest/cases/00303/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ffc176f3e --- /dev/null +++ b/latest/cases/00303/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 1.05; +k2 @Record 'k2' { } .= 1.15; + diff --git a/latest/cases/00303/l2v5/index.heta b/latest/cases/00303/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00303/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00303/l2v5/json/output.json b/latest/cases/00303/l2v5/json/output.json new file mode 100644 index 000000000..e8796765b --- /dev/null +++ b/latest/cases/00303/l2v5/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.05" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.15" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00303/l3v2/heta-code/output.heta b/latest/cases/00303/l3v2/heta-code/output.heta new file mode 100644 index 000000000..566273084 --- /dev/null +++ b/latest/cases/00303/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00303/l3v2/index.heta b/latest/cases/00303/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00303/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00303/l3v2/json/output.json b/latest/cases/00303/l3v2/json/output.json new file mode 100644 index 000000000..aed292d08 --- /dev/null +++ b/latest/cases/00303/l3v2/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.05 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.15 + } +] \ No newline at end of file diff --git a/latest/cases/00303/model-sbml-l2v5.xml b/latest/cases/00303/model-sbml-l2v5.xml new file mode 100644 index 000000000..55f929176 --- /dev/null +++ b/latest/cases/00303/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00303/model-sbml-l3v2.xml b/latest/cases/00303/model-sbml-l3v2.xml new file mode 100644 index 000000000..a3afe7fd2 --- /dev/null +++ b/latest/cases/00303/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00303/output.heta b/latest/cases/00303/output.heta new file mode 100644 index 000000000..fdf77776c --- /dev/null +++ b/latest/cases/00303/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Both +species S1 and S3 are labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the initial value +must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00303/synopsis.txt b/latest/cases/00303/synopsis.txt new file mode 100644 index 000000000..ed61c4daa --- /dev/null +++ b/latest/cases/00303/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Both +species S1 and S3 are labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the initial value +must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00304/l2v5/heta-code/output.heta b/latest/cases/00304/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4f98992e0 --- /dev/null +++ b/latest/cases/00304/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.15 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 1.05; +k2 @Record 'k2' { } .= 1.15; + diff --git a/latest/cases/00304/l2v5/index.heta b/latest/cases/00304/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00304/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00304/l2v5/json/output.json b/latest/cases/00304/l2v5/json/output.json new file mode 100644 index 000000000..2a01aff63 --- /dev/null +++ b/latest/cases/00304/l2v5/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.05" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.15" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00304/l3v2/heta-code/output.heta b/latest/cases/00304/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ca1b31c04 --- /dev/null +++ b/latest/cases/00304/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00304/l3v2/index.heta b/latest/cases/00304/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00304/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00304/l3v2/json/output.json b/latest/cases/00304/l3v2/json/output.json new file mode 100644 index 000000000..fc7d89276 --- /dev/null +++ b/latest/cases/00304/l3v2/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.05 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.15 + } +] \ No newline at end of file diff --git a/latest/cases/00304/model-sbml-l2v5.xml b/latest/cases/00304/model-sbml-l2v5.xml new file mode 100644 index 000000000..43f4e5c00 --- /dev/null +++ b/latest/cases/00304/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00304/model-sbml-l3v2.xml b/latest/cases/00304/model-sbml-l3v2.xml new file mode 100644 index 000000000..df9b2149e --- /dev/null +++ b/latest/cases/00304/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00304/output.heta b/latest/cases/00304/output.heta new file mode 100644 index 000000000..d60d3dd92 --- /dev/null +++ b/latest/cases/00304/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ConstantSpecies, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S1 +is labeled as both constant and an SBML boundary condition, and therefore cannot +be changed by rules or reactions. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.1 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00304/synopsis.txt b/latest/cases/00304/synopsis.txt new file mode 100644 index 000000000..2f0be85aa --- /dev/null +++ b/latest/cases/00304/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ConstantSpecies, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S1 +is labeled as both constant and an SBML boundary condition, and therefore cannot +be changed by rules or reactions. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00305/l2v5/heta-code/output.heta b/latest/cases/00305/l2v5/heta-code/output.heta new file mode 100644 index 000000000..11f95b7db --- /dev/null +++ b/latest/cases/00305/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 1.05; +k2 @Record 'k2' { } .= 1.15; + diff --git a/latest/cases/00305/l2v5/index.heta b/latest/cases/00305/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00305/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00305/l2v5/json/output.json b/latest/cases/00305/l2v5/json/output.json new file mode 100644 index 000000000..ac58ac61c --- /dev/null +++ b/latest/cases/00305/l2v5/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.05" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.15" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00305/l3v2/heta-code/output.heta b/latest/cases/00305/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9dcbe703e --- /dev/null +++ b/latest/cases/00305/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00305/l3v2/index.heta b/latest/cases/00305/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00305/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00305/l3v2/json/output.json b/latest/cases/00305/l3v2/json/output.json new file mode 100644 index 000000000..81337d1d1 --- /dev/null +++ b/latest/cases/00305/l3v2/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.05 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.15 + } +] \ No newline at end of file diff --git a/latest/cases/00305/model-sbml-l2v5.xml b/latest/cases/00305/model-sbml-l2v5.xml new file mode 100644 index 000000000..dbe840751 --- /dev/null +++ b/latest/cases/00305/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00305/model-sbml-l3v2.xml b/latest/cases/00305/model-sbml-l3v2.xml new file mode 100644 index 000000000..4306a531b --- /dev/null +++ b/latest/cases/00305/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00305/output.heta b/latest/cases/00305/output.heta new file mode 100644 index 000000000..897d836a0 --- /dev/null +++ b/latest/cases/00305/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ConstantSpecies, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S2 +is labeled as both constant and an SBML boundary condition, and therefore +cannot be changed by rules or reactions. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00305/synopsis.txt b/latest/cases/00305/synopsis.txt new file mode 100644 index 000000000..aeee0d9cf --- /dev/null +++ b/latest/cases/00305/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ConstantSpecies, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S2 +is labeled as both constant and an SBML boundary condition, and therefore +cannot be changed by rules or reactions. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00306/l2v5/heta-code/output.heta b/latest/cases/00306/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cf52593e5 --- /dev/null +++ b/latest/cases/00306/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 0.005; +k2 @Record 'k2' { } .= 5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00306/l2v5/index.heta b/latest/cases/00306/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00306/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00306/l2v5/json/output.json b/latest/cases/00306/l2v5/json/output.json new file mode 100644 index 000000000..e53a8619a --- /dev/null +++ b/latest/cases/00306/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.005" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00306/l3v2/heta-code/output.heta b/latest/cases/00306/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dc9208e14 --- /dev/null +++ b/latest/cases/00306/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.005; +k2 @Const 'k2' { } = 5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00306/l3v2/index.heta b/latest/cases/00306/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00306/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00306/l3v2/json/output.json b/latest/cases/00306/l3v2/json/output.json new file mode 100644 index 000000000..62887c17a --- /dev/null +++ b/latest/cases/00306/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.005 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00306/model-sbml-l2v5.xml b/latest/cases/00306/model-sbml-l2v5.xml new file mode 100644 index 000000000..ba09580f3 --- /dev/null +++ b/latest/cases/00306/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00306/model-sbml-l3v2.xml b/latest/cases/00306/model-sbml-l3v2.xml new file mode 100644 index 000000000..2abe13a2b --- /dev/null +++ b/latest/cases/00306/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00306/output.heta b/latest/cases/00306/output.heta new file mode 100644 index 000000000..830fe441f --- /dev/null +++ b/latest/cases/00306/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S2 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.5 \x 10^-2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.005; +k2 @Const 'k2' { } = 5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00306/synopsis.txt b/latest/cases/00306/synopsis.txt new file mode 100644 index 000000000..6ea598233 --- /dev/null +++ b/latest/cases/00306/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S2 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.5 \x 10^-2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00307/l2v5/heta-code/output.heta b/latest/cases/00307/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f4a568ccc --- /dev/null +++ b/latest/cases/00307/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 0.005; +k2 @Record 'k2' { } .= 5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00307/l2v5/index.heta b/latest/cases/00307/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00307/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00307/l2v5/json/output.json b/latest/cases/00307/l2v5/json/output.json new file mode 100644 index 000000000..d7bff6eb4 --- /dev/null +++ b/latest/cases/00307/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.005" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00307/l3v2/heta-code/output.heta b/latest/cases/00307/l3v2/heta-code/output.heta new file mode 100644 index 000000000..017e35477 --- /dev/null +++ b/latest/cases/00307/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.005; +k2 @Const 'k2' { } = 5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00307/l3v2/index.heta b/latest/cases/00307/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00307/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00307/l3v2/json/output.json b/latest/cases/00307/l3v2/json/output.json new file mode 100644 index 000000000..411507af3 --- /dev/null +++ b/latest/cases/00307/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.005 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00307/model-sbml-l2v5.xml b/latest/cases/00307/model-sbml-l2v5.xml new file mode 100644 index 000000000..14eb6e833 --- /dev/null +++ b/latest/cases/00307/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00307/model-sbml-l3v2.xml b/latest/cases/00307/model-sbml-l3v2.xml new file mode 100644 index 000000000..621b0dfb8 --- /dev/null +++ b/latest/cases/00307/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00307/output.heta b/latest/cases/00307/output.heta new file mode 100644 index 000000000..8025d560e --- /dev/null +++ b/latest/cases/00307/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S3 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.5 \x 10^-2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.005; +k2 @Const 'k2' { } = 5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00307/synopsis.txt b/latest/cases/00307/synopsis.txt new file mode 100644 index 000000000..bc6cd1916 --- /dev/null +++ b/latest/cases/00307/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, BoundaryCondition, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S3 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.5 \x 10^-2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00308/l2v5/heta-code/output.heta b/latest/cases/00308/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0dbeaf642 --- /dev/null +++ b/latest/cases/00308/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; +S5 @Species 'S5' { units: substance/volume, boundary: true, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S5], reversible: false, }; +reaction1 := compartment * k1 * S1 * S5; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Record 'k1' { } .= 0.005; +k2 @Record 'k2' { } .= 5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00308/l2v5/index.heta b/latest/cases/00308/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00308/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00308/l2v5/json/output.json b/latest/cases/00308/l2v5/json/output.json new file mode 100644 index 000000000..35e583a53 --- /dev/null +++ b/latest/cases/00308/l2v5/json/output.json @@ -0,0 +1,167 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S5" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.005" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00308/l3v2/heta-code/output.heta b/latest/cases/00308/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7ab5c84cc --- /dev/null +++ b/latest/cases/00308/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; +S5 @Species 'S5' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S5], reversible: false, }; +reaction1 := compartment * k1 * S1 * S5; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.005; +k2 @Const 'k2' { } = 5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00308/l3v2/index.heta b/latest/cases/00308/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00308/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00308/l3v2/json/output.json b/latest/cases/00308/l3v2/json/output.json new file mode 100644 index 000000000..20abe64f3 --- /dev/null +++ b/latest/cases/00308/l3v2/json/output.json @@ -0,0 +1,137 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25e-5 / compartment", + "ode_": "k3 * S2" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S5" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.005 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00308/model-sbml-l2v5.xml b/latest/cases/00308/model-sbml-l2v5.xml new file mode 100644 index 000000000..00fce536c --- /dev/null +++ b/latest/cases/00308/model-sbml-l2v5.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S5 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00308/model-sbml-l3v2.xml b/latest/cases/00308/model-sbml-l3v2.xml new file mode 100644 index 000000000..c8f17378f --- /dev/null +++ b/latest/cases/00308/model-sbml-l3v2.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S5 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00308/output.heta b/latest/cases/00308/output.heta new file mode 100644 index 000000000..9e88c8468 --- /dev/null +++ b/latest/cases/00308/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S5 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S5 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Initial amount of S5 |$ 1 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.5 \x 10^-2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment; +S4 := k3 * S2; +S5 @Species 'S5' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S5], reversible: false, }; +reaction1 := compartment * k1 * S1 * S5; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; + +k1 @Const 'k1' { } = 0.005; +k2 @Const 'k2' { } = 5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00308/synopsis.txt b/latest/cases/00308/synopsis.txt new file mode 100644 index 000000000..416aef720 --- /dev/null +++ b/latest/cases/00308/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S5 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S5 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Initial amount of S5 |$ 1 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.5 \x 10^-2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00309/l2v5/heta-code/output.heta b/latest/cases/00309/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0eed493c7 --- /dev/null +++ b/latest/cases/00309/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, }; +S3 := k1 * S4; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Record 'k1' { } .= 1.05; +k2 @Record 'k2' { } .= 1.15; + diff --git a/latest/cases/00309/l2v5/index.heta b/latest/cases/00309/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00309/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00309/l2v5/json/output.json b/latest/cases/00309/l2v5/json/output.json new file mode 100644 index 000000000..924ec9208 --- /dev/null +++ b/latest/cases/00309/l2v5/json/output.json @@ -0,0 +1,116 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S4" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.05" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.15" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00309/l3v2/heta-code/output.heta b/latest/cases/00309/l3v2/heta-code/output.heta new file mode 100644 index 000000000..23250e13e --- /dev/null +++ b/latest/cases/00309/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S4; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00309/l3v2/index.heta b/latest/cases/00309/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00309/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00309/l3v2/json/output.json b/latest/cases/00309/l3v2/json/output.json new file mode 100644 index 000000000..40bb69ed2 --- /dev/null +++ b/latest/cases/00309/l3v2/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S4" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.05 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.15 + } +] \ No newline at end of file diff --git a/latest/cases/00309/model-sbml-l2v5.xml b/latest/cases/00309/model-sbml-l2v5.xml new file mode 100644 index 000000000..971dbac9a --- /dev/null +++ b/latest/cases/00309/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + k1 + S4 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00309/model-sbml-l3v2.xml b/latest/cases/00309/model-sbml-l3v2.xml new file mode 100644 index 000000000..ae2f4e4b6 --- /dev/null +++ b/latest/cases/00309/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S4 + + + + + + + + + + + + + + + + + compartment + k2 + S1 + + + + + + + diff --git a/latest/cases/00309/output.heta b/latest/cases/00309/output.heta new file mode 100644 index 000000000..afb0fac8a --- /dev/null +++ b/latest/cases/00309/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S4 +is labeled as constant and therefore cannot be changed by rules or +reactions. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S4$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, }; +S3 := k1 * S4; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.015 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/00309/synopsis.txt b/latest/cases/00309/synopsis.txt new file mode 100644 index 000000000..3e7e8fcc4 --- /dev/null +++ b/latest/cases/00309/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S4 +is labeled as constant and therefore cannot be changed by rules or +reactions. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $compartment * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S4$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00310/l2v5/heta-code/output.heta b/latest/cases/00310/l2v5/heta-code/output.heta new file mode 100644 index 000000000..fb849ac94 --- /dev/null +++ b/latest/cases/00310/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 0.15; +C := p1 * p2; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +k1 @Record 'k1' { } .= 0.9; +p1 @Record 'p1' { } .= 0.1; +p2 @Record 'p2' { } .= 1.5; + diff --git a/latest/cases/00310/l2v5/index.heta b/latest/cases/00310/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00310/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00310/l2v5/json/output.json b/latest/cases/00310/l2v5/json/output.json new file mode 100644 index 000000000..0b0695de1 --- /dev/null +++ b/latest/cases/00310/l2v5/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.15", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00310/l3v2/heta-code/output.heta b/latest/cases/00310/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e2acaf8f1 --- /dev/null +++ b/latest/cases/00310/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 0.15; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.9; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00310/l3v2/index.heta b/latest/cases/00310/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00310/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00310/l3v2/json/output.json b/latest/cases/00310/l3v2/json/output.json new file mode 100644 index 000000000..9e86dad5f --- /dev/null +++ b/latest/cases/00310/l3v2/json/output.json @@ -0,0 +1,91 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.15", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.9 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00310/model-sbml-l2v5.xml b/latest/cases/00310/model-sbml-l2v5.xml new file mode 100644 index 000000000..87b59b036 --- /dev/null +++ b/latest/cases/00310/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00310/model-sbml-l3v2.xml b/latest/cases/00310/model-sbml-l3v2.xml new file mode 100644 index 000000000..3fde8ad2c --- /dev/null +++ b/latest/cases/00310/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00310/output.heta b/latest/cases/00310/output.heta new file mode 100644 index 000000000..51e66ef51 --- /dev/null +++ b/latest/cases/00310/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a compartment + whose volume is varying. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case the initial value declared for C is consistent +with that calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment C |$ 0.15$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 0.15; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.9; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00310/synopsis.txt b/latest/cases/00310/synopsis.txt new file mode 100644 index 000000000..30e18e751 --- /dev/null +++ b/latest/cases/00310/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a compartment + whose volume is varying. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case the initial value declared for C is consistent +with that calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment C |$ 0.15$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00311/l2v5/heta-code/output.heta b/latest/cases/00311/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5a2cd708f --- /dev/null +++ b/latest/cases/00311/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, } .= 1; +compartment := p1 * p2; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +k1 @Record 'k1' { } .= 0.9; +p1 @Record 'p1' { } .= 0.1; +p2 @Record 'p2' { } .= 1.5; + diff --git a/latest/cases/00311/l2v5/index.heta b/latest/cases/00311/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00311/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00311/l2v5/json/output.json b/latest/cases/00311/l2v5/json/output.json new file mode 100644 index 000000000..5aa22cf58 --- /dev/null +++ b/latest/cases/00311/l2v5/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00311/l3v2/heta-code/output.heta b/latest/cases/00311/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d7e5b8976 --- /dev/null +++ b/latest/cases/00311/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 1; +compartment := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.9; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00311/l3v2/index.heta b/latest/cases/00311/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00311/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00311/l3v2/json/output.json b/latest/cases/00311/l3v2/json/output.json new file mode 100644 index 000000000..fbd15d285 --- /dev/null +++ b/latest/cases/00311/l3v2/json/output.json @@ -0,0 +1,91 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.9 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00311/model-sbml-l2v5.xml b/latest/cases/00311/model-sbml-l2v5.xml new file mode 100644 index 000000000..d382f4fa2 --- /dev/null +++ b/latest/cases/00311/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00311/model-sbml-l3v2.xml b/latest/cases/00311/model-sbml-l3v2.xml new file mode 100644 index 000000000..39610f104 --- /dev/null +++ b/latest/cases/00311/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00311/output.heta b/latest/cases/00311/output.heta new file mode 100644 index 000000000..f25e699f7 --- /dev/null +++ b/latest/cases/00311/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a compartment + whose volume is varying. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called "compartment". There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules. The assignmentRule assigns value to compartment +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case, the initial value declared for compartment "compartment" is +inconsistent with that calculated by the assignmentRule; the calculated +value should be used. Note that since this assignmentRule must always +remain true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, } .= 1; +compartment := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.9; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00311/synopsis.txt b/latest/cases/00311/synopsis.txt new file mode 100644 index 000000000..026318442 --- /dev/null +++ b/latest/cases/00311/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a compartment + whose volume is varying. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called "compartment". There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules. The assignmentRule assigns value to compartment +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | compartment | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case, the initial value declared for compartment "compartment" is +inconsistent with that calculated by the assignmentRule; the calculated +value should be used. Note that since this assignmentRule must always +remain true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00312/l2v5/heta-code/output.heta b/latest/cases/00312/l2v5/heta-code/output.heta new file mode 100644 index 000000000..aea202df0 --- /dev/null +++ b/latest/cases/00312/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, }; +C := p1 * p2; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +k1 @Record 'k1' { } .= 0.9; +p1 @Record 'p1' { } .= 0.1; +p2 @Record 'p2' { } .= 1.5; + diff --git a/latest/cases/00312/l2v5/index.heta b/latest/cases/00312/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00312/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00312/l2v5/json/output.json b/latest/cases/00312/l2v5/json/output.json new file mode 100644 index 000000000..7a833a15b --- /dev/null +++ b/latest/cases/00312/l2v5/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00312/l3v2/heta-code/output.heta b/latest/cases/00312/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4508471d5 --- /dev/null +++ b/latest/cases/00312/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, }; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.9; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00312/l3v2/index.heta b/latest/cases/00312/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00312/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00312/l3v2/json/output.json b/latest/cases/00312/l3v2/json/output.json new file mode 100644 index 000000000..7c824f1ee --- /dev/null +++ b/latest/cases/00312/l3v2/json/output.json @@ -0,0 +1,90 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.9 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00312/model-sbml-l2v5.xml b/latest/cases/00312/model-sbml-l2v5.xml new file mode 100644 index 000000000..e1599499b --- /dev/null +++ b/latest/cases/00312/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00312/model-sbml-l3v2.xml b/latest/cases/00312/model-sbml-l3v2.xml new file mode 100644 index 000000000..d3c7b2fb3 --- /dev/null +++ b/latest/cases/00312/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00312/output.heta b/latest/cases/00312/output.heta new file mode 100644 index 000000000..ebe65a00a --- /dev/null +++ b/latest/cases/00312/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a compartment + whose volume is varying. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case, the initial value is not declared for compartment +C and must be calculated by the assignmentRule. Note that +since this assignmentRule must always remain true, it should be considered +during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment C |$ undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, }; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.9; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00312/synopsis.txt b/latest/cases/00312/synopsis.txt new file mode 100644 index 000000000..e49c5ca6e --- /dev/null +++ b/latest/cases/00312/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a compartment + whose volume is varying. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case, the initial value is not declared for compartment +C and must be calculated by the assignmentRule. Note that +since this assignmentRule must always remain true, it should be considered +during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 0.9$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment C |$ undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00313/l2v5/heta-code/output.heta b/latest/cases/00313/l2v5/heta-code/output.heta new file mode 100644 index 000000000..531ae3e6f --- /dev/null +++ b/latest/cases/00313/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 1; +C := p1 * p2; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2.5; +p1 @Record 'p1' { } .= 0.1; +p2 @Record 'p2' { } .= 1; + diff --git a/latest/cases/00313/l2v5/index.heta b/latest/cases/00313/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00313/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00313/l2v5/json/output.json b/latest/cases/00313/l2v5/json/output.json new file mode 100644 index 000000000..00963e67e --- /dev/null +++ b/latest/cases/00313/l2v5/json/output.json @@ -0,0 +1,164 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00313/l3v2/heta-code/output.heta b/latest/cases/00313/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c3edfeb90 --- /dev/null +++ b/latest/cases/00313/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.5; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00313/l3v2/index.heta b/latest/cases/00313/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00313/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00313/l3v2/json/output.json b/latest/cases/00313/l3v2/json/output.json new file mode 100644 index 000000000..deefeb05e --- /dev/null +++ b/latest/cases/00313/l3v2/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00313/model-sbml-l2v5.xml b/latest/cases/00313/model-sbml-l2v5.xml new file mode 100644 index 000000000..e4c4259c7 --- /dev/null +++ b/latest/cases/00313/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00313/model-sbml-l3v2.xml b/latest/cases/00313/model-sbml-l3v2.xml new file mode 100644 index 000000000..6f3480343 --- /dev/null +++ b/latest/cases/00313/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00313/output.heta b/latest/cases/00313/output.heta new file mode 100644 index 000000000..efdf8b0d8 --- /dev/null +++ b/latest/cases/00313/output.heta @@ -0,0 +1,73 @@ +/* +category: Test +synopsis: Basic reaction with two species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are three +species called S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case, the initial value declared for compartment C is +inconsistent with that calculated by the assignmentRule; the calculated +value should be used. Note that since this assignmentRule must always +remain true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.0$ |mole second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.5; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00313/synopsis.txt b/latest/cases/00313/synopsis.txt new file mode 100644 index 000000000..546a0ffdf --- /dev/null +++ b/latest/cases/00313/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic reaction with two species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are three +species called S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case, the initial value declared for compartment C is +inconsistent with that calculated by the assignmentRule; the calculated +value should be used. Note that since this assignmentRule must always +remain true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.0$ |mole second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00314/l2v5/heta-code/output.heta b/latest/cases/00314/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1b401e82a --- /dev/null +++ b/latest/cases/00314/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 0.1; +C := p1 * p2; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 25; +p1 @Record 'p1' { } .= 0.1; +p2 @Record 'p2' { } .= 1; + diff --git a/latest/cases/00314/l2v5/index.heta b/latest/cases/00314/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00314/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00314/l2v5/json/output.json b/latest/cases/00314/l2v5/json/output.json new file mode 100644 index 000000000..ec597c0f4 --- /dev/null +++ b/latest/cases/00314/l2v5/json/output.json @@ -0,0 +1,164 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00314/l3v2/heta-code/output.heta b/latest/cases/00314/l3v2/heta-code/output.heta new file mode 100644 index 000000000..33073fc0f --- /dev/null +++ b/latest/cases/00314/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 0.1; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.2; + +p2 @Record 'p2' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 25; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00314/l3v2/index.heta b/latest/cases/00314/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00314/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00314/l3v2/json/output.json b/latest/cases/00314/l3v2/json/output.json new file mode 100644 index 000000000..8b664d62d --- /dev/null +++ b/latest/cases/00314/l3v2/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00314/model-sbml-l2v5.xml b/latest/cases/00314/model-sbml-l2v5.xml new file mode 100644 index 000000000..211eab6e1 --- /dev/null +++ b/latest/cases/00314/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.2 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00314/model-sbml-l3v2.xml b/latest/cases/00314/model-sbml-l3v2.xml new file mode 100644 index 000000000..d09319b81 --- /dev/null +++ b/latest/cases/00314/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.2 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00314/output.heta b/latest/cases/00314/output.heta new file mode 100644 index 000000000..a349a96b1 --- /dev/null +++ b/latest/cases/00314/output.heta @@ -0,0 +1,73 @@ +/* +category: Test +synopsis: Basic reaction with two species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are three +species called S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.2 |] + +In this case, the initial value declared for compartment C is +consistent with that calculated by the assignmentRule. Note that since +this assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 25$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.0$ |mole second^-1^ | +|Volume of compartment C |$ 0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 0.1; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.2; + +p2 @Record 'p2' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 25; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00314/synopsis.txt b/latest/cases/00314/synopsis.txt new file mode 100644 index 000000000..32e4b0ef3 --- /dev/null +++ b/latest/cases/00314/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic reaction with two species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are three +species called S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.2 |] + +In this case, the initial value declared for compartment C is +consistent with that calculated by the assignmentRule. Note that since +this assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 25$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.0$ |mole second^-1^ | +|Volume of compartment C |$ 0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00315/l2v5/heta-code/output.heta b/latest/cases/00315/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ab49e58b0 --- /dev/null +++ b/latest/cases/00315/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, }; +C := p1 * p2; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.1; +p2 @Record 'p2' { } .= 1; + diff --git a/latest/cases/00315/l2v5/index.heta b/latest/cases/00315/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00315/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00315/l2v5/json/output.json b/latest/cases/00315/l2v5/json/output.json new file mode 100644 index 000000000..48fdaaa97 --- /dev/null +++ b/latest/cases/00315/l2v5/json/output.json @@ -0,0 +1,163 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00315/l3v2/heta-code/output.heta b/latest/cases/00315/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1081927ea --- /dev/null +++ b/latest/cases/00315/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, }; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00315/l3v2/index.heta b/latest/cases/00315/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00315/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00315/l3v2/json/output.json b/latest/cases/00315/l3v2/json/output.json new file mode 100644 index 000000000..481cab24f --- /dev/null +++ b/latest/cases/00315/l3v2/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00315/model-sbml-l2v5.xml b/latest/cases/00315/model-sbml-l2v5.xml new file mode 100644 index 000000000..a2a3454fe --- /dev/null +++ b/latest/cases/00315/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00315/model-sbml-l3v2.xml b/latest/cases/00315/model-sbml-l3v2.xml new file mode 100644 index 000000000..1c2cf8738 --- /dev/null +++ b/latest/cases/00315/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00315/output.heta b/latest/cases/00315/output.heta new file mode 100644 index 000000000..7f4de8ec8 --- /dev/null +++ b/latest/cases/00315/output.heta @@ -0,0 +1,73 @@ +/* +category: Test +synopsis: Basic reaction with two species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are three +species called S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case, the initial value is not declared for compartment +C and must be calculated by the assignmentRule. Note that +since this assignmentRule must always remain true, it should be considered +during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$ 0.2$ |mole | +|Initial amount of S3 |$ 0.1$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.0$ |mole second^-1^ | +|Volume of compartment C |$ undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, }; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00315/synopsis.txt b/latest/cases/00315/synopsis.txt new file mode 100644 index 000000000..064848853 --- /dev/null +++ b/latest/cases/00315/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic reaction with two species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are three +species called S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1 |] + +In this case, the initial value is not declared for compartment +C and must be calculated by the assignmentRule. Note that +since this assignmentRule must always remain true, it should be considered +during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.1$ |mole | +|Initial amount of S2 |$ 0.2$ |mole | +|Initial amount of S3 |$ 0.1$ |mole | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre mole^-1^ | +|Value of parameter p2 |$ 1.0$ |mole second^-1^ | +|Volume of compartment C |$ undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00316/l2v5/heta-code/output.heta b/latest/cases/00316/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ca2ec5c3c --- /dev/null +++ b/latest/cases/00316/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 1; +C := p1 * p2; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.1 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +k1 @Record 'k1' { } .= 0.0365; +k2 @Record 'k2' { } .= 0.0025; +p1 @Record 'p1' { } .= 0.1; +p2 @Record 'p2' { } .= 1.5; + diff --git a/latest/cases/00316/l2v5/index.heta b/latest/cases/00316/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00316/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00316/l2v5/json/output.json b/latest/cases/00316/l2v5/json/output.json new file mode 100644 index 000000000..aec613810 --- /dev/null +++ b/latest/cases/00316/l2v5/json/output.json @@ -0,0 +1,182 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.0365" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0025" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00316/l3v2/heta-code/output.heta b/latest/cases/00316/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0985338be --- /dev/null +++ b/latest/cases/00316/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.0365; +k2 @Const 'k2' { } = 0.0025; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00316/l3v2/index.heta b/latest/cases/00316/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00316/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00316/l3v2/json/output.json b/latest/cases/00316/l3v2/json/output.json new file mode 100644 index 000000000..d3a32df2e --- /dev/null +++ b/latest/cases/00316/l3v2/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.0365 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0025 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00316/model-sbml-l2v5.xml b/latest/cases/00316/model-sbml-l2v5.xml new file mode 100644 index 000000000..725ccdab2 --- /dev/null +++ b/latest/cases/00316/model-sbml-l2v5.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00316/model-sbml-l3v2.xml b/latest/cases/00316/model-sbml-l3v2.xml new file mode 100644 index 000000000..ccb9196a0 --- /dev/null +++ b/latest/cases/00316/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00316/output.heta b/latest/cases/00316/output.heta new file mode 100644 index 000000000..febd30d85 --- /dev/null +++ b/latest/cases/00316/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1$ |] + +In this case, the initial value declared for compartment C is +inconsistent with that calculated by the assignmentRule; the calculated +value should be used. Note that since this assignmentRule must always +remain true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.1$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.0365$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.0025$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre^2^ mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 1; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.0365; +k2 @Const 'k2' { } = 0.0025; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00316/synopsis.txt b/latest/cases/00316/synopsis.txt new file mode 100644 index 000000000..6e56ea2ca --- /dev/null +++ b/latest/cases/00316/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1$ |] + +In this case, the initial value declared for compartment C is +inconsistent with that calculated by the assignmentRule; the calculated +value should be used. Note that since this assignmentRule must always +remain true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.1$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.0365$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.0025$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre^2^ mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00317/l2v5/heta-code/output.heta b/latest/cases/00317/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6ae3f03c7 --- /dev/null +++ b/latest/cases/00317/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 0.1; +C := p1 * p2; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.1 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +k1 @Record 'k1' { } .= 0.0365; +k2 @Record 'k2' { } .= 0.0025; +p1 @Record 'p1' { } .= 0.1; +p2 @Record 'p2' { } .= 1.5; + diff --git a/latest/cases/00317/l2v5/index.heta b/latest/cases/00317/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00317/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00317/l2v5/json/output.json b/latest/cases/00317/l2v5/json/output.json new file mode 100644 index 000000000..8bf838f1f --- /dev/null +++ b/latest/cases/00317/l2v5/json/output.json @@ -0,0 +1,182 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.0365" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0025" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00317/l3v2/heta-code/output.heta b/latest/cases/00317/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fd8e96ecd --- /dev/null +++ b/latest/cases/00317/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 0.1; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.0365; +k2 @Const 'k2' { } = 0.0025; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00317/l3v2/index.heta b/latest/cases/00317/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00317/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00317/l3v2/json/output.json b/latest/cases/00317/l3v2/json/output.json new file mode 100644 index 000000000..016e58cc6 --- /dev/null +++ b/latest/cases/00317/l3v2/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.1", + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.0365 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0025 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00317/model-sbml-l2v5.xml b/latest/cases/00317/model-sbml-l2v5.xml new file mode 100644 index 000000000..6116281ed --- /dev/null +++ b/latest/cases/00317/model-sbml-l2v5.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00317/model-sbml-l3v2.xml b/latest/cases/00317/model-sbml-l3v2.xml new file mode 100644 index 000000000..1c3e62835 --- /dev/null +++ b/latest/cases/00317/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00317/output.heta b/latest/cases/00317/output.heta new file mode 100644 index 000000000..d1d40a36f --- /dev/null +++ b/latest/cases/00317/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1$ |] + +In this case, the initial value declared for compartment C is +consistent with that calculated by the assignmentRule. Note that since +this assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.1$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.0365$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.0025$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre^2^ mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment C |$ 0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 0.1; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 1.5; + +k1 @Const 'k1' { } = 0.0365; +k2 @Const 'k2' { } = 0.0025; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00317/synopsis.txt b/latest/cases/00317/synopsis.txt new file mode 100644 index 000000000..02a2c9329 --- /dev/null +++ b/latest/cases/00317/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1$ |] + +In this case, the initial value declared for compartment C is +consistent with that calculated by the assignmentRule. Note that since +this assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.1$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 0.0365$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.0025$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre^2^ mole^-1^ | +|Value of parameter p2 |$ 1.5$ |mole second^-1^ | +|Volume of compartment C |$ 0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00318/l2v5/heta-code/output.heta b/latest/cases/00318/l2v5/heta-code/output.heta new file mode 100644 index 000000000..20add0a10 --- /dev/null +++ b/latest/cases/00318/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, }; +C := p1 * p2; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.1 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +k1 @Record 'k1' { } .= 0.0365; +k2 @Record 'k2' { } .= 0.0025; +p1 @Record 'p1' { } .= 0.1; +p2 @Record 'p2' { } .= 0.9; + diff --git a/latest/cases/00318/l2v5/index.heta b/latest/cases/00318/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00318/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00318/l2v5/json/output.json b/latest/cases/00318/l2v5/json/output.json new file mode 100644 index 000000000..e4398ecb7 --- /dev/null +++ b/latest/cases/00318/l2v5/json/output.json @@ -0,0 +1,181 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.0365" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0025" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00318/l3v2/heta-code/output.heta b/latest/cases/00318/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4a3d2b5aa --- /dev/null +++ b/latest/cases/00318/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, }; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 0.9; + +k1 @Const 'k1' { } = 0.0365; +k2 @Const 'k2' { } = 0.0025; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00318/l3v2/index.heta b/latest/cases/00318/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00318/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00318/l3v2/json/output.json b/latest/cases/00318/l3v2/json/output.json new file mode 100644 index 000000000..1ba21e4f0 --- /dev/null +++ b/latest/cases/00318/l3v2/json/output.json @@ -0,0 +1,151 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "ode_": "p1 * p2" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.0365 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0025 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.1 + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Process", + "id": "p2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "p2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00318/model-sbml-l2v5.xml b/latest/cases/00318/model-sbml-l2v5.xml new file mode 100644 index 000000000..9af6980dc --- /dev/null +++ b/latest/cases/00318/model-sbml-l2v5.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00318/model-sbml-l3v2.xml b/latest/cases/00318/model-sbml-l3v2.xml new file mode 100644 index 000000000..732c37751 --- /dev/null +++ b/latest/cases/00318/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + + + + + + 0.1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00318/output.heta b/latest/cases/00318/output.heta new file mode 100644 index 000000000..858a081b8 --- /dev/null +++ b/latest/cases/00318/output.heta @@ -0,0 +1,74 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1$ |] + +In this case, the initial value is not declared for compartment +C and must be calculated by the assignmentRule. Note that +since this assignmentRule must always remain true, it should be considered +during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.1$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 7.5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 2.5$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre^2^ mole^-1^ | +|Volume of compartment C |$ undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, }; +C := p1 * p2; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +p2_proc @Process { actors: = p2, aux: {{"metaid":"rule2"}}, }; +p2_proc := 0.1; + +p2 @Record 'p2' { } .= 0.9; + +k1 @Const 'k1' { } = 0.0365; +k2 @Const 'k2' { } = 0.0025; +p1 @Const 'p1' { } = 0.1; + diff --git a/latest/cases/00318/synopsis.txt b/latest/cases/00318/synopsis.txt new file mode 100644 index 000000000..a19865e0f --- /dev/null +++ b/latest/cases/00318/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment whose + volume is varying. +componentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one varying compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two rules. The assignmentRule assigns value to C +and the rateRule determines the rate at which p2 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | C | $p1 * p2$ | + | Rate | p2 | $0.1$ |] + +In this case, the initial value is not declared for compartment +C and must be calculated by the assignmentRule. Note that +since this assignmentRule must always remain true, it should be considered +during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 1.5$ |mole | +|Initial amount of S3 |$ 1.1$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 7.5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 2.5$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.1$ |litre^2^ mole^-1^ | +|Volume of compartment C |$ undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00319/l2v5/heta-code/output.heta b/latest/cases/00319/l2v5/heta-code/output.heta new file mode 100644 index 000000000..de9a11c68 --- /dev/null +++ b/latest/cases/00319/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.65; + +k1 @Record 'k1' { } .= 1.546; + diff --git a/latest/cases/00319/l2v5/index.heta b/latest/cases/00319/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00319/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00319/l2v5/json/output.json b/latest/cases/00319/l2v5/json/output.json new file mode 100644 index 000000000..178e36e9c --- /dev/null +++ b/latest/cases/00319/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.546" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.65" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00319/l3v2/heta-code/output.heta b/latest/cases/00319/l3v2/heta-code/output.heta new file mode 100644 index 000000000..05e1fe21b --- /dev/null +++ b/latest/cases/00319/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.65; + +k1 @Const 'k1' { } = 1.546; + diff --git a/latest/cases/00319/l3v2/index.heta b/latest/cases/00319/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00319/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00319/l3v2/json/output.json b/latest/cases/00319/l3v2/json/output.json new file mode 100644 index 000000000..55211596a --- /dev/null +++ b/latest/cases/00319/l3v2/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.546 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.65" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00319/model-sbml-l2v5.xml b/latest/cases/00319/model-sbml-l2v5.xml new file mode 100644 index 000000000..fae7134f6 --- /dev/null +++ b/latest/cases/00319/model-sbml-l2v5.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + 0.65 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00319/model-sbml-l3v2.xml b/latest/cases/00319/model-sbml-l3v2.xml new file mode 100644 index 000000000..81cca6abe --- /dev/null +++ b/latest/cases/00319/model-sbml-l3v2.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.65 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00319/output.heta b/latest/cases/00319/output.heta new file mode 100644 index 000000000..95dbc61c4 --- /dev/null +++ b/latest/cases/00319/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a 2D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 2-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.65$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.546$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.65; + +k1 @Const 'k1' { } = 1.546; + diff --git a/latest/cases/00319/synopsis.txt b/latest/cases/00319/synopsis.txt new file mode 100644 index 000000000..6701579fa --- /dev/null +++ b/latest/cases/00319/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a 2D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 2-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.65$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.546$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00320/l2v5/heta-code/output.heta b/latest/cases/00320/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b20301f6a --- /dev/null +++ b/latest/cases/00320/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.65; + +k1 @Record 'k1' { } .= 1.546; + diff --git a/latest/cases/00320/l2v5/index.heta b/latest/cases/00320/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00320/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00320/l2v5/json/output.json b/latest/cases/00320/l2v5/json/output.json new file mode 100644 index 000000000..4679fdc23 --- /dev/null +++ b/latest/cases/00320/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.546" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.65" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00320/l3v2/heta-code/output.heta b/latest/cases/00320/l3v2/heta-code/output.heta new file mode 100644 index 000000000..724e494f4 --- /dev/null +++ b/latest/cases/00320/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.65; + +k1 @Const 'k1' { } = 1.546; + diff --git a/latest/cases/00320/l3v2/index.heta b/latest/cases/00320/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00320/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00320/l3v2/json/output.json b/latest/cases/00320/l3v2/json/output.json new file mode 100644 index 000000000..1abe0c836 --- /dev/null +++ b/latest/cases/00320/l3v2/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.546 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.65" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00320/model-sbml-l2v5.xml b/latest/cases/00320/model-sbml-l2v5.xml new file mode 100644 index 000000000..655d7bd36 --- /dev/null +++ b/latest/cases/00320/model-sbml-l2v5.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + 0.65 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00320/model-sbml-l3v2.xml b/latest/cases/00320/model-sbml-l3v2.xml new file mode 100644 index 000000000..2ae6be80f --- /dev/null +++ b/latest/cases/00320/model-sbml-l3v2.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.65 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00320/output.heta b/latest/cases/00320/output.heta new file mode 100644 index 000000000..33eefed38 --- /dev/null +++ b/latest/cases/00320/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a 1D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 1-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.65$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.546$ |second^-1^ | +|length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.65; + +k1 @Const 'k1' { } = 1.546; + diff --git a/latest/cases/00320/synopsis.txt b/latest/cases/00320/synopsis.txt new file mode 100644 index 000000000..fb956625c --- /dev/null +++ b/latest/cases/00320/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a 1D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 1-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.65$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.546$ |second^-1^ | +|length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00321/l2v5/heta-code/output.heta b/latest/cases/00321/l2v5/heta-code/output.heta new file mode 100644 index 000000000..73b6df8fb --- /dev/null +++ b/latest/cases/00321/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.65; + +k1 @Record 'k1' { } .= 1.546; + diff --git a/latest/cases/00321/l2v5/index.heta b/latest/cases/00321/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00321/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00321/l2v5/json/output.json b/latest/cases/00321/l2v5/json/output.json new file mode 100644 index 000000000..a8effd9f2 --- /dev/null +++ b/latest/cases/00321/l2v5/json/output.json @@ -0,0 +1,115 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.546" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.65" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00321/l3v2/heta-code/output.heta b/latest/cases/00321/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3529ac97d --- /dev/null +++ b/latest/cases/00321/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.65; + +k1 @Const 'k1' { } = 1.546; + diff --git a/latest/cases/00321/l3v2/index.heta b/latest/cases/00321/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00321/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00321/l3v2/json/output.json b/latest/cases/00321/l3v2/json/output.json new file mode 100644 index 000000000..47bd16cd4 --- /dev/null +++ b/latest/cases/00321/l3v2/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.546 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.65" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00321/model-sbml-l2v5.xml b/latest/cases/00321/model-sbml-l2v5.xml new file mode 100644 index 000000000..520fb8985 --- /dev/null +++ b/latest/cases/00321/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + 0.65 + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00321/model-sbml-l3v2.xml b/latest/cases/00321/model-sbml-l3v2.xml new file mode 100644 index 000000000..830ac65d1 --- /dev/null +++ b/latest/cases/00321/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.65 + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00321/output.heta b/latest/cases/00321/output.heta new file mode 100644 index 000000000..30720c2ca --- /dev/null +++ b/latest/cases/00321/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a 0D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 0-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.65$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.546$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.65; + +k1 @Const 'k1' { } = 1.546; + diff --git a/latest/cases/00321/synopsis.txt b/latest/cases/00321/synopsis.txt new file mode 100644 index 000000000..530da5f2d --- /dev/null +++ b/latest/cases/00321/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a 0D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. Compartment +"compartment" is 0-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.65$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.546$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00322/l2v5/heta-code/output.heta b/latest/cases/00322/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e3e17f549 --- /dev/null +++ b/latest/cases/00322/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 0.04 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 100); + +k1 @Record 'k1' { } .= 69; +k2 @Record 'k2' { } .= 0.023; + diff --git a/latest/cases/00322/l2v5/index.heta b/latest/cases/00322/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00322/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00322/l2v5/json/output.json b/latest/cases/00322/l2v5/json/output.json new file mode 100644 index 000000000..ab210842f --- /dev/null +++ b/latest/cases/00322/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.04 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "69" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.023" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 100)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00322/l3v2/heta-code/output.heta b/latest/cases/00322/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3e2e33cf8 --- /dev/null +++ b/latest/cases/00322/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.04 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 100); + +k1 @Const 'k1' { } = 69; +k2 @Const 'k2' { } = 0.023; + diff --git a/latest/cases/00322/l3v2/index.heta b/latest/cases/00322/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00322/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00322/l3v2/json/output.json b/latest/cases/00322/l3v2/json/output.json new file mode 100644 index 000000000..43ade6855 --- /dev/null +++ b/latest/cases/00322/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.04 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 69 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.023 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 100)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00322/model-sbml-l2v5.xml b/latest/cases/00322/model-sbml-l2v5.xml new file mode 100644 index 000000000..057545257 --- /dev/null +++ b/latest/cases/00322/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 1 100 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00322/model-sbml-l3v2.xml b/latest/cases/00322/model-sbml-l3v2.xml new file mode 100644 index 000000000..e9c032c26 --- /dev/null +++ b/latest/cases/00322/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 100 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00322/output.heta b/latest/cases/00322/output.heta new file mode 100644 index 000000000..799b286da --- /dev/null +++ b/latest/cases/00322/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a 2D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$4.0 \x 10^-2$ |mole | +|Initial amount of S4 |$ 1 \x 10^-2$ |mole | +|Value of parameter k1 |$0.69 \x 10^2$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.23 \x 10^-1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.04 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 100); + +k1 @Const 'k1' { } = 69; +k2 @Const 'k2' { } = 0.023; + diff --git a/latest/cases/00322/synopsis.txt b/latest/cases/00322/synopsis.txt new file mode 100644 index 000000000..5447411e9 --- /dev/null +++ b/latest/cases/00322/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a 2D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$4.0 \x 10^-2$ |mole | +|Initial amount of S4 |$ 1 \x 10^-2$ |mole | +|Value of parameter k1 |$0.69 \x 10^2$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.23 \x 10^-1$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00323/l2v5/heta-code/output.heta b/latest/cases/00323/l2v5/heta-code/output.heta new file mode 100644 index 000000000..24387f2ab --- /dev/null +++ b/latest/cases/00323/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1.5e-4 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 2e-4 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 4e-4 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 10000); + +k1 @Record 'k1' { } .= 6900; +k2 @Record 'k2' { } .= 0.0023; + diff --git a/latest/cases/00323/l2v5/index.heta b/latest/cases/00323/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00323/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00323/l2v5/json/output.json b/latest/cases/00323/l2v5/json/output.json new file mode 100644 index 000000000..1a76e73e8 --- /dev/null +++ b/latest/cases/00323/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "4e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "6900" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0023" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 10000)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00323/l3v2/heta-code/output.heta b/latest/cases/00323/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e074bf614 --- /dev/null +++ b/latest/cases/00323/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 4e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 10000); + +k1 @Const 'k1' { } = 6900; +k2 @Const 'k2' { } = 0.0023; + diff --git a/latest/cases/00323/l3v2/index.heta b/latest/cases/00323/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00323/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00323/l3v2/json/output.json b/latest/cases/00323/l3v2/json/output.json new file mode 100644 index 000000000..0be72ac83 --- /dev/null +++ b/latest/cases/00323/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "4e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 6900 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0023 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 10000)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00323/model-sbml-l2v5.xml b/latest/cases/00323/model-sbml-l2v5.xml new file mode 100644 index 000000000..921212a9c --- /dev/null +++ b/latest/cases/00323/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 1 10000 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00323/model-sbml-l3v2.xml b/latest/cases/00323/model-sbml-l3v2.xml new file mode 100644 index 000000000..ffb1bff61 --- /dev/null +++ b/latest/cases/00323/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 10000 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00323/output.heta b/latest/cases/00323/output.heta new file mode 100644 index 000000000..ed248d24a --- /dev/null +++ b/latest/cases/00323/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a 1D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$4.0 \x 10^-4$ |mole | +|Initial amount of S4 |$ 1 \x 10^-4$ |mole | +|Value of parameter k1 |$0.69 \x 10^4$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.23 \x 10^-2$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-4 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 4e-4 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 10000); + +k1 @Const 'k1' { } = 6900; +k2 @Const 'k2' { } = 0.0023; + diff --git a/latest/cases/00323/synopsis.txt b/latest/cases/00323/synopsis.txt new file mode 100644 index 000000000..9f6310583 --- /dev/null +++ b/latest/cases/00323/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a 1D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$4.0 \x 10^-4$ |mole | +|Initial amount of S4 |$ 1 \x 10^-4$ |mole | +|Value of parameter k1 |$0.69 \x 10^4$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.23 \x 10^-2$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00324/l2v5/heta-code/output.heta b/latest/cases/00324/l2v5/heta-code/output.heta new file mode 100644 index 000000000..775208585 --- /dev/null +++ b/latest/cases/00324/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.015; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.04; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 100); + +k1 @Record 'k1' { } .= 69; +k2 @Record 'k2' { } .= 0.023; + diff --git a/latest/cases/00324/l2v5/index.heta b/latest/cases/00324/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00324/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00324/l2v5/json/output.json b/latest/cases/00324/l2v5/json/output.json new file mode 100644 index 000000000..57a9008e6 --- /dev/null +++ b/latest/cases/00324/l2v5/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.04" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "69" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.023" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 100)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00324/l3v2/heta-code/output.heta b/latest/cases/00324/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dd56b21e6 --- /dev/null +++ b/latest/cases/00324/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.015; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.04; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 100); + +k1 @Const 'k1' { } = 69; +k2 @Const 'k2' { } = 0.023; + diff --git a/latest/cases/00324/l3v2/index.heta b/latest/cases/00324/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00324/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00324/l3v2/json/output.json b/latest/cases/00324/l3v2/json/output.json new file mode 100644 index 000000000..5074fca0d --- /dev/null +++ b/latest/cases/00324/l3v2/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.04" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 69 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.023 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 100)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00324/model-sbml-l2v5.xml b/latest/cases/00324/model-sbml-l2v5.xml new file mode 100644 index 000000000..24372114b --- /dev/null +++ b/latest/cases/00324/model-sbml-l2v5.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + 1 100 + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00324/model-sbml-l3v2.xml b/latest/cases/00324/model-sbml-l3v2.xml new file mode 100644 index 000000000..fe80137a7 --- /dev/null +++ b/latest/cases/00324/model-sbml-l3v2.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 100 + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00324/output.heta b/latest/cases/00324/output.heta new file mode 100644 index 000000000..3744a5e0a --- /dev/null +++ b/latest/cases/00324/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a 0D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$4.0 \x 10^-2$ |mole | +|Initial amount of S4 |$ 1 \x 10^-2$ |mole | +|Value of parameter k1 |$0.69 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.23 \x 10^-1$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.015; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.04; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 100); + +k1 @Const 'k1' { } = 69; +k2 @Const 'k2' { } = 0.023; + diff --git a/latest/cases/00324/synopsis.txt b/latest/cases/00324/synopsis.txt new file mode 100644 index 000000000..14556abf4 --- /dev/null +++ b/latest/cases/00324/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a 0D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$4.0 \x 10^-2$ |mole | +|Initial amount of S4 |$ 1 \x 10^-2$ |mole | +|Value of parameter k1 |$0.69 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.23 \x 10^-1$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00325/l2v5/heta-code/output.heta b/latest/cases/00325/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5f42fb4ee --- /dev/null +++ b/latest/cases/00325/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 1.5 / compartment; +S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00325/l2v5/index.heta b/latest/cases/00325/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00325/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00325/l2v5/json/output.json b/latest/cases/00325/l2v5/json/output.json new file mode 100644 index 000000000..d0ed0643f --- /dev/null +++ b/latest/cases/00325/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00325/l3v2/heta-code/output.heta b/latest/cases/00325/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dfb49168a --- /dev/null +++ b/latest/cases/00325/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00325/l3v2/index.heta b/latest/cases/00325/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00325/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00325/l3v2/json/output.json b/latest/cases/00325/l3v2/json/output.json new file mode 100644 index 000000000..3073e51d4 --- /dev/null +++ b/latest/cases/00325/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00325/model-sbml-l2v5.xml b/latest/cases/00325/model-sbml-l2v5.xml new file mode 100644 index 000000000..e89463234 --- /dev/null +++ b/latest/cases/00325/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00325/model-sbml-l3v2.xml b/latest/cases/00325/model-sbml-l3v2.xml new file mode 100644 index 000000000..35e749ee8 --- /dev/null +++ b/latest/cases/00325/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00325/output.heta b/latest/cases/00325/output.heta new file mode 100644 index 000000000..86c16ee39 --- /dev/null +++ b/latest/cases/00325/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a 2D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment; +S4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00325/synopsis.txt b/latest/cases/00325/synopsis.txt new file mode 100644 index 000000000..d1728e911 --- /dev/null +++ b/latest/cases/00325/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a 2D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment "compartment" |$ 1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00326/l2v5/heta-code/output.heta b/latest/cases/00326/l2v5/heta-code/output.heta new file mode 100644 index 000000000..894c4d541 --- /dev/null +++ b/latest/cases/00326/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/length, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: substance/length, compartment: compartment, } .= 1.5 / compartment; +S4 @Species 'S4' { units: substance/length, compartment: compartment, } .= 4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00326/l2v5/index.heta b/latest/cases/00326/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00326/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00326/l2v5/json/output.json b/latest/cases/00326/l2v5/json/output.json new file mode 100644 index 000000000..cbd1892da --- /dev/null +++ b/latest/cases/00326/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00326/l3v2/heta-code/output.heta b/latest/cases/00326/l3v2/heta-code/output.heta new file mode 100644 index 000000000..017c5a3e9 --- /dev/null +++ b/latest/cases/00326/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00326/l3v2/index.heta b/latest/cases/00326/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00326/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00326/l3v2/json/output.json b/latest/cases/00326/l3v2/json/output.json new file mode 100644 index 000000000..fcd7be541 --- /dev/null +++ b/latest/cases/00326/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00326/model-sbml-l2v5.xml b/latest/cases/00326/model-sbml-l2v5.xml new file mode 100644 index 000000000..b400d19c4 --- /dev/null +++ b/latest/cases/00326/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00326/model-sbml-l3v2.xml b/latest/cases/00326/model-sbml-l3v2.xml new file mode 100644 index 000000000..afdce4974 --- /dev/null +++ b/latest/cases/00326/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00326/output.heta b/latest/cases/00326/output.heta new file mode 100644 index 000000000..041ff0e70 --- /dev/null +++ b/latest/cases/00326/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a 1D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment; +S4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00326/synopsis.txt b/latest/cases/00326/synopsis.txt new file mode 100644 index 000000000..d6e9b64fc --- /dev/null +++ b/latest/cases/00326/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a 1D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Length of compartment "compartment" |$ 1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00327/l2v5/heta-code/output.heta b/latest/cases/00327/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b02cdf493 --- /dev/null +++ b/latest/cases/00327/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 2; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00327/l2v5/index.heta b/latest/cases/00327/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00327/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00327/l2v5/json/output.json b/latest/cases/00327/l2v5/json/output.json new file mode 100644 index 000000000..4c82c90dc --- /dev/null +++ b/latest/cases/00327/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00327/l3v2/heta-code/output.heta b/latest/cases/00327/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2c2cb9dd8 --- /dev/null +++ b/latest/cases/00327/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00327/l3v2/index.heta b/latest/cases/00327/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00327/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00327/l3v2/json/output.json b/latest/cases/00327/l3v2/json/output.json new file mode 100644 index 000000000..892b3c677 --- /dev/null +++ b/latest/cases/00327/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00327/model-sbml-l2v5.xml b/latest/cases/00327/model-sbml-l2v5.xml new file mode 100644 index 000000000..eba4ccd8e --- /dev/null +++ b/latest/cases/00327/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00327/model-sbml-l3v2.xml b/latest/cases/00327/model-sbml-l3v2.xml new file mode 100644 index 000000000..aec7e126e --- /dev/null +++ b/latest/cases/00327/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00327/output.heta b/latest/cases/00327/output.heta new file mode 100644 index 000000000..029cf7185 --- /dev/null +++ b/latest/cases/00327/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a 0D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00327/synopsis.txt b/latest/cases/00327/synopsis.txt new file mode 100644 index 000000000..9d4cdd8a3 --- /dev/null +++ b/latest/cases/00327/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a 0D compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 0-dimensional. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00328/l2v5/heta-code/output.heta b/latest/cases/00328/l2v5/heta-code/output.heta new file mode 100644 index 000000000..302330a3b --- /dev/null +++ b/latest/cases/00328/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00328/l2v5/index.heta b/latest/cases/00328/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00328/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00328/l2v5/json/output.json b/latest/cases/00328/l2v5/json/output.json new file mode 100644 index 000000000..b754e8dcd --- /dev/null +++ b/latest/cases/00328/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00328/l3v2/heta-code/output.heta b/latest/cases/00328/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c4a0b8e4f --- /dev/null +++ b/latest/cases/00328/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00328/l3v2/index.heta b/latest/cases/00328/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00328/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00328/l3v2/json/output.json b/latest/cases/00328/l3v2/json/output.json new file mode 100644 index 000000000..303634b41 --- /dev/null +++ b/latest/cases/00328/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00328/model-sbml-l2v5.xml b/latest/cases/00328/model-sbml-l2v5.xml new file mode 100644 index 000000000..1d556d297 --- /dev/null +++ b/latest/cases/00328/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00328/model-sbml-l3v2.xml b/latest/cases/00328/model-sbml-l3v2.xml new file mode 100644 index 000000000..e76dffd98 --- /dev/null +++ b/latest/cases/00328/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00328/output.heta b/latest/cases/00328/output.heta new file mode 100644 index 000000000..3cc7ff267 --- /dev/null +++ b/latest/cases/00328/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 0.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00328/synopsis.txt b/latest/cases/00328/synopsis.txt new file mode 100644 index 000000000..2780eb4d6 --- /dev/null +++ b/latest/cases/00328/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 0.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00329/l2v5/heta-code/output.heta b/latest/cases/00329/l2v5/heta-code/output.heta new file mode 100644 index 000000000..58c65d615 --- /dev/null +++ b/latest/cases/00329/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1.75; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00329/l2v5/index.heta b/latest/cases/00329/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00329/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00329/l2v5/json/output.json b/latest/cases/00329/l2v5/json/output.json new file mode 100644 index 000000000..ef2fee6d7 --- /dev/null +++ b/latest/cases/00329/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1.75" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00329/l3v2/heta-code/output.heta b/latest/cases/00329/l3v2/heta-code/output.heta new file mode 100644 index 000000000..31122c130 --- /dev/null +++ b/latest/cases/00329/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1.75; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00329/l3v2/index.heta b/latest/cases/00329/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00329/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00329/l3v2/json/output.json b/latest/cases/00329/l3v2/json/output.json new file mode 100644 index 000000000..47b3d0f52 --- /dev/null +++ b/latest/cases/00329/l3v2/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1.75" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00329/model-sbml-l2v5.xml b/latest/cases/00329/model-sbml-l2v5.xml new file mode 100644 index 000000000..f5e0191b1 --- /dev/null +++ b/latest/cases/00329/model-sbml-l2v5.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00329/model-sbml-l3v2.xml b/latest/cases/00329/model-sbml-l3v2.xml new file mode 100644 index 000000000..befba5b70 --- /dev/null +++ b/latest/cases/00329/model-sbml-l3v2.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00329/output.heta b/latest/cases/00329/output.heta new file mode 100644 index 000000000..e7930e407 --- /dev/null +++ b/latest/cases/00329/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.75$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1.75; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00329/synopsis.txt b/latest/cases/00329/synopsis.txt new file mode 100644 index 000000000..8d37279a0 --- /dev/null +++ b/latest/cases/00329/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and one parameter named k1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment "compartment" |$ 1.75$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00330/l2v5/heta-code/output.heta b/latest/cases/00330/l2v5/heta-code/output.heta new file mode 100644 index 000000000..70e444904 --- /dev/null +++ b/latest/cases/00330/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 0.93; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 100); + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 0.025; + diff --git a/latest/cases/00330/l2v5/index.heta b/latest/cases/00330/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00330/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00330/l2v5/json/output.json b/latest/cases/00330/l2v5/json/output.json new file mode 100644 index 000000000..a7e668546 --- /dev/null +++ b/latest/cases/00330/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "0.93" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.025" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 100)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00330/l3v2/heta-code/output.heta b/latest/cases/00330/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1609d330d --- /dev/null +++ b/latest/cases/00330/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.93; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 100); + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 0.025; + diff --git a/latest/cases/00330/l3v2/index.heta b/latest/cases/00330/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00330/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00330/l3v2/json/output.json b/latest/cases/00330/l3v2/json/output.json new file mode 100644 index 000000000..3040e5f79 --- /dev/null +++ b/latest/cases/00330/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "0.93" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 100)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00330/model-sbml-l2v5.xml b/latest/cases/00330/model-sbml-l2v5.xml new file mode 100644 index 000000000..5f5dfd8aa --- /dev/null +++ b/latest/cases/00330/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 1 100 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00330/model-sbml-l3v2.xml b/latest/cases/00330/model-sbml-l3v2.xml new file mode 100644 index 000000000..77bc5371a --- /dev/null +++ b/latest/cases/00330/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 100 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00330/output.heta b/latest/cases/00330/output.heta new file mode 100644 index 000000000..f35d8014f --- /dev/null +++ b/latest/cases/00330/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.5 \x 10^-2$ |mole | +|Initial amount of S4 |$ 1 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.93; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.02 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 100); + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 0.025; + diff --git a/latest/cases/00330/synopsis.txt b/latest/cases/00330/synopsis.txt new file mode 100644 index 000000000..719b1e2e5 --- /dev/null +++ b/latest/cases/00330/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.5 \x 10^-2$ |mole | +|Initial amount of S4 |$ 1 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00331/l2v5/heta-code/output.heta b/latest/cases/00331/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8b5d2f55e --- /dev/null +++ b/latest/cases/00331/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Record 'k1' { } .= 1.75; +k2 @Record 'k2' { } .= 0.015; + diff --git a/latest/cases/00331/l2v5/index.heta b/latest/cases/00331/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00331/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00331/l2v5/json/output.json b/latest/cases/00331/l2v5/json/output.json new file mode 100644 index 000000000..f9dcafcff --- /dev/null +++ b/latest/cases/00331/l2v5/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00331/l3v2/heta-code/output.heta b/latest/cases/00331/l3v2/heta-code/output.heta new file mode 100644 index 000000000..555b962d3 --- /dev/null +++ b/latest/cases/00331/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.015; + diff --git a/latest/cases/00331/l3v2/index.heta b/latest/cases/00331/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00331/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00331/l3v2/json/output.json b/latest/cases/00331/l3v2/json/output.json new file mode 100644 index 000000000..82fe48e64 --- /dev/null +++ b/latest/cases/00331/l3v2/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.015 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00331/model-sbml-l2v5.xml b/latest/cases/00331/model-sbml-l2v5.xml new file mode 100644 index 000000000..cbe7079cc --- /dev/null +++ b/latest/cases/00331/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00331/model-sbml-l3v2.xml b/latest/cases/00331/model-sbml-l3v2.xml new file mode 100644 index 000000000..fb985b1b2 --- /dev/null +++ b/latest/cases/00331/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00331/output.heta b/latest/cases/00331/output.heta new file mode 100644 index 000000000..472bc5248 --- /dev/null +++ b/latest/cases/00331/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-2$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.015; + diff --git a/latest/cases/00331/synopsis.txt b/latest/cases/00331/synopsis.txt new file mode 100644 index 000000000..4e81d57c7 --- /dev/null +++ b/latest/cases/00331/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-2$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00332/l2v5/heta-code/output.heta b/latest/cases/00332/l2v5/heta-code/output.heta new file mode 100644 index 000000000..330816f97 --- /dev/null +++ b/latest/cases/00332/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Record 'k1' { } .= 7.5e+5; +k2 @Record 'k2' { } .= 2.5e-4; + diff --git a/latest/cases/00332/l2v5/index.heta b/latest/cases/00332/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00332/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00332/l2v5/json/output.json b/latest/cases/00332/l2v5/json/output.json new file mode 100644 index 000000000..4b8dba9ba --- /dev/null +++ b/latest/cases/00332/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5e-4" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00332/l3v2/heta-code/output.heta b/latest/cases/00332/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0d86ba19f --- /dev/null +++ b/latest/cases/00332/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00332/l3v2/index.heta b/latest/cases/00332/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00332/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00332/l3v2/json/output.json b/latest/cases/00332/l3v2/json/output.json new file mode 100644 index 000000000..837a5200c --- /dev/null +++ b/latest/cases/00332/l3v2/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.00025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00332/model-sbml-l2v5.xml b/latest/cases/00332/model-sbml-l2v5.xml new file mode 100644 index 000000000..cc7faa216 --- /dev/null +++ b/latest/cases/00332/model-sbml-l2v5.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00332/model-sbml-l3v2.xml b/latest/cases/00332/model-sbml-l3v2.xml new file mode 100644 index 000000000..dd81798ef --- /dev/null +++ b/latest/cases/00332/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00332/output.heta b/latest/cases/00332/output.heta new file mode 100644 index 000000000..7e37b52e8 --- /dev/null +++ b/latest/cases/00332/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00332/synopsis.txt b/latest/cases/00332/synopsis.txt new file mode 100644 index 000000000..aa5993e7f --- /dev/null +++ b/latest/cases/00332/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/00333/l2v5/heta-code/output.heta b/latest/cases/00333/l2v5/heta-code/output.heta new file mode 100644 index 000000000..aeb9c9874 --- /dev/null +++ b/latest/cases/00333/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.0015; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.002; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.0015; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.004; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Record 'k1' { } .= 0.693; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00333/l2v5/index.heta b/latest/cases/00333/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00333/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00333/l2v5/json/output.json b/latest/cases/00333/l2v5/json/output.json new file mode 100644 index 000000000..41e5ae9f5 --- /dev/null +++ b/latest/cases/00333/l2v5/json/output.json @@ -0,0 +1,151 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.004" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.693" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00333/l3v2/heta-code/output.heta b/latest/cases/00333/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1315f6c4a --- /dev/null +++ b/latest/cases/00333/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.004; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00333/l3v2/index.heta b/latest/cases/00333/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00333/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00333/l3v2/json/output.json b/latest/cases/00333/l3v2/json/output.json new file mode 100644 index 000000000..d2ba46110 --- /dev/null +++ b/latest/cases/00333/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.004" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.693 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00333/model-sbml-l2v5.xml b/latest/cases/00333/model-sbml-l2v5.xml new file mode 100644 index 000000000..f57003a93 --- /dev/null +++ b/latest/cases/00333/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00333/model-sbml-l3v2.xml b/latest/cases/00333/model-sbml-l3v2.xml new file mode 100644 index 000000000..422e90dd1 --- /dev/null +++ b/latest/cases/00333/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/00333/output.heta b/latest/cases/00333/output.heta new file mode 100644 index 000000000..c890aaedf --- /dev/null +++ b/latest/cases/00333/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains one reaction defined as: + +[{width:25em,=}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains two rules: + +[{width:25em,=}| *Type* | *Variable* | *Formula* | +| Rate | S3 | $k1 * 0.5 10^-3$ | +| Rate | S4 | $-k2 * 0.5 10^-3$ |] + +The initial conditions are as follows: + +[{width:35em,=}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only (meaning that +the attribute %hasOnlySubstanceUnits% is set to true). Thus, they must be +treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.004; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00333/synopsis.txt b/latest/cases/00333/synopsis.txt new file mode 100644 index 000000000..0b1086288 --- /dev/null +++ b/latest/cases/00333/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains one reaction defined as: + +[{width:25em,=}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains two rules: + +[{width:25em,=}| *Type* | *Variable* | *Formula* | +| Rate | S3 | $k1 * 0.5 10^-3$ | +| Rate | S4 | $-k2 * 0.5 10^-3$ |] + +The initial conditions are as follows: + +[{width:35em,=}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species have been declared as having substance units only (meaning that +the attribute %hasOnlySubstanceUnits% is set to true). Thus, they must be +treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00334/l2v5/heta-code/output.heta b/latest/cases/00334/l2v5/heta-code/output.heta new file mode 100644 index 000000000..377bf9520 --- /dev/null +++ b/latest/cases/00334/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1.5e-4 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Record 'k1' { } .= 1.75; +k2 @Record 'k2' { } .= 1.5e-5; + diff --git a/latest/cases/00334/l2v5/index.heta b/latest/cases/00334/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00334/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00334/l2v5/json/output.json b/latest/cases/00334/l2v5/json/output.json new file mode 100644 index 000000000..5049e523c --- /dev/null +++ b/latest/cases/00334/l2v5/json/output.json @@ -0,0 +1,121 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.5e-5" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00334/l3v2/heta-code/output.heta b/latest/cases/00334/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a7688ec9c --- /dev/null +++ b/latest/cases/00334/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.000015; + diff --git a/latest/cases/00334/l3v2/index.heta b/latest/cases/00334/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00334/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00334/l3v2/json/output.json b/latest/cases/00334/l3v2/json/output.json new file mode 100644 index 000000000..329e37adf --- /dev/null +++ b/latest/cases/00334/l3v2/json/output.json @@ -0,0 +1,93 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.000015 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00334/model-sbml-l2v5.xml b/latest/cases/00334/model-sbml-l2v5.xml new file mode 100644 index 000000000..812fe507c --- /dev/null +++ b/latest/cases/00334/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00334/model-sbml-l3v2.xml b/latest/cases/00334/model-sbml-l3v2.xml new file mode 100644 index 000000000..fb9ffb33a --- /dev/null +++ b/latest/cases/00334/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00334/output.heta b/latest/cases/00334/output.heta new file mode 100644 index 000000000..f16e5c806 --- /dev/null +++ b/latest/cases/00334/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S3 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-5$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.000015; + diff --git a/latest/cases/00334/synopsis.txt b/latest/cases/00334/synopsis.txt new file mode 100644 index 000000000..e270c2be9 --- /dev/null +++ b/latest/cases/00334/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S3 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-5$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00335/l2v5/heta-code/output.heta b/latest/cases/00335/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3fdb09150 --- /dev/null +++ b/latest/cases/00335/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Record 'k1' { } .= 1.75; +k2 @Record 'k2' { } .= 1.5e-4; + diff --git a/latest/cases/00335/l2v5/index.heta b/latest/cases/00335/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00335/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00335/l2v5/json/output.json b/latest/cases/00335/l2v5/json/output.json new file mode 100644 index 000000000..c3fbb6088 --- /dev/null +++ b/latest/cases/00335/l2v5/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.5e-4" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00335/l3v2/heta-code/output.heta b/latest/cases/00335/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fef7321dd --- /dev/null +++ b/latest/cases/00335/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.00015; + diff --git a/latest/cases/00335/l3v2/index.heta b/latest/cases/00335/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00335/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00335/l3v2/json/output.json b/latest/cases/00335/l3v2/json/output.json new file mode 100644 index 000000000..47fcfc690 --- /dev/null +++ b/latest/cases/00335/l3v2/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.00015 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00335/model-sbml-l2v5.xml b/latest/cases/00335/model-sbml-l2v5.xml new file mode 100644 index 000000000..790d2fc6b --- /dev/null +++ b/latest/cases/00335/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00335/model-sbml-l3v2.xml b/latest/cases/00335/model-sbml-l3v2.xml new file mode 100644 index 000000000..534faa9e4 --- /dev/null +++ b/latest/cases/00335/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00335/output.heta b/latest/cases/00335/output.heta new file mode 100644 index 000000000..5a7f3551b --- /dev/null +++ b/latest/cases/00335/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S1 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-4$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.00015; + diff --git a/latest/cases/00335/synopsis.txt b/latest/cases/00335/synopsis.txt new file mode 100644 index 000000000..1112c62a7 --- /dev/null +++ b/latest/cases/00335/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S1 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-4$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00336/l2v5/heta-code/output.heta b/latest/cases/00336/l2v5/heta-code/output.heta new file mode 100644 index 000000000..631ffbb75 --- /dev/null +++ b/latest/cases/00336/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Record 'k1' { } .= 1.75; +k2 @Record 'k2' { } .= 0.0015; + diff --git a/latest/cases/00336/l2v5/index.heta b/latest/cases/00336/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00336/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00336/l2v5/json/output.json b/latest/cases/00336/l2v5/json/output.json new file mode 100644 index 000000000..e5ec155ac --- /dev/null +++ b/latest/cases/00336/l2v5/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0015" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00336/l3v2/heta-code/output.heta b/latest/cases/00336/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b7bdb00cf --- /dev/null +++ b/latest/cases/00336/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.0015; + diff --git a/latest/cases/00336/l3v2/index.heta b/latest/cases/00336/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00336/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00336/l3v2/json/output.json b/latest/cases/00336/l3v2/json/output.json new file mode 100644 index 000000000..9e7cc9156 --- /dev/null +++ b/latest/cases/00336/l3v2/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0015 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00336/model-sbml-l2v5.xml b/latest/cases/00336/model-sbml-l2v5.xml new file mode 100644 index 000000000..7842a6114 --- /dev/null +++ b/latest/cases/00336/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00336/model-sbml-l3v2.xml b/latest/cases/00336/model-sbml-l3v2.xml new file mode 100644 index 000000000..bb9e33ff8 --- /dev/null +++ b/latest/cases/00336/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00336/output.heta b/latest/cases/00336/output.heta new file mode 100644 index 000000000..0ef726780 --- /dev/null +++ b/latest/cases/00336/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S2 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-3$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.01 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.0015; + diff --git a/latest/cases/00336/synopsis.txt b/latest/cases/00336/synopsis.txt new file mode 100644 index 000000000..8422f8096 --- /dev/null +++ b/latest/cases/00336/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Species S2 +is labeled as an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-3$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00337/l2v5/heta-code/output.heta b/latest/cases/00337/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f344a6905 --- /dev/null +++ b/latest/cases/00337/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.15 / compartment; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.1 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.1 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Record 'k1' { } .= 1.75; +k2 @Record 'k2' { } .= 0.015; + diff --git a/latest/cases/00337/l2v5/index.heta b/latest/cases/00337/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00337/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00337/l2v5/json/output.json b/latest/cases/00337/l2v5/json/output.json new file mode 100644 index 000000000..4e48b4eca --- /dev/null +++ b/latest/cases/00337/l2v5/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00337/l3v2/heta-code/output.heta b/latest/cases/00337/l3v2/heta-code/output.heta new file mode 100644 index 000000000..decad6294 --- /dev/null +++ b/latest/cases/00337/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.015; + diff --git a/latest/cases/00337/l3v2/index.heta b/latest/cases/00337/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00337/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00337/l3v2/json/output.json b/latest/cases/00337/l3v2/json/output.json new file mode 100644 index 000000000..7e9ad621b --- /dev/null +++ b/latest/cases/00337/l3v2/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.015 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00337/model-sbml-l2v5.xml b/latest/cases/00337/model-sbml-l2v5.xml new file mode 100644 index 000000000..f22faccf2 --- /dev/null +++ b/latest/cases/00337/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00337/model-sbml-l3v2.xml b/latest/cases/00337/model-sbml-l3v2.xml new file mode 100644 index 000000000..d63aa70e5 --- /dev/null +++ b/latest/cases/00337/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00337/output.heta b/latest/cases/00337/output.heta new file mode 100644 index 000000000..70535da20 --- /dev/null +++ b/latest/cases/00337/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Both +species S2 and S3 are labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-2$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.1 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.015; + diff --git a/latest/cases/00337/synopsis.txt b/latest/cases/00337/synopsis.txt new file mode 100644 index 000000000..7880193fb --- /dev/null +++ b/latest/cases/00337/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. Both +species S2 and S3 are labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-2$ |mole | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00338/l2v5/heta-code/output.heta b/latest/cases/00338/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ac7561103 --- /dev/null +++ b/latest/cases/00338/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Record 'k1' { } .= 7.5e+5; +k2 @Record 'k2' { } .= 2.5e-4; + diff --git a/latest/cases/00338/l2v5/index.heta b/latest/cases/00338/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00338/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00338/l2v5/json/output.json b/latest/cases/00338/l2v5/json/output.json new file mode 100644 index 000000000..8fc16d237 --- /dev/null +++ b/latest/cases/00338/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5e-4" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00338/l3v2/heta-code/output.heta b/latest/cases/00338/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e7f8aed02 --- /dev/null +++ b/latest/cases/00338/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00338/l3v2/index.heta b/latest/cases/00338/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00338/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00338/l3v2/json/output.json b/latest/cases/00338/l3v2/json/output.json new file mode 100644 index 000000000..34323d43b --- /dev/null +++ b/latest/cases/00338/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.00025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00338/model-sbml-l2v5.xml b/latest/cases/00338/model-sbml-l2v5.xml new file mode 100644 index 000000000..03ab98e9d --- /dev/null +++ b/latest/cases/00338/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00338/model-sbml-l3v2.xml b/latest/cases/00338/model-sbml-l3v2.xml new file mode 100644 index 000000000..1fd8156b5 --- /dev/null +++ b/latest/cases/00338/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00338/output.heta b/latest/cases/00338/output.heta new file mode 100644 index 000000000..fda1150d4 --- /dev/null +++ b/latest/cases/00338/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S1 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00338/synopsis.txt b/latest/cases/00338/synopsis.txt new file mode 100644 index 000000000..ff4f9dde5 --- /dev/null +++ b/latest/cases/00338/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S1 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00339/l2v5/heta-code/output.heta b/latest/cases/00339/l2v5/heta-code/output.heta new file mode 100644 index 000000000..752900383 --- /dev/null +++ b/latest/cases/00339/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Record 'k1' { } .= 7.5e+5; +k2 @Record 'k2' { } .= 2.5e-4; + diff --git a/latest/cases/00339/l2v5/index.heta b/latest/cases/00339/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00339/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00339/l2v5/json/output.json b/latest/cases/00339/l2v5/json/output.json new file mode 100644 index 000000000..008a09765 --- /dev/null +++ b/latest/cases/00339/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5e-4" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00339/l3v2/heta-code/output.heta b/latest/cases/00339/l3v2/heta-code/output.heta new file mode 100644 index 000000000..11c002733 --- /dev/null +++ b/latest/cases/00339/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00339/l3v2/index.heta b/latest/cases/00339/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00339/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00339/l3v2/json/output.json b/latest/cases/00339/l3v2/json/output.json new file mode 100644 index 000000000..fb8be6b6f --- /dev/null +++ b/latest/cases/00339/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.00025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00339/model-sbml-l2v5.xml b/latest/cases/00339/model-sbml-l2v5.xml new file mode 100644 index 000000000..df3404569 --- /dev/null +++ b/latest/cases/00339/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00339/model-sbml-l3v2.xml b/latest/cases/00339/model-sbml-l3v2.xml new file mode 100644 index 000000000..f891e7fe9 --- /dev/null +++ b/latest/cases/00339/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00339/output.heta b/latest/cases/00339/output.heta new file mode 100644 index 000000000..38d3ce9f4 --- /dev/null +++ b/latest/cases/00339/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S3 is labeled as an SBML boundary species. The model contains two +reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00339/synopsis.txt b/latest/cases/00339/synopsis.txt new file mode 100644 index 000000000..b1631547d --- /dev/null +++ b/latest/cases/00339/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S3 is labeled as an SBML boundary species. The model contains two +reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00340/l2v5/heta-code/output.heta b/latest/cases/00340/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a60f87f24 --- /dev/null +++ b/latest/cases/00340/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Record 'k1' { } .= 7.5e+5; +k2 @Record 'k2' { } .= 2.5e-4; + diff --git a/latest/cases/00340/l2v5/index.heta b/latest/cases/00340/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00340/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00340/l2v5/json/output.json b/latest/cases/00340/l2v5/json/output.json new file mode 100644 index 000000000..415576b0e --- /dev/null +++ b/latest/cases/00340/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5e-4" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00340/l3v2/heta-code/output.heta b/latest/cases/00340/l3v2/heta-code/output.heta new file mode 100644 index 000000000..528241555 --- /dev/null +++ b/latest/cases/00340/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00340/l3v2/index.heta b/latest/cases/00340/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00340/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00340/l3v2/json/output.json b/latest/cases/00340/l3v2/json/output.json new file mode 100644 index 000000000..852398913 --- /dev/null +++ b/latest/cases/00340/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.00025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00340/model-sbml-l2v5.xml b/latest/cases/00340/model-sbml-l2v5.xml new file mode 100644 index 000000000..b424d1ffa --- /dev/null +++ b/latest/cases/00340/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00340/model-sbml-l3v2.xml b/latest/cases/00340/model-sbml-l3v2.xml new file mode 100644 index 000000000..4943a21f2 --- /dev/null +++ b/latest/cases/00340/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00340/output.heta b/latest/cases/00340/output.heta new file mode 100644 index 000000000..50a68ca9d --- /dev/null +++ b/latest/cases/00340/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S4 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00340/synopsis.txt b/latest/cases/00340/synopsis.txt new file mode 100644 index 000000000..5c76591ce --- /dev/null +++ b/latest/cases/00340/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S4 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00341/l2v5/heta-code/output.heta b/latest/cases/00341/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ac7561103 --- /dev/null +++ b/latest/cases/00341/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Record 'k1' { } .= 7.5e+5; +k2 @Record 'k2' { } .= 2.5e-4; + diff --git a/latest/cases/00341/l2v5/index.heta b/latest/cases/00341/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00341/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00341/l2v5/json/output.json b/latest/cases/00341/l2v5/json/output.json new file mode 100644 index 000000000..8fc16d237 --- /dev/null +++ b/latest/cases/00341/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5e-4" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00341/l3v2/heta-code/output.heta b/latest/cases/00341/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e7f8aed02 --- /dev/null +++ b/latest/cases/00341/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00341/l3v2/index.heta b/latest/cases/00341/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00341/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00341/l3v2/json/output.json b/latest/cases/00341/l3v2/json/output.json new file mode 100644 index 000000000..34323d43b --- /dev/null +++ b/latest/cases/00341/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.00025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00341/model-sbml-l2v5.xml b/latest/cases/00341/model-sbml-l2v5.xml new file mode 100644 index 000000000..c7e7c5ffe --- /dev/null +++ b/latest/cases/00341/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00341/model-sbml-l3v2.xml b/latest/cases/00341/model-sbml-l3v2.xml new file mode 100644 index 000000000..9a3726b92 --- /dev/null +++ b/latest/cases/00341/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00341/output.heta b/latest/cases/00341/output.heta new file mode 100644 index 000000000..886a8daeb --- /dev/null +++ b/latest/cases/00341/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. Both +species S1 and S4 are labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00341/synopsis.txt b/latest/cases/00341/synopsis.txt new file mode 100644 index 000000000..777eb5349 --- /dev/null +++ b/latest/cases/00341/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. Both +species S1 and S4 are labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00342/l2v5/heta-code/output.heta b/latest/cases/00342/l2v5/heta-code/output.heta new file mode 100644 index 000000000..752900383 --- /dev/null +++ b/latest/cases/00342/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Record 'k1' { } .= 7.5e+5; +k2 @Record 'k2' { } .= 2.5e-4; + diff --git a/latest/cases/00342/l2v5/index.heta b/latest/cases/00342/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00342/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00342/l2v5/json/output.json b/latest/cases/00342/l2v5/json/output.json new file mode 100644 index 000000000..008a09765 --- /dev/null +++ b/latest/cases/00342/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5e-4" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00342/l3v2/heta-code/output.heta b/latest/cases/00342/l3v2/heta-code/output.heta new file mode 100644 index 000000000..11c002733 --- /dev/null +++ b/latest/cases/00342/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00342/l3v2/index.heta b/latest/cases/00342/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00342/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00342/l3v2/json/output.json b/latest/cases/00342/l3v2/json/output.json new file mode 100644 index 000000000..fb8be6b6f --- /dev/null +++ b/latest/cases/00342/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "compartment * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.00025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00342/model-sbml-l2v5.xml b/latest/cases/00342/model-sbml-l2v5.xml new file mode 100644 index 000000000..27daaf57f --- /dev/null +++ b/latest/cases/00342/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00342/model-sbml-l3v2.xml b/latest/cases/00342/model-sbml-l3v2.xml new file mode 100644 index 000000000..bac768428 --- /dev/null +++ b/latest/cases/00342/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/00342/output.heta b/latest/cases/00342/output.heta new file mode 100644 index 000000000..6428f204a --- /dev/null +++ b/latest/cases/00342/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. Both +species S3 and S4 are labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := compartment * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := compartment * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/00342/synopsis.txt b/latest/cases/00342/synopsis.txt new file mode 100644 index 000000000..f5de0586a --- /dev/null +++ b/latest/cases/00342/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. Both +species S3 and S4 are labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00343/l2v5/heta-code/output.heta b/latest/cases/00343/l2v5/heta-code/output.heta new file mode 100644 index 000000000..048a6bcdc --- /dev/null +++ b/latest/cases/00343/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Record 'k1' { } .= 0.693; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00343/l2v5/index.heta b/latest/cases/00343/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00343/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00343/l2v5/json/output.json b/latest/cases/00343/l2v5/json/output.json new file mode 100644 index 000000000..8ef90da9c --- /dev/null +++ b/latest/cases/00343/l2v5/json/output.json @@ -0,0 +1,148 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.693" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00343/l3v2/heta-code/output.heta b/latest/cases/00343/l3v2/heta-code/output.heta new file mode 100644 index 000000000..88ad58036 --- /dev/null +++ b/latest/cases/00343/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00343/l3v2/index.heta b/latest/cases/00343/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00343/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00343/l3v2/json/output.json b/latest/cases/00343/l3v2/json/output.json new file mode 100644 index 000000000..6ec3d5f69 --- /dev/null +++ b/latest/cases/00343/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.693 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00343/model-sbml-l2v5.xml b/latest/cases/00343/model-sbml-l2v5.xml new file mode 100644 index 000000000..c967aeafe --- /dev/null +++ b/latest/cases/00343/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00343/model-sbml-l3v2.xml b/latest/cases/00343/model-sbml-l3v2.xml new file mode 100644 index 000000000..f517b8dc0 --- /dev/null +++ b/latest/cases/00343/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00343/output.heta b/latest/cases/00343/output.heta new file mode 100644 index 000000000..bd50e97e6 --- /dev/null +++ b/latest/cases/00343/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S1 is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00343/synopsis.txt b/latest/cases/00343/synopsis.txt new file mode 100644 index 000000000..bf492f991 --- /dev/null +++ b/latest/cases/00343/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S1 is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00344/l2v5/heta-code/output.heta b/latest/cases/00344/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d7ec0c5ce --- /dev/null +++ b/latest/cases/00344/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Record 'k1' { } .= 0.693; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00344/l2v5/index.heta b/latest/cases/00344/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00344/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00344/l2v5/json/output.json b/latest/cases/00344/l2v5/json/output.json new file mode 100644 index 000000000..5890a6ed0 --- /dev/null +++ b/latest/cases/00344/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.693" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00344/l3v2/heta-code/output.heta b/latest/cases/00344/l3v2/heta-code/output.heta new file mode 100644 index 000000000..33bfb4f41 --- /dev/null +++ b/latest/cases/00344/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00344/l3v2/index.heta b/latest/cases/00344/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00344/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00344/l3v2/json/output.json b/latest/cases/00344/l3v2/json/output.json new file mode 100644 index 000000000..11acb390b --- /dev/null +++ b/latest/cases/00344/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.693 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00344/model-sbml-l2v5.xml b/latest/cases/00344/model-sbml-l2v5.xml new file mode 100644 index 000000000..6758dd693 --- /dev/null +++ b/latest/cases/00344/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00344/model-sbml-l3v2.xml b/latest/cases/00344/model-sbml-l3v2.xml new file mode 100644 index 000000000..d78ffaca7 --- /dev/null +++ b/latest/cases/00344/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00344/output.heta b/latest/cases/00344/output.heta new file mode 100644 index 000000000..dd4f753ac --- /dev/null +++ b/latest/cases/00344/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S3 is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00344/synopsis.txt b/latest/cases/00344/synopsis.txt new file mode 100644 index 000000000..ebf7de2bb --- /dev/null +++ b/latest/cases/00344/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S3 is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00345/l2v5/heta-code/output.heta b/latest/cases/00345/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d7ec0c5ce --- /dev/null +++ b/latest/cases/00345/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Record 'k1' { } .= 0.693; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00345/l2v5/index.heta b/latest/cases/00345/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00345/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00345/l2v5/json/output.json b/latest/cases/00345/l2v5/json/output.json new file mode 100644 index 000000000..5890a6ed0 --- /dev/null +++ b/latest/cases/00345/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.693" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00345/l3v2/heta-code/output.heta b/latest/cases/00345/l3v2/heta-code/output.heta new file mode 100644 index 000000000..33bfb4f41 --- /dev/null +++ b/latest/cases/00345/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00345/l3v2/index.heta b/latest/cases/00345/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00345/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00345/l3v2/json/output.json b/latest/cases/00345/l3v2/json/output.json new file mode 100644 index 000000000..11acb390b --- /dev/null +++ b/latest/cases/00345/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.693 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00345/model-sbml-l2v5.xml b/latest/cases/00345/model-sbml-l2v5.xml new file mode 100644 index 000000000..96110b336 --- /dev/null +++ b/latest/cases/00345/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00345/model-sbml-l3v2.xml b/latest/cases/00345/model-sbml-l3v2.xml new file mode 100644 index 000000000..13cbab0bf --- /dev/null +++ b/latest/cases/00345/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00345/output.heta b/latest/cases/00345/output.heta new file mode 100644 index 000000000..cea361922 --- /dev/null +++ b/latest/cases/00345/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S4 is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00345/synopsis.txt b/latest/cases/00345/synopsis.txt new file mode 100644 index 000000000..67acb2d80 --- /dev/null +++ b/latest/cases/00345/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Species S4 is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00346/l2v5/heta-code/output.heta b/latest/cases/00346/l2v5/heta-code/output.heta new file mode 100644 index 000000000..048a6bcdc --- /dev/null +++ b/latest/cases/00346/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Record 'k1' { } .= 0.693; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00346/l2v5/index.heta b/latest/cases/00346/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00346/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00346/l2v5/json/output.json b/latest/cases/00346/l2v5/json/output.json new file mode 100644 index 000000000..8ef90da9c --- /dev/null +++ b/latest/cases/00346/l2v5/json/output.json @@ -0,0 +1,148 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.693" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00346/l3v2/heta-code/output.heta b/latest/cases/00346/l3v2/heta-code/output.heta new file mode 100644 index 000000000..88ad58036 --- /dev/null +++ b/latest/cases/00346/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00346/l3v2/index.heta b/latest/cases/00346/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00346/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00346/l3v2/json/output.json b/latest/cases/00346/l3v2/json/output.json new file mode 100644 index 000000000..6ec3d5f69 --- /dev/null +++ b/latest/cases/00346/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "boundary": true, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.693 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00346/model-sbml-l2v5.xml b/latest/cases/00346/model-sbml-l2v5.xml new file mode 100644 index 000000000..e55cefcce --- /dev/null +++ b/latest/cases/00346/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00346/model-sbml-l3v2.xml b/latest/cases/00346/model-sbml-l3v2.xml new file mode 100644 index 000000000..b65444bea --- /dev/null +++ b/latest/cases/00346/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00346/output.heta b/latest/cases/00346/output.heta new file mode 100644 index 000000000..74c221148 --- /dev/null +++ b/latest/cases/00346/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. Both +species S1 and S4 are labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00346/synopsis.txt b/latest/cases/00346/synopsis.txt new file mode 100644 index 000000000..04f1d8e8b --- /dev/null +++ b/latest/cases/00346/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. Both +species S1 and S4 are labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00347/l2v5/heta-code/output.heta b/latest/cases/00347/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d7ec0c5ce --- /dev/null +++ b/latest/cases/00347/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: substance/volume, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Record 'k1' { } .= 0.693; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00347/l2v5/index.heta b/latest/cases/00347/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00347/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00347/l2v5/json/output.json b/latest/cases/00347/l2v5/json/output.json new file mode 100644 index 000000000..5890a6ed0 --- /dev/null +++ b/latest/cases/00347/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.693" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00347/l3v2/heta-code/output.heta b/latest/cases/00347/l3v2/heta-code/output.heta new file mode 100644 index 000000000..33bfb4f41 --- /dev/null +++ b/latest/cases/00347/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00347/l3v2/index.heta b/latest/cases/00347/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00347/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00347/l3v2/json/output.json b/latest/cases/00347/l3v2/json/output.json new file mode 100644 index 000000000..11acb390b --- /dev/null +++ b/latest/cases/00347/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.004 / compartment" + }, + "compartment": "compartment" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "compartment * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.693 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00347/model-sbml-l2v5.xml b/latest/cases/00347/model-sbml-l2v5.xml new file mode 100644 index 000000000..7684659ef --- /dev/null +++ b/latest/cases/00347/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00347/model-sbml-l3v2.xml b/latest/cases/00347/model-sbml-l3v2.xml new file mode 100644 index 000000000..71866e54e --- /dev/null +++ b/latest/cases/00347/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/00347/output.heta b/latest/cases/00347/output.heta new file mode 100644 index 000000000..cb9899ba3 --- /dev/null +++ b/latest/cases/00347/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. Both +species S3 and S4 are labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment; +S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment; +S4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := compartment * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00347/synopsis.txt b/latest/cases/00347/synopsis.txt new file mode 100644 index 000000000..e24adb76f --- /dev/null +++ b/latest/cases/00347/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. Both +species S3 and S4 are labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * compartment$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 10^-3$ | + | Rate | S4 | $-k2 * 0.5 10^-3$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00348/l2v5/heta-code/output.heta b/latest/cases/00348/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3ddf80ef5 --- /dev/null +++ b/latest/cases/00348/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00348/l2v5/index.heta b/latest/cases/00348/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00348/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00348/l2v5/json/output.json b/latest/cases/00348/l2v5/json/output.json new file mode 100644 index 000000000..66e952b39 --- /dev/null +++ b/latest/cases/00348/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00348/l3v2/heta-code/output.heta b/latest/cases/00348/l3v2/heta-code/output.heta new file mode 100644 index 000000000..efdc2cdf5 --- /dev/null +++ b/latest/cases/00348/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00348/l3v2/index.heta b/latest/cases/00348/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00348/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00348/l3v2/json/output.json b/latest/cases/00348/l3v2/json/output.json new file mode 100644 index 000000000..5838333cb --- /dev/null +++ b/latest/cases/00348/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00348/model-sbml-l2v5.xml b/latest/cases/00348/model-sbml-l2v5.xml new file mode 100644 index 000000000..1256606f5 --- /dev/null +++ b/latest/cases/00348/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00348/model-sbml-l3v2.xml b/latest/cases/00348/model-sbml-l3v2.xml new file mode 100644 index 000000000..235c82fdf --- /dev/null +++ b/latest/cases/00348/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00348/output.heta b/latest/cases/00348/output.heta new file mode 100644 index 000000000..c6ed246ae --- /dev/null +++ b/latest/cases/00348/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00348/synopsis.txt b/latest/cases/00348/synopsis.txt new file mode 100644 index 000000000..28927b4eb --- /dev/null +++ b/latest/cases/00348/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00349/l2v5/heta-code/output.heta b/latest/cases/00349/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c926f44b1 --- /dev/null +++ b/latest/cases/00349/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00349/l2v5/index.heta b/latest/cases/00349/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00349/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00349/l2v5/json/output.json b/latest/cases/00349/l2v5/json/output.json new file mode 100644 index 000000000..58d3ccfb5 --- /dev/null +++ b/latest/cases/00349/l2v5/json/output.json @@ -0,0 +1,146 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00349/l3v2/heta-code/output.heta b/latest/cases/00349/l3v2/heta-code/output.heta new file mode 100644 index 000000000..eb0cfd169 --- /dev/null +++ b/latest/cases/00349/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00349/l3v2/index.heta b/latest/cases/00349/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00349/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00349/l3v2/json/output.json b/latest/cases/00349/l3v2/json/output.json new file mode 100644 index 000000000..4dcf79ab6 --- /dev/null +++ b/latest/cases/00349/l3v2/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + } +] \ No newline at end of file diff --git a/latest/cases/00349/model-sbml-l2v5.xml b/latest/cases/00349/model-sbml-l2v5.xml new file mode 100644 index 000000000..343bff122 --- /dev/null +++ b/latest/cases/00349/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00349/model-sbml-l3v2.xml b/latest/cases/00349/model-sbml-l3v2.xml new file mode 100644 index 000000000..7b760e4fc --- /dev/null +++ b/latest/cases/00349/model-sbml-l3v2.xml @@ -0,0 +1,113 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00349/output.heta b/latest/cases/00349/output.heta new file mode 100644 index 000000000..dd442a0ac --- /dev/null +++ b/latest/cases/00349/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00349/synopsis.txt b/latest/cases/00349/synopsis.txt new file mode 100644 index 000000000..9059b3cee --- /dev/null +++ b/latest/cases/00349/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00350/l2v5/heta-code/output.heta b/latest/cases/00350/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e7fa7e879 --- /dev/null +++ b/latest/cases/00350/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00350/l2v5/index.heta b/latest/cases/00350/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00350/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00350/l2v5/json/output.json b/latest/cases/00350/l2v5/json/output.json new file mode 100644 index 000000000..18b152575 --- /dev/null +++ b/latest/cases/00350/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00350/l3v2/heta-code/output.heta b/latest/cases/00350/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6d08a2f33 --- /dev/null +++ b/latest/cases/00350/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00350/l3v2/index.heta b/latest/cases/00350/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00350/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00350/l3v2/json/output.json b/latest/cases/00350/l3v2/json/output.json new file mode 100644 index 000000000..a8aeaabfc --- /dev/null +++ b/latest/cases/00350/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00350/model-sbml-l2v5.xml b/latest/cases/00350/model-sbml-l2v5.xml new file mode 100644 index 000000000..1da1f17a9 --- /dev/null +++ b/latest/cases/00350/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00350/model-sbml-l3v2.xml b/latest/cases/00350/model-sbml-l3v2.xml new file mode 100644 index 000000000..8c95e35f1 --- /dev/null +++ b/latest/cases/00350/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00350/output.heta b/latest/cases/00350/output.heta new file mode 100644 index 000000000..4a9e383a6 --- /dev/null +++ b/latest/cases/00350/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00350/synopsis.txt b/latest/cases/00350/synopsis.txt new file mode 100644 index 000000000..c8b5cee86 --- /dev/null +++ b/latest/cases/00350/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00351/l2v5/heta-code/output.heta b/latest/cases/00351/l2v5/heta-code/output.heta new file mode 100644 index 000000000..747077e0e --- /dev/null +++ b/latest/cases/00351/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001 / C; +S1 [event1]= (1 / 500); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.0012 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.002 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 750; +k2 @Record 'k2' { } .= 250; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00351/l2v5/index.heta b/latest/cases/00351/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00351/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00351/l2v5/json/output.json b/latest/cases/00351/l2v5/json/output.json new file mode 100644 index 000000000..a488f71a3 --- /dev/null +++ b/latest/cases/00351/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C", + "event1": "(1 / 500)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "750" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "250" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00351/l3v2/heta-code/output.heta b/latest/cases/00351/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fe11dd0bb --- /dev/null +++ b/latest/cases/00351/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S1 [event1]= (1 / 500); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.002 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00351/l3v2/index.heta b/latest/cases/00351/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00351/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00351/l3v2/json/output.json b/latest/cases/00351/l3v2/json/output.json new file mode 100644 index 000000000..ac12379c8 --- /dev/null +++ b/latest/cases/00351/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C", + "event1": "(1 / 500)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 250 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + } +] \ No newline at end of file diff --git a/latest/cases/00351/model-sbml-l2v5.xml b/latest/cases/00351/model-sbml-l2v5.xml new file mode 100644 index 000000000..4fffd640a --- /dev/null +++ b/latest/cases/00351/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 500 + + + + + + + diff --git a/latest/cases/00351/model-sbml-l3v2.xml b/latest/cases/00351/model-sbml-l3v2.xml new file mode 100644 index 000000000..a8c2a3420 --- /dev/null +++ b/latest/cases/00351/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 500 + + + + + + + diff --git a/latest/cases/00351/output.heta b/latest/cases/00351/output.heta new file mode 100644 index 000000000..77e914925 --- /dev/null +++ b/latest/cases/00351/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns value to species S1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S1 [event1]= (1 / 500); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.002 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00351/synopsis.txt b/latest/cases/00351/synopsis.txt new file mode 100644 index 000000000..c016411a8 --- /dev/null +++ b/latest/cases/00351/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns value to species S1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00352/l2v5/heta-code/output.heta b/latest/cases/00352/l2v5/heta-code/output.heta new file mode 100644 index 000000000..662cea6fc --- /dev/null +++ b/latest/cases/00352/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S1 [event1]= (1 / 50); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.012 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.02 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.01 / C; +S4 [event2]= (1 / 100); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 25; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (9 / 400), }; + diff --git a/latest/cases/00352/l2v5/index.heta b/latest/cases/00352/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00352/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00352/l2v5/json/output.json b/latest/cases/00352/l2v5/json/output.json new file mode 100644 index 000000000..d5a8988c1 --- /dev/null +++ b/latest/cases/00352/l2v5/json/output.json @@ -0,0 +1,164 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C", + "event1": "(1 / 50)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C", + "event2": "(1 / 100)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > (9 / 400)" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00352/l3v2/heta-code/output.heta b/latest/cases/00352/l3v2/heta-code/output.heta new file mode 100644 index 000000000..28328170d --- /dev/null +++ b/latest/cases/00352/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S1 [event1]= (1 / 50); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.01 / C; +S4 [event2]= (1 / 100); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (9 / 400), }; + diff --git a/latest/cases/00352/l3v2/index.heta b/latest/cases/00352/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00352/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00352/l3v2/json/output.json b/latest/cases/00352/l3v2/json/output.json new file mode 100644 index 000000000..498dc8ac9 --- /dev/null +++ b/latest/cases/00352/l3v2/json/output.json @@ -0,0 +1,136 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C", + "event1": "(1 / 50)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C", + "event2": "(1 / 100)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > (9 / 400)" + } +] \ No newline at end of file diff --git a/latest/cases/00352/model-sbml-l2v5.xml b/latest/cases/00352/model-sbml-l2v5.xml new file mode 100644 index 000000000..fed36956e --- /dev/null +++ b/latest/cases/00352/model-sbml-l2v5.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 50 + + + + + + + + + + S3 + 9 400 + + + + + + + 1 100 + + + + + + + diff --git a/latest/cases/00352/model-sbml-l3v2.xml b/latest/cases/00352/model-sbml-l3v2.xml new file mode 100644 index 000000000..8e8fdb21f --- /dev/null +++ b/latest/cases/00352/model-sbml-l3v2.xml @@ -0,0 +1,117 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 50 + + + + + + + + + + S3 + 9 400 + + + + + + + 1 100 + + + + + + + diff --git a/latest/cases/00352/output.heta b/latest/cases/00352/output.heta new file mode 100644 index 000000000..bdeedde53 --- /dev/null +++ b/latest/cases/00352/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign value to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-2$ |] + | Event2 | $S3 > 2.25 \x 10^-2$ | $-$ | $S4 -> 1 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S1 [event1]= (1 / 50); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.01 / C; +S4 [event2]= (1 / 100); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (9 / 400), }; + diff --git a/latest/cases/00352/synopsis.txt b/latest/cases/00352/synopsis.txt new file mode 100644 index 000000000..d8dacf33c --- /dev/null +++ b/latest/cases/00352/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign value to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-2$ |] + | Event2 | $S3 > 2.25 \x 10^-2$ | $-$ | $S4 -> 1 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00353/l2v5/heta-code/output.heta b/latest/cases/00353/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a60afef78 --- /dev/null +++ b/latest/cases/00353/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1 / C; +S1 [event1]= (1 / 5); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.12 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.2 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.1 / C; +S4 [event1]= (1 / 20); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 2.5; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00353/l2v5/index.heta b/latest/cases/00353/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00353/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00353/l2v5/json/output.json b/latest/cases/00353/l2v5/json/output.json new file mode 100644 index 000000000..3649cf228 --- /dev/null +++ b/latest/cases/00353/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C", + "event1": "(1 / 5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.12 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C", + "event1": "(1 / 20)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00353/l3v2/heta-code/output.heta b/latest/cases/00353/l3v2/heta-code/output.heta new file mode 100644 index 000000000..913fd88bc --- /dev/null +++ b/latest/cases/00353/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S1 [event1]= (1 / 5); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1 / C; +S4 [event1]= (1 / 20); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00353/l3v2/index.heta b/latest/cases/00353/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00353/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00353/l3v2/json/output.json b/latest/cases/00353/l3v2/json/output.json new file mode 100644 index 000000000..46f28a09b --- /dev/null +++ b/latest/cases/00353/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C", + "event1": "(1 / 5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.12 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C", + "event1": "(1 / 20)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + } +] \ No newline at end of file diff --git a/latest/cases/00353/model-sbml-l2v5.xml b/latest/cases/00353/model-sbml-l2v5.xml new file mode 100644 index 000000000..f1cf6473d --- /dev/null +++ b/latest/cases/00353/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5 + + + + + 1 20 + + + + + + + diff --git a/latest/cases/00353/model-sbml-l3v2.xml b/latest/cases/00353/model-sbml-l3v2.xml new file mode 100644 index 000000000..ffd573903 --- /dev/null +++ b/latest/cases/00353/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5 + + + + + 1 20 + + + + + + + diff --git a/latest/cases/00353/output.heta b/latest/cases/00353/output.heta new file mode 100644 index 000000000..2b0fb1c13 --- /dev/null +++ b/latest/cases/00353/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-1$ |] + | | | | $S4 -> 0.5 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S1 [event1]= (1 / 5); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1 / C; +S4 [event1]= (1 / 20); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00353/synopsis.txt b/latest/cases/00353/synopsis.txt new file mode 100644 index 000000000..1d9c16c9b --- /dev/null +++ b/latest/cases/00353/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-1$ |] + | | | | $S4 -> 0.5 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00354/l2v5/heta-code/output.heta b/latest/cases/00354/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b19a2b763 --- /dev/null +++ b/latest/cases/00354/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.8; +k4 @Record 'k4' { } .= 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00354/l2v5/index.heta b/latest/cases/00354/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00354/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00354/l2v5/json/output.json b/latest/cases/00354/l2v5/json/output.json new file mode 100644 index 000000000..0cf9e2cc3 --- /dev/null +++ b/latest/cases/00354/l2v5/json/output.json @@ -0,0 +1,164 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.8" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00354/l3v2/heta-code/output.heta b/latest/cases/00354/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d818d3899 --- /dev/null +++ b/latest/cases/00354/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00354/l3v2/index.heta b/latest/cases/00354/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00354/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00354/l3v2/json/output.json b/latest/cases/00354/l3v2/json/output.json new file mode 100644 index 000000000..614cb5cbe --- /dev/null +++ b/latest/cases/00354/l3v2/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.8 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.2 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00354/model-sbml-l2v5.xml b/latest/cases/00354/model-sbml-l2v5.xml new file mode 100644 index 000000000..f538d9c7d --- /dev/null +++ b/latest/cases/00354/model-sbml-l2v5.xml @@ -0,0 +1,103 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00354/model-sbml-l3v2.xml b/latest/cases/00354/model-sbml-l3v2.xml new file mode 100644 index 000000000..fd5173e30 --- /dev/null +++ b/latest/cases/00354/model-sbml-l3v2.xml @@ -0,0 +1,120 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00354/output.heta b/latest/cases/00354/output.heta new file mode 100644 index 000000000..4e550e260 --- /dev/null +++ b/latest/cases/00354/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +The eventAssignment uses the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00354/synopsis.txt b/latest/cases/00354/synopsis.txt new file mode 100644 index 000000000..ce2031355 --- /dev/null +++ b/latest/cases/00354/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +The eventAssignment uses the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00355/l2v5/build.log b/latest/cases/00355/l2v5/build.log new file mode 100644 index 000000000..ce5f30203 --- /dev/null +++ b/latest/cases/00355/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00355/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00355/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00355/model-sbml-l2v5.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 93 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00355/l2v5/index.heta b/latest/cases/00355/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00355/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00355/l3v2/build.log b/latest/cases/00355/l3v2/build.log new file mode 100644 index 000000000..33e84b270 --- /dev/null +++ b/latest/cases/00355/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00355/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00355/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00355/model-sbml-l3v2.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 88 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00355/l3v2/index.heta b/latest/cases/00355/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00355/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00355/model-sbml-l2v5.xml b/latest/cases/00355/model-sbml-l2v5.xml new file mode 100644 index 000000000..11d28229a --- /dev/null +++ b/latest/cases/00355/model-sbml-l2v5.xml @@ -0,0 +1,97 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.5 + + + + + + + 1.2 + + + + + + + diff --git a/latest/cases/00355/model-sbml-l3v2.xml b/latest/cases/00355/model-sbml-l3v2.xml new file mode 100644 index 000000000..ddcd1fbaf --- /dev/null +++ b/latest/cases/00355/model-sbml-l3v2.xml @@ -0,0 +1,114 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.5 + + + + + + + 1.2 + + + + + + + diff --git a/latest/cases/00355/synopsis.txt b/latest/cases/00355/synopsis.txt new file mode 100644 index 000000000..6c6462fff --- /dev/null +++ b/latest/cases/00355/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.5)$ | $-$ | $S2 = 1.2$ |] + +The event trigger uses the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | lessthan | x, y | $x < y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00356/l2v5/heta-code/output.heta b/latest/cases/00356/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a624d1bd3 --- /dev/null +++ b/latest/cases/00356/l2v5/heta-code/output.heta @@ -0,0 +1,32 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; +divide #defineFunction { arguments: [x, y], math: x * pow(y, (-1)), }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event2]= divide(k3, k4); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.5; +k4 @Record 'k4' { } .= 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00356/l2v5/index.heta b/latest/cases/00356/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00356/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00356/l2v5/json/output.json b/latest/cases/00356/l2v5/json/output.json new file mode 100644 index 000000000..dddcd6917 --- /dev/null +++ b/latest/cases/00356/l2v5/json/output.json @@ -0,0 +1,180 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event2": "divide(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + }, + { + "id": "divide", + "arguments": [ + "x", + "y" + ], + "math": "x * pow(y, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00356/l3v2/heta-code/output.heta b/latest/cases/00356/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8cdb3c359 --- /dev/null +++ b/latest/cases/00356/l3v2/heta-code/output.heta @@ -0,0 +1,27 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; +divide #defineFunction { arguments: [x, y], math: x * pow(y, (-1)), }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= divide(k3, k4); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.5; +k4 @Const 'k4' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00356/l3v2/index.heta b/latest/cases/00356/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00356/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00356/l3v2/json/output.json b/latest/cases/00356/l3v2/json/output.json new file mode 100644 index 000000000..e74312276 --- /dev/null +++ b/latest/cases/00356/l3v2/json/output.json @@ -0,0 +1,148 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event2": "divide(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.5 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.2" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + }, + { + "id": "divide", + "arguments": [ + "x", + "y" + ], + "math": "x * pow(y, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00356/model-sbml-l2v5.xml b/latest/cases/00356/model-sbml-l2v5.xml new file mode 100644 index 000000000..cdd078119 --- /dev/null +++ b/latest/cases/00356/model-sbml-l2v5.xml @@ -0,0 +1,146 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + add + k3 + k4 + + + + + + + + + + + S3 + 1.2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00356/model-sbml-l3v2.xml b/latest/cases/00356/model-sbml-l3v2.xml new file mode 100644 index 000000000..154f4d181 --- /dev/null +++ b/latest/cases/00356/model-sbml-l3v2.xml @@ -0,0 +1,163 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + add + k3 + k4 + + + + + + + + + + + S3 + 1.2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00356/output.heta b/latest/cases/00356/output.heta new file mode 100644 index 000000000..1d93e12cb --- /dev/null +++ b/latest/cases/00356/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = add(k3, k4)$ | + | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1 * divide(k3, k4)$ |] + +Both eventAssignments use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; +divide #defineFunction { arguments: [x, y], math: x * pow(y, (-1)), }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= divide(k3, k4); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.5; +k4 @Const 'k4' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00356/synopsis.txt b/latest/cases/00356/synopsis.txt new file mode 100644 index 000000000..54923de33 --- /dev/null +++ b/latest/cases/00356/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = add(k3, k4)$ | + | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1 * divide(k3, k4)$ |] + +Both eventAssignments use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00357/l2v5/build.log b/latest/cases/00357/l2v5/build.log new file mode 100644 index 000000000..7e909569e --- /dev/null +++ b/latest/cases/00357/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00357/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00357/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00357/model-sbml-l2v5.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 96 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00357/l2v5/index.heta b/latest/cases/00357/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00357/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00357/l3v2/build.log b/latest/cases/00357/l3v2/build.log new file mode 100644 index 000000000..a34110f9a --- /dev/null +++ b/latest/cases/00357/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00357/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00357/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00357/model-sbml-l3v2.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 91 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00357/l3v2/index.heta b/latest/cases/00357/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00357/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00357/model-sbml-l2v5.xml b/latest/cases/00357/model-sbml-l2v5.xml new file mode 100644 index 000000000..ab3d0d1f5 --- /dev/null +++ b/latest/cases/00357/model-sbml-l2v5.xml @@ -0,0 +1,142 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.77 + + + + + + + 1.2 + + + + + + + + + + S3 + 1.2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00357/model-sbml-l3v2.xml b/latest/cases/00357/model-sbml-l3v2.xml new file mode 100644 index 000000000..5730ef585 --- /dev/null +++ b/latest/cases/00357/model-sbml-l3v2.xml @@ -0,0 +1,159 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.77 + + + + + + + 1.2 + + + + + + + + + + S3 + 1.2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00357/synopsis.txt b/latest/cases/00357/synopsis.txt new file mode 100644 index 000000000..7357f23ca --- /dev/null +++ b/latest/cases/00357/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.77)$ | $-$ | $S2 = 1.2$ | + | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1 * divide(k3, k4)$ |] + +Both events use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | lessthan | x, y | $x < y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00358/l2v5/build.log b/latest/cases/00358/l2v5/build.log new file mode 100644 index 000000000..bb1b5d9be --- /dev/null +++ b/latest/cases/00358/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00358/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00358/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00358/model-sbml-l2v5.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 93 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00358/l2v5/index.heta b/latest/cases/00358/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00358/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00358/l3v2/build.log b/latest/cases/00358/l3v2/build.log new file mode 100644 index 000000000..b9626f575 --- /dev/null +++ b/latest/cases/00358/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00358/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00358/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00358/model-sbml-l3v2.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 88 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00358/l3v2/index.heta b/latest/cases/00358/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00358/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00358/model-sbml-l2v5.xml b/latest/cases/00358/model-sbml-l2v5.xml new file mode 100644 index 000000000..00c41fe22 --- /dev/null +++ b/latest/cases/00358/model-sbml-l2v5.xml @@ -0,0 +1,102 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.7 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00358/model-sbml-l3v2.xml b/latest/cases/00358/model-sbml-l3v2.xml new file mode 100644 index 000000000..0e519bc44 --- /dev/null +++ b/latest/cases/00358/model-sbml-l3v2.xml @@ -0,0 +1,119 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.7 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00358/synopsis.txt b/latest/cases/00358/synopsis.txt new file mode 100644 index 000000000..c203375bd --- /dev/null +++ b/latest/cases/00358/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.7)$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The event trigger uses the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | lessthan | x, y | $x < y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00359/l2v5/build.log b/latest/cases/00359/l2v5/build.log new file mode 100644 index 000000000..3209e685a --- /dev/null +++ b/latest/cases/00359/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00359/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00359/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00359/model-sbml-l2v5.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 95 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00359/l2v5/index.heta b/latest/cases/00359/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00359/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00359/l3v2/build.log b/latest/cases/00359/l3v2/build.log new file mode 100644 index 000000000..db96061ff --- /dev/null +++ b/latest/cases/00359/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00359/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00359/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00359/model-sbml-l3v2.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 90 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00359/l3v2/index.heta b/latest/cases/00359/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00359/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00359/model-sbml-l2v5.xml b/latest/cases/00359/model-sbml-l2v5.xml new file mode 100644 index 000000000..1bfe7bccd --- /dev/null +++ b/latest/cases/00359/model-sbml-l2v5.xml @@ -0,0 +1,125 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.6 + + + + + + + 1.5 + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00359/model-sbml-l3v2.xml b/latest/cases/00359/model-sbml-l3v2.xml new file mode 100644 index 000000000..4621bd2e5 --- /dev/null +++ b/latest/cases/00359/model-sbml-l3v2.xml @@ -0,0 +1,142 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.6 + + + + + + + 1.5 + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00359/synopsis.txt b/latest/cases/00359/synopsis.txt new file mode 100644 index 000000000..d4449e8cd --- /dev/null +++ b/latest/cases/00359/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.6)$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = add(k3, k4)$ |] + +Both the event trigger and assignment use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ | +| lessthan | x, y | $x < y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00360/l2v5/heta-code/output.heta b/latest/cases/00360/l2v5/heta-code/output.heta new file mode 100644 index 000000000..10269f3f3 --- /dev/null +++ b/latest/cases/00360/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/area, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/area, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.8; +k2 @Record 'k2' { } .= 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.7, }; + diff --git a/latest/cases/00360/l2v5/index.heta b/latest/cases/00360/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00360/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00360/l2v5/json/output.json b/latest/cases/00360/l2v5/json/output.json new file mode 100644 index 000000000..1a084b75c --- /dev/null +++ b/latest/cases/00360/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.8" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.7" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00360/l3v2/heta-code/output.heta b/latest/cases/00360/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c09214fb4 --- /dev/null +++ b/latest/cases/00360/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.8; +k2 @Const 'k2' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.7, }; + diff --git a/latest/cases/00360/l3v2/index.heta b/latest/cases/00360/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00360/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00360/l3v2/json/output.json b/latest/cases/00360/l3v2/json/output.json new file mode 100644 index 000000000..80ee20441 --- /dev/null +++ b/latest/cases/00360/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.8 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.2 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.7" + } +] \ No newline at end of file diff --git a/latest/cases/00360/model-sbml-l2v5.xml b/latest/cases/00360/model-sbml-l2v5.xml new file mode 100644 index 000000000..8fc66f91b --- /dev/null +++ b/latest/cases/00360/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00360/model-sbml-l3v2.xml b/latest/cases/00360/model-sbml-l3v2.xml new file mode 100644 index 000000000..38a0736e6 --- /dev/null +++ b/latest/cases/00360/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00360/output.heta b/latest/cases/00360/output.heta new file mode 100644 index 000000000..e585426db --- /dev/null +++ b/latest/cases/00360/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.7$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.8$ |metre^2 mole^-1^ second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Area of compartment C |$1$ |metre^2 |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.8; +k2 @Const 'k2' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.7, }; + diff --git a/latest/cases/00360/synopsis.txt b/latest/cases/00360/synopsis.txt new file mode 100644 index 000000000..510d9ad0f --- /dev/null +++ b/latest/cases/00360/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.7$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.8$ |metre^2 mole^-1^ second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Area of compartment C |$1$ |metre^2 |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00361/l2v5/heta-code/output.heta b/latest/cases/00361/l2v5/heta-code/output.heta new file mode 100644 index 000000000..abefffa8c --- /dev/null +++ b/latest/cases/00361/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/length, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/length, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.8; +k2 @Record 'k2' { } .= 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.6, }; + diff --git a/latest/cases/00361/l2v5/index.heta b/latest/cases/00361/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00361/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00361/l2v5/json/output.json b/latest/cases/00361/l2v5/json/output.json new file mode 100644 index 000000000..654aa834e --- /dev/null +++ b/latest/cases/00361/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.8" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.6" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00361/l3v2/heta-code/output.heta b/latest/cases/00361/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f230b994d --- /dev/null +++ b/latest/cases/00361/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.8; +k2 @Const 'k2' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.6, }; + diff --git a/latest/cases/00361/l3v2/index.heta b/latest/cases/00361/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00361/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00361/l3v2/json/output.json b/latest/cases/00361/l3v2/json/output.json new file mode 100644 index 000000000..b2636bfdf --- /dev/null +++ b/latest/cases/00361/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.8 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.2 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.6" + } +] \ No newline at end of file diff --git a/latest/cases/00361/model-sbml-l2v5.xml b/latest/cases/00361/model-sbml-l2v5.xml new file mode 100644 index 000000000..a7508079f --- /dev/null +++ b/latest/cases/00361/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.6 + + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00361/model-sbml-l3v2.xml b/latest/cases/00361/model-sbml-l3v2.xml new file mode 100644 index 000000000..51d5874c3 --- /dev/null +++ b/latest/cases/00361/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.6 + + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00361/output.heta b/latest/cases/00361/output.heta new file mode 100644 index 000000000..3db6ddf16 --- /dev/null +++ b/latest/cases/00361/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.6$ | $-$ | $S2 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.8$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.8; +k2 @Const 'k2' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.6, }; + diff --git a/latest/cases/00361/synopsis.txt b/latest/cases/00361/synopsis.txt new file mode 100644 index 000000000..48fa5fcb9 --- /dev/null +++ b/latest/cases/00361/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.6$ | $-$ | $S2 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.8$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00362/l2v5/heta-code/output.heta b/latest/cases/00362/l2v5/heta-code/output.heta new file mode 100644 index 000000000..fb9fd9228 --- /dev/null +++ b/latest/cases/00362/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: C, isAmount: true, } .= 1; +S2 @Species 'S2' { units: substance, compartment: C, isAmount: true, } .= 2; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: substance, compartment: C, isAmount: true, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 0.8; +k2 @Record 'k2' { } .= 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.7, }; + diff --git a/latest/cases/00362/l2v5/index.heta b/latest/cases/00362/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00362/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00362/l2v5/json/output.json b/latest/cases/00362/l2v5/json/output.json new file mode 100644 index 000000000..270c10614 --- /dev/null +++ b/latest/cases/00362/l2v5/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2", + "event1": "1.25" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.8" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.7" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00362/l3v2/heta-code/output.heta b/latest/cases/00362/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ff5f61853 --- /dev/null +++ b/latest/cases/00362/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.8; +k2 @Const 'k2' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.7, }; + diff --git a/latest/cases/00362/l3v2/index.heta b/latest/cases/00362/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00362/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00362/l3v2/json/output.json b/latest/cases/00362/l3v2/json/output.json new file mode 100644 index 000000000..7b511d89f --- /dev/null +++ b/latest/cases/00362/l3v2/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2", + "event1": "1.25" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.8 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.2 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.7" + } +] \ No newline at end of file diff --git a/latest/cases/00362/model-sbml-l2v5.xml b/latest/cases/00362/model-sbml-l2v5.xml new file mode 100644 index 000000000..37c28b12c --- /dev/null +++ b/latest/cases/00362/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + + 1.25 + + + + + + + diff --git a/latest/cases/00362/model-sbml-l3v2.xml b/latest/cases/00362/model-sbml-l3v2.xml new file mode 100644 index 000000000..2541b9d97 --- /dev/null +++ b/latest/cases/00362/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + + 1.25 + + + + + + + diff --git a/latest/cases/00362/output.heta b/latest/cases/00362/output.heta new file mode 100644 index 000000000..9058cd5fd --- /dev/null +++ b/latest/cases/00362/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 0D compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.7$ | $-$ | $S2 = 1.25$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.8$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.8; +k2 @Const 'k2' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.7, }; + diff --git a/latest/cases/00362/synopsis.txt b/latest/cases/00362/synopsis.txt new file mode 100644 index 000000000..8db181dfd --- /dev/null +++ b/latest/cases/00362/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic two reactions with three species in one 0D compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.7$ | $-$ | $S2 = 1.25$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.8$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00363/l2v5/heta-code/output.heta b/latest/cases/00363/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ce6154dd2 --- /dev/null +++ b/latest/cases/00363/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: substance/area, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/area, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.075; +k2 @Record 'k2' { } .= 0.025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00363/l2v5/index.heta b/latest/cases/00363/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00363/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00363/l2v5/json/output.json b/latest/cases/00363/l2v5/json/output.json new file mode 100644 index 000000000..a5c14ab13 --- /dev/null +++ b/latest/cases/00363/l2v5/json/output.json @@ -0,0 +1,146 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.075" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.025" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00363/l3v2/heta-code/output.heta b/latest/cases/00363/l3v2/heta-code/output.heta new file mode 100644 index 000000000..32c741a12 --- /dev/null +++ b/latest/cases/00363/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.075; +k2 @Const 'k2' { } = 0.025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00363/l3v2/index.heta b/latest/cases/00363/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00363/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00363/l3v2/json/output.json b/latest/cases/00363/l3v2/json/output.json new file mode 100644 index 000000000..6039afbe8 --- /dev/null +++ b/latest/cases/00363/l3v2/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.075 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.025 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + } +] \ No newline at end of file diff --git a/latest/cases/00363/model-sbml-l2v5.xml b/latest/cases/00363/model-sbml-l2v5.xml new file mode 100644 index 000000000..4d633827f --- /dev/null +++ b/latest/cases/00363/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00363/model-sbml-l3v2.xml b/latest/cases/00363/model-sbml-l3v2.xml new file mode 100644 index 000000000..c3855a7c8 --- /dev/null +++ b/latest/cases/00363/model-sbml-l3v2.xml @@ -0,0 +1,113 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00363/output.heta b/latest/cases/00363/output.heta new file mode 100644 index 000000000..ada772b69 --- /dev/null +++ b/latest/cases/00363/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.075$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025$ |second^-1^ | +|Area of compartment C |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.075; +k2 @Const 'k2' { } = 0.025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00363/synopsis.txt b/latest/cases/00363/synopsis.txt new file mode 100644 index 000000000..bd3f0a0da --- /dev/null +++ b/latest/cases/00363/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.075$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025$ |second^-1^ | +|Area of compartment C |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00364/l2v5/heta-code/output.heta b/latest/cases/00364/l2v5/heta-code/output.heta new file mode 100644 index 000000000..dc4451673 --- /dev/null +++ b/latest/cases/00364/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: substance/length, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/length, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.075; +k2 @Record 'k2' { } .= 0.025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.65, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00364/l2v5/index.heta b/latest/cases/00364/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00364/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00364/l2v5/json/output.json b/latest/cases/00364/l2v5/json/output.json new file mode 100644 index 000000000..ffff7c567 --- /dev/null +++ b/latest/cases/00364/l2v5/json/output.json @@ -0,0 +1,146 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.075" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.025" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.65" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00364/l3v2/heta-code/output.heta b/latest/cases/00364/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ac6ee1986 --- /dev/null +++ b/latest/cases/00364/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.075; +k2 @Const 'k2' { } = 0.025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.65, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00364/l3v2/index.heta b/latest/cases/00364/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00364/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00364/l3v2/json/output.json b/latest/cases/00364/l3v2/json/output.json new file mode 100644 index 000000000..619c097eb --- /dev/null +++ b/latest/cases/00364/l3v2/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.075 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.025 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.65" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.2" + } +] \ No newline at end of file diff --git a/latest/cases/00364/model-sbml-l2v5.xml b/latest/cases/00364/model-sbml-l2v5.xml new file mode 100644 index 000000000..24a0d54a9 --- /dev/null +++ b/latest/cases/00364/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + + 1 + + + + + + + + + + S3 + 1.2 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00364/model-sbml-l3v2.xml b/latest/cases/00364/model-sbml-l3v2.xml new file mode 100644 index 000000000..ebd90826a --- /dev/null +++ b/latest/cases/00364/model-sbml-l3v2.xml @@ -0,0 +1,113 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + + 1 + + + + + + + + + + S3 + 1.2 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00364/output.heta b/latest/cases/00364/output.heta new file mode 100644 index 000000000..574c456e6 --- /dev/null +++ b/latest/cases/00364/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.075$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025$ |second^-1^ | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.075; +k2 @Const 'k2' { } = 0.025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.65, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00364/synopsis.txt b/latest/cases/00364/synopsis.txt new file mode 100644 index 000000000..736e27b5d --- /dev/null +++ b/latest/cases/00364/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.075$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025$ |second^-1^ | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00365/l2v5/heta-code/output.heta b/latest/cases/00365/l2v5/heta-code/output.heta new file mode 100644 index 000000000..97f9f5e0f --- /dev/null +++ b/latest/cases/00365/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: C, isAmount: true, } .= 1; +S1 [event2]= 0.95; +S2 @Species 'S2' { units: substance, compartment: C, isAmount: true, } .= 2; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance, compartment: C, isAmount: true, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 0.075; +k2 @Record 'k2' { } .= 0.025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.7, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00365/l2v5/index.heta b/latest/cases/00365/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00365/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00365/l2v5/json/output.json b/latest/cases/00365/l2v5/json/output.json new file mode 100644 index 000000000..1f4d8b958 --- /dev/null +++ b/latest/cases/00365/l2v5/json/output.json @@ -0,0 +1,148 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1", + "event2": "0.95" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2", + "event1": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.075" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.025" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.7" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00365/l3v2/heta-code/output.heta b/latest/cases/00365/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bed17c1a9 --- /dev/null +++ b/latest/cases/00365/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 1; +S1 [event2]= 0.95; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.075; +k2 @Const 'k2' { } = 0.025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.7, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00365/l3v2/index.heta b/latest/cases/00365/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00365/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00365/l3v2/json/output.json b/latest/cases/00365/l3v2/json/output.json new file mode 100644 index 000000000..0ba607eac --- /dev/null +++ b/latest/cases/00365/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1", + "event2": "0.95" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2", + "event1": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.075 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.025 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.7" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.2" + } +] \ No newline at end of file diff --git a/latest/cases/00365/model-sbml-l2v5.xml b/latest/cases/00365/model-sbml-l2v5.xml new file mode 100644 index 000000000..7988c4547 --- /dev/null +++ b/latest/cases/00365/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + + 1 + + + + + + + + + + S3 + 1.2 + + + + + + + 0.95 + + + + + + + diff --git a/latest/cases/00365/model-sbml-l3v2.xml b/latest/cases/00365/model-sbml-l3v2.xml new file mode 100644 index 000000000..3a75955d0 --- /dev/null +++ b/latest/cases/00365/model-sbml-l3v2.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + + 1 + + + + + + + + + + S3 + 1.2 + + + + + + + 0.95 + + + + + + + diff --git a/latest/cases/00365/output.heta b/latest/cases/00365/output.heta new file mode 100644 index 000000000..389a49244 --- /dev/null +++ b/latest/cases/00365/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 0D compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.075$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 1; +S1 [event2]= 0.95; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.075; +k2 @Const 'k2' { } = 0.025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.7, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00365/synopsis.txt b/latest/cases/00365/synopsis.txt new file mode 100644 index 000000000..e3dcc4ef4 --- /dev/null +++ b/latest/cases/00365/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic two reactions with three species in one 0D compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.075$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00366/l2v5/heta-code/output.heta b/latest/cases/00366/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ef7a7a6c6 --- /dev/null +++ b/latest/cases/00366/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: substance/area, compartment: C, } .= 2 / C; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: substance/area, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00366/l2v5/index.heta b/latest/cases/00366/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00366/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00366/l2v5/json/output.json b/latest/cases/00366/l2v5/json/output.json new file mode 100644 index 000000000..96e153bf4 --- /dev/null +++ b/latest/cases/00366/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "2 / C", + "event1": "1.25" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00366/l3v2/heta-code/output.heta b/latest/cases/00366/l3v2/heta-code/output.heta new file mode 100644 index 000000000..67bd0af6c --- /dev/null +++ b/latest/cases/00366/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2 / C; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00366/l3v2/index.heta b/latest/cases/00366/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00366/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00366/l3v2/json/output.json b/latest/cases/00366/l3v2/json/output.json new file mode 100644 index 000000000..fbdf7f155 --- /dev/null +++ b/latest/cases/00366/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "2 / C", + "event1": "1.25" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + } +] \ No newline at end of file diff --git a/latest/cases/00366/model-sbml-l2v5.xml b/latest/cases/00366/model-sbml-l2v5.xml new file mode 100644 index 000000000..c38a95d2a --- /dev/null +++ b/latest/cases/00366/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.25 + + + + + 1 + + + + + + + diff --git a/latest/cases/00366/model-sbml-l3v2.xml b/latest/cases/00366/model-sbml-l3v2.xml new file mode 100644 index 000000000..cc8880ede --- /dev/null +++ b/latest/cases/00366/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.25 + + + + + 1 + + + + + + + diff --git a/latest/cases/00366/output.heta b/latest/cases/00366/output.heta new file mode 100644 index 000000000..b6d175070 --- /dev/null +++ b/latest/cases/00366/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns value to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.25$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Area of compartment C |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2 / C; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00366/synopsis.txt b/latest/cases/00366/synopsis.txt new file mode 100644 index 000000000..e21167787 --- /dev/null +++ b/latest/cases/00366/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns value to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.25$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Area of compartment C |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00367/l2v5/heta-code/output.heta b/latest/cases/00367/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c0eee01d8 --- /dev/null +++ b/latest/cases/00367/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: C, } .= 1 / C; +S1 [event1]= 0.6; +S2 @Species 'S2' { units: substance/length, compartment: C, } .= 2 / C; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: substance/length, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.45, }; + diff --git a/latest/cases/00367/l2v5/index.heta b/latest/cases/00367/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00367/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00367/l2v5/json/output.json b/latest/cases/00367/l2v5/json/output.json new file mode 100644 index 000000000..13107aeff --- /dev/null +++ b/latest/cases/00367/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / C", + "event1": "0.6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / C", + "event1": "1.25" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.45" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00367/l3v2/heta-code/output.heta b/latest/cases/00367/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2efe4ae05 --- /dev/null +++ b/latest/cases/00367/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S1 [event1]= 0.6; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.45, }; + diff --git a/latest/cases/00367/l3v2/index.heta b/latest/cases/00367/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00367/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00367/l3v2/json/output.json b/latest/cases/00367/l3v2/json/output.json new file mode 100644 index 000000000..7e403b213 --- /dev/null +++ b/latest/cases/00367/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / C", + "event1": "0.6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / C", + "event1": "1.25" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.45" + } +] \ No newline at end of file diff --git a/latest/cases/00367/model-sbml-l2v5.xml b/latest/cases/00367/model-sbml-l2v5.xml new file mode 100644 index 000000000..dbaa746be --- /dev/null +++ b/latest/cases/00367/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.45 + + + + + + + 1.25 + + + + + 0.6 + + + + + + + diff --git a/latest/cases/00367/model-sbml-l3v2.xml b/latest/cases/00367/model-sbml-l3v2.xml new file mode 100644 index 000000000..72e762575 --- /dev/null +++ b/latest/cases/00367/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.45 + + + + + + + 1.25 + + + + + 0.6 + + + + + + + diff --git a/latest/cases/00367/output.heta b/latest/cases/00367/output.heta new file mode 100644 index 000000000..041105a0e --- /dev/null +++ b/latest/cases/00367/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | +| Event1 | $S1 < 0.45$ | $-$ | $S2 = 1.25$ | +| | | | $S1 = 0.6$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S1 [event1]= 0.6; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.45, }; + diff --git a/latest/cases/00367/synopsis.txt b/latest/cases/00367/synopsis.txt new file mode 100644 index 000000000..febfe5dfe --- /dev/null +++ b/latest/cases/00367/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | +| Event1 | $S1 < 0.45$ | $-$ | $S2 = 1.25$ | +| | | | $S1 = 0.6$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00368/l2v5/heta-code/output.heta b/latest/cases/00368/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6c490aabb --- /dev/null +++ b/latest/cases/00368/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: C, isAmount: true, } .= 1; +S1 [event1]= 0.5; +S2 @Species 'S2' { units: substance, compartment: C, isAmount: true, } .= 2; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: substance, compartment: C, isAmount: true, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00368/l2v5/index.heta b/latest/cases/00368/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00368/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00368/l2v5/json/output.json b/latest/cases/00368/l2v5/json/output.json new file mode 100644 index 000000000..97d3d280a --- /dev/null +++ b/latest/cases/00368/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1", + "event1": "0.5" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2", + "event1": "1.25" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00368/l3v2/heta-code/output.heta b/latest/cases/00368/l3v2/heta-code/output.heta new file mode 100644 index 000000000..48e968ab9 --- /dev/null +++ b/latest/cases/00368/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 1; +S1 [event1]= 0.5; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00368/l3v2/index.heta b/latest/cases/00368/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00368/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00368/l3v2/json/output.json b/latest/cases/00368/l3v2/json/output.json new file mode 100644 index 000000000..2375af8a1 --- /dev/null +++ b/latest/cases/00368/l3v2/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1", + "event1": "0.5" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2", + "event1": "1.25" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00368/model-sbml-l2v5.xml b/latest/cases/00368/model-sbml-l2v5.xml new file mode 100644 index 000000000..b29c65b15 --- /dev/null +++ b/latest/cases/00368/model-sbml-l2v5.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.25 + + + + + 0.5 + + + + + + + diff --git a/latest/cases/00368/model-sbml-l3v2.xml b/latest/cases/00368/model-sbml-l3v2.xml new file mode 100644 index 000000000..6ed76f29e --- /dev/null +++ b/latest/cases/00368/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.25 + + + + + 0.5 + + + + + + + diff --git a/latest/cases/00368/output.heta b/latest/cases/00368/output.heta new file mode 100644 index 000000000..e49767639 --- /dev/null +++ b/latest/cases/00368/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one 0D compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.45$ | $-$ | $S2 = 1.25$ | + | | | | $S1 = 0.6$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 1; +S1 [event1]= 0.5; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2; +S2 [event1]= 1.25; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00368/synopsis.txt b/latest/cases/00368/synopsis.txt new file mode 100644 index 000000000..76f51be7c --- /dev/null +++ b/latest/cases/00368/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic two reactions with three species in one 0D compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.45$ | $-$ | $S2 = 1.25$ | + | | | | $S1 = 0.6$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00369/l2v5/heta-code/output.heta b/latest/cases/00369/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b42d25a5d --- /dev/null +++ b/latest/cases/00369/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00369/l2v5/index.heta b/latest/cases/00369/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00369/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00369/l2v5/json/output.json b/latest/cases/00369/l2v5/json/output.json new file mode 100644 index 000000000..0b5920344 --- /dev/null +++ b/latest/cases/00369/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00369/l3v2/heta-code/output.heta b/latest/cases/00369/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f046cf577 --- /dev/null +++ b/latest/cases/00369/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00369/l3v2/index.heta b/latest/cases/00369/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00369/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00369/l3v2/json/output.json b/latest/cases/00369/l3v2/json/output.json new file mode 100644 index 000000000..417235d59 --- /dev/null +++ b/latest/cases/00369/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00369/model-sbml-l2v5.xml b/latest/cases/00369/model-sbml-l2v5.xml new file mode 100644 index 000000000..786a2ae2d --- /dev/null +++ b/latest/cases/00369/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00369/model-sbml-l3v2.xml b/latest/cases/00369/model-sbml-l3v2.xml new file mode 100644 index 000000000..a0ce3725e --- /dev/null +++ b/latest/cases/00369/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00369/output.heta b/latest/cases/00369/output.heta new file mode 100644 index 000000000..448e32baa --- /dev/null +++ b/latest/cases/00369/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00369/synopsis.txt b/latest/cases/00369/synopsis.txt new file mode 100644 index 000000000..445467e33 --- /dev/null +++ b/latest/cases/00369/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00370/l2v5/heta-code/output.heta b/latest/cases/00370/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c219b63b5 --- /dev/null +++ b/latest/cases/00370/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.43; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1, }; + diff --git a/latest/cases/00370/l2v5/index.heta b/latest/cases/00370/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00370/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00370/l2v5/json/output.json b/latest/cases/00370/l2v5/json/output.json new file mode 100644 index 000000000..49854dcaa --- /dev/null +++ b/latest/cases/00370/l2v5/json/output.json @@ -0,0 +1,146 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.43" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00370/l3v2/heta-code/output.heta b/latest/cases/00370/l3v2/heta-code/output.heta new file mode 100644 index 000000000..57f15ea28 --- /dev/null +++ b/latest/cases/00370/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.43; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1, }; + diff --git a/latest/cases/00370/l3v2/index.heta b/latest/cases/00370/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00370/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00370/l3v2/json/output.json b/latest/cases/00370/l3v2/json/output.json new file mode 100644 index 000000000..5ac4c390f --- /dev/null +++ b/latest/cases/00370/l3v2/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.43" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1" + } +] \ No newline at end of file diff --git a/latest/cases/00370/model-sbml-l2v5.xml b/latest/cases/00370/model-sbml-l2v5.xml new file mode 100644 index 000000000..676f6a44d --- /dev/null +++ b/latest/cases/00370/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1 + + + + + + + + + + S3 + 1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00370/model-sbml-l3v2.xml b/latest/cases/00370/model-sbml-l3v2.xml new file mode 100644 index 000000000..2acee5cac --- /dev/null +++ b/latest/cases/00370/model-sbml-l3v2.xml @@ -0,0 +1,113 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1 + + + + + + + + + + S3 + 1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00370/output.heta b/latest/cases/00370/output.heta new file mode 100644 index 000000000..347d77493 --- /dev/null +++ b/latest/cases/00370/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1.43$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.43; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1, }; + diff --git a/latest/cases/00370/synopsis.txt b/latest/cases/00370/synopsis.txt new file mode 100644 index 000000000..498727009 --- /dev/null +++ b/latest/cases/00370/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1.43$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00371/l2v5/heta-code/output.heta b/latest/cases/00371/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3ba93ffc9 --- /dev/null +++ b/latest/cases/00371/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.9; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.65, }; + diff --git a/latest/cases/00371/l2v5/index.heta b/latest/cases/00371/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00371/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00371/l2v5/json/output.json b/latest/cases/00371/l2v5/json/output.json new file mode 100644 index 000000000..9050d2dcb --- /dev/null +++ b/latest/cases/00371/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.9" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.65" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00371/l3v2/heta-code/output.heta b/latest/cases/00371/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e9de72350 --- /dev/null +++ b/latest/cases/00371/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.65, }; + diff --git a/latest/cases/00371/l3v2/index.heta b/latest/cases/00371/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00371/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00371/l3v2/json/output.json b/latest/cases/00371/l3v2/json/output.json new file mode 100644 index 000000000..4c93eda17 --- /dev/null +++ b/latest/cases/00371/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.9" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.65" + } +] \ No newline at end of file diff --git a/latest/cases/00371/model-sbml-l2v5.xml b/latest/cases/00371/model-sbml-l2v5.xml new file mode 100644 index 000000000..84f3271be --- /dev/null +++ b/latest/cases/00371/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00371/model-sbml-l3v2.xml b/latest/cases/00371/model-sbml-l3v2.xml new file mode 100644 index 000000000..f1a061178 --- /dev/null +++ b/latest/cases/00371/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00371/output.heta b/latest/cases/00371/output.heta new file mode 100644 index 000000000..b6a8346aa --- /dev/null +++ b/latest/cases/00371/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.9$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.65, }; + diff --git a/latest/cases/00371/synopsis.txt b/latest/cases/00371/synopsis.txt new file mode 100644 index 000000000..a13be2aa3 --- /dev/null +++ b/latest/cases/00371/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.9$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00372/l2v5/heta-code/output.heta b/latest/cases/00372/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a81c34d12 --- /dev/null +++ b/latest/cases/00372/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.24; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.002 / C; +S1 [event1]= 0.004; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.0022 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 750; +k2 @Record 'k2' { } .= 0.05; + +event1 @DSwitcher 'event1' { trigger: S4 > 0.01, }; + diff --git a/latest/cases/00372/l2v5/index.heta b/latest/cases/00372/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00372/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00372/l2v5/json/output.json b/latest/cases/00372/l2v5/json/output.json new file mode 100644 index 000000000..a074f3152 --- /dev/null +++ b/latest/cases/00372/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.24" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C", + "event1": "0.004" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0022 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "750" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.05" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > 0.01" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00372/l3v2/heta-code/output.heta b/latest/cases/00372/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d32d020df --- /dev/null +++ b/latest/cases/00372/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.24; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.002 / C; +S1 [event1]= 0.004; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0022 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 0.05; + +event1 @DSwitcher 'event1' { trigger: S4 > 0.01, }; + diff --git a/latest/cases/00372/l3v2/index.heta b/latest/cases/00372/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00372/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00372/l3v2/json/output.json b/latest/cases/00372/l3v2/json/output.json new file mode 100644 index 000000000..8c9ade9e8 --- /dev/null +++ b/latest/cases/00372/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.24" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C", + "event1": "0.004" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0022 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.05 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > 0.01" + } +] \ No newline at end of file diff --git a/latest/cases/00372/model-sbml-l2v5.xml b/latest/cases/00372/model-sbml-l2v5.xml new file mode 100644 index 000000000..e48c700a2 --- /dev/null +++ b/latest/cases/00372/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + 0.01 + + + + + + + 0.004 + + + + + + + diff --git a/latest/cases/00372/model-sbml-l3v2.xml b/latest/cases/00372/model-sbml-l3v2.xml new file mode 100644 index 000000000..edc8c24d7 --- /dev/null +++ b/latest/cases/00372/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + 0.01 + + + + + + + 0.004 + + + + + + + diff --git a/latest/cases/00372/output.heta b/latest/cases/00372/output.heta new file mode 100644 index 000000000..f35df3a78 --- /dev/null +++ b/latest/cases/00372/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.2 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Initial amount of S4 |$0.5 \x 10^-3$ |mole | +|Value of parameter k1 |$750$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.05$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.24$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.24; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.002 / C; +S1 [event1]= 0.004; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0022 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 0.05; + +event1 @DSwitcher 'event1' { trigger: S4 > 0.01, }; + diff --git a/latest/cases/00372/synopsis.txt b/latest/cases/00372/synopsis.txt new file mode 100644 index 000000000..d165a0e62 --- /dev/null +++ b/latest/cases/00372/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.2 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Initial amount of S4 |$0.5 \x 10^-3$ |mole | +|Value of parameter k1 |$750$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.05$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.24$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00373/l2v5/heta-code/output.heta b/latest/cases/00373/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c04630435 --- /dev/null +++ b/latest/cases/00373/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1 / C; +S1 [event1]= 1.4; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.12 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.2 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.1 / C; +S4 [event2]= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 0.0025; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S2 < 0.03, }; + diff --git a/latest/cases/00373/l2v5/index.heta b/latest/cases/00373/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00373/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00373/l2v5/json/output.json b/latest/cases/00373/l2v5/json/output.json new file mode 100644 index 000000000..525cf3587 --- /dev/null +++ b/latest/cases/00373/l2v5/json/output.json @@ -0,0 +1,164 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C", + "event1": "1.4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.12 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C", + "event2": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0025" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S2 < 0.03" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00373/l3v2/heta-code/output.heta b/latest/cases/00373/l3v2/heta-code/output.heta new file mode 100644 index 000000000..100880380 --- /dev/null +++ b/latest/cases/00373/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S1 [event1]= 1.4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1 / C; +S4 [event2]= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.0025; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S2 < 0.03, }; + diff --git a/latest/cases/00373/l3v2/index.heta b/latest/cases/00373/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00373/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00373/l3v2/json/output.json b/latest/cases/00373/l3v2/json/output.json new file mode 100644 index 000000000..9c045ee56 --- /dev/null +++ b/latest/cases/00373/l3v2/json/output.json @@ -0,0 +1,136 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C", + "event1": "1.4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.12 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C", + "event2": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0025 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S2 < 0.03" + } +] \ No newline at end of file diff --git a/latest/cases/00373/model-sbml-l2v5.xml b/latest/cases/00373/model-sbml-l2v5.xml new file mode 100644 index 000000000..b550e0b3c --- /dev/null +++ b/latest/cases/00373/model-sbml-l2v5.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1.4 + + + + + + + + + + S2 + 0.03 + + + + + + + 0.1 + + + + + + + diff --git a/latest/cases/00373/model-sbml-l3v2.xml b/latest/cases/00373/model-sbml-l3v2.xml new file mode 100644 index 000000000..0518a1152 --- /dev/null +++ b/latest/cases/00373/model-sbml-l3v2.xml @@ -0,0 +1,117 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1.4 + + + + + + + + + + S2 + 0.03 + + + + + + + 0.1 + + + + + + + diff --git a/latest/cases/00373/output.heta b/latest/cases/00373/output.heta new file mode 100644 index 000000000..252db19b5 --- /dev/null +++ b/latest/cases/00373/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 1.4$ |] + | Event2 | $S2 < 0.03$ | $-$ | $S4 -> 1 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S1 [event1]= 1.4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1 / C; +S4 [event2]= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.0025; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S2 < 0.03, }; + diff --git a/latest/cases/00373/synopsis.txt b/latest/cases/00373/synopsis.txt new file mode 100644 index 000000000..af91e9d3c --- /dev/null +++ b/latest/cases/00373/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 1.4$ |] + | Event2 | $S2 < 0.03$ | $-$ | $S4 -> 1 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00374/l2v5/heta-code/output.heta b/latest/cases/00374/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2ecd707ef --- /dev/null +++ b/latest/cases/00374/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.25; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 4e-4; +S1 [event1]= (1 / 5000); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 4.8e-4; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 8e-4; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4e-4; +S4 [event1]= (1 / 5000); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 250; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00374/l2v5/index.heta b/latest/cases/00374/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00374/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00374/l2v5/json/output.json b/latest/cases/00374/l2v5/json/output.json new file mode 100644 index 000000000..c41dedb63 --- /dev/null +++ b/latest/cases/00374/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.25" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "4e-4", + "event1": "(1 / 5000)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "4.8e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "8e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4e-4", + "event1": "(1 / 5000)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "250" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00374/l3v2/heta-code/output.heta b/latest/cases/00374/l3v2/heta-code/output.heta new file mode 100644 index 000000000..85282bed1 --- /dev/null +++ b/latest/cases/00374/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.25; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 4e-4; +S1 [event1]= (1 / 5000); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 4.8e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 8e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4e-4; +S4 [event1]= (1 / 5000); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 250; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00374/l3v2/index.heta b/latest/cases/00374/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00374/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00374/l3v2/json/output.json b/latest/cases/00374/l3v2/json/output.json new file mode 100644 index 000000000..9de958af1 --- /dev/null +++ b/latest/cases/00374/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.25" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "4e-4", + "event1": "(1 / 5000)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "4.8e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "8e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4e-4", + "event1": "(1 / 5000)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 250 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + } +] \ No newline at end of file diff --git a/latest/cases/00374/model-sbml-l2v5.xml b/latest/cases/00374/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef5fc7433 --- /dev/null +++ b/latest/cases/00374/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5000 + + + + + 1 5000 + + + + + + + diff --git a/latest/cases/00374/model-sbml-l3v2.xml b/latest/cases/00374/model-sbml-l3v2.xml new file mode 100644 index 000000000..ac73b32e0 --- /dev/null +++ b/latest/cases/00374/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5000 + + + + + 1 5000 + + + + + + + diff --git a/latest/cases/00374/output.heta b/latest/cases/00374/output.heta new file mode 100644 index 000000000..c35d0696e --- /dev/null +++ b/latest/cases/00374/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | +| Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-4$ | +| | | | $S4 -> 2 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$4.0 \x 10^-4$ |mole | +|Initial amount of S2 |$4.8 \x 10^-4$ |mole | +|Initial amount of S3 |$8.0 \x 10^-4$ |mole | +|Initial amount of S4 |$4.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.25$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.25; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 4e-4; +S1 [event1]= (1 / 5000); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 4.8e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 8e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4e-4; +S4 [event1]= (1 / 5000); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 250; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00374/synopsis.txt b/latest/cases/00374/synopsis.txt new file mode 100644 index 000000000..162fddbb2 --- /dev/null +++ b/latest/cases/00374/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | +| Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-4$ | +| | | | $S4 -> 2 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$4.0 \x 10^-4$ |mole | +|Initial amount of S2 |$4.8 \x 10^-4$ |mole | +|Initial amount of S3 |$8.0 \x 10^-4$ |mole | +|Initial amount of S4 |$4.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.25$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00375/l2v5/heta-code/output.heta b/latest/cases/00375/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e1cd9896d --- /dev/null +++ b/latest/cases/00375/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00375/l2v5/index.heta b/latest/cases/00375/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00375/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00375/l2v5/json/output.json b/latest/cases/00375/l2v5/json/output.json new file mode 100644 index 000000000..f5e8c96f4 --- /dev/null +++ b/latest/cases/00375/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00375/l3v2/heta-code/output.heta b/latest/cases/00375/l3v2/heta-code/output.heta new file mode 100644 index 000000000..63d671cf9 --- /dev/null +++ b/latest/cases/00375/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00375/l3v2/index.heta b/latest/cases/00375/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00375/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00375/l3v2/json/output.json b/latest/cases/00375/l3v2/json/output.json new file mode 100644 index 000000000..a0a06e2aa --- /dev/null +++ b/latest/cases/00375/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00375/model-sbml-l2v5.xml b/latest/cases/00375/model-sbml-l2v5.xml new file mode 100644 index 000000000..1420737b6 --- /dev/null +++ b/latest/cases/00375/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00375/model-sbml-l3v2.xml b/latest/cases/00375/model-sbml-l3v2.xml new file mode 100644 index 000000000..2e8174560 --- /dev/null +++ b/latest/cases/00375/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00375/output.heta b/latest/cases/00375/output.heta new file mode 100644 index 000000000..926d56851 --- /dev/null +++ b/latest/cases/00375/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S2 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00375/synopsis.txt b/latest/cases/00375/synopsis.txt new file mode 100644 index 000000000..f93cb25e8 --- /dev/null +++ b/latest/cases/00375/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S2 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00376/l2v5/heta-code/output.heta b/latest/cases/00376/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0e1ddb9dc --- /dev/null +++ b/latest/cases/00376/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00376/l2v5/index.heta b/latest/cases/00376/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00376/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00376/l2v5/json/output.json b/latest/cases/00376/l2v5/json/output.json new file mode 100644 index 000000000..f6928e71c --- /dev/null +++ b/latest/cases/00376/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00376/l3v2/heta-code/output.heta b/latest/cases/00376/l3v2/heta-code/output.heta new file mode 100644 index 000000000..789fe3890 --- /dev/null +++ b/latest/cases/00376/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00376/l3v2/index.heta b/latest/cases/00376/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00376/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00376/l3v2/json/output.json b/latest/cases/00376/l3v2/json/output.json new file mode 100644 index 000000000..9175ff62f --- /dev/null +++ b/latest/cases/00376/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00376/model-sbml-l2v5.xml b/latest/cases/00376/model-sbml-l2v5.xml new file mode 100644 index 000000000..5f7d8c6d5 --- /dev/null +++ b/latest/cases/00376/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00376/model-sbml-l3v2.xml b/latest/cases/00376/model-sbml-l3v2.xml new file mode 100644 index 000000000..d6363d6a7 --- /dev/null +++ b/latest/cases/00376/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00376/output.heta b/latest/cases/00376/output.heta new file mode 100644 index 000000000..0988fb5b0 --- /dev/null +++ b/latest/cases/00376/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00376/synopsis.txt b/latest/cases/00376/synopsis.txt new file mode 100644 index 000000000..f9c735395 --- /dev/null +++ b/latest/cases/00376/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00377/l2v5/heta-code/output.heta b/latest/cases/00377/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c4c4c20b6 --- /dev/null +++ b/latest/cases/00377/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.1; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00377/l2v5/index.heta b/latest/cases/00377/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00377/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00377/l2v5/json/output.json b/latest/cases/00377/l2v5/json/output.json new file mode 100644 index 000000000..79e25fdd5 --- /dev/null +++ b/latest/cases/00377/l2v5/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00377/l3v2/heta-code/output.heta b/latest/cases/00377/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1214b4f81 --- /dev/null +++ b/latest/cases/00377/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00377/l3v2/index.heta b/latest/cases/00377/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00377/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00377/l3v2/json/output.json b/latest/cases/00377/l3v2/json/output.json new file mode 100644 index 000000000..a1c949dd7 --- /dev/null +++ b/latest/cases/00377/l3v2/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00377/model-sbml-l2v5.xml b/latest/cases/00377/model-sbml-l2v5.xml new file mode 100644 index 000000000..156265bf5 --- /dev/null +++ b/latest/cases/00377/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.1 + + + + + + + diff --git a/latest/cases/00377/model-sbml-l3v2.xml b/latest/cases/00377/model-sbml-l3v2.xml new file mode 100644 index 000000000..71fa0d242 --- /dev/null +++ b/latest/cases/00377/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.1 + + + + + + + diff --git a/latest/cases/00377/output.heta b/latest/cases/00377/output.heta new file mode 100644 index 000000000..2e0bc8f6c --- /dev/null +++ b/latest/cases/00377/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Both species S2 +and S3 are labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00377/synopsis.txt b/latest/cases/00377/synopsis.txt new file mode 100644 index 000000000..81e9f67b5 --- /dev/null +++ b/latest/cases/00377/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Both species S2 +and S3 are labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00378/l2v5/heta-code/output.heta b/latest/cases/00378/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0b67fbcb4 --- /dev/null +++ b/latest/cases/00378/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00378/l2v5/index.heta b/latest/cases/00378/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00378/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00378/l2v5/json/output.json b/latest/cases/00378/l2v5/json/output.json new file mode 100644 index 000000000..27326cd3e --- /dev/null +++ b/latest/cases/00378/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00378/l3v2/heta-code/output.heta b/latest/cases/00378/l3v2/heta-code/output.heta new file mode 100644 index 000000000..abeb44cee --- /dev/null +++ b/latest/cases/00378/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00378/l3v2/index.heta b/latest/cases/00378/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00378/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00378/l3v2/json/output.json b/latest/cases/00378/l3v2/json/output.json new file mode 100644 index 000000000..6c32695da --- /dev/null +++ b/latest/cases/00378/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + } +] \ No newline at end of file diff --git a/latest/cases/00378/model-sbml-l2v5.xml b/latest/cases/00378/model-sbml-l2v5.xml new file mode 100644 index 000000000..17d3ed206 --- /dev/null +++ b/latest/cases/00378/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00378/model-sbml-l3v2.xml b/latest/cases/00378/model-sbml-l3v2.xml new file mode 100644 index 000000000..53ba7472b --- /dev/null +++ b/latest/cases/00378/model-sbml-l3v2.xml @@ -0,0 +1,113 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00378/output.heta b/latest/cases/00378/output.heta new file mode 100644 index 000000000..394fadfe4 --- /dev/null +++ b/latest/cases/00378/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S2 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00378/synopsis.txt b/latest/cases/00378/synopsis.txt new file mode 100644 index 000000000..a3099781a --- /dev/null +++ b/latest/cases/00378/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S2 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00379/l2v5/heta-code/output.heta b/latest/cases/00379/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9da14582d --- /dev/null +++ b/latest/cases/00379/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00379/l2v5/index.heta b/latest/cases/00379/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00379/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00379/l2v5/json/output.json b/latest/cases/00379/l2v5/json/output.json new file mode 100644 index 000000000..173fc4330 --- /dev/null +++ b/latest/cases/00379/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00379/l3v2/heta-code/output.heta b/latest/cases/00379/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9d8179aa0 --- /dev/null +++ b/latest/cases/00379/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00379/l3v2/index.heta b/latest/cases/00379/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00379/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00379/l3v2/json/output.json b/latest/cases/00379/l3v2/json/output.json new file mode 100644 index 000000000..948f02eb0 --- /dev/null +++ b/latest/cases/00379/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + } +] \ No newline at end of file diff --git a/latest/cases/00379/model-sbml-l2v5.xml b/latest/cases/00379/model-sbml-l2v5.xml new file mode 100644 index 000000000..bfa2b5fee --- /dev/null +++ b/latest/cases/00379/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00379/model-sbml-l3v2.xml b/latest/cases/00379/model-sbml-l3v2.xml new file mode 100644 index 000000000..7849ac11e --- /dev/null +++ b/latest/cases/00379/model-sbml-l3v2.xml @@ -0,0 +1,113 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00379/output.heta b/latest/cases/00379/output.heta new file mode 100644 index 000000000..c504244dd --- /dev/null +++ b/latest/cases/00379/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assigns values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00379/synopsis.txt b/latest/cases/00379/synopsis.txt new file mode 100644 index 000000000..ded0bfebb --- /dev/null +++ b/latest/cases/00379/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assigns values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00380/l2v5/heta-code/output.heta b/latest/cases/00380/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ba9a6c764 --- /dev/null +++ b/latest/cases/00380/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event2]= 1.1; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.1; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00380/l2v5/index.heta b/latest/cases/00380/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00380/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00380/l2v5/json/output.json b/latest/cases/00380/l2v5/json/output.json new file mode 100644 index 000000000..26ca5c49c --- /dev/null +++ b/latest/cases/00380/l2v5/json/output.json @@ -0,0 +1,148 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event2": "1.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00380/l3v2/heta-code/output.heta b/latest/cases/00380/l3v2/heta-code/output.heta new file mode 100644 index 000000000..32d12465d --- /dev/null +++ b/latest/cases/00380/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1.1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00380/l3v2/index.heta b/latest/cases/00380/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00380/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00380/l3v2/json/output.json b/latest/cases/00380/l3v2/json/output.json new file mode 100644 index 000000000..95a719bec --- /dev/null +++ b/latest/cases/00380/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event2": "1.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + } +] \ No newline at end of file diff --git a/latest/cases/00380/model-sbml-l2v5.xml b/latest/cases/00380/model-sbml-l2v5.xml new file mode 100644 index 000000000..c033bad7c --- /dev/null +++ b/latest/cases/00380/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1.1 + + + + + + + diff --git a/latest/cases/00380/model-sbml-l3v2.xml b/latest/cases/00380/model-sbml-l3v2.xml new file mode 100644 index 000000000..72d9dc59a --- /dev/null +++ b/latest/cases/00380/model-sbml-l3v2.xml @@ -0,0 +1,113 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1.1 + + + + + + + diff --git a/latest/cases/00380/output.heta b/latest/cases/00380/output.heta new file mode 100644 index 000000000..42f21f0f1 --- /dev/null +++ b/latest/cases/00380/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Both species S2 +and S3 are labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 1.1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00380/synopsis.txt b/latest/cases/00380/synopsis.txt new file mode 100644 index 000000000..de9d1bfde --- /dev/null +++ b/latest/cases/00380/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Both species S2 +and S3 are labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00381/l2v5/heta-code/output.heta b/latest/cases/00381/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9653839ea --- /dev/null +++ b/latest/cases/00381/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00381/l2v5/index.heta b/latest/cases/00381/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00381/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00381/l2v5/json/output.json b/latest/cases/00381/l2v5/json/output.json new file mode 100644 index 000000000..2a8c02b61 --- /dev/null +++ b/latest/cases/00381/l2v5/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00381/l3v2/heta-code/output.heta b/latest/cases/00381/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4c4ec7f8f --- /dev/null +++ b/latest/cases/00381/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00381/l3v2/index.heta b/latest/cases/00381/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00381/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00381/l3v2/json/output.json b/latest/cases/00381/l3v2/json/output.json new file mode 100644 index 000000000..3e740158d --- /dev/null +++ b/latest/cases/00381/l3v2/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00381/model-sbml-l2v5.xml b/latest/cases/00381/model-sbml-l2v5.xml new file mode 100644 index 000000000..fe1e80d06 --- /dev/null +++ b/latest/cases/00381/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00381/model-sbml-l3v2.xml b/latest/cases/00381/model-sbml-l3v2.xml new file mode 100644 index 000000000..dfb44a378 --- /dev/null +++ b/latest/cases/00381/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00381/output.heta b/latest/cases/00381/output.heta new file mode 100644 index 000000000..d67708e84 --- /dev/null +++ b/latest/cases/00381/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S2 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00381/synopsis.txt b/latest/cases/00381/synopsis.txt new file mode 100644 index 000000000..539aeedf2 --- /dev/null +++ b/latest/cases/00381/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S2 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00382/l2v5/heta-code/output.heta b/latest/cases/00382/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ade7412c8 --- /dev/null +++ b/latest/cases/00382/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00382/l2v5/index.heta b/latest/cases/00382/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00382/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00382/l2v5/json/output.json b/latest/cases/00382/l2v5/json/output.json new file mode 100644 index 000000000..be7b04af0 --- /dev/null +++ b/latest/cases/00382/l2v5/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00382/l3v2/heta-code/output.heta b/latest/cases/00382/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fbde5a6d8 --- /dev/null +++ b/latest/cases/00382/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00382/l3v2/index.heta b/latest/cases/00382/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00382/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00382/l3v2/json/output.json b/latest/cases/00382/l3v2/json/output.json new file mode 100644 index 000000000..e73059bf1 --- /dev/null +++ b/latest/cases/00382/l3v2/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00382/model-sbml-l2v5.xml b/latest/cases/00382/model-sbml-l2v5.xml new file mode 100644 index 000000000..ed84d4ead --- /dev/null +++ b/latest/cases/00382/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00382/model-sbml-l3v2.xml b/latest/cases/00382/model-sbml-l3v2.xml new file mode 100644 index 000000000..8d9a7bcc4 --- /dev/null +++ b/latest/cases/00382/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00382/output.heta b/latest/cases/00382/output.heta new file mode 100644 index 000000000..7b7adb55e --- /dev/null +++ b/latest/cases/00382/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00382/synopsis.txt b/latest/cases/00382/synopsis.txt new file mode 100644 index 000000000..da2bf4a0f --- /dev/null +++ b/latest/cases/00382/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00383/l2v5/heta-code/output.heta b/latest/cases/00383/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f6e9225ec --- /dev/null +++ b/latest/cases/00383/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00383/l2v5/index.heta b/latest/cases/00383/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00383/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00383/l2v5/json/output.json b/latest/cases/00383/l2v5/json/output.json new file mode 100644 index 000000000..34182fa2f --- /dev/null +++ b/latest/cases/00383/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00383/l3v2/heta-code/output.heta b/latest/cases/00383/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8fc4a8929 --- /dev/null +++ b/latest/cases/00383/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00383/l3v2/index.heta b/latest/cases/00383/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00383/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00383/l3v2/json/output.json b/latest/cases/00383/l3v2/json/output.json new file mode 100644 index 000000000..30537ecf9 --- /dev/null +++ b/latest/cases/00383/l3v2/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00383/model-sbml-l2v5.xml b/latest/cases/00383/model-sbml-l2v5.xml new file mode 100644 index 000000000..23393dc45 --- /dev/null +++ b/latest/cases/00383/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00383/model-sbml-l3v2.xml b/latest/cases/00383/model-sbml-l3v2.xml new file mode 100644 index 000000000..0b0f869c9 --- /dev/null +++ b/latest/cases/00383/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00383/output.heta b/latest/cases/00383/output.heta new file mode 100644 index 000000000..b82dfabc0 --- /dev/null +++ b/latest/cases/00383/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Both species S2 +and S3 are labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00383/synopsis.txt b/latest/cases/00383/synopsis.txt new file mode 100644 index 000000000..65fc325ea --- /dev/null +++ b/latest/cases/00383/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Both species S2 +and S3 are labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00384/l2v5/heta-code/output.heta b/latest/cases/00384/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4489135d0 --- /dev/null +++ b/latest/cases/00384/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4 / C; +S1 [event1]= (1 / 5000); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.2e-4 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2e-4 / C; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00384/l2v5/index.heta b/latest/cases/00384/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00384/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00384/l2v5/json/output.json b/latest/cases/00384/l2v5/json/output.json new file mode 100644 index 000000000..8cec43930 --- /dev/null +++ b/latest/cases/00384/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C", + "event1": "(1 / 5000)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00384/l3v2/heta-code/output.heta b/latest/cases/00384/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d76370fd7 --- /dev/null +++ b/latest/cases/00384/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S1 [event1]= (1 / 5000); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00384/l3v2/index.heta b/latest/cases/00384/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00384/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00384/l3v2/json/output.json b/latest/cases/00384/l3v2/json/output.json new file mode 100644 index 000000000..f2183a146 --- /dev/null +++ b/latest/cases/00384/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C", + "event1": "(1 / 5000)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + } +] \ No newline at end of file diff --git a/latest/cases/00384/model-sbml-l2v5.xml b/latest/cases/00384/model-sbml-l2v5.xml new file mode 100644 index 000000000..02e4a1949 --- /dev/null +++ b/latest/cases/00384/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5000 + + + + + + + diff --git a/latest/cases/00384/model-sbml-l3v2.xml b/latest/cases/00384/model-sbml-l3v2.xml new file mode 100644 index 000000000..61bdbfd1c --- /dev/null +++ b/latest/cases/00384/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5000 + + + + + + + diff --git a/latest/cases/00384/output.heta b/latest/cases/00384/output.heta new file mode 100644 index 000000000..193d362a5 --- /dev/null +++ b/latest/cases/00384/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S1 [event1]= (1 / 5000); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00384/synopsis.txt b/latest/cases/00384/synopsis.txt new file mode 100644 index 000000000..072ab2ff7 --- /dev/null +++ b/latest/cases/00384/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00385/l2v5/heta-code/output.heta b/latest/cases/00385/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e16dea1e8 --- /dev/null +++ b/latest/cases/00385/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001 / C; +S1 [event1]= 0.002; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.0012 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.0019 / C; +S3 [event2]= (1 / 1000); +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 750; +k2 @Record 'k2' { } .= 250; + +event1 @DSwitcher 'event1' { trigger: S2 < S4, }; +event2 @DSwitcher 'event2' { trigger: S3 > 0.002, }; + diff --git a/latest/cases/00385/l2v5/index.heta b/latest/cases/00385/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00385/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00385/l2v5/json/output.json b/latest/cases/00385/l2v5/json/output.json new file mode 100644 index 000000000..d2ccbed86 --- /dev/null +++ b/latest/cases/00385/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C", + "event1": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0019 / C", + "event2": "(1 / 1000)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "750" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "250" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S2 < S4" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 0.002" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00385/l3v2/heta-code/output.heta b/latest/cases/00385/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ad23ffe56 --- /dev/null +++ b/latest/cases/00385/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S1 [event1]= 0.002; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.0019 / C; +S3 [event2]= (1 / 1000); +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + +event1 @DSwitcher 'event1' { trigger: S2 < S4, }; +event2 @DSwitcher 'event2' { trigger: S3 > 0.002, }; + diff --git a/latest/cases/00385/l3v2/index.heta b/latest/cases/00385/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00385/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00385/l3v2/json/output.json b/latest/cases/00385/l3v2/json/output.json new file mode 100644 index 000000000..758c53c5b --- /dev/null +++ b/latest/cases/00385/l3v2/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C", + "event1": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0019 / C", + "event2": "(1 / 1000)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 250 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S2 < S4" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 0.002" + } +] \ No newline at end of file diff --git a/latest/cases/00385/model-sbml-l2v5.xml b/latest/cases/00385/model-sbml-l2v5.xml new file mode 100644 index 000000000..ed21aa5e9 --- /dev/null +++ b/latest/cases/00385/model-sbml-l2v5.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S4 + + + + + + + 0.002 + + + + + + + + + + S3 + 0.002 + + + + + + + 1 1000 + + + + + + + diff --git a/latest/cases/00385/model-sbml-l3v2.xml b/latest/cases/00385/model-sbml-l3v2.xml new file mode 100644 index 000000000..6cc42eefd --- /dev/null +++ b/latest/cases/00385/model-sbml-l3v2.xml @@ -0,0 +1,118 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S4 + + + + + + + 0.002 + + + + + + + + + + S3 + 0.002 + + + + + + + 1 1000 + + + + + + + diff --git a/latest/cases/00385/output.heta b/latest/cases/00385/output.heta new file mode 100644 index 000000000..626b795ee --- /dev/null +++ b/latest/cases/00385/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S2 < S4$ | $-$ | $S1 -> 2 \x 10^-3$ |] + | Event2 | $S3 > 2 \x 10^-3$ | $-$ | $S3 -> 1 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.9 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S1 [event1]= 0.002; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.0019 / C; +S3 [event2]= (1 / 1000); +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + +event1 @DSwitcher 'event1' { trigger: S2 < S4, }; +event2 @DSwitcher 'event2' { trigger: S3 > 0.002, }; + diff --git a/latest/cases/00385/synopsis.txt b/latest/cases/00385/synopsis.txt new file mode 100644 index 000000000..c87e5ec50 --- /dev/null +++ b/latest/cases/00385/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S2 < S4$ | $-$ | $S1 -> 2 \x 10^-3$ |] + | Event2 | $S3 > 2 \x 10^-3$ | $-$ | $S3 -> 1 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.9 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00386/l2v5/heta-code/output.heta b/latest/cases/00386/l2v5/heta-code/output.heta new file mode 100644 index 000000000..24bc5537f --- /dev/null +++ b/latest/cases/00386/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S1 [event1]= (1 / 50); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.012 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.02 / C; +S3 [event1]= (1 / 200); +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 25; + +event1 @DSwitcher 'event1' { trigger: S2 < S4, }; + diff --git a/latest/cases/00386/l2v5/index.heta b/latest/cases/00386/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00386/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00386/l2v5/json/output.json b/latest/cases/00386/l2v5/json/output.json new file mode 100644 index 000000000..e34c87f57 --- /dev/null +++ b/latest/cases/00386/l2v5/json/output.json @@ -0,0 +1,156 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C", + "event1": "(1 / 50)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C", + "event1": "(1 / 200)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S2 < S4" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00386/l3v2/heta-code/output.heta b/latest/cases/00386/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3e013ce23 --- /dev/null +++ b/latest/cases/00386/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S1 [event1]= (1 / 50); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 [event1]= (1 / 200); +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + +event1 @DSwitcher 'event1' { trigger: S2 < S4, }; + diff --git a/latest/cases/00386/l3v2/index.heta b/latest/cases/00386/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00386/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00386/l3v2/json/output.json b/latest/cases/00386/l3v2/json/output.json new file mode 100644 index 000000000..45490dc55 --- /dev/null +++ b/latest/cases/00386/l3v2/json/output.json @@ -0,0 +1,128 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C", + "event1": "(1 / 50)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C", + "event1": "(1 / 200)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S2 < S4" + } +] \ No newline at end of file diff --git a/latest/cases/00386/model-sbml-l2v5.xml b/latest/cases/00386/model-sbml-l2v5.xml new file mode 100644 index 000000000..532080abf --- /dev/null +++ b/latest/cases/00386/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S4 + + + + + + + 1 50 + + + + + 1 200 + + + + + + + diff --git a/latest/cases/00386/model-sbml-l3v2.xml b/latest/cases/00386/model-sbml-l3v2.xml new file mode 100644 index 000000000..7d02711d2 --- /dev/null +++ b/latest/cases/00386/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S4 + + + + + + + 1 50 + + + + + 1 200 + + + + + + + diff --git a/latest/cases/00386/output.heta b/latest/cases/00386/output.heta new file mode 100644 index 000000000..05c740f50 --- /dev/null +++ b/latest/cases/00386/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S2 < S4$ | $-$ | $S1 -> 2 \x 10^-2$ |] + | | | | $S3 -> 0.5 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S1 [event1]= (1 / 50); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 [event1]= (1 / 200); +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + +event1 @DSwitcher 'event1' { trigger: S2 < S4, }; + diff --git a/latest/cases/00386/synopsis.txt b/latest/cases/00386/synopsis.txt new file mode 100644 index 000000000..5113e8a28 --- /dev/null +++ b/latest/cases/00386/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S2 < S4$ | $-$ | $S1 -> 2 \x 10^-2$ |] + | | | | $S3 -> 0.5 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00387/l2v5/heta-code/output.heta b/latest/cases/00387/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a9c900c88 --- /dev/null +++ b/latest/cases/00387/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00387/l2v5/index.heta b/latest/cases/00387/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00387/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00387/l2v5/json/output.json b/latest/cases/00387/l2v5/json/output.json new file mode 100644 index 000000000..34b835ad4 --- /dev/null +++ b/latest/cases/00387/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00387/l3v2/heta-code/output.heta b/latest/cases/00387/l3v2/heta-code/output.heta new file mode 100644 index 000000000..61650e4c1 --- /dev/null +++ b/latest/cases/00387/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00387/l3v2/index.heta b/latest/cases/00387/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00387/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00387/l3v2/json/output.json b/latest/cases/00387/l3v2/json/output.json new file mode 100644 index 000000000..8b17bad4e --- /dev/null +++ b/latest/cases/00387/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00387/model-sbml-l2v5.xml b/latest/cases/00387/model-sbml-l2v5.xml new file mode 100644 index 000000000..faaaa830b --- /dev/null +++ b/latest/cases/00387/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00387/model-sbml-l3v2.xml b/latest/cases/00387/model-sbml-l3v2.xml new file mode 100644 index 000000000..47d281e7c --- /dev/null +++ b/latest/cases/00387/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00387/output.heta b/latest/cases/00387/output.heta new file mode 100644 index 000000000..2e548f334 --- /dev/null +++ b/latest/cases/00387/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00387/synopsis.txt b/latest/cases/00387/synopsis.txt new file mode 100644 index 000000000..ca39fe5b8 --- /dev/null +++ b/latest/cases/00387/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00388/l2v5/build.log b/latest/cases/00388/l2v5/build.log new file mode 100644 index 000000000..de6f36098 --- /dev/null +++ b/latest/cases/00388/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00388/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00388/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00388/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00388/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00388/l2v5/index.heta b/latest/cases/00388/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00388/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00388/l3v2/index.heta b/latest/cases/00388/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00388/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00388/model-sbml-l2v5.xml b/latest/cases/00388/model-sbml-l2v5.xml new file mode 100644 index 000000000..8d0c43336 --- /dev/null +++ b/latest/cases/00388/model-sbml-l2v5.xml @@ -0,0 +1,89 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00388/synopsis.txt b/latest/cases/00388/synopsis.txt new file mode 100644 index 000000000..bd16f74ed --- /dev/null +++ b/latest/cases/00388/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (2 * p1) S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00389/l2v5/heta-code/output.heta b/latest/cases/00389/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c77abffb3 --- /dev/null +++ b/latest/cases/00389/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00389/l2v5/index.heta b/latest/cases/00389/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00389/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00389/l2v5/json/output.json b/latest/cases/00389/l2v5/json/output.json new file mode 100644 index 000000000..b04998163 --- /dev/null +++ b/latest/cases/00389/l2v5/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00389/l3v2/heta-code/output.heta b/latest/cases/00389/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c99a6d709 --- /dev/null +++ b/latest/cases/00389/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00389/l3v2/index.heta b/latest/cases/00389/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00389/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00389/l3v2/json/output.json b/latest/cases/00389/l3v2/json/output.json new file mode 100644 index 000000000..84727b579 --- /dev/null +++ b/latest/cases/00389/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00389/model-sbml-l2v5.xml b/latest/cases/00389/model-sbml-l2v5.xml new file mode 100644 index 000000000..f7e59be66 --- /dev/null +++ b/latest/cases/00389/model-sbml-l2v5.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00389/model-sbml-l3v2.xml b/latest/cases/00389/model-sbml-l3v2.xml new file mode 100644 index 000000000..fd034a2ad --- /dev/null +++ b/latest/cases/00389/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00389/output.heta b/latest/cases/00389/output.heta new file mode 100644 index 000000000..846b788d6 --- /dev/null +++ b/latest/cases/00389/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 + +S2 defines another local parameter k. Note that these parameters have a +scope local to the defining reaction. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of local parameter k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00389/synopsis.txt b/latest/cases/00389/synopsis.txt new file mode 100644 index 000000000..305ec0c80 --- /dev/null +++ b/latest/cases/00389/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 + +S2 defines another local parameter k. Note that these parameters have a +scope local to the defining reaction. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of local parameter k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00390/l2v5/heta-code/output.heta b/latest/cases/00390/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f9d334bc6 --- /dev/null +++ b/latest/cases/00390/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1 / C; +S1 [event1]= (1 / 5); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.12 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.2 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.1 / C; +S4 [event2]= (1 / 10); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: 2*S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 2.5; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (1 / 4), }; + diff --git a/latest/cases/00390/l2v5/index.heta b/latest/cases/00390/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00390/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00390/l2v5/json/output.json b/latest/cases/00390/l2v5/json/output.json new file mode 100644 index 000000000..ab1748cda --- /dev/null +++ b/latest/cases/00390/l2v5/json/output.json @@ -0,0 +1,164 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C", + "event1": "(1 / 5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.12 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C", + "event2": "(1 / 10)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -2 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > (1 / 4)" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00390/l3v2/heta-code/output.heta b/latest/cases/00390/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d2fad62c9 --- /dev/null +++ b/latest/cases/00390/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S1 [event1]= (1 / 5); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1 / C; +S4 [event2]= (1 / 10); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: 2*S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (1 / 4), }; + diff --git a/latest/cases/00390/l3v2/index.heta b/latest/cases/00390/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00390/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00390/l3v2/json/output.json b/latest/cases/00390/l3v2/json/output.json new file mode 100644 index 000000000..4c63d7465 --- /dev/null +++ b/latest/cases/00390/l3v2/json/output.json @@ -0,0 +1,136 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C", + "event1": "(1 / 5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.12 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C", + "event2": "(1 / 10)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -2 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > (1 / 4)" + } +] \ No newline at end of file diff --git a/latest/cases/00390/model-sbml-l2v5.xml b/latest/cases/00390/model-sbml-l2v5.xml new file mode 100644 index 000000000..1bee9f0bd --- /dev/null +++ b/latest/cases/00390/model-sbml-l2v5.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5 + + + + + + + + + + S3 + 1 4 + + + + + + + 1 10 + + + + + + + diff --git a/latest/cases/00390/model-sbml-l3v2.xml b/latest/cases/00390/model-sbml-l3v2.xml new file mode 100644 index 000000000..c12bfd255 --- /dev/null +++ b/latest/cases/00390/model-sbml-l3v2.xml @@ -0,0 +1,117 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5 + + + + + + + + + + S3 + 1 4 + + + + + + + 1 10 + + + + + + + diff --git a/latest/cases/00390/output.heta b/latest/cases/00390/output.heta new file mode 100644 index 000000000..727f035d9 --- /dev/null +++ b/latest/cases/00390/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> 2S3 + S4 | $k1 * S1 * S2 * C$ | +| 2S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-1$ |] + | Event2 | $S3 > 2.5 \x 10^-1$ | $-$ | $S4 -> 1 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S1 [event1]= (1 / 5); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1 / C; +S4 [event2]= (1 / 10); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: 2*S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (1 / 4), }; + diff --git a/latest/cases/00390/synopsis.txt b/latest/cases/00390/synopsis.txt new file mode 100644 index 000000000..b36e670ff --- /dev/null +++ b/latest/cases/00390/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> 2S3 + S4 | $k1 * S1 * S2 * C$ | +| 2S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-1$ |] + | Event2 | $S3 > 2.5 \x 10^-1$ | $-$ | $S4 -> 1 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00391/l2v5/build.log b/latest/cases/00391/l2v5/build.log new file mode 100644 index 000000000..702d83542 --- /dev/null +++ b/latest/cases/00391/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00391/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00391/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00391/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00391/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00391/l2v5/index.heta b/latest/cases/00391/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00391/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00391/l3v2/index.heta b/latest/cases/00391/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00391/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00391/model-sbml-l2v5.xml b/latest/cases/00391/model-sbml-l2v5.xml new file mode 100644 index 000000000..81e99946a --- /dev/null +++ b/latest/cases/00391/model-sbml-l2v5.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5000 + + + + + + + + + + S3 + 1 4000 + + + + + + + 1 10000 + + + + + + + diff --git a/latest/cases/00391/synopsis.txt b/latest/cases/00391/synopsis.txt new file mode 100644 index 000000000..171114c01 --- /dev/null +++ b/latest/cases/00391/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p1)S3 + S4 | $k1 * S1 * S2 * C$ | +| 2S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-4$ |] + | Event2 | $S3 > 2.5 \x 10^-4$ | $-$ | $S4 -> 1 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00392/l2v5/heta-code/output.heta b/latest/cases/00392/l2v5/heta-code/output.heta new file mode 100644 index 000000000..43794138c --- /dev/null +++ b/latest/cases/00392/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001 / C; +S1 [event1]= (1 / 500); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.0012 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.002 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.001 / C; +S4 [event2]= (1 / 1000); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3 * S4; + +k__reaction1_local @Const { } = 750; +k__reaction2_local @Const { } = 250; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (9 / 4000), }; + diff --git a/latest/cases/00392/l2v5/index.heta b/latest/cases/00392/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00392/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00392/l2v5/json/output.json b/latest/cases/00392/l2v5/json/output.json new file mode 100644 index 000000000..6d66836b2 --- /dev/null +++ b/latest/cases/00392/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C", + "event1": "(1 / 500)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C", + "event2": "(1 / 1000)" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 750 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 250 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > (9 / 4000)" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00392/l3v2/heta-code/output.heta b/latest/cases/00392/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3527d6cf1 --- /dev/null +++ b/latest/cases/00392/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S1 [event1]= (1 / 500); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.002 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.001 / C; +S4 [event2]= (1 / 1000); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3 * S4; + +k__reaction1_local @Const { } = 750; +k__reaction2_local @Const { } = 250; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (9 / 4000), }; + diff --git a/latest/cases/00392/l3v2/index.heta b/latest/cases/00392/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00392/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00392/l3v2/json/output.json b/latest/cases/00392/l3v2/json/output.json new file mode 100644 index 000000000..6ce0dce23 --- /dev/null +++ b/latest/cases/00392/l3v2/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C", + "event1": "(1 / 500)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C", + "event2": "(1 / 1000)" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 750 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 250 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > (9 / 4000)" + } +] \ No newline at end of file diff --git a/latest/cases/00392/model-sbml-l2v5.xml b/latest/cases/00392/model-sbml-l2v5.xml new file mode 100644 index 000000000..b9a16d04d --- /dev/null +++ b/latest/cases/00392/model-sbml-l2v5.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + + C + k + S3 + S4 + + + + + + + + + + + + + + + S4 + S2 + + + + + + + 1 500 + + + + + + + + + + S3 + 9 4000 + + + + + + + 1 1000 + + + + + + + diff --git a/latest/cases/00392/model-sbml-l3v2.xml b/latest/cases/00392/model-sbml-l3v2.xml new file mode 100644 index 000000000..f7078729a --- /dev/null +++ b/latest/cases/00392/model-sbml-l3v2.xml @@ -0,0 +1,119 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + + C + k + S3 + S4 + + + + + + + + + + + + + + + S4 + S2 + + + + + + + 1 500 + + + + + + + + + + S3 + 9 4000 + + + + + + + 1 1000 + + + + + + + diff --git a/latest/cases/00392/output.heta b/latest/cases/00392/output.heta new file mode 100644 index 000000000..5a137051e --- /dev/null +++ b/latest/cases/00392/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k * S3 * S4 * C$ |] + +Reaction S1 + S2 -> S3 + S4 defines one local parameter k. Reaction S3 + +S4 -> S1 + S2 defines another (different) local parameter k. Note that +these parmeters have a scope local to the defining reaction. + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-3$ |] + | Event2 | $S3 > 2.25 \x 10^-3$ | $-$ | $S4 -> 1 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of local parameter k |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S1 [event1]= (1 / 500); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.002 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.001 / C; +S4 [event2]= (1 / 1000); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3 * S4; + +k__reaction1_local @Const { } = 750; +k__reaction2_local @Const { } = 250; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (9 / 4000), }; + diff --git a/latest/cases/00392/synopsis.txt b/latest/cases/00392/synopsis.txt new file mode 100644 index 000000000..c8e84c7d9 --- /dev/null +++ b/latest/cases/00392/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k * S3 * S4 * C$ |] + +Reaction S1 + S2 -> S3 + S4 defines one local parameter k. Reaction S3 + +S4 -> S1 + S2 defines another (different) local parameter k. Note that +these parmeters have a scope local to the defining reaction. + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-3$ |] + | Event2 | $S3 > 2.25 \x 10^-3$ | $-$ | $S4 -> 1 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of local parameter k |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00393/l2v5/heta-code/output.heta b/latest/cases/00393/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3e42d3371 --- /dev/null +++ b/latest/cases/00393/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.75; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00393/l2v5/index.heta b/latest/cases/00393/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00393/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00393/l2v5/json/output.json b/latest/cases/00393/l2v5/json/output.json new file mode 100644 index 000000000..3e05772e7 --- /dev/null +++ b/latest/cases/00393/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.75" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00393/l3v2/heta-code/output.heta b/latest/cases/00393/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d494e41f9 --- /dev/null +++ b/latest/cases/00393/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.75; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00393/l3v2/index.heta b/latest/cases/00393/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00393/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00393/l3v2/json/output.json b/latest/cases/00393/l3v2/json/output.json new file mode 100644 index 000000000..06c6424e9 --- /dev/null +++ b/latest/cases/00393/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.75" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00393/model-sbml-l2v5.xml b/latest/cases/00393/model-sbml-l2v5.xml new file mode 100644 index 000000000..f23b6b625 --- /dev/null +++ b/latest/cases/00393/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.75 + + + + + 1 + + + + + + + diff --git a/latest/cases/00393/model-sbml-l3v2.xml b/latest/cases/00393/model-sbml-l3v2.xml new file mode 100644 index 000000000..21057b5bb --- /dev/null +++ b/latest/cases/00393/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.75 + + + + + 1 + + + + + + + diff --git a/latest/cases/00393/output.heta b/latest/cases/00393/output.heta new file mode 100644 index 000000000..9a83cf443 --- /dev/null +++ b/latest/cases/00393/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.75$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.75; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00393/synopsis.txt b/latest/cases/00393/synopsis.txt new file mode 100644 index 000000000..7587c2a2b --- /dev/null +++ b/latest/cases/00393/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.75$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00394/l2v5/build.log b/latest/cases/00394/l2v5/build.log new file mode 100644 index 000000000..70318cf2b --- /dev/null +++ b/latest/cases/00394/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00394/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00394/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00394/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00394/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00394/l2v5/index.heta b/latest/cases/00394/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00394/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00394/l3v2/index.heta b/latest/cases/00394/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00394/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00394/model-sbml-l2v5.xml b/latest/cases/00394/model-sbml-l2v5.xml new file mode 100644 index 000000000..bf0913969 --- /dev/null +++ b/latest/cases/00394/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.75 + + + + + 1 + + + + + + + diff --git a/latest/cases/00394/synopsis.txt b/latest/cases/00394/synopsis.txt new file mode 100644 index 000000000..2e68df256 --- /dev/null +++ b/latest/cases/00394/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.75$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$ 0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00395/l2v5/heta-code/output.heta b/latest/cases/00395/l2v5/heta-code/output.heta new file mode 100644 index 000000000..65fb2ae3a --- /dev/null +++ b/latest/cases/00395/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00395/l2v5/index.heta b/latest/cases/00395/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00395/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00395/l2v5/json/output.json b/latest/cases/00395/l2v5/json/output.json new file mode 100644 index 000000000..4462c47f0 --- /dev/null +++ b/latest/cases/00395/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00395/l3v2/heta-code/output.heta b/latest/cases/00395/l3v2/heta-code/output.heta new file mode 100644 index 000000000..355ce65ee --- /dev/null +++ b/latest/cases/00395/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00395/l3v2/index.heta b/latest/cases/00395/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00395/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00395/l3v2/json/output.json b/latest/cases/00395/l3v2/json/output.json new file mode 100644 index 000000000..a5c3e6b37 --- /dev/null +++ b/latest/cases/00395/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00395/model-sbml-l2v5.xml b/latest/cases/00395/model-sbml-l2v5.xml new file mode 100644 index 000000000..555d64671 --- /dev/null +++ b/latest/cases/00395/model-sbml-l2v5.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00395/model-sbml-l3v2.xml b/latest/cases/00395/model-sbml-l3v2.xml new file mode 100644 index 000000000..c2e8c77ca --- /dev/null +++ b/latest/cases/00395/model-sbml-l3v2.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00395/output.heta b/latest/cases/00395/output.heta new file mode 100644 index 000000000..a4e6abc3c --- /dev/null +++ b/latest/cases/00395/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 + +S2 defines another (different) local parameter k. Note that these +parmeters have a scope local to the defining reaction. + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of local parameter k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00395/synopsis.txt b/latest/cases/00395/synopsis.txt new file mode 100644 index 000000000..0f8ead51b --- /dev/null +++ b/latest/cases/00395/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 + +S2 defines another (different) local parameter k. Note that these +parmeters have a scope local to the defining reaction. + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of local parameter k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00396/l2v5/heta-code/output.heta b/latest/cases/00396/l2v5/heta-code/output.heta new file mode 100644 index 000000000..23a05c2b5 --- /dev/null +++ b/latest/cases/00396/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1; +S3 @Record 'S3' { } .= 1; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00396/l2v5/index.heta b/latest/cases/00396/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00396/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00396/l2v5/json/output.json b/latest/cases/00396/l2v5/json/output.json new file mode 100644 index 000000000..c6525d935 --- /dev/null +++ b/latest/cases/00396/l2v5/json/output.json @@ -0,0 +1,125 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00396/l3v2/heta-code/output.heta b/latest/cases/00396/l3v2/heta-code/output.heta new file mode 100644 index 000000000..86be5d8b1 --- /dev/null +++ b/latest/cases/00396/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00396/l3v2/index.heta b/latest/cases/00396/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00396/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00396/l3v2/json/output.json b/latest/cases/00396/l3v2/json/output.json new file mode 100644 index 000000000..e861bfc2f --- /dev/null +++ b/latest/cases/00396/l3v2/json/output.json @@ -0,0 +1,97 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00396/model-sbml-l2v5.xml b/latest/cases/00396/model-sbml-l2v5.xml new file mode 100644 index 000000000..e0d8059ab --- /dev/null +++ b/latest/cases/00396/model-sbml-l2v5.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00396/model-sbml-l3v2.xml b/latest/cases/00396/model-sbml-l3v2.xml new file mode 100644 index 000000000..36c09b9e4 --- /dev/null +++ b/latest/cases/00396/model-sbml-l3v2.xml @@ -0,0 +1,98 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00396/output.heta b/latest/cases/00396/output.heta new file mode 100644 index 000000000..ec5fc4aa5 --- /dev/null +++ b/latest/cases/00396/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Model using parameters and rules only with + one event that assigns value to a parameter. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains one event that assigns value to parameter S2 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00396/synopsis.txt b/latest/cases/00396/synopsis.txt new file mode 100644 index 000000000..96223c4e3 --- /dev/null +++ b/latest/cases/00396/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Model using parameters and rules only with + one event that assigns value to a parameter. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains one event that assigns value to parameter S2 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00397/l2v5/heta-code/output.heta b/latest/cases/00397/l2v5/heta-code/output.heta new file mode 100644 index 000000000..011d0a7b8 --- /dev/null +++ b/latest/cases/00397/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event2]= 1; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1; +S3 @Record 'S3' { } .= 1; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00397/l2v5/index.heta b/latest/cases/00397/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00397/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00397/l2v5/json/output.json b/latest/cases/00397/l2v5/json/output.json new file mode 100644 index 000000000..766f19ba8 --- /dev/null +++ b/latest/cases/00397/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event2": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00397/l3v2/heta-code/output.heta b/latest/cases/00397/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fbdf6eee9 --- /dev/null +++ b/latest/cases/00397/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event2]= 1; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00397/l3v2/index.heta b/latest/cases/00397/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00397/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00397/l3v2/json/output.json b/latest/cases/00397/l3v2/json/output.json new file mode 100644 index 000000000..0ecf182ab --- /dev/null +++ b/latest/cases/00397/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event2": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + } +] \ No newline at end of file diff --git a/latest/cases/00397/model-sbml-l2v5.xml b/latest/cases/00397/model-sbml-l2v5.xml new file mode 100644 index 000000000..9d2c81401 --- /dev/null +++ b/latest/cases/00397/model-sbml-l2v5.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00397/model-sbml-l3v2.xml b/latest/cases/00397/model-sbml-l3v2.xml new file mode 100644 index 000000000..96bed84b3 --- /dev/null +++ b/latest/cases/00397/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00397/output.heta b/latest/cases/00397/output.heta new file mode 100644 index 000000000..03d107fa2 --- /dev/null +++ b/latest/cases/00397/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Model using parameters and rules only with + one event that assigns value to a parameter. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains two events, that assign value to parameters S2 and S1 respectively, defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event2]= 1; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00397/synopsis.txt b/latest/cases/00397/synopsis.txt new file mode 100644 index 000000000..767f9e752 --- /dev/null +++ b/latest/cases/00397/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Model using parameters and rules only with + one event that assigns value to a parameter. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains two events, that assign value to parameters S2 and S1 respectively, defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00398/l2v5/heta-code/output.heta b/latest/cases/00398/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9cb4ab29c --- /dev/null +++ b/latest/cases/00398/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= 1; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1.5; +S3 @Record 'S3' { } .= 1; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00398/l2v5/index.heta b/latest/cases/00398/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00398/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00398/l2v5/json/output.json b/latest/cases/00398/l2v5/json/output.json new file mode 100644 index 000000000..674f30418 --- /dev/null +++ b/latest/cases/00398/l2v5/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1.5" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00398/l3v2/heta-code/output.heta b/latest/cases/00398/l3v2/heta-code/output.heta new file mode 100644 index 000000000..592748da7 --- /dev/null +++ b/latest/cases/00398/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= 1; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1.5; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00398/l3v2/index.heta b/latest/cases/00398/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00398/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00398/l3v2/json/output.json b/latest/cases/00398/l3v2/json/output.json new file mode 100644 index 000000000..4f7b0829e --- /dev/null +++ b/latest/cases/00398/l3v2/json/output.json @@ -0,0 +1,98 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "1" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1.5" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00398/model-sbml-l2v5.xml b/latest/cases/00398/model-sbml-l2v5.xml new file mode 100644 index 000000000..ad9933b42 --- /dev/null +++ b/latest/cases/00398/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00398/model-sbml-l3v2.xml b/latest/cases/00398/model-sbml-l3v2.xml new file mode 100644 index 000000000..0445c671e --- /dev/null +++ b/latest/cases/00398/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00398/output.heta b/latest/cases/00398/output.heta new file mode 100644 index 000000000..62b20d5a5 --- /dev/null +++ b/latest/cases/00398/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Model using parameters and rules only with + one event that assigns value to two parameters. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains two events, that assign value to parameters S2 and S1 respectively, defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= 1; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1.5; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00398/synopsis.txt b/latest/cases/00398/synopsis.txt new file mode 100644 index 000000000..ee69fdfe8 --- /dev/null +++ b/latest/cases/00398/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Model using parameters and rules only with + one event that assigns value to two parameters. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains two events, that assign value to parameters S2 and S1 respectively, defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00399/l2v5/heta-code/output.heta b/latest/cases/00399/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f982f059c --- /dev/null +++ b/latest/cases/00399/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= S2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00399/l2v5/index.heta b/latest/cases/00399/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00399/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00399/l2v5/json/output.json b/latest/cases/00399/l2v5/json/output.json new file mode 100644 index 000000000..8f056fcac --- /dev/null +++ b/latest/cases/00399/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00399/l3v2/heta-code/output.heta b/latest/cases/00399/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cbbe11753 --- /dev/null +++ b/latest/cases/00399/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00399/l3v2/index.heta b/latest/cases/00399/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00399/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00399/l3v2/json/output.json b/latest/cases/00399/l3v2/json/output.json new file mode 100644 index 000000000..ad15e020e --- /dev/null +++ b/latest/cases/00399/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00399/model-sbml-l2v5.xml b/latest/cases/00399/model-sbml-l2v5.xml new file mode 100644 index 000000000..ffb6c1201 --- /dev/null +++ b/latest/cases/00399/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00399/model-sbml-l3v2.xml b/latest/cases/00399/model-sbml-l3v2.xml new file mode 100644 index 000000000..ac8c10514 --- /dev/null +++ b/latest/cases/00399/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00399/output.heta b/latest/cases/00399/output.heta new file mode 100644 index 000000000..0963da594 --- /dev/null +++ b/latest/cases/00399/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00399/synopsis.txt b/latest/cases/00399/synopsis.txt new file mode 100644 index 000000000..e0042238f --- /dev/null +++ b/latest/cases/00399/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00400/l2v5/heta-code/output.heta b/latest/cases/00400/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0e0ac4eb8 --- /dev/null +++ b/latest/cases/00400/l2v5/heta-code/output.heta @@ -0,0 +1,30 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= S2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S1, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.55; +k3 @Record 'k3' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00400/l2v5/index.heta b/latest/cases/00400/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00400/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00400/l2v5/json/output.json b/latest/cases/00400/l2v5/json/output.json new file mode 100644 index 000000000..8d13a5d09 --- /dev/null +++ b/latest/cases/00400/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.55" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00400/l3v2/heta-code/output.heta b/latest/cases/00400/l3v2/heta-code/output.heta new file mode 100644 index 000000000..acc89304b --- /dev/null +++ b/latest/cases/00400/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S1, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.55; +k3 @Const 'k3' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00400/l3v2/index.heta b/latest/cases/00400/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00400/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00400/l3v2/json/output.json b/latest/cases/00400/l3v2/json/output.json new file mode 100644 index 000000000..e78c53df0 --- /dev/null +++ b/latest/cases/00400/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.55 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00400/model-sbml-l2v5.xml b/latest/cases/00400/model-sbml-l2v5.xml new file mode 100644 index 000000000..477b17076 --- /dev/null +++ b/latest/cases/00400/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00400/model-sbml-l3v2.xml b/latest/cases/00400/model-sbml-l3v2.xml new file mode 100644 index 000000000..d1117e46a --- /dev/null +++ b/latest/cases/00400/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00400/output.heta b/latest/cases/00400/output.heta new file mode 100644 index 000000000..89b2e1629 --- /dev/null +++ b/latest/cases/00400/output.heta @@ -0,0 +1,72 @@ +/* +category: Test +synopsis: Basic three reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S1 | $k3 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S1, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.55; +k3 @Const 'k3' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00400/synopsis.txt b/latest/cases/00400/synopsis.txt new file mode 100644 index 000000000..3b6db2a6c --- /dev/null +++ b/latest/cases/00400/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Basic three reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S1 | $k3 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00401/l2v5/heta-code/output.heta b/latest/cases/00401/l2v5/heta-code/output.heta new file mode 100644 index 000000000..701f8e7d1 --- /dev/null +++ b/latest/cases/00401/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event1]= S2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= S3; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; +S3 [event1]= S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S1, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.55; +k3 @Record 'k3' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00401/l2v5/index.heta b/latest/cases/00401/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00401/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00401/l2v5/json/output.json b/latest/cases/00401/l2v5/json/output.json new file mode 100644 index 000000000..a40f798f3 --- /dev/null +++ b/latest/cases/00401/l2v5/json/output.json @@ -0,0 +1,160 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "S3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event1": "S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.55" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00401/l3v2/heta-code/output.heta b/latest/cases/00401/l3v2/heta-code/output.heta new file mode 100644 index 000000000..80f08ff17 --- /dev/null +++ b/latest/cases/00401/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= S3; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S3 [event1]= S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S1, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.55; +k3 @Const 'k3' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00401/l3v2/index.heta b/latest/cases/00401/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00401/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00401/l3v2/json/output.json b/latest/cases/00401/l3v2/json/output.json new file mode 100644 index 000000000..37a35daa8 --- /dev/null +++ b/latest/cases/00401/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "S3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event1": "S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.55 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00401/model-sbml-l2v5.xml b/latest/cases/00401/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef33951cb --- /dev/null +++ b/latest/cases/00401/model-sbml-l2v5.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + S3 + + + + + S2 + + + + + S1 + + + + + + + diff --git a/latest/cases/00401/model-sbml-l3v2.xml b/latest/cases/00401/model-sbml-l3v2.xml new file mode 100644 index 000000000..f8b3bdc0f --- /dev/null +++ b/latest/cases/00401/model-sbml-l3v2.xml @@ -0,0 +1,121 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + S3 + + + + + S2 + + + + + S1 + + + + + + + diff --git a/latest/cases/00401/output.heta b/latest/cases/00401/output.heta new file mode 100644 index 000000000..4906bd0c2 --- /dev/null +++ b/latest/cases/00401/output.heta @@ -0,0 +1,74 @@ +/* +category: Test +synopsis: Basic three reactions with three species in one compartment + and one event that assigns value to three species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S1 | $k3 * S3 * C$ |] + +The model contains one event that assigns values to species S1, S2 and S3: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = S3$ | + | | | | $S1 = S2$ | + | | | | $S3 = S1$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event1]= S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= S3; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S3 [event1]= S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S1, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.55; +k3 @Const 'k3' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00401/synopsis.txt b/latest/cases/00401/synopsis.txt new file mode 100644 index 000000000..8b6e10320 --- /dev/null +++ b/latest/cases/00401/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic three reactions with three species in one compartment + and one event that assigns value to three species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S1 | $k3 * S3 * C$ |] + +The model contains one event that assigns values to species S1, S2 and S3: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = S3$ | + | | | | $S1 = S2$ | + | | | | $S3 = S1$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00402/l2v5/heta-code/output.heta b/latest/cases/00402/l2v5/heta-code/output.heta new file mode 100644 index 000000000..859107221 --- /dev/null +++ b/latest/cases/00402/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= S2; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1.5; +S3 @Record 'S3' { } .= 1; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00402/l2v5/index.heta b/latest/cases/00402/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00402/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00402/l2v5/json/output.json b/latest/cases/00402/l2v5/json/output.json new file mode 100644 index 000000000..a8555df7d --- /dev/null +++ b/latest/cases/00402/l2v5/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "S2" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1.5" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00402/l3v2/heta-code/output.heta b/latest/cases/00402/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0f78342e8 --- /dev/null +++ b/latest/cases/00402/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= S2; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1.5; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00402/l3v2/index.heta b/latest/cases/00402/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00402/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00402/l3v2/json/output.json b/latest/cases/00402/l3v2/json/output.json new file mode 100644 index 000000000..5412eb209 --- /dev/null +++ b/latest/cases/00402/l3v2/json/output.json @@ -0,0 +1,98 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "S2" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1.5" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k1 * S1 * S2 + (-1) * k2 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00402/model-sbml-l2v5.xml b/latest/cases/00402/model-sbml-l2v5.xml new file mode 100644 index 000000000..ae35637b9 --- /dev/null +++ b/latest/cases/00402/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00402/model-sbml-l3v2.xml b/latest/cases/00402/model-sbml-l3v2.xml new file mode 100644 index 000000000..709a76041 --- /dev/null +++ b/latest/cases/00402/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00402/output.heta b/latest/cases/00402/output.heta new file mode 100644 index 000000000..27c6c86cb --- /dev/null +++ b/latest/cases/00402/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Model using parameters and rules only with + and one event that assigns value to two parameters. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains one event that assigns values to parameters S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k1 * S1 * S2 + (-1) * k2 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= S2; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1.5; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00402/synopsis.txt b/latest/cases/00402/synopsis.txt new file mode 100644 index 000000000..bbd3b0f1a --- /dev/null +++ b/latest/cases/00402/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Model using parameters and rules only with + and one event that assigns value to two parameters. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains one event that assigns values to parameters S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00403/l2v5/heta-code/output.heta b/latest/cases/00403/l2v5/heta-code/output.heta new file mode 100644 index 000000000..71d2af603 --- /dev/null +++ b/latest/cases/00403/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k3 * S3 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k2 * S2 + (-1) * k3 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= S2; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1.5; +S3 @Record 'S3' { } .= 1; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.55; +k3 @Record 'k3' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00403/l2v5/index.heta b/latest/cases/00403/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00403/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00403/l2v5/json/output.json b/latest/cases/00403/l2v5/json/output.json new file mode 100644 index 000000000..37f7fad87 --- /dev/null +++ b/latest/cases/00403/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "S2" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1.5" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.55" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k3 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k3 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00403/l3v2/heta-code/output.heta b/latest/cases/00403/l3v2/heta-code/output.heta new file mode 100644 index 000000000..780a056a7 --- /dev/null +++ b/latest/cases/00403/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k3 * S3 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k2 * S2 + (-1) * k3 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= S2; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1.5; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.55; +k3 @Const 'k3' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00403/l3v2/index.heta b/latest/cases/00403/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00403/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00403/l3v2/json/output.json b/latest/cases/00403/l3v2/json/output.json new file mode 100644 index 000000000..a12c4b300 --- /dev/null +++ b/latest/cases/00403/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "S2" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "1.5" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.55 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.25 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k3 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k3 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00403/model-sbml-l2v5.xml b/latest/cases/00403/model-sbml-l2v5.xml new file mode 100644 index 000000000..2384a7f4a --- /dev/null +++ b/latest/cases/00403/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00403/model-sbml-l3v2.xml b/latest/cases/00403/model-sbml-l3v2.xml new file mode 100644 index 000000000..7072fbeb9 --- /dev/null +++ b/latest/cases/00403/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00403/output.heta b/latest/cases/00403/output.heta new file mode 100644 index 000000000..676e062dc --- /dev/null +++ b/latest/cases/00403/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Model using parameters and rules only with + and one event that assigns value to two parameters. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and three constant +parameters called k1, k2 and k3. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k3 * S3 - k1 * S1$ | + | Rate | S2 | $k1 * S1 - k2 * S2$ | + | Rate | S3 | $k2 * S2 - k3 * S3$ |] + +The model contains one event that assigns values to both parameters S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k3 * S3 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k2 * S2 + (-1) * k3 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= S2; +S2 @Record 'S2' { } .= 2; +S2 [event1]= 1.5; +S3 @Record 'S3' { } .= 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.55; +k3 @Const 'k3' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00403/synopsis.txt b/latest/cases/00403/synopsis.txt new file mode 100644 index 000000000..397843da4 --- /dev/null +++ b/latest/cases/00403/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Model using parameters and rules only with + and one event that assigns value to two parameters. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and three constant +parameters called k1, k2 and k3. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k3 * S3 - k1 * S1$ | + | Rate | S2 | $k1 * S1 - k2 * S2$ | + | Rate | S3 | $k2 * S2 - k3 * S3$ |] + +The model contains one event that assigns values to both parameters S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00404/l2v5/heta-code/output.heta b/latest/cases/00404/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8b7d1c1fa --- /dev/null +++ b/latest/cases/00404/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k3 * S3 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k2 * S2 + (-1) * k3 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= S2; +S2 @Record 'S2' { } .= 2; +S2 [event1]= S3; +S3 @Record 'S3' { } .= 1; +S3 [event1]= S1; +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.55; +k3 @Record 'k3' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00404/l2v5/index.heta b/latest/cases/00404/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00404/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00404/l2v5/json/output.json b/latest/cases/00404/l2v5/json/output.json new file mode 100644 index 000000000..ab963b6c5 --- /dev/null +++ b/latest/cases/00404/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "S2" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "S3" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1", + "event1": "S1" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.55" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k3 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k3 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00404/l3v2/heta-code/output.heta b/latest/cases/00404/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9769b7a36 --- /dev/null +++ b/latest/cases/00404/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k3 * S3 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k2 * S2 + (-1) * k3 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= S2; +S2 @Record 'S2' { } .= 2; +S2 [event1]= S3; +S3 @Record 'S3' { } .= 1; +S3 [event1]= S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.55; +k3 @Const 'k3' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00404/l3v2/index.heta b/latest/cases/00404/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00404/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00404/l3v2/json/output.json b/latest/cases/00404/l3v2/json/output.json new file mode 100644 index 000000000..3584e5dde --- /dev/null +++ b/latest/cases/00404/l3v2/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S1", + "title": "S1", + "assignments": { + "start_": "1", + "event1": "S2" + } + }, + { + "class": "Record", + "id": "S2", + "title": "S2", + "assignments": { + "start_": "2", + "event1": "S3" + } + }, + { + "class": "Record", + "id": "S3", + "title": "S3", + "assignments": { + "start_": "1", + "event1": "S1" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.55 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.25 + }, + { + "class": "Process", + "id": "S1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k3 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * S1 + (-1) * k2 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "k2 * S2 + (-1) * k3 * S3" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00404/model-sbml-l2v5.xml b/latest/cases/00404/model-sbml-l2v5.xml new file mode 100644 index 000000000..e7bf19e47 --- /dev/null +++ b/latest/cases/00404/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + S3 + + + + + S2 + + + + + S1 + + + + + + + diff --git a/latest/cases/00404/model-sbml-l3v2.xml b/latest/cases/00404/model-sbml-l3v2.xml new file mode 100644 index 000000000..847e25309 --- /dev/null +++ b/latest/cases/00404/model-sbml-l3v2.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + S3 + + + + + S2 + + + + + S1 + + + + + + + diff --git a/latest/cases/00404/output.heta b/latest/cases/00404/output.heta new file mode 100644 index 000000000..fac3188bf --- /dev/null +++ b/latest/cases/00404/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Model using parameters and rules only with + and one event that assigns value to three parameters. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and three constant +parameters called k1, k2 and k3. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k3 * S3 - k1 * S1$ | + | Rate | S2 | $k1 * S1 - k2 * S2$ | + | Rate | S3 | $k2 * S2 - k3 * S3$ |] + +The model contains one event that assigns values to parameters S1, S2 and +S3: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = S3$ | + | | | | $S1 = S2$ | + | | | | $S3 = S1$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +S1_proc @Process { actors: = S1, aux: {{"metaid":"rule1"}}, }; +S1_proc := k3 * S3 + (-1) * k1 * S1; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k1 * S1 + (-1) * k2 * S2; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule3"}}, }; +S3_proc := k2 * S2 + (-1) * k3 * S3; + +S1 @Record 'S1' { } .= 1; +S1 [event1]= S2; +S2 @Record 'S2' { } .= 2; +S2 [event1]= S3; +S3 @Record 'S3' { } .= 1; +S3 [event1]= S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.55; +k3 @Const 'k3' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00404/synopsis.txt b/latest/cases/00404/synopsis.txt new file mode 100644 index 000000000..5c68c93e7 --- /dev/null +++ b/latest/cases/00404/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Model using parameters and rules only with + and one event that assigns value to three parameters. +componentTags: Parameter, RateRule, EventNoDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and three constant +parameters called k1, k2 and k3. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k3 * S3 - k1 * S1$ | + | Rate | S2 | $k1 * S1 - k2 * S2$ | + | Rate | S3 | $k2 * S2 - k3 * S3$ |] + +The model contains one event that assigns values to parameters S1, S2 and +S3: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = S3$ | + | | | | $S1 = S2$ | + | | | | $S3 = S1$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00405/l2v5/build.log b/latest/cases/00405/l2v5/build.log new file mode 100644 index 000000000..b6685abf0 --- /dev/null +++ b/latest/cases/00405/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00405/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00405/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00405/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00405/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00405/l2v5/index.heta b/latest/cases/00405/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00405/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00405/l3v2/build.log b/latest/cases/00405/l3v2/build.log new file mode 100644 index 000000000..1ab5c5f95 --- /dev/null +++ b/latest/cases/00405/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00405/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00405/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00405/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00405/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00405/l3v2/index.heta b/latest/cases/00405/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00405/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00405/model-sbml-l2v5.xml b/latest/cases/00405/model-sbml-l2v5.xml new file mode 100644 index 000000000..42bb4b378 --- /dev/null +++ b/latest/cases/00405/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00405/model-sbml-l3v2.xml b/latest/cases/00405/model-sbml-l3v2.xml new file mode 100644 index 000000000..a4e519f73 --- /dev/null +++ b/latest/cases/00405/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00405/synopsis.txt b/latest/cases/00405/synopsis.txt new file mode 100644 index 000000000..7f8c56e1a --- /dev/null +++ b/latest/cases/00405/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00406/l2v5/build.log b/latest/cases/00406/l2v5/build.log new file mode 100644 index 000000000..6e5ce9512 --- /dev/null +++ b/latest/cases/00406/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00406/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00406/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00406/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00406/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00406/l2v5/index.heta b/latest/cases/00406/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00406/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00406/l3v2/build.log b/latest/cases/00406/l3v2/build.log new file mode 100644 index 000000000..fa3bc88f4 --- /dev/null +++ b/latest/cases/00406/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00406/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00406/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00406/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00406/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00406/l3v2/index.heta b/latest/cases/00406/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00406/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00406/model-sbml-l2v5.xml b/latest/cases/00406/model-sbml-l2v5.xml new file mode 100644 index 000000000..ee345b351 --- /dev/null +++ b/latest/cases/00406/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 0.25 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00406/model-sbml-l3v2.xml b/latest/cases/00406/model-sbml-l3v2.xml new file mode 100644 index 000000000..e32f767d9 --- /dev/null +++ b/latest/cases/00406/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 0.25 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00406/synopsis.txt b/latest/cases/00406/synopsis.txt new file mode 100644 index 000000000..f9e923f84 --- /dev/null +++ b/latest/cases/00406/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $0.25$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00407/l2v5/build.log b/latest/cases/00407/l2v5/build.log new file mode 100644 index 000000000..dd4a6d3c4 --- /dev/null +++ b/latest/cases/00407/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00407/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00407/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00407/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00407/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00407/l2v5/index.heta b/latest/cases/00407/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00407/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00407/l3v2/build.log b/latest/cases/00407/l3v2/build.log new file mode 100644 index 000000000..2f1451bf7 --- /dev/null +++ b/latest/cases/00407/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00407/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00407/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00407/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00407/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00407/l3v2/index.heta b/latest/cases/00407/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00407/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00407/model-sbml-l2v5.xml b/latest/cases/00407/model-sbml-l2v5.xml new file mode 100644 index 000000000..5efcf956f --- /dev/null +++ b/latest/cases/00407/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00407/model-sbml-l3v2.xml b/latest/cases/00407/model-sbml-l3v2.xml new file mode 100644 index 000000000..5bc23a7f2 --- /dev/null +++ b/latest/cases/00407/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00407/synopsis.txt b/latest/cases/00407/synopsis.txt new file mode 100644 index 000000000..7cab4b505 --- /dev/null +++ b/latest/cases/00407/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00408/l2v5/build.log b/latest/cases/00408/l2v5/build.log new file mode 100644 index 000000000..baf8c7f1f --- /dev/null +++ b/latest/cases/00408/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00408/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00408/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00408/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00408/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00408/l2v5/index.heta b/latest/cases/00408/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00408/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00408/l3v2/build.log b/latest/cases/00408/l3v2/build.log new file mode 100644 index 000000000..62cb03927 --- /dev/null +++ b/latest/cases/00408/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00408/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00408/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00408/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00408/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00408/l3v2/index.heta b/latest/cases/00408/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00408/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00408/model-sbml-l2v5.xml b/latest/cases/00408/model-sbml-l2v5.xml new file mode 100644 index 000000000..3df8066fa --- /dev/null +++ b/latest/cases/00408/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1 + + + + + + 1 5000 + + + + + + + diff --git a/latest/cases/00408/model-sbml-l3v2.xml b/latest/cases/00408/model-sbml-l3v2.xml new file mode 100644 index 000000000..0ee07d1c9 --- /dev/null +++ b/latest/cases/00408/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1 + + + + + + 1 5000 + + + + + + + diff --git a/latest/cases/00408/synopsis.txt b/latest/cases/00408/synopsis.txt new file mode 100644 index 000000000..c285c2655 --- /dev/null +++ b/latest/cases/00408/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $1$ | $S1 -> 2 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00409/l2v5/build.log b/latest/cases/00409/l2v5/build.log new file mode 100644 index 000000000..5eac48916 --- /dev/null +++ b/latest/cases/00409/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00409/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00409/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00409/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00409/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00409/l2v5/index.heta b/latest/cases/00409/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00409/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00409/l3v2/build.log b/latest/cases/00409/l3v2/build.log new file mode 100644 index 000000000..63d304e4d --- /dev/null +++ b/latest/cases/00409/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00409/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00409/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00409/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00409/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00409/l3v2/index.heta b/latest/cases/00409/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00409/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00409/model-sbml-l2v5.xml b/latest/cases/00409/model-sbml-l2v5.xml new file mode 100644 index 000000000..14d444c2a --- /dev/null +++ b/latest/cases/00409/model-sbml-l2v5.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 500 + + + + + + + + + + S3 + 9 4000 + + + + + + 0.75 + + + + + + 1 1000 + + + + + + + diff --git a/latest/cases/00409/model-sbml-l3v2.xml b/latest/cases/00409/model-sbml-l3v2.xml new file mode 100644 index 000000000..7760872d4 --- /dev/null +++ b/latest/cases/00409/model-sbml-l3v2.xml @@ -0,0 +1,127 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 500 + + + + + + + + + + S3 + 9 4000 + + + + + + 0.75 + + + + + + 1 1000 + + + + + + + diff --git a/latest/cases/00409/synopsis.txt b/latest/cases/00409/synopsis.txt new file mode 100644 index 000000000..3331c8c99 --- /dev/null +++ b/latest/cases/00409/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $0.5$ | $S1 -> 2 \x 10^-3$ |] + | Event2 | $S3 > 2.25 \x 10^-3$ | $0.75$ | $S4 -> 1 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00410/l2v5/build.log b/latest/cases/00410/l2v5/build.log new file mode 100644 index 000000000..01af11aed --- /dev/null +++ b/latest/cases/00410/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00410/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00410/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00410/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00410/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00410/l2v5/index.heta b/latest/cases/00410/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00410/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00410/l3v2/build.log b/latest/cases/00410/l3v2/build.log new file mode 100644 index 000000000..575d6e56c --- /dev/null +++ b/latest/cases/00410/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00410/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00410/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00410/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00410/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00410/l3v2/index.heta b/latest/cases/00410/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00410/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00410/model-sbml-l2v5.xml b/latest/cases/00410/model-sbml-l2v5.xml new file mode 100644 index 000000000..c89c1fb3a --- /dev/null +++ b/latest/cases/00410/model-sbml-l2v5.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1.2 + + + + + + 1 50 + + + + + 1 200 + + + + + + + diff --git a/latest/cases/00410/model-sbml-l3v2.xml b/latest/cases/00410/model-sbml-l3v2.xml new file mode 100644 index 000000000..6035c9557 --- /dev/null +++ b/latest/cases/00410/model-sbml-l3v2.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1.2 + + + + + + 1 50 + + + + + 1 200 + + + + + + + diff --git a/latest/cases/00410/synopsis.txt b/latest/cases/00410/synopsis.txt new file mode 100644 index 000000000..5e61690b4 --- /dev/null +++ b/latest/cases/00410/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assign values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $1.2$ | $S1 -> 2 \x 10^-2$ |] + | | | | $S4 -> 0.5 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00411/l2v5/build.log b/latest/cases/00411/l2v5/build.log new file mode 100644 index 000000000..20f83504b --- /dev/null +++ b/latest/cases/00411/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00411/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00411/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00411/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00411/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00411/l2v5/index.heta b/latest/cases/00411/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00411/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00411/l3v2/build.log b/latest/cases/00411/l3v2/build.log new file mode 100644 index 000000000..3da7a17da --- /dev/null +++ b/latest/cases/00411/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00411/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00411/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00411/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00411/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00411/l3v2/index.heta b/latest/cases/00411/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00411/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00411/model-sbml-l2v5.xml b/latest/cases/00411/model-sbml-l2v5.xml new file mode 100644 index 000000000..1ebabf956 --- /dev/null +++ b/latest/cases/00411/model-sbml-l2v5.xml @@ -0,0 +1,108 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 0.5 + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00411/model-sbml-l3v2.xml b/latest/cases/00411/model-sbml-l3v2.xml new file mode 100644 index 000000000..cefd83f42 --- /dev/null +++ b/latest/cases/00411/model-sbml-l3v2.xml @@ -0,0 +1,125 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 0.5 + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00411/synopsis.txt b/latest/cases/00411/synopsis.txt new file mode 100644 index 000000000..ce6111ea6 --- /dev/null +++ b/latest/cases/00411/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function, + subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $0.5$ | $S2 = add(k3, k4)$ |] + +The eventAssignment uses a functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00412/l2v5/build.log b/latest/cases/00412/l2v5/build.log new file mode 100644 index 000000000..5eb28b8bf --- /dev/null +++ b/latest/cases/00412/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00412/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00412/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00412/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00412/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00412/l2v5/index.heta b/latest/cases/00412/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00412/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00412/l3v2/build.log b/latest/cases/00412/l3v2/build.log new file mode 100644 index 000000000..051c3656a --- /dev/null +++ b/latest/cases/00412/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00412/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00412/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00412/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00412/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00412/l3v2/index.heta b/latest/cases/00412/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00412/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00412/model-sbml-l2v5.xml b/latest/cases/00412/model-sbml-l2v5.xml new file mode 100644 index 000000000..32648d386 --- /dev/null +++ b/latest/cases/00412/model-sbml-l2v5.xml @@ -0,0 +1,102 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.5 + + + + + + 2.5 + + + + + + 1.2 + + + + + + + diff --git a/latest/cases/00412/model-sbml-l3v2.xml b/latest/cases/00412/model-sbml-l3v2.xml new file mode 100644 index 000000000..0b153b99b --- /dev/null +++ b/latest/cases/00412/model-sbml-l3v2.xml @@ -0,0 +1,119 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.5 + + + + + + 2.5 + + + + + + 1.2 + + + + + + + diff --git a/latest/cases/00412/synopsis.txt b/latest/cases/00412/synopsis.txt new file mode 100644 index 000000000..cd10f4955 --- /dev/null +++ b/latest/cases/00412/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function, + subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.5)$ | $2.5$ | $S2 = 1.2$ |] + +The event trigger uses a functionDefinition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | lessthan | x, y | $x < y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00413/l2v5/build.log b/latest/cases/00413/l2v5/build.log new file mode 100644 index 000000000..50b80196c --- /dev/null +++ b/latest/cases/00413/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00413/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00413/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00413/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00413/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00413/l2v5/index.heta b/latest/cases/00413/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00413/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00413/l3v2/build.log b/latest/cases/00413/l3v2/build.log new file mode 100644 index 000000000..3670f204a --- /dev/null +++ b/latest/cases/00413/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00413/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00413/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00413/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00413/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00413/l3v2/index.heta b/latest/cases/00413/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00413/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00413/model-sbml-l2v5.xml b/latest/cases/00413/model-sbml-l2v5.xml new file mode 100644 index 000000000..3d310eda6 --- /dev/null +++ b/latest/cases/00413/model-sbml-l2v5.xml @@ -0,0 +1,156 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.25 + + + + + + + add + k3 + k4 + + + + + + + + + + + S3 + 1.2 + + + + + + 1.5 + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00413/model-sbml-l3v2.xml b/latest/cases/00413/model-sbml-l3v2.xml new file mode 100644 index 000000000..6dd1b489a --- /dev/null +++ b/latest/cases/00413/model-sbml-l3v2.xml @@ -0,0 +1,173 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.25 + + + + + + + add + k3 + k4 + + + + + + + + + + + S3 + 1.2 + + + + + + 1.5 + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00413/synopsis.txt b/latest/cases/00413/synopsis.txt new file mode 100644 index 000000000..3b9fe809e --- /dev/null +++ b/latest/cases/00413/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events, subject to delays, that assigns value to a +species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, FunctionDefinition +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $0.25$ | $S2 = add(k3, k4)$ | + | Event2 | $S3 > 1.2$ | $1.5$ | $S1 = 1 * divide(k3, k4)$ |] + +Both eventAssignments use functionDefinitions defined as follows: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00414/l2v5/build.log b/latest/cases/00414/l2v5/build.log new file mode 100644 index 000000000..222dea424 --- /dev/null +++ b/latest/cases/00414/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00414/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00414/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00414/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00414/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00414/l2v5/index.heta b/latest/cases/00414/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00414/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00414/l3v2/build.log b/latest/cases/00414/l3v2/build.log new file mode 100644 index 000000000..681d17682 --- /dev/null +++ b/latest/cases/00414/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00414/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00414/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00414/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00414/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00414/l3v2/index.heta b/latest/cases/00414/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00414/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00414/model-sbml-l2v5.xml b/latest/cases/00414/model-sbml-l2v5.xml new file mode 100644 index 000000000..4c1235ac3 --- /dev/null +++ b/latest/cases/00414/model-sbml-l2v5.xml @@ -0,0 +1,152 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.77 + + + + + + 1 + + + + + + 1.2 + + + + + + + + + + S3 + 1.2 + + + + + + 1.2 + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00414/model-sbml-l3v2.xml b/latest/cases/00414/model-sbml-l3v2.xml new file mode 100644 index 000000000..8b2c8176c --- /dev/null +++ b/latest/cases/00414/model-sbml-l3v2.xml @@ -0,0 +1,169 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.77 + + + + + + 1 + + + + + + 1.2 + + + + + + + + + + S3 + 1.2 + + + + + + 1.2 + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00414/synopsis.txt b/latest/cases/00414/synopsis.txt new file mode 100644 index 000000000..602221b1d --- /dev/null +++ b/latest/cases/00414/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events, subject to delays, that assign value to a +species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, FunctionDefinition +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.77)$ | $1$ | $S2 = 1.2$ | + | Event2 | $S3 > 1.2$ | $1.2$ | $S1 = 1 * divide(k3, k4)$ |] + +Both events use functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | lessthan | x, y | $x < y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00415/l2v5/build.log b/latest/cases/00415/l2v5/build.log new file mode 100644 index 000000000..bf3ddee61 --- /dev/null +++ b/latest/cases/00415/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00415/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00415/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00415/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00415/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00415/l2v5/index.heta b/latest/cases/00415/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00415/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00415/l3v2/build.log b/latest/cases/00415/l3v2/build.log new file mode 100644 index 000000000..2c9939d7b --- /dev/null +++ b/latest/cases/00415/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00415/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00415/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00415/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00415/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00415/l3v2/index.heta b/latest/cases/00415/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00415/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00415/model-sbml-l2v5.xml b/latest/cases/00415/model-sbml-l2v5.xml new file mode 100644 index 000000000..baf21adcb --- /dev/null +++ b/latest/cases/00415/model-sbml-l2v5.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.7 + + + + + + 0.25 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00415/model-sbml-l3v2.xml b/latest/cases/00415/model-sbml-l3v2.xml new file mode 100644 index 000000000..481d46067 --- /dev/null +++ b/latest/cases/00415/model-sbml-l3v2.xml @@ -0,0 +1,124 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.7 + + + + + + 0.25 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00415/synopsis.txt b/latest/cases/00415/synopsis.txt new file mode 100644 index 000000000..de1b8418c --- /dev/null +++ b/latest/cases/00415/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event, subject to a delay, that assigns value to a +species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.7)$ | $0.25$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The event trigger uses the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | lessthan | x, y | $x < y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier +to use the model in a discrete stochastic simulator, but (as per usual +SBML principles) their symbols represent their values in concentration +units where they appear in expressions. + diff --git a/latest/cases/00416/l2v5/build.log b/latest/cases/00416/l2v5/build.log new file mode 100644 index 000000000..70ab6492f --- /dev/null +++ b/latest/cases/00416/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00416/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00416/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00416/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00416/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00416/l2v5/index.heta b/latest/cases/00416/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00416/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00416/l3v2/build.log b/latest/cases/00416/l3v2/build.log new file mode 100644 index 000000000..c7cbff3af --- /dev/null +++ b/latest/cases/00416/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00416/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00416/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00416/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00416/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00416/l3v2/index.heta b/latest/cases/00416/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00416/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00416/model-sbml-l2v5.xml b/latest/cases/00416/model-sbml-l2v5.xml new file mode 100644 index 000000000..55deaed54 --- /dev/null +++ b/latest/cases/00416/model-sbml-l2v5.xml @@ -0,0 +1,130 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.6 + + + + + + 2 + + + + + + 1.5 + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00416/model-sbml-l3v2.xml b/latest/cases/00416/model-sbml-l3v2.xml new file mode 100644 index 000000000..9143203fb --- /dev/null +++ b/latest/cases/00416/model-sbml-l3v2.xml @@ -0,0 +1,147 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.6 + + + + + + 2 + + + + + + 1.5 + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00416/synopsis.txt b/latest/cases/00416/synopsis.txt new file mode 100644 index 000000000..1bd127685 --- /dev/null +++ b/latest/cases/00416/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event, subject to a delay, that assigns value to a +species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.6)$ | $2$ | $S2 = 1.5$ | + | | | | $S1 = add(k3, k4)$ |] + +Both the event trigger and assignment use functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ | + | lessthan | x, y | $x < y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00417/l2v5/build.log b/latest/cases/00417/l2v5/build.log new file mode 100644 index 000000000..04d42d0d3 --- /dev/null +++ b/latest/cases/00417/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00417/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00417/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00417/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00417/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00417/l2v5/index.heta b/latest/cases/00417/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00417/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00417/l3v2/build.log b/latest/cases/00417/l3v2/build.log new file mode 100644 index 000000000..53247e6cc --- /dev/null +++ b/latest/cases/00417/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00417/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00417/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00417/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00417/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00417/l3v2/index.heta b/latest/cases/00417/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00417/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00417/model-sbml-l2v5.xml b/latest/cases/00417/model-sbml-l2v5.xml new file mode 100644 index 000000000..504a4cc3b --- /dev/null +++ b/latest/cases/00417/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + 1.2 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00417/model-sbml-l3v2.xml b/latest/cases/00417/model-sbml-l3v2.xml new file mode 100644 index 000000000..2464e81d6 --- /dev/null +++ b/latest/cases/00417/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + 1.2 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00417/synopsis.txt b/latest/cases/00417/synopsis.txt new file mode 100644 index 000000000..00b9d5e4d --- /dev/null +++ b/latest/cases/00417/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and one event that assigns value to a species, subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.7$ | $1.2$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.8$ |metre^2 mole^-1^ second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Area of compartment C |$1$ |metre^2 |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00418/l2v5/build.log b/latest/cases/00418/l2v5/build.log new file mode 100644 index 000000000..ba592f779 --- /dev/null +++ b/latest/cases/00418/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00418/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00418/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00418/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00418/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00418/l2v5/index.heta b/latest/cases/00418/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00418/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00418/l3v2/build.log b/latest/cases/00418/l3v2/build.log new file mode 100644 index 000000000..9240498f4 --- /dev/null +++ b/latest/cases/00418/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00418/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00418/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00418/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00418/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00418/l3v2/index.heta b/latest/cases/00418/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00418/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00418/model-sbml-l2v5.xml b/latest/cases/00418/model-sbml-l2v5.xml new file mode 100644 index 000000000..40247e1db --- /dev/null +++ b/latest/cases/00418/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.6 + + + + + + 2 + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00418/model-sbml-l3v2.xml b/latest/cases/00418/model-sbml-l3v2.xml new file mode 100644 index 000000000..feb95ebf8 --- /dev/null +++ b/latest/cases/00418/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.6 + + + + + + 2 + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00418/synopsis.txt b/latest/cases/00418/synopsis.txt new file mode 100644 index 000000000..2e25024f9 --- /dev/null +++ b/latest/cases/00418/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.6$ | $2$ | $S2 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.8$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00419/l2v5/build.log b/latest/cases/00419/l2v5/build.log new file mode 100644 index 000000000..7a00d8986 --- /dev/null +++ b/latest/cases/00419/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00419/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00419/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00419/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00419/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00419/l2v5/index.heta b/latest/cases/00419/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00419/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00419/l3v2/build.log b/latest/cases/00419/l3v2/build.log new file mode 100644 index 000000000..ace6060f8 --- /dev/null +++ b/latest/cases/00419/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00419/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00419/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00419/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00419/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00419/l3v2/index.heta b/latest/cases/00419/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00419/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00419/model-sbml-l2v5.xml b/latest/cases/00419/model-sbml-l2v5.xml new file mode 100644 index 000000000..8570107d4 --- /dev/null +++ b/latest/cases/00419/model-sbml-l2v5.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + 0.5 + + + + + + 1.25 + + + + + + + diff --git a/latest/cases/00419/model-sbml-l3v2.xml b/latest/cases/00419/model-sbml-l3v2.xml new file mode 100644 index 000000000..973809892 --- /dev/null +++ b/latest/cases/00419/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + 0.5 + + + + + + 1.25 + + + + + + + diff --git a/latest/cases/00419/synopsis.txt b/latest/cases/00419/synopsis.txt new file mode 100644 index 000000000..91173a4f7 --- /dev/null +++ b/latest/cases/00419/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic two reactions with three species in one 0D compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.7$ | $0.5$ | $S2 = 1.25$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.8$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00420/l2v5/build.log b/latest/cases/00420/l2v5/build.log new file mode 100644 index 000000000..ef7f5aadc --- /dev/null +++ b/latest/cases/00420/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00420/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00420/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00420/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00420/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00420/l2v5/index.heta b/latest/cases/00420/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00420/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00420/l3v2/build.log b/latest/cases/00420/l3v2/build.log new file mode 100644 index 000000000..8b4a05473 --- /dev/null +++ b/latest/cases/00420/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00420/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00420/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00420/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00420/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00420/l3v2/index.heta b/latest/cases/00420/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00420/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00420/model-sbml-l2v5.xml b/latest/cases/00420/model-sbml-l2v5.xml new file mode 100644 index 000000000..0a911f6c6 --- /dev/null +++ b/latest/cases/00420/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 5 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 10 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00420/model-sbml-l3v2.xml b/latest/cases/00420/model-sbml-l3v2.xml new file mode 100644 index 000000000..fa0cf68b0 --- /dev/null +++ b/latest/cases/00420/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 5 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 10 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00420/synopsis.txt b/latest/cases/00420/synopsis.txt new file mode 100644 index 000000000..8279cb1a1 --- /dev/null +++ b/latest/cases/00420/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $5$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $10$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.075$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025$ |second^-1^ | +|Area of compartment C |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00421/l2v5/build.log b/latest/cases/00421/l2v5/build.log new file mode 100644 index 000000000..2dcda7d19 --- /dev/null +++ b/latest/cases/00421/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00421/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00421/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00421/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00421/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00421/l2v5/index.heta b/latest/cases/00421/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00421/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00421/l3v2/build.log b/latest/cases/00421/l3v2/build.log new file mode 100644 index 000000000..b825133af --- /dev/null +++ b/latest/cases/00421/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00421/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00421/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00421/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00421/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00421/l3v2/index.heta b/latest/cases/00421/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00421/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00421/model-sbml-l2v5.xml b/latest/cases/00421/model-sbml-l2v5.xml new file mode 100644 index 000000000..474b6c532 --- /dev/null +++ b/latest/cases/00421/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + 7.5 + + + + + + 1 + + + + + + + + + + S3 + 1.2 + + + + + + 4.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00421/model-sbml-l3v2.xml b/latest/cases/00421/model-sbml-l3v2.xml new file mode 100644 index 000000000..5e88cb31d --- /dev/null +++ b/latest/cases/00421/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + 7.5 + + + + + + 1 + + + + + + + + + + S3 + 1.2 + + + + + + 4.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00421/synopsis.txt b/latest/cases/00421/synopsis.txt new file mode 100644 index 000000000..d7187a25d --- /dev/null +++ b/latest/cases/00421/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $7.5$ | $S2 = 1$ | + | Event2 | $S3 > 1.2$ | $4.5$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.075$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025$ |second^-1^ | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00422/l2v5/build.log b/latest/cases/00422/l2v5/build.log new file mode 100644 index 000000000..379c4a8c9 --- /dev/null +++ b/latest/cases/00422/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00422/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00422/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00422/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00422/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00422/l2v5/index.heta b/latest/cases/00422/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00422/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00422/l3v2/build.log b/latest/cases/00422/l3v2/build.log new file mode 100644 index 000000000..320e07a49 --- /dev/null +++ b/latest/cases/00422/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00422/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00422/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00422/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00422/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00422/l3v2/index.heta b/latest/cases/00422/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00422/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00422/model-sbml-l2v5.xml b/latest/cases/00422/model-sbml-l2v5.xml new file mode 100644 index 000000000..293a2e80c --- /dev/null +++ b/latest/cases/00422/model-sbml-l2v5.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + 8 + + + + + + 1 + + + + + + + + + + S3 + 1.2 + + + + + + 12 + + + + + + 0.95 + + + + + + + diff --git a/latest/cases/00422/model-sbml-l3v2.xml b/latest/cases/00422/model-sbml-l3v2.xml new file mode 100644 index 000000000..53ef5cd44 --- /dev/null +++ b/latest/cases/00422/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.7 + + + + + + 8 + + + + + + 1 + + + + + + + + + + S3 + 1.2 + + + + + + 12 + + + + + + 0.95 + + + + + + + diff --git a/latest/cases/00422/synopsis.txt b/latest/cases/00422/synopsis.txt new file mode 100644 index 000000000..ace0efc76 --- /dev/null +++ b/latest/cases/00422/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic two reactions with three species in one 0D compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, 0D-Compartment, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $8$ | $S2 = 1$ | + | Event2 | $S3 > 1.2$ | $12$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.075$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.025$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00423/l2v5/build.log b/latest/cases/00423/l2v5/build.log new file mode 100644 index 000000000..c023b7c26 --- /dev/null +++ b/latest/cases/00423/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00423/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00423/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00423/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00423/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00423/l2v5/index.heta b/latest/cases/00423/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00423/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00423/l3v2/build.log b/latest/cases/00423/l3v2/build.log new file mode 100644 index 000000000..8d5105c5f --- /dev/null +++ b/latest/cases/00423/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00423/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00423/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00423/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00423/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00423/l3v2/index.heta b/latest/cases/00423/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00423/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00423/model-sbml-l2v5.xml b/latest/cases/00423/model-sbml-l2v5.xml new file mode 100644 index 000000000..99c8f6445 --- /dev/null +++ b/latest/cases/00423/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 1 + + + + + + 1.25 + + + + + 1 + + + + + + + diff --git a/latest/cases/00423/model-sbml-l3v2.xml b/latest/cases/00423/model-sbml-l3v2.xml new file mode 100644 index 000000000..348638cc3 --- /dev/null +++ b/latest/cases/00423/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 1 + + + + + + 1.25 + + + + + 1 + + + + + + + diff --git a/latest/cases/00423/synopsis.txt b/latest/cases/00423/synopsis.txt new file mode 100644 index 000000000..c85def212 --- /dev/null +++ b/latest/cases/00423/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 2D compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $1$ | $S2 = 1.25$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Area of compartment C |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00424/l2v5/build.log b/latest/cases/00424/l2v5/build.log new file mode 100644 index 000000000..18cbf13d5 --- /dev/null +++ b/latest/cases/00424/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00424/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00424/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00424/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00424/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00424/l2v5/index.heta b/latest/cases/00424/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00424/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00424/l3v2/build.log b/latest/cases/00424/l3v2/build.log new file mode 100644 index 000000000..67bd19f3f --- /dev/null +++ b/latest/cases/00424/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00424/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00424/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00424/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00424/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00424/l3v2/index.heta b/latest/cases/00424/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00424/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00424/model-sbml-l2v5.xml b/latest/cases/00424/model-sbml-l2v5.xml new file mode 100644 index 000000000..84c35da3b --- /dev/null +++ b/latest/cases/00424/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.45 + + + + + + 2.25 + + + + + + 1.25 + + + + + 0.6 + + + + + + + diff --git a/latest/cases/00424/model-sbml-l3v2.xml b/latest/cases/00424/model-sbml-l3v2.xml new file mode 100644 index 000000000..f80b294b4 --- /dev/null +++ b/latest/cases/00424/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.45 + + + + + + 2.25 + + + + + + 1.25 + + + + + 0.6 + + + + + + + diff --git a/latest/cases/00424/synopsis.txt b/latest/cases/00424/synopsis.txt new file mode 100644 index 000000000..4f8db968c --- /dev/null +++ b/latest/cases/00424/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 1D compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.45$ | $2.25$ | $S2 = 1.25$ | + | | | | $S1 = 0.6$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00425/l2v5/build.log b/latest/cases/00425/l2v5/build.log new file mode 100644 index 000000000..7418543c6 --- /dev/null +++ b/latest/cases/00425/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00425/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00425/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00425/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00425/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00425/l2v5/index.heta b/latest/cases/00425/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00425/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00425/l3v2/build.log b/latest/cases/00425/l3v2/build.log new file mode 100644 index 000000000..808167f8d --- /dev/null +++ b/latest/cases/00425/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00425/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00425/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00425/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00425/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00425/l3v2/index.heta b/latest/cases/00425/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00425/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00425/model-sbml-l2v5.xml b/latest/cases/00425/model-sbml-l2v5.xml new file mode 100644 index 000000000..db749f744 --- /dev/null +++ b/latest/cases/00425/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 3 + + + + + + 1.25 + + + + + 0.5 + + + + + + + diff --git a/latest/cases/00425/model-sbml-l3v2.xml b/latest/cases/00425/model-sbml-l3v2.xml new file mode 100644 index 000000000..4aa6ae0d7 --- /dev/null +++ b/latest/cases/00425/model-sbml-l3v2.xml @@ -0,0 +1,98 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 3 + + + + + + 1.25 + + + + + 0.5 + + + + + + + diff --git a/latest/cases/00425/synopsis.txt b/latest/cases/00425/synopsis.txt new file mode 100644 index 000000000..117906aca --- /dev/null +++ b/latest/cases/00425/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic two reactions with three species in one 0D compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.45$ | $3$ | $S2 = 1.25$ | + | | | | $S1 = 0.6$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00426/l2v5/build.log b/latest/cases/00426/l2v5/build.log new file mode 100644 index 000000000..2605b0a99 --- /dev/null +++ b/latest/cases/00426/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00426/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00426/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00426/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00426/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00426/l2v5/index.heta b/latest/cases/00426/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00426/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00426/l3v2/build.log b/latest/cases/00426/l3v2/build.log new file mode 100644 index 000000000..7456bad9c --- /dev/null +++ b/latest/cases/00426/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00426/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00426/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00426/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00426/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00426/l3v2/index.heta b/latest/cases/00426/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00426/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00426/model-sbml-l2v5.xml b/latest/cases/00426/model-sbml-l2v5.xml new file mode 100644 index 000000000..e5f1f6177 --- /dev/null +++ b/latest/cases/00426/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 5.7 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00426/model-sbml-l3v2.xml b/latest/cases/00426/model-sbml-l3v2.xml new file mode 100644 index 000000000..b4817dbc6 --- /dev/null +++ b/latest/cases/00426/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 5.7 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00426/synopsis.txt b/latest/cases/00426/synopsis.txt new file mode 100644 index 000000000..742f533f4 --- /dev/null +++ b/latest/cases/00426/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $5.7$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00427/l2v5/build.log b/latest/cases/00427/l2v5/build.log new file mode 100644 index 000000000..77f48e5df --- /dev/null +++ b/latest/cases/00427/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00427/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00427/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00427/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00427/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00427/l2v5/index.heta b/latest/cases/00427/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00427/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00427/l3v2/build.log b/latest/cases/00427/l3v2/build.log new file mode 100644 index 000000000..d254d4829 --- /dev/null +++ b/latest/cases/00427/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00427/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00427/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00427/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00427/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00427/l3v2/index.heta b/latest/cases/00427/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00427/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00427/model-sbml-l2v5.xml b/latest/cases/00427/model-sbml-l2v5.xml new file mode 100644 index 000000000..48a3305ea --- /dev/null +++ b/latest/cases/00427/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 0.75 + + + + + + 1 + + + + + + + + + + S3 + 1 + + + + + + 1.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00427/model-sbml-l3v2.xml b/latest/cases/00427/model-sbml-l3v2.xml new file mode 100644 index 000000000..37deb6436 --- /dev/null +++ b/latest/cases/00427/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 0.75 + + + + + + 1 + + + + + + + + + + S3 + 1 + + + + + + 1.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00427/synopsis.txt b/latest/cases/00427/synopsis.txt new file mode 100644 index 000000000..f7de84847 --- /dev/null +++ b/latest/cases/00427/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, NonUnityCompartment, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $0.75$ | $S2 = 1$ | + | Event2 | $S3 > 1$ | $1.5$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1.43$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00428/l2v5/build.log b/latest/cases/00428/l2v5/build.log new file mode 100644 index 000000000..a533f077d --- /dev/null +++ b/latest/cases/00428/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00428/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00428/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00428/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00428/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00428/l2v5/index.heta b/latest/cases/00428/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00428/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00428/l3v2/build.log b/latest/cases/00428/l3v2/build.log new file mode 100644 index 000000000..38d624890 --- /dev/null +++ b/latest/cases/00428/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00428/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00428/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00428/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00428/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00428/l3v2/index.heta b/latest/cases/00428/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00428/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00428/model-sbml-l2v5.xml b/latest/cases/00428/model-sbml-l2v5.xml new file mode 100644 index 000000000..7cb2e1fcd --- /dev/null +++ b/latest/cases/00428/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + 1 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00428/model-sbml-l3v2.xml b/latest/cases/00428/model-sbml-l3v2.xml new file mode 100644 index 000000000..5d64fac1a --- /dev/null +++ b/latest/cases/00428/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + 1 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00428/synopsis.txt b/latest/cases/00428/synopsis.txt new file mode 100644 index 000000000..96148d9cd --- /dev/null +++ b/latest/cases/00428/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $1$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.9$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00429/l2v5/build.log b/latest/cases/00429/l2v5/build.log new file mode 100644 index 000000000..1dd88fe23 --- /dev/null +++ b/latest/cases/00429/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00429/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00429/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00429/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00429/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00429/l2v5/index.heta b/latest/cases/00429/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00429/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00429/l3v2/build.log b/latest/cases/00429/l3v2/build.log new file mode 100644 index 000000000..e9444af31 --- /dev/null +++ b/latest/cases/00429/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00429/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00429/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00429/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00429/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00429/l3v2/index.heta b/latest/cases/00429/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00429/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00429/model-sbml-l2v5.xml b/latest/cases/00429/model-sbml-l2v5.xml new file mode 100644 index 000000000..aff84299d --- /dev/null +++ b/latest/cases/00429/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1.2 + + + + + + 1 50 + + + + + + + diff --git a/latest/cases/00429/model-sbml-l3v2.xml b/latest/cases/00429/model-sbml-l3v2.xml new file mode 100644 index 000000000..55752b724 --- /dev/null +++ b/latest/cases/00429/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1.2 + + + + + + 1 50 + + + + + + + diff --git a/latest/cases/00429/synopsis.txt b/latest/cases/00429/synopsis.txt new file mode 100644 index 000000000..ed822ce27 --- /dev/null +++ b/latest/cases/00429/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns value to species S1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $1.2$ | $S1 -> 2 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.24$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00430/l2v5/build.log b/latest/cases/00430/l2v5/build.log new file mode 100644 index 000000000..43880e8dc --- /dev/null +++ b/latest/cases/00430/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00430/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00430/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00430/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00430/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00430/l2v5/index.heta b/latest/cases/00430/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00430/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00430/l3v2/build.log b/latest/cases/00430/l3v2/build.log new file mode 100644 index 000000000..17ab4213b --- /dev/null +++ b/latest/cases/00430/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00430/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00430/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00430/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00430/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00430/l3v2/index.heta b/latest/cases/00430/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00430/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00430/model-sbml-l2v5.xml b/latest/cases/00430/model-sbml-l2v5.xml new file mode 100644 index 000000000..12d749c91 --- /dev/null +++ b/latest/cases/00430/model-sbml-l2v5.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 500 + + + + + + + + + + S3 + 1 50 + + + + + + 1 + + + + + + 1 1000 + + + + + + + diff --git a/latest/cases/00430/model-sbml-l3v2.xml b/latest/cases/00430/model-sbml-l3v2.xml new file mode 100644 index 000000000..03a2e9e37 --- /dev/null +++ b/latest/cases/00430/model-sbml-l3v2.xml @@ -0,0 +1,127 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 500 + + + + + + + + + + S3 + 1 50 + + + + + + 1 + + + + + + 1 1000 + + + + + + + diff --git a/latest/cases/00430/synopsis.txt b/latest/cases/00430/synopsis.txt new file mode 100644 index 000000000..33c452cd0 --- /dev/null +++ b/latest/cases/00430/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign value to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $0.5$ | $S1 -> 2 \x 10^-3$ |] + | Event2 | $S3 > 2.25 \x 10^-3$ | $1$ | $S4 -> 1 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00431/l2v5/build.log b/latest/cases/00431/l2v5/build.log new file mode 100644 index 000000000..54a6facf3 --- /dev/null +++ b/latest/cases/00431/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00431/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00431/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00431/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00431/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00431/l2v5/index.heta b/latest/cases/00431/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00431/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00431/l3v2/build.log b/latest/cases/00431/l3v2/build.log new file mode 100644 index 000000000..1c8bb7d10 --- /dev/null +++ b/latest/cases/00431/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00431/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00431/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00431/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00431/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00431/l3v2/index.heta b/latest/cases/00431/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00431/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00431/model-sbml-l2v5.xml b/latest/cases/00431/model-sbml-l2v5.xml new file mode 100644 index 000000000..d9492ee97 --- /dev/null +++ b/latest/cases/00431/model-sbml-l2v5.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 2.5 + + + + + + 1 5 + + + + + 1 20 + + + + + + + diff --git a/latest/cases/00431/model-sbml-l3v2.xml b/latest/cases/00431/model-sbml-l3v2.xml new file mode 100644 index 000000000..4511bc4aa --- /dev/null +++ b/latest/cases/00431/model-sbml-l3v2.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 2.5 + + + + + + 1 5 + + + + + 1 20 + + + + + + + diff --git a/latest/cases/00431/synopsis.txt b/latest/cases/00431/synopsis.txt new file mode 100644 index 000000000..01c379e7f --- /dev/null +++ b/latest/cases/00431/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $2.5$ | $S1 -> 2 \x 10^-1$ |] + | | | | $S4 -> 0.5 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.25$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00432/l2v5/build.log b/latest/cases/00432/l2v5/build.log new file mode 100644 index 000000000..681d95401 --- /dev/null +++ b/latest/cases/00432/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00432/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00432/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00432/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00432/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00432/l2v5/index.heta b/latest/cases/00432/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00432/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00432/l3v2/build.log b/latest/cases/00432/l3v2/build.log new file mode 100644 index 000000000..1407c1945 --- /dev/null +++ b/latest/cases/00432/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00432/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00432/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00432/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00432/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00432/l3v2/index.heta b/latest/cases/00432/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00432/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00432/model-sbml-l2v5.xml b/latest/cases/00432/model-sbml-l2v5.xml new file mode 100644 index 000000000..9c0efd0a9 --- /dev/null +++ b/latest/cases/00432/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00432/model-sbml-l3v2.xml b/latest/cases/00432/model-sbml-l3v2.xml new file mode 100644 index 000000000..3afc405f8 --- /dev/null +++ b/latest/cases/00432/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00432/synopsis.txt b/latest/cases/00432/synopsis.txt new file mode 100644 index 000000000..e8376dcc8 --- /dev/null +++ b/latest/cases/00432/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S2 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1.5$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00433/l2v5/build.log b/latest/cases/00433/l2v5/build.log new file mode 100644 index 000000000..f452199ce --- /dev/null +++ b/latest/cases/00433/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00433/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00433/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00433/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00433/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00433/l2v5/index.heta b/latest/cases/00433/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00433/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00433/l3v2/build.log b/latest/cases/00433/l3v2/build.log new file mode 100644 index 000000000..2dea8d8d8 --- /dev/null +++ b/latest/cases/00433/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00433/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00433/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00433/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00433/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00433/l3v2/index.heta b/latest/cases/00433/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00433/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00433/model-sbml-l2v5.xml b/latest/cases/00433/model-sbml-l2v5.xml new file mode 100644 index 000000000..2eccade8f --- /dev/null +++ b/latest/cases/00433/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.2 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00433/model-sbml-l3v2.xml b/latest/cases/00433/model-sbml-l3v2.xml new file mode 100644 index 000000000..8e8b5fcad --- /dev/null +++ b/latest/cases/00433/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.2 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00433/synopsis.txt b/latest/cases/00433/synopsis.txt new file mode 100644 index 000000000..99e824be9 --- /dev/null +++ b/latest/cases/00433/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.2$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00434/l2v5/build.log b/latest/cases/00434/l2v5/build.log new file mode 100644 index 000000000..34db5095a --- /dev/null +++ b/latest/cases/00434/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00434/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00434/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00434/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00434/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00434/l2v5/index.heta b/latest/cases/00434/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00434/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00434/l3v2/build.log b/latest/cases/00434/l3v2/build.log new file mode 100644 index 000000000..1e5c1066f --- /dev/null +++ b/latest/cases/00434/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00434/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00434/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00434/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00434/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00434/l3v2/index.heta b/latest/cases/00434/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00434/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00434/model-sbml-l2v5.xml b/latest/cases/00434/model-sbml-l2v5.xml new file mode 100644 index 000000000..fc551212c --- /dev/null +++ b/latest/cases/00434/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 3.4 + + + + + + 1.1 + + + + + + + diff --git a/latest/cases/00434/model-sbml-l3v2.xml b/latest/cases/00434/model-sbml-l3v2.xml new file mode 100644 index 000000000..beb8dd2db --- /dev/null +++ b/latest/cases/00434/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 3.4 + + + + + + 1.1 + + + + + + + diff --git a/latest/cases/00434/synopsis.txt b/latest/cases/00434/synopsis.txt new file mode 100644 index 000000000..3ba808392 --- /dev/null +++ b/latest/cases/00434/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Both species S2 +and S3 are labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $3.4$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00435/l2v5/build.log b/latest/cases/00435/l2v5/build.log new file mode 100644 index 000000000..45260d84f --- /dev/null +++ b/latest/cases/00435/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00435/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00435/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00435/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00435/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00435/l2v5/index.heta b/latest/cases/00435/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00435/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00435/l3v2/build.log b/latest/cases/00435/l3v2/build.log new file mode 100644 index 000000000..2de15ceba --- /dev/null +++ b/latest/cases/00435/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00435/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00435/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00435/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00435/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00435/l3v2/index.heta b/latest/cases/00435/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00435/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00435/model-sbml-l2v5.xml b/latest/cases/00435/model-sbml-l2v5.xml new file mode 100644 index 000000000..ae475ddbf --- /dev/null +++ b/latest/cases/00435/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.5 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 1.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00435/model-sbml-l3v2.xml b/latest/cases/00435/model-sbml-l3v2.xml new file mode 100644 index 000000000..5c6fec356 --- /dev/null +++ b/latest/cases/00435/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.5 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 1.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00435/synopsis.txt b/latest/cases/00435/synopsis.txt new file mode 100644 index 000000000..2b2c0d75f --- /dev/null +++ b/latest/cases/00435/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, BoundaryCondition, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S2 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $0.5$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $1.3$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00436/l2v5/build.log b/latest/cases/00436/l2v5/build.log new file mode 100644 index 000000000..08af85342 --- /dev/null +++ b/latest/cases/00436/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00436/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00436/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00436/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00436/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00436/l2v5/index.heta b/latest/cases/00436/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00436/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00436/l3v2/build.log b/latest/cases/00436/l3v2/build.log new file mode 100644 index 000000000..a82c29a4b --- /dev/null +++ b/latest/cases/00436/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00436/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00436/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00436/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00436/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00436/l3v2/index.heta b/latest/cases/00436/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00436/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00436/model-sbml-l2v5.xml b/latest/cases/00436/model-sbml-l2v5.xml new file mode 100644 index 000000000..0b7cc5f6b --- /dev/null +++ b/latest/cases/00436/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00436/model-sbml-l3v2.xml b/latest/cases/00436/model-sbml-l3v2.xml new file mode 100644 index 000000000..7840bf7b6 --- /dev/null +++ b/latest/cases/00436/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00436/synopsis.txt b/latest/cases/00436/synopsis.txt new file mode 100644 index 000000000..94838738a --- /dev/null +++ b/latest/cases/00436/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.5$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $2.5$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00437/l2v5/build.log b/latest/cases/00437/l2v5/build.log new file mode 100644 index 000000000..ade964060 --- /dev/null +++ b/latest/cases/00437/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00437/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00437/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00437/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00437/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00437/l2v5/index.heta b/latest/cases/00437/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00437/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00437/l3v2/build.log b/latest/cases/00437/l3v2/build.log new file mode 100644 index 000000000..82777980a --- /dev/null +++ b/latest/cases/00437/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00437/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00437/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00437/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00437/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00437/l3v2/index.heta b/latest/cases/00437/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00437/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00437/model-sbml-l2v5.xml b/latest/cases/00437/model-sbml-l2v5.xml new file mode 100644 index 000000000..037eee67b --- /dev/null +++ b/latest/cases/00437/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + 1.1 + + + + + + + + + + S3 + 1.4 + + + + + + 1.5 + + + + + + 1.1 + + + + + + + diff --git a/latest/cases/00437/model-sbml-l3v2.xml b/latest/cases/00437/model-sbml-l3v2.xml new file mode 100644 index 000000000..cf0450021 --- /dev/null +++ b/latest/cases/00437/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + 1.1 + + + + + + + + + + S3 + 1.4 + + + + + + 1.5 + + + + + + 1.1 + + + + + + + diff --git a/latest/cases/00437/synopsis.txt b/latest/cases/00437/synopsis.txt new file mode 100644 index 000000000..a1cabbc6b --- /dev/null +++ b/latest/cases/00437/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Both species S2 +and S3 are labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1.5$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $1.5$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00438/l2v5/build.log b/latest/cases/00438/l2v5/build.log new file mode 100644 index 000000000..413a0bccf --- /dev/null +++ b/latest/cases/00438/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00438/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00438/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00438/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00438/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00438/l2v5/index.heta b/latest/cases/00438/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00438/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00438/l3v2/build.log b/latest/cases/00438/l3v2/build.log new file mode 100644 index 000000000..0d86a24a4 --- /dev/null +++ b/latest/cases/00438/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00438/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00438/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00438/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00438/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00438/l3v2/index.heta b/latest/cases/00438/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00438/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00438/model-sbml-l2v5.xml b/latest/cases/00438/model-sbml-l2v5.xml new file mode 100644 index 000000000..2759ed57d --- /dev/null +++ b/latest/cases/00438/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00438/model-sbml-l3v2.xml b/latest/cases/00438/model-sbml-l3v2.xml new file mode 100644 index 000000000..3f2160c9e --- /dev/null +++ b/latest/cases/00438/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00438/synopsis.txt b/latest/cases/00438/synopsis.txt new file mode 100644 index 000000000..a8fd90ae3 --- /dev/null +++ b/latest/cases/00438/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S2 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00439/l2v5/build.log b/latest/cases/00439/l2v5/build.log new file mode 100644 index 000000000..ec67b80ad --- /dev/null +++ b/latest/cases/00439/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00439/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00439/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00439/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00439/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00439/l2v5/index.heta b/latest/cases/00439/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00439/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00439/l3v2/build.log b/latest/cases/00439/l3v2/build.log new file mode 100644 index 000000000..ddc2dc670 --- /dev/null +++ b/latest/cases/00439/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00439/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00439/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00439/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00439/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00439/l3v2/index.heta b/latest/cases/00439/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00439/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00439/model-sbml-l2v5.xml b/latest/cases/00439/model-sbml-l2v5.xml new file mode 100644 index 000000000..bc7dc83ad --- /dev/null +++ b/latest/cases/00439/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.75 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00439/model-sbml-l3v2.xml b/latest/cases/00439/model-sbml-l3v2.xml new file mode 100644 index 000000000..ae1141619 --- /dev/null +++ b/latest/cases/00439/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.75 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00439/synopsis.txt b/latest/cases/00439/synopsis.txt new file mode 100644 index 000000000..cb3acd8d6 --- /dev/null +++ b/latest/cases/00439/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $0.75$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00440/l2v5/build.log b/latest/cases/00440/l2v5/build.log new file mode 100644 index 000000000..6652a1764 --- /dev/null +++ b/latest/cases/00440/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00440/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00440/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00440/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00440/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00440/l2v5/index.heta b/latest/cases/00440/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00440/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00440/l3v2/build.log b/latest/cases/00440/l3v2/build.log new file mode 100644 index 000000000..19915cf19 --- /dev/null +++ b/latest/cases/00440/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00440/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00440/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00440/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00440/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00440/l3v2/index.heta b/latest/cases/00440/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00440/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00440/model-sbml-l2v5.xml b/latest/cases/00440/model-sbml-l2v5.xml new file mode 100644 index 000000000..033cfc661 --- /dev/null +++ b/latest/cases/00440/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.3 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00440/model-sbml-l3v2.xml b/latest/cases/00440/model-sbml-l3v2.xml new file mode 100644 index 000000000..3925eba00 --- /dev/null +++ b/latest/cases/00440/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.3 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00440/synopsis.txt b/latest/cases/00440/synopsis.txt new file mode 100644 index 000000000..6ac38e816 --- /dev/null +++ b/latest/cases/00440/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. Both species S2 +and S3 are labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.3$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00441/l2v5/build.log b/latest/cases/00441/l2v5/build.log new file mode 100644 index 000000000..51e0a999f --- /dev/null +++ b/latest/cases/00441/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00441/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00441/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00441/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00441/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00441/l2v5/index.heta b/latest/cases/00441/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00441/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00441/l3v2/build.log b/latest/cases/00441/l3v2/build.log new file mode 100644 index 000000000..0cb5625f5 --- /dev/null +++ b/latest/cases/00441/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00441/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00441/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00441/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00441/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00441/l3v2/index.heta b/latest/cases/00441/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00441/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00441/model-sbml-l2v5.xml b/latest/cases/00441/model-sbml-l2v5.xml new file mode 100644 index 000000000..d361b73e0 --- /dev/null +++ b/latest/cases/00441/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1.3 + + + + + + 1 5 + + + + + + + diff --git a/latest/cases/00441/model-sbml-l3v2.xml b/latest/cases/00441/model-sbml-l3v2.xml new file mode 100644 index 000000000..f64eca304 --- /dev/null +++ b/latest/cases/00441/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1.3 + + + + + + 1 5 + + + + + + + diff --git a/latest/cases/00441/synopsis.txt b/latest/cases/00441/synopsis.txt new file mode 100644 index 000000000..d5967d52a --- /dev/null +++ b/latest/cases/00441/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns value to species S1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $1.3$ | $S1 -> 2 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00442/l2v5/build.log b/latest/cases/00442/l2v5/build.log new file mode 100644 index 000000000..ebf325c07 --- /dev/null +++ b/latest/cases/00442/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00442/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00442/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00442/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00442/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00442/l2v5/index.heta b/latest/cases/00442/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00442/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00442/l3v2/build.log b/latest/cases/00442/l3v2/build.log new file mode 100644 index 000000000..4710ca94b --- /dev/null +++ b/latest/cases/00442/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00442/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00442/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00442/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00442/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00442/l3v2/index.heta b/latest/cases/00442/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00442/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00442/model-sbml-l2v5.xml b/latest/cases/00442/model-sbml-l2v5.xml new file mode 100644 index 000000000..43c0f5444 --- /dev/null +++ b/latest/cases/00442/model-sbml-l2v5.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S4 + + + + + + 1 + + + + + + 1 5000 + + + + + + + + + + S3 + 1 5000 + + + + + + 1.5 + + + + + + 1 10000 + + + + + + + diff --git a/latest/cases/00442/model-sbml-l3v2.xml b/latest/cases/00442/model-sbml-l3v2.xml new file mode 100644 index 000000000..c87aae892 --- /dev/null +++ b/latest/cases/00442/model-sbml-l3v2.xml @@ -0,0 +1,128 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S4 + + + + + + 1 + + + + + + 1 5000 + + + + + + + + + + S3 + 1 5000 + + + + + + 1.5 + + + + + + 1 10000 + + + + + + + diff --git a/latest/cases/00442/synopsis.txt b/latest/cases/00442/synopsis.txt new file mode 100644 index 000000000..b661b4e8e --- /dev/null +++ b/latest/cases/00442/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, ConstantSpecies, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign value to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S2 < S4$ | $1$ | $S1 -> 2 \x 10^-4$ |] + | Event2 | $S3 > 2 \x 10^-4$ | $1.5$ | $S3 -> 1 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.9 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00443/l2v5/build.log b/latest/cases/00443/l2v5/build.log new file mode 100644 index 000000000..cc86584a3 --- /dev/null +++ b/latest/cases/00443/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00443/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00443/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00443/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00443/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00443/l2v5/index.heta b/latest/cases/00443/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00443/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00443/l3v2/build.log b/latest/cases/00443/l3v2/build.log new file mode 100644 index 000000000..a325a6812 --- /dev/null +++ b/latest/cases/00443/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00443/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00443/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00443/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00443/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00443/l3v2/index.heta b/latest/cases/00443/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00443/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00443/model-sbml-l2v5.xml b/latest/cases/00443/model-sbml-l2v5.xml new file mode 100644 index 000000000..07c272a32 --- /dev/null +++ b/latest/cases/00443/model-sbml-l2v5.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S4 + + + + + + 1.75 + + + + + + 1 500 + + + + + 1 2000 + + + + + + + diff --git a/latest/cases/00443/model-sbml-l3v2.xml b/latest/cases/00443/model-sbml-l3v2.xml new file mode 100644 index 000000000..1ccbf82dc --- /dev/null +++ b/latest/cases/00443/model-sbml-l3v2.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S4 + + + + + + 1.75 + + + + + + 1 500 + + + + + 1 2000 + + + + + + + diff --git a/latest/cases/00443/synopsis.txt b/latest/cases/00443/synopsis.txt new file mode 100644 index 000000000..0380ae52e --- /dev/null +++ b/latest/cases/00443/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S2 < S4$ | $1.75$ | $S1 -> 2 \x 10^-3$ |] + | | | | $S3 -> 0.5 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.0 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00444/l2v5/build.log b/latest/cases/00444/l2v5/build.log new file mode 100644 index 000000000..113c65030 --- /dev/null +++ b/latest/cases/00444/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00444/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00444/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00444/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00444/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00444/l2v5/index.heta b/latest/cases/00444/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00444/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00444/l3v2/build.log b/latest/cases/00444/l3v2/build.log new file mode 100644 index 000000000..8d0c1a626 --- /dev/null +++ b/latest/cases/00444/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00444/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00444/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00444/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00444/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00444/l3v2/index.heta b/latest/cases/00444/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00444/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00444/model-sbml-l2v5.xml b/latest/cases/00444/model-sbml-l2v5.xml new file mode 100644 index 000000000..4b5a1b616 --- /dev/null +++ b/latest/cases/00444/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.9 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00444/model-sbml-l3v2.xml b/latest/cases/00444/model-sbml-l3v2.xml new file mode 100644 index 000000000..6b589d245 --- /dev/null +++ b/latest/cases/00444/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.9 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00444/synopsis.txt b/latest/cases/00444/synopsis.txt new file mode 100644 index 000000000..79cf90043 --- /dev/null +++ b/latest/cases/00444/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1.9$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00445/l2v5/build.log b/latest/cases/00445/l2v5/build.log new file mode 100644 index 000000000..13e81c548 --- /dev/null +++ b/latest/cases/00445/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00445/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00445/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00445/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00445/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00445/l2v5/index.heta b/latest/cases/00445/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00445/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00445/l3v2/index.heta b/latest/cases/00445/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00445/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00445/model-sbml-l2v5.xml b/latest/cases/00445/model-sbml-l2v5.xml new file mode 100644 index 000000000..8504cfba6 --- /dev/null +++ b/latest/cases/00445/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.95 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00445/synopsis.txt b/latest/cases/00445/synopsis.txt new file mode 100644 index 000000000..fc18d851e --- /dev/null +++ b/latest/cases/00445/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (2 * p1) S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $0.95$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00446/l2v5/build.log b/latest/cases/00446/l2v5/build.log new file mode 100644 index 000000000..de20161f3 --- /dev/null +++ b/latest/cases/00446/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00446/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00446/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00446/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00446/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00446/l2v5/index.heta b/latest/cases/00446/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00446/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00446/l3v2/build.log b/latest/cases/00446/l3v2/build.log new file mode 100644 index 000000000..712789935 --- /dev/null +++ b/latest/cases/00446/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00446/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00446/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00446/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00446/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00446/l3v2/index.heta b/latest/cases/00446/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00446/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00446/model-sbml-l2v5.xml b/latest/cases/00446/model-sbml-l2v5.xml new file mode 100644 index 000000000..7a121e8c5 --- /dev/null +++ b/latest/cases/00446/model-sbml-l2v5.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00446/model-sbml-l3v2.xml b/latest/cases/00446/model-sbml-l3v2.xml new file mode 100644 index 000000000..d2a4fa56d --- /dev/null +++ b/latest/cases/00446/model-sbml-l3v2.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00446/synopsis.txt b/latest/cases/00446/synopsis.txt new file mode 100644 index 000000000..f7aaaf3b2 --- /dev/null +++ b/latest/cases/00446/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, EventWithDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| $S1 + S2 -> S3$ | $k * S1 * S2 * C$ | +| $S3 -> S1 + S2$ | $k * S3 * C$ |] + +Reaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1 ++ S2$ defines another (different) local parameter k. Note that these +parameters have a scope local to the defining reaction. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.5$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of local parameter k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00447/l2v5/build.log b/latest/cases/00447/l2v5/build.log new file mode 100644 index 000000000..1a60c8d2b --- /dev/null +++ b/latest/cases/00447/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00447/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00447/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00447/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00447/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00447/l2v5/index.heta b/latest/cases/00447/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00447/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00447/l3v2/build.log b/latest/cases/00447/l3v2/build.log new file mode 100644 index 000000000..f8d1f5a4f --- /dev/null +++ b/latest/cases/00447/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00447/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00447/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00447/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00447/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00447/l3v2/index.heta b/latest/cases/00447/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00447/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00447/model-sbml-l2v5.xml b/latest/cases/00447/model-sbml-l2v5.xml new file mode 100644 index 000000000..2e57f6b82 --- /dev/null +++ b/latest/cases/00447/model-sbml-l2v5.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 50 + + + + + + + + + + S3 + 1 40 + + + + + + 1.5 + + + + + + 1 100 + + + + + + + diff --git a/latest/cases/00447/model-sbml-l3v2.xml b/latest/cases/00447/model-sbml-l3v2.xml new file mode 100644 index 000000000..ced08997e --- /dev/null +++ b/latest/cases/00447/model-sbml-l3v2.xml @@ -0,0 +1,127 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 50 + + + + + + + + + + S3 + 1 40 + + + + + + 1.5 + + + + + + 1 100 + + + + + + + diff --git a/latest/cases/00447/synopsis.txt b/latest/cases/00447/synopsis.txt new file mode 100644 index 000000000..607730214 --- /dev/null +++ b/latest/cases/00447/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> 2S3 + S4 | $k1 * S1 * S2 * C$ | +| 2S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign value to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $0.5$ | $S1 -> 2 \x 10^-2$ |] + | Event2 | $S3 > 2.5 \x 10^-2$ | $1.5$ | $S4 -> 1 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00448/l2v5/build.log b/latest/cases/00448/l2v5/build.log new file mode 100644 index 000000000..6c55d874c --- /dev/null +++ b/latest/cases/00448/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00448/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00448/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00448/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00448/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00448/l2v5/index.heta b/latest/cases/00448/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00448/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00448/l3v2/index.heta b/latest/cases/00448/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00448/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00448/model-sbml-l2v5.xml b/latest/cases/00448/model-sbml-l2v5.xml new file mode 100644 index 000000000..17ad68a0e --- /dev/null +++ b/latest/cases/00448/model-sbml-l2v5.xml @@ -0,0 +1,121 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 5 + + + + + + + + + + S3 + 1 4 + + + + + + 1.5 + + + + + + 1 10 + + + + + + + diff --git a/latest/cases/00448/synopsis.txt b/latest/cases/00448/synopsis.txt new file mode 100644 index 000000000..cc6cdd2f0 --- /dev/null +++ b/latest/cases/00448/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p1)S3 + S4 | $k1 * S1 * S2 * C$ | +| 2S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign value to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $0.5$ | $S1 -> 2 \x 10^-1$ |] + | Event2 | $S3 > 2.5 \x 10^-1$ | $1.5$ | $S4 -> 1 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00449/l2v5/build.log b/latest/cases/00449/l2v5/build.log new file mode 100644 index 000000000..e12c94b94 --- /dev/null +++ b/latest/cases/00449/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00449/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00449/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00449/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00449/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00449/l2v5/index.heta b/latest/cases/00449/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00449/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00449/l3v2/build.log b/latest/cases/00449/l3v2/build.log new file mode 100644 index 000000000..61e7ce285 --- /dev/null +++ b/latest/cases/00449/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00449/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00449/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00449/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00449/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00449/l3v2/index.heta b/latest/cases/00449/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00449/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00449/model-sbml-l2v5.xml b/latest/cases/00449/model-sbml-l2v5.xml new file mode 100644 index 000000000..681140003 --- /dev/null +++ b/latest/cases/00449/model-sbml-l2v5.xml @@ -0,0 +1,112 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + + C + k + S3 + S4 + + + + + + + + + + + + + + + S4 + S2 + + + + + + 1.5 + + + + + + 1 5000 + + + + + + + + + + S3 + 9 40000 + + + + + + 0.5 + + + + + + 1 10000 + + + + + + + diff --git a/latest/cases/00449/model-sbml-l3v2.xml b/latest/cases/00449/model-sbml-l3v2.xml new file mode 100644 index 000000000..8f1a0b28c --- /dev/null +++ b/latest/cases/00449/model-sbml-l3v2.xml @@ -0,0 +1,129 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + + C + k + S3 + S4 + + + + + + + + + + + + + + + S4 + S2 + + + + + + 1.5 + + + + + + 1 5000 + + + + + + + + + + S3 + 9 40000 + + + + + + 0.5 + + + + + + 1 10000 + + + + + + + diff --git a/latest/cases/00449/synopsis.txt b/latest/cases/00449/synopsis.txt new file mode 100644 index 000000000..5c28e762a --- /dev/null +++ b/latest/cases/00449/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, EventWithDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k * S3 * S4 * C$ |] + +Reaction $S1 + S2 -> S3 + S4$ defines one local parameter k. Reaction $S3 ++ S4 -> S1 + S2$ defines another (different) local parameter k. Note that +these parameters have a scope local to the defining reaction. + +The model contains two events that assign value to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $1.5$ | $S1 -> 2 \x 10^-4$ |] + | Event2 | $S3 > 2.25 \x 10^-4$ | $0.5$ | $S4 -> 1 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of local parameter k |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00450/l2v5/build.log b/latest/cases/00450/l2v5/build.log new file mode 100644 index 000000000..a2c0ef194 --- /dev/null +++ b/latest/cases/00450/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00450/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00450/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00450/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00450/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00450/l2v5/index.heta b/latest/cases/00450/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00450/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00450/l3v2/build.log b/latest/cases/00450/l3v2/build.log new file mode 100644 index 000000000..90839689c --- /dev/null +++ b/latest/cases/00450/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00450/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00450/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00450/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00450/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00450/l3v2/index.heta b/latest/cases/00450/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00450/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00450/model-sbml-l2v5.xml b/latest/cases/00450/model-sbml-l2v5.xml new file mode 100644 index 000000000..9be68382b --- /dev/null +++ b/latest/cases/00450/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.75 + + + + + 1 + + + + + + + diff --git a/latest/cases/00450/model-sbml-l3v2.xml b/latest/cases/00450/model-sbml-l3v2.xml new file mode 100644 index 000000000..2ab6bcfec --- /dev/null +++ b/latest/cases/00450/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.75 + + + + + 1 + + + + + + + diff --git a/latest/cases/00450/synopsis.txt b/latest/cases/00450/synopsis.txt new file mode 100644 index 000000000..2ff60ddd2 --- /dev/null +++ b/latest/cases/00450/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, NonUnityStoichiometry, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2$ | $S2 = 1.75$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00451/l2v5/build.log b/latest/cases/00451/l2v5/build.log new file mode 100644 index 000000000..c244f9291 --- /dev/null +++ b/latest/cases/00451/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00451/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00451/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00451/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00451/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00451/l2v5/index.heta b/latest/cases/00451/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00451/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00451/l3v2/index.heta b/latest/cases/00451/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00451/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00451/model-sbml-l2v5.xml b/latest/cases/00451/model-sbml-l2v5.xml new file mode 100644 index 000000000..215416252 --- /dev/null +++ b/latest/cases/00451/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.2 + + + + + + 1.75 + + + + + 1 + + + + + + + diff --git a/latest/cases/00451/synopsis.txt b/latest/cases/00451/synopsis.txt new file mode 100644 index 000000000..1d8d69a57 --- /dev/null +++ b/latest/cases/00451/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.2$ | $S2 = 1.75$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00452/l2v5/build.log b/latest/cases/00452/l2v5/build.log new file mode 100644 index 000000000..2f1210927 --- /dev/null +++ b/latest/cases/00452/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00452/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00452/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00452/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00452/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00452/l2v5/index.heta b/latest/cases/00452/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00452/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00452/l3v2/build.log b/latest/cases/00452/l3v2/build.log new file mode 100644 index 000000000..e3f8953a9 --- /dev/null +++ b/latest/cases/00452/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00452/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00452/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00452/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00452/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00452/l3v2/index.heta b/latest/cases/00452/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00452/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00452/model-sbml-l2v5.xml b/latest/cases/00452/model-sbml-l2v5.xml new file mode 100644 index 000000000..d628d31fe --- /dev/null +++ b/latest/cases/00452/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.7 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00452/model-sbml-l3v2.xml b/latest/cases/00452/model-sbml-l3v2.xml new file mode 100644 index 000000000..4f5b38057 --- /dev/null +++ b/latest/cases/00452/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.7 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00452/synopsis.txt b/latest/cases/00452/synopsis.txt new file mode 100644 index 000000000..110028634 --- /dev/null +++ b/latest/cases/00452/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, EventWithDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1 ++ S2$ defines another (different) local parameter k. Note that these +paramters have a scope local to the defining reaction. + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $0.7$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of local parameter k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00453/l2v5/build.log b/latest/cases/00453/l2v5/build.log new file mode 100644 index 000000000..b620b3ccf --- /dev/null +++ b/latest/cases/00453/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00453/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00453/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00453/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00453/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00453/l2v5/index.heta b/latest/cases/00453/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00453/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00453/l3v2/build.log b/latest/cases/00453/l3v2/build.log new file mode 100644 index 000000000..0d8f1397d --- /dev/null +++ b/latest/cases/00453/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00453/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00453/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00453/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00453/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00453/l3v2/index.heta b/latest/cases/00453/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00453/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00453/model-sbml-l2v5.xml b/latest/cases/00453/model-sbml-l2v5.xml new file mode 100644 index 000000000..2577bd37d --- /dev/null +++ b/latest/cases/00453/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00453/model-sbml-l3v2.xml b/latest/cases/00453/model-sbml-l3v2.xml new file mode 100644 index 000000000..5a40f5916 --- /dev/null +++ b/latest/cases/00453/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00453/synopsis.txt b/latest/cases/00453/synopsis.txt new file mode 100644 index 000000000..e39718c30 --- /dev/null +++ b/latest/cases/00453/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Model using parameters and rules only with + one event that assigns value to a parameter, subject to a delay. +componentTags: Parameter, RateRule, EventWithDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains one event that assigns value to parameter S2 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1.1$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00454/l2v5/build.log b/latest/cases/00454/l2v5/build.log new file mode 100644 index 000000000..40cacd751 --- /dev/null +++ b/latest/cases/00454/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00454/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00454/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00454/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00454/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00454/l2v5/index.heta b/latest/cases/00454/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00454/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00454/l3v2/build.log b/latest/cases/00454/l3v2/build.log new file mode 100644 index 000000000..adafab2da --- /dev/null +++ b/latest/cases/00454/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00454/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00454/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00454/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00454/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00454/l3v2/index.heta b/latest/cases/00454/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00454/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00454/model-sbml-l2v5.xml b/latest/cases/00454/model-sbml-l2v5.xml new file mode 100644 index 000000000..9ad697f94 --- /dev/null +++ b/latest/cases/00454/model-sbml-l2v5.xml @@ -0,0 +1,119 @@ + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 1.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00454/model-sbml-l3v2.xml b/latest/cases/00454/model-sbml-l3v2.xml new file mode 100644 index 000000000..a0338e6be --- /dev/null +++ b/latest/cases/00454/model-sbml-l3v2.xml @@ -0,0 +1,126 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 1.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00454/synopsis.txt b/latest/cases/00454/synopsis.txt new file mode 100644 index 000000000..74d7fc9b2 --- /dev/null +++ b/latest/cases/00454/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Model using parameters and rules only with + one event that assigns value to a parameter, subject to a delay. +componentTags: Parameter, RateRule, EventWithDelay +testTags: NonConstantParameter, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains two events that assign values to parameters S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $1.5$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00455/l2v5/build.log b/latest/cases/00455/l2v5/build.log new file mode 100644 index 000000000..7cb603109 --- /dev/null +++ b/latest/cases/00455/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00455/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00455/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00455/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00455/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00455/l2v5/index.heta b/latest/cases/00455/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00455/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00455/l3v2/build.log b/latest/cases/00455/l3v2/build.log new file mode 100644 index 000000000..e7a3169b6 --- /dev/null +++ b/latest/cases/00455/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00455/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00455/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00455/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00455/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00455/l3v2/index.heta b/latest/cases/00455/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00455/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00455/model-sbml-l2v5.xml b/latest/cases/00455/model-sbml-l2v5.xml new file mode 100644 index 000000000..c84bd5748 --- /dev/null +++ b/latest/cases/00455/model-sbml-l2v5.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.4 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00455/model-sbml-l3v2.xml b/latest/cases/00455/model-sbml-l3v2.xml new file mode 100644 index 000000000..08a4bd06e --- /dev/null +++ b/latest/cases/00455/model-sbml-l3v2.xml @@ -0,0 +1,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.4 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00455/synopsis.txt b/latest/cases/00455/synopsis.txt new file mode 100644 index 000000000..87991065f --- /dev/null +++ b/latest/cases/00455/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Model using parameters and rules only with + one event that assigns value to two parameters, subject to a delay. +componentTags: Parameter, RateRule, EventWithDelay +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains one event that assigns values to both parameters S2 and +S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.4$ | $S2 = 1$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00456/l2v5/build.log b/latest/cases/00456/l2v5/build.log new file mode 100644 index 000000000..c237cdc31 --- /dev/null +++ b/latest/cases/00456/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00456/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00456/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00456/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00456/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00456/l2v5/index.heta b/latest/cases/00456/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00456/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00456/l3v2/build.log b/latest/cases/00456/l3v2/build.log new file mode 100644 index 000000000..885d98e0a --- /dev/null +++ b/latest/cases/00456/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00456/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00456/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00456/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00456/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00456/l3v2/index.heta b/latest/cases/00456/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00456/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00456/model-sbml-l2v5.xml b/latest/cases/00456/model-sbml-l2v5.xml new file mode 100644 index 000000000..2a898994d --- /dev/null +++ b/latest/cases/00456/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00456/model-sbml-l3v2.xml b/latest/cases/00456/model-sbml-l3v2.xml new file mode 100644 index 000000000..39439f16c --- /dev/null +++ b/latest/cases/00456/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00456/synopsis.txt b/latest/cases/00456/synopsis.txt new file mode 100644 index 000000000..f6fe468e4 --- /dev/null +++ b/latest/cases/00456/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00457/l2v5/build.log b/latest/cases/00457/l2v5/build.log new file mode 100644 index 000000000..093ef8a0c --- /dev/null +++ b/latest/cases/00457/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00457/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00457/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00457/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00457/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00457/l2v5/index.heta b/latest/cases/00457/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00457/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00457/l3v2/build.log b/latest/cases/00457/l3v2/build.log new file mode 100644 index 000000000..d8d92c0de --- /dev/null +++ b/latest/cases/00457/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00457/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00457/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00457/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00457/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00457/l3v2/index.heta b/latest/cases/00457/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00457/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00457/model-sbml-l2v5.xml b/latest/cases/00457/model-sbml-l2v5.xml new file mode 100644 index 000000000..47eabdbbd --- /dev/null +++ b/latest/cases/00457/model-sbml-l2v5.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00457/model-sbml-l3v2.xml b/latest/cases/00457/model-sbml-l3v2.xml new file mode 100644 index 000000000..530d2af60 --- /dev/null +++ b/latest/cases/00457/model-sbml-l3v2.xml @@ -0,0 +1,121 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00457/synopsis.txt b/latest/cases/00457/synopsis.txt new file mode 100644 index 000000000..dbdbda653 --- /dev/null +++ b/latest/cases/00457/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Basic three reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S1 | $k3 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1.5$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00458/l2v5/build.log b/latest/cases/00458/l2v5/build.log new file mode 100644 index 000000000..b6f98c35a --- /dev/null +++ b/latest/cases/00458/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00458/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00458/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00458/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00458/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00458/l2v5/index.heta b/latest/cases/00458/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00458/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00458/l3v2/build.log b/latest/cases/00458/l3v2/build.log new file mode 100644 index 000000000..0ca5539c3 --- /dev/null +++ b/latest/cases/00458/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00458/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00458/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00458/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00458/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00458/l3v2/index.heta b/latest/cases/00458/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00458/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00458/model-sbml-l2v5.xml b/latest/cases/00458/model-sbml-l2v5.xml new file mode 100644 index 000000000..7e4be8bcd --- /dev/null +++ b/latest/cases/00458/model-sbml-l2v5.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + S3 + + + + + S2 + + + + + S1 + + + + + + + diff --git a/latest/cases/00458/model-sbml-l3v2.xml b/latest/cases/00458/model-sbml-l3v2.xml new file mode 100644 index 000000000..d29d4dc69 --- /dev/null +++ b/latest/cases/00458/model-sbml-l3v2.xml @@ -0,0 +1,126 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + S3 + + + + + S2 + + + + + S1 + + + + + + + diff --git a/latest/cases/00458/synopsis.txt b/latest/cases/00458/synopsis.txt new file mode 100644 index 000000000..5f7d58203 --- /dev/null +++ b/latest/cases/00458/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic three reactions with three species in one compartment + and one event that assigns value to three species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S1 | $k3 * S3 * C$ |] + +The model contains one event that assigns values to species S1, S2 and S3: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1.5$ | $S2 = S3$ | + | | | | $S1 = S2$ | + | | | | $S3 = S1$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00459/l2v5/build.log b/latest/cases/00459/l2v5/build.log new file mode 100644 index 000000000..c9b7f8161 --- /dev/null +++ b/latest/cases/00459/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00459/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00459/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00459/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00459/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00459/l2v5/index.heta b/latest/cases/00459/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00459/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00459/l3v2/build.log b/latest/cases/00459/l3v2/build.log new file mode 100644 index 000000000..a0dfff58b --- /dev/null +++ b/latest/cases/00459/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00459/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00459/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00459/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00459/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00459/l3v2/index.heta b/latest/cases/00459/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00459/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00459/model-sbml-l2v5.xml b/latest/cases/00459/model-sbml-l2v5.xml new file mode 100644 index 000000000..b5140d61b --- /dev/null +++ b/latest/cases/00459/model-sbml-l2v5.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00459/model-sbml-l3v2.xml b/latest/cases/00459/model-sbml-l3v2.xml new file mode 100644 index 000000000..043bb1ddf --- /dev/null +++ b/latest/cases/00459/model-sbml-l3v2.xml @@ -0,0 +1,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + S2 + + + + + + + + + + + k1 + S1 + S2 + + + + -1 + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00459/synopsis.txt b/latest/cases/00459/synopsis.txt new file mode 100644 index 000000000..e42b160b4 --- /dev/null +++ b/latest/cases/00459/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Model using parameters and rules only with + and one event that assigns value to two parameters, subject to a delay. +componentTags: Parameter, RateRule, EventWithDelay +testTags: NonConstantParameter, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and two constant +parameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ | + | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |] + +The model contains one event that assigns values to both parameters S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00460/l2v5/build.log b/latest/cases/00460/l2v5/build.log new file mode 100644 index 000000000..e44dfeee5 --- /dev/null +++ b/latest/cases/00460/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00460/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00460/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00460/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00460/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00460/l2v5/index.heta b/latest/cases/00460/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00460/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00460/l3v2/build.log b/latest/cases/00460/l3v2/build.log new file mode 100644 index 000000000..42c57673e --- /dev/null +++ b/latest/cases/00460/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00460/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00460/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00460/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00460/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00460/l3v2/index.heta b/latest/cases/00460/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00460/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00460/model-sbml-l2v5.xml b/latest/cases/00460/model-sbml-l2v5.xml new file mode 100644 index 000000000..6dd4a5aa2 --- /dev/null +++ b/latest/cases/00460/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00460/model-sbml-l3v2.xml b/latest/cases/00460/model-sbml-l3v2.xml new file mode 100644 index 000000000..a600b1bfb --- /dev/null +++ b/latest/cases/00460/model-sbml-l3v2.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00460/synopsis.txt b/latest/cases/00460/synopsis.txt new file mode 100644 index 000000000..dd28a8062 --- /dev/null +++ b/latest/cases/00460/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Model using parameters and rules only with + and one event that assigns value to two parameters, subject to a delay. +componentTags: Parameter, RateRule, EventWithDelay +testTags: NonConstantParameter, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and three constant +parameters called k1, k2 and k3. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k3 * S3 - k1 * S1$ | + | Rate | S2 | $k1 * S1 - k2 * S2$ | + | Rate | S3 | $k2 * S2 - k3 * S3$ |] + +The model contains one event that assigns values to both parameters S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1.5$ | $S2 = 1.5$ | + | | | | $S1 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00461/l2v5/build.log b/latest/cases/00461/l2v5/build.log new file mode 100644 index 000000000..bc220bba1 --- /dev/null +++ b/latest/cases/00461/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00461/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00461/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00461/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00461/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00461/l2v5/index.heta b/latest/cases/00461/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00461/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00461/l3v2/build.log b/latest/cases/00461/l3v2/build.log new file mode 100644 index 000000000..f1b4fd487 --- /dev/null +++ b/latest/cases/00461/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00461/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00461/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00461/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00461/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00461/l3v2/index.heta b/latest/cases/00461/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00461/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00461/model-sbml-l2v5.xml b/latest/cases/00461/model-sbml-l2v5.xml new file mode 100644 index 000000000..efce0ae84 --- /dev/null +++ b/latest/cases/00461/model-sbml-l2v5.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + S3 + + + + + S2 + + + + + S1 + + + + + + + diff --git a/latest/cases/00461/model-sbml-l3v2.xml b/latest/cases/00461/model-sbml-l3v2.xml new file mode 100644 index 000000000..7637511aa --- /dev/null +++ b/latest/cases/00461/model-sbml-l3v2.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + k1 + S1 + + + + -1 + k2 + S2 + + + + + + + + + + + k2 + S2 + + + + -1 + k3 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 1.5 + + + + + + S3 + + + + + S2 + + + + + S1 + + + + + + + diff --git a/latest/cases/00461/synopsis.txt b/latest/cases/00461/synopsis.txt new file mode 100644 index 000000000..45d413aa3 --- /dev/null +++ b/latest/cases/00461/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Model using parameters and rules only with + and one event that assigns value to three parameters, subject to a delay. +componentTags: Parameter, RateRule, EventWithDelay +testTags: NonConstantParameter, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called S1, S2 and S3 and three constant +parameters called k1, k2 and k3. (Note that indeed S1, S2 and S3 are parameters and +not species in this model.) + +The model contains three rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S1 | $k3 * S3 - k1 * S1$ | + | Rate | S2 | $k1 * S1 - k2 * S2$ | + | Rate | S3 | $k2 * S2 - k3 * S3$ |] + +The model contains one event that assigns values to parameters S1, S2 and S3: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1.5$ | $S2 = S3$ | + | | | | $S1 = S2$ | + | | | | $S3 = S1$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S1 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |any | +|Initial amount of S2 |$2.0$ |same as S1 | +|Initial amount of S3 |$1.0$ |same as S1 | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.55$ |second^-1^ | +|Value of parameter k3 |$0.25$ |second^-1^ |] + + diff --git a/latest/cases/00462/l2v5/heta-code/output.heta b/latest/cases/00462/l2v5/heta-code/output.heta new file mode 100644 index 000000000..01b11820a --- /dev/null +++ b/latest/cases/00462/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5e-4; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00462/l2v5/index.heta b/latest/cases/00462/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00462/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00462/l2v5/json/output.json b/latest/cases/00462/l2v5/json/output.json new file mode 100644 index 000000000..10e6d4860 --- /dev/null +++ b/latest/cases/00462/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00462/l3v2/heta-code/output.heta b/latest/cases/00462/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9fcd5d0e4 --- /dev/null +++ b/latest/cases/00462/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00462/l3v2/index.heta b/latest/cases/00462/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00462/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00462/l3v2/json/output.json b/latest/cases/00462/l3v2/json/output.json new file mode 100644 index 000000000..a46b01a1c --- /dev/null +++ b/latest/cases/00462/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00462/model-sbml-l2v5.xml b/latest/cases/00462/model-sbml-l2v5.xml new file mode 100644 index 000000000..c1ab83994 --- /dev/null +++ b/latest/cases/00462/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00462/model-sbml-l3v2.xml b/latest/cases/00462/model-sbml-l3v2.xml new file mode 100644 index 000000000..a28cb2323 --- /dev/null +++ b/latest/cases/00462/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00462/output.heta b/latest/cases/00462/output.heta new file mode 100644 index 000000000..c0ad4854b --- /dev/null +++ b/latest/cases/00462/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k1. The model contains one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model does not contain any rules. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00462/synopsis.txt b/latest/cases/00462/synopsis.txt new file mode 100644 index 000000000..dabb353b4 --- /dev/null +++ b/latest/cases/00462/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k1. The model contains one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model does not contain any rules. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00463/l2v5/heta-code/output.heta b/latest/cases/00463/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ccfbc74b3 --- /dev/null +++ b/latest/cases/00463/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.15; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00463/l2v5/index.heta b/latest/cases/00463/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00463/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00463/l2v5/json/output.json b/latest/cases/00463/l2v5/json/output.json new file mode 100644 index 000000000..965e40594 --- /dev/null +++ b/latest/cases/00463/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00463/l3v2/heta-code/output.heta b/latest/cases/00463/l3v2/heta-code/output.heta new file mode 100644 index 000000000..061335b51 --- /dev/null +++ b/latest/cases/00463/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.15; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00463/l3v2/index.heta b/latest/cases/00463/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00463/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00463/l3v2/json/output.json b/latest/cases/00463/l3v2/json/output.json new file mode 100644 index 000000000..3b1ab4d67 --- /dev/null +++ b/latest/cases/00463/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00463/model-sbml-l2v5.xml b/latest/cases/00463/model-sbml-l2v5.xml new file mode 100644 index 000000000..c960f1d7e --- /dev/null +++ b/latest/cases/00463/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00463/model-sbml-l3v2.xml b/latest/cases/00463/model-sbml-l3v2.xml new file mode 100644 index 000000000..9cb73f855 --- /dev/null +++ b/latest/cases/00463/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00463/output.heta b/latest/cases/00463/output.heta new file mode 100644 index 000000000..bee0d08b7 --- /dev/null +++ b/latest/cases/00463/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment and nonzero initial concentrations. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.15; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00463/synopsis.txt b/latest/cases/00463/synopsis.txt new file mode 100644 index 000000000..b29623827 --- /dev/null +++ b/latest/cases/00463/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment and nonzero initial concentrations. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00464/l2v5/heta-code/output.heta b/latest/cases/00464/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4f0b54cec --- /dev/null +++ b/latest/cases/00464/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.0015; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := C * k2 * S2; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 0.5; + diff --git a/latest/cases/00464/l2v5/index.heta b/latest/cases/00464/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00464/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00464/l2v5/json/output.json b/latest/cases/00464/l2v5/json/output.json new file mode 100644 index 000000000..c32272ee2 --- /dev/null +++ b/latest/cases/00464/l2v5/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00464/l3v2/heta-code/output.heta b/latest/cases/00464/l3v2/heta-code/output.heta new file mode 100644 index 000000000..77888d498 --- /dev/null +++ b/latest/cases/00464/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0015; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := C * k2 * S2; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00464/l3v2/index.heta b/latest/cases/00464/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00464/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00464/l3v2/json/output.json b/latest/cases/00464/l3v2/json/output.json new file mode 100644 index 000000000..c61ecd21b --- /dev/null +++ b/latest/cases/00464/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00464/model-sbml-l2v5.xml b/latest/cases/00464/model-sbml-l2v5.xml new file mode 100644 index 000000000..8a141425b --- /dev/null +++ b/latest/cases/00464/model-sbml-l2v5.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + diff --git a/latest/cases/00464/model-sbml-l3v2.xml b/latest/cases/00464/model-sbml-l3v2.xml new file mode 100644 index 000000000..1c6c94899 --- /dev/null +++ b/latest/cases/00464/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + diff --git a/latest/cases/00464/output.heta b/latest/cases/00464/output.heta new file mode 100644 index 000000000..b46d99a80 --- /dev/null +++ b/latest/cases/00464/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment, nonzero initial concentrations, and identical reaction rates. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S1 | $k2 * S2 * C$ |] + +The rate constants are identical in both directions, leading to a system +where the species concentrations remain the same. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$0.5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0015; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, }; +reaction2 := C * k2 * S2; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00464/synopsis.txt b/latest/cases/00464/synopsis.txt new file mode 100644 index 000000000..d74126e19 --- /dev/null +++ b/latest/cases/00464/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment, nonzero initial concentrations, and identical reaction rates. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S1 | $k2 * S2 * C$ |] + +The rate constants are identical in both directions, leading to a system +where the species concentrations remain the same. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$0.5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00465/l2v5/heta-code/output.heta b/latest/cases/00465/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0341d6d0a --- /dev/null +++ b/latest/cases/00465/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00465/l2v5/index.heta b/latest/cases/00465/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00465/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00465/l2v5/json/output.json b/latest/cases/00465/l2v5/json/output.json new file mode 100644 index 000000000..c428723fe --- /dev/null +++ b/latest/cases/00465/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00465/l3v2/heta-code/output.heta b/latest/cases/00465/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c3f04204f --- /dev/null +++ b/latest/cases/00465/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00465/l3v2/index.heta b/latest/cases/00465/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00465/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00465/l3v2/json/output.json b/latest/cases/00465/l3v2/json/output.json new file mode 100644 index 000000000..9acbbe19a --- /dev/null +++ b/latest/cases/00465/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00465/model-sbml-l2v5.xml b/latest/cases/00465/model-sbml-l2v5.xml new file mode 100644 index 000000000..f7acd45b7 --- /dev/null +++ b/latest/cases/00465/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00465/model-sbml-l3v2.xml b/latest/cases/00465/model-sbml-l3v2.xml new file mode 100644 index 000000000..c6c68abc9 --- /dev/null +++ b/latest/cases/00465/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00465/output.heta b/latest/cases/00465/output.heta new file mode 100644 index 000000000..5b5e8b010 --- /dev/null +++ b/latest/cases/00465/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00465/synopsis.txt b/latest/cases/00465/synopsis.txt new file mode 100644 index 000000000..83677d7a6 --- /dev/null +++ b/latest/cases/00465/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + + diff --git a/latest/cases/00466/l2v5/heta-code/output.heta b/latest/cases/00466/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c672de0dd --- /dev/null +++ b/latest/cases/00466/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1e-4; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00466/l2v5/index.heta b/latest/cases/00466/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00466/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00466/l2v5/json/output.json b/latest/cases/00466/l2v5/json/output.json new file mode 100644 index 000000000..5cbef3337 --- /dev/null +++ b/latest/cases/00466/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00466/l3v2/heta-code/output.heta b/latest/cases/00466/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d31deb816 --- /dev/null +++ b/latest/cases/00466/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00466/l3v2/index.heta b/latest/cases/00466/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00466/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00466/l3v2/json/output.json b/latest/cases/00466/l3v2/json/output.json new file mode 100644 index 000000000..5ecb64a7c --- /dev/null +++ b/latest/cases/00466/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + } +] \ No newline at end of file diff --git a/latest/cases/00466/model-sbml-l2v5.xml b/latest/cases/00466/model-sbml-l2v5.xml new file mode 100644 index 000000000..82c91d6db --- /dev/null +++ b/latest/cases/00466/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00466/model-sbml-l3v2.xml b/latest/cases/00466/model-sbml-l3v2.xml new file mode 100644 index 000000000..2d9517982 --- /dev/null +++ b/latest/cases/00466/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00466/output.heta b/latest/cases/00466/output.heta new file mode 100644 index 000000000..03b72ba1c --- /dev/null +++ b/latest/cases/00466/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one C. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00466/synopsis.txt b/latest/cases/00466/synopsis.txt new file mode 100644 index 000000000..9958b8229 --- /dev/null +++ b/latest/cases/00466/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic two reactions with four species in one C. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00467/l2v5/heta-code/output.heta b/latest/cases/00467/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5f1f83a0a --- /dev/null +++ b/latest/cases/00467/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Record 'k1' { } .= 10; +k2 @Record 'k2' { } .= 0.9; +k3 @Record 'k3' { } .= 0.7; + diff --git a/latest/cases/00467/l2v5/index.heta b/latest/cases/00467/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00467/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00467/l2v5/json/output.json b/latest/cases/00467/l2v5/json/output.json new file mode 100644 index 000000000..5f70b6fb1 --- /dev/null +++ b/latest/cases/00467/l2v5/json/output.json @@ -0,0 +1,173 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "10" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00467/l3v2/heta-code/output.heta b/latest/cases/00467/l3v2/heta-code/output.heta new file mode 100644 index 000000000..af7467ad0 --- /dev/null +++ b/latest/cases/00467/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 10; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00467/l3v2/index.heta b/latest/cases/00467/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00467/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00467/l3v2/json/output.json b/latest/cases/00467/l3v2/json/output.json new file mode 100644 index 000000000..773ae7a39 --- /dev/null +++ b/latest/cases/00467/l3v2/json/output.json @@ -0,0 +1,143 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 10 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.9 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00467/model-sbml-l2v5.xml b/latest/cases/00467/model-sbml-l2v5.xml new file mode 100644 index 000000000..95ddc51d2 --- /dev/null +++ b/latest/cases/00467/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00467/model-sbml-l3v2.xml b/latest/cases/00467/model-sbml-l3v2.xml new file mode 100644 index 000000000..ff23aed57 --- /dev/null +++ b/latest/cases/00467/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00467/output.heta b/latest/cases/00467/output.heta new file mode 100644 index 000000000..fe9e96e71 --- /dev/null +++ b/latest/cases/00467/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Three reactions with four species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and three parameters called k1, k2 and k3. The model +contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1.0 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.9$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 10; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00467/synopsis.txt b/latest/cases/00467/synopsis.txt new file mode 100644 index 000000000..d5f8de29e --- /dev/null +++ b/latest/cases/00467/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Three reactions with four species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and three parameters called k1, k2 and k3. The model +contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1.0 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.9$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + + diff --git a/latest/cases/00468/l2v5/heta-code/output.heta b/latest/cases/00468/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a6abffe55 --- /dev/null +++ b/latest/cases/00468/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00468/l2v5/index.heta b/latest/cases/00468/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00468/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00468/l2v5/json/output.json b/latest/cases/00468/l2v5/json/output.json new file mode 100644 index 000000000..42cf6f10e --- /dev/null +++ b/latest/cases/00468/l2v5/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00468/l3v2/heta-code/output.heta b/latest/cases/00468/l3v2/heta-code/output.heta new file mode 100644 index 000000000..26f7e735f --- /dev/null +++ b/latest/cases/00468/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00468/l3v2/index.heta b/latest/cases/00468/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00468/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00468/l3v2/json/output.json b/latest/cases/00468/l3v2/json/output.json new file mode 100644 index 000000000..5779d3b90 --- /dev/null +++ b/latest/cases/00468/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00468/model-sbml-l2v5.xml b/latest/cases/00468/model-sbml-l2v5.xml new file mode 100644 index 000000000..2f88e9915 --- /dev/null +++ b/latest/cases/00468/model-sbml-l2v5.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00468/model-sbml-l3v2.xml b/latest/cases/00468/model-sbml-l3v2.xml new file mode 100644 index 000000000..df5fbb1f9 --- /dev/null +++ b/latest/cases/00468/model-sbml-l3v2.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00468/output.heta b/latest/cases/00468/output.heta new file mode 100644 index 000000000..18d04411b --- /dev/null +++ b/latest/cases/00468/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. +There are four species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S4 | $k3 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$0.7$ |second^-1^ | +|Value of parameter k2 |$0.5$ |second^-1^ | +|Value of parameter k3 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00468/synopsis.txt b/latest/cases/00468/synopsis.txt new file mode 100644 index 000000000..d03347da6 --- /dev/null +++ b/latest/cases/00468/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. +There are four species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S4 | $k3 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$0.7$ |second^-1^ | +|Value of parameter k2 |$0.5$ |second^-1^ | +|Value of parameter k3 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00469/l2v5/heta-code/output.heta b/latest/cases/00469/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a4c076cb9 --- /dev/null +++ b/latest/cases/00469/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= k2 / 100; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00469/l2v5/index.heta b/latest/cases/00469/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00469/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00469/l2v5/json/output.json b/latest/cases/00469/l2v5/json/output.json new file mode 100644 index 000000000..5832beb4a --- /dev/null +++ b/latest/cases/00469/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "k2 / 100" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00057/l3v2/build.log b/latest/cases/00469/l3v2/build.log similarity index 54% rename from latest/cases/00057/l3v2/build.log rename to latest/cases/00469/l3v2/build.log index 9bd0ab98f..655bd3431 100644 --- a/latest/cases/00057/l3v2/build.log +++ b/latest/cases/00469/l3v2/build.log @@ -1,10 +1,9 @@ [info] Namespace "nameless" was set as "concrete" -[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00057/l3v2". +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00469/l3v2". [info] Compilation of module "index.heta" of type "heta"... -[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00057/l3v2/index.heta"... -[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00057/model-sbml-l3v2.xml"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00469/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00469/model-sbml-l3v2.xml"... [info] Setting references in elements, total length 85 -[error] Component "k" is not found in space "nameless" as expected in expression: reaction1 [ode_]= compartment * k * S1; -[error] Component "k" is not found in space "nameless" as expected in expression: reaction2 [ode_]= compartment * k * S2; +[error] No required "num" property for "k1" of Const. [info] Checking for circular references in Records. [warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00469/l3v2/index.heta b/latest/cases/00469/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00469/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00469/model-sbml-l2v5.xml b/latest/cases/00469/model-sbml-l2v5.xml new file mode 100644 index 000000000..27444475b --- /dev/null +++ b/latest/cases/00469/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k2 + 100 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00469/model-sbml-l3v2.xml b/latest/cases/00469/model-sbml-l3v2.xml new file mode 100644 index 000000000..54d19bdc2 --- /dev/null +++ b/latest/cases/00469/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + 100 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00469/output.heta b/latest/cases/00469/output.heta new file mode 100644 index 000000000..a437bf8c8 --- /dev/null +++ b/latest/cases/00469/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k1 has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= k2 / 100; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00469/synopsis.txt b/latest/cases/00469/synopsis.txt new file mode 100644 index 000000000..9d580bd9f --- /dev/null +++ b/latest/cases/00469/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k1 has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00470/l2v5/heta-code/output.heta b/latest/cases/00470/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a4c076cb9 --- /dev/null +++ b/latest/cases/00470/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= k2 / 100; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00470/l2v5/index.heta b/latest/cases/00470/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00470/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00470/l2v5/json/output.json b/latest/cases/00470/l2v5/json/output.json new file mode 100644 index 000000000..5832beb4a --- /dev/null +++ b/latest/cases/00470/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "k2 / 100" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00470/l3v2/heta-code/output.heta b/latest/cases/00470/l3v2/heta-code/output.heta new file mode 100644 index 000000000..24be22dee --- /dev/null +++ b/latest/cases/00470/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 100; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00470/l3v2/index.heta b/latest/cases/00470/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00470/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00470/l3v2/json/output.json b/latest/cases/00470/l3v2/json/output.json new file mode 100644 index 000000000..00fbc17e8 --- /dev/null +++ b/latest/cases/00470/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 100 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00470/model-sbml-l2v5.xml b/latest/cases/00470/model-sbml-l2v5.xml new file mode 100644 index 000000000..61253c57f --- /dev/null +++ b/latest/cases/00470/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k2 + 100 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00470/model-sbml-l3v2.xml b/latest/cases/00470/model-sbml-l3v2.xml new file mode 100644 index 000000000..cdbc59de2 --- /dev/null +++ b/latest/cases/00470/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + 100 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00470/output.heta b/latest/cases/00470/output.heta new file mode 100644 index 000000000..a9fba482d --- /dev/null +++ b/latest/cases/00470/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for parameter k1 is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$100$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 100; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00470/synopsis.txt b/latest/cases/00470/synopsis.txt new file mode 100644 index 000000000..c88ba9e14 --- /dev/null +++ b/latest/cases/00470/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for parameter k1 is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$100$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00471/l2v5/heta-code/output.heta b/latest/cases/00471/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cfec286cf --- /dev/null +++ b/latest/cases/00471/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= k2 / 50; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00471/l2v5/index.heta b/latest/cases/00471/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00471/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00471/l2v5/json/output.json b/latest/cases/00471/l2v5/json/output.json new file mode 100644 index 000000000..4122fd82b --- /dev/null +++ b/latest/cases/00471/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00471/l3v2/heta-code/output.heta b/latest/cases/00471/l3v2/heta-code/output.heta new file mode 100644 index 000000000..955e16c1e --- /dev/null +++ b/latest/cases/00471/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k2 / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00471/l3v2/index.heta b/latest/cases/00471/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00471/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00471/l3v2/json/output.json b/latest/cases/00471/l3v2/json/output.json new file mode 100644 index 000000000..256b887c8 --- /dev/null +++ b/latest/cases/00471/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00471/model-sbml-l2v5.xml b/latest/cases/00471/model-sbml-l2v5.xml new file mode 100644 index 000000000..6b5ebf115 --- /dev/null +++ b/latest/cases/00471/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k2 + 50 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00471/model-sbml-l3v2.xml b/latest/cases/00471/model-sbml-l3v2.xml new file mode 100644 index 000000000..cd7cc4202 --- /dev/null +++ b/latest/cases/00471/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + 50 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00471/output.heta b/latest/cases/00471/output.heta new file mode 100644 index 000000000..3a4e5aa76 --- /dev/null +++ b/latest/cases/00471/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5.4$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k2 / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00471/synopsis.txt b/latest/cases/00471/synopsis.txt new file mode 100644 index 000000000..609eacc41 --- /dev/null +++ b/latest/cases/00471/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5.4$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00472/l2v5/heta-code/output.heta b/latest/cases/00472/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cfec286cf --- /dev/null +++ b/latest/cases/00472/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= k2 / 50; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00472/l2v5/index.heta b/latest/cases/00472/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00472/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00472/l2v5/json/output.json b/latest/cases/00472/l2v5/json/output.json new file mode 100644 index 000000000..4122fd82b --- /dev/null +++ b/latest/cases/00472/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00472/l3v2/heta-code/output.heta b/latest/cases/00472/l3v2/heta-code/output.heta new file mode 100644 index 000000000..955e16c1e --- /dev/null +++ b/latest/cases/00472/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k2 / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00472/l3v2/index.heta b/latest/cases/00472/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00472/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00472/l3v2/json/output.json b/latest/cases/00472/l3v2/json/output.json new file mode 100644 index 000000000..256b887c8 --- /dev/null +++ b/latest/cases/00472/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00472/model-sbml-l2v5.xml b/latest/cases/00472/model-sbml-l2v5.xml new file mode 100644 index 000000000..a939e2079 --- /dev/null +++ b/latest/cases/00472/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k2 + 50 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00472/model-sbml-l3v2.xml b/latest/cases/00472/model-sbml-l3v2.xml new file mode 100644 index 000000000..814f5b9af --- /dev/null +++ b/latest/cases/00472/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + 50 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00472/output.heta b/latest/cases/00472/output.heta new file mode 100644 index 000000000..71e9da5c0 --- /dev/null +++ b/latest/cases/00472/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k2 / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00472/synopsis.txt b/latest/cases/00472/synopsis.txt new file mode 100644 index 000000000..b750bda45 --- /dev/null +++ b/latest/cases/00472/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00473/l2v5/heta-code/output.heta b/latest/cases/00473/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cfec286cf --- /dev/null +++ b/latest/cases/00473/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= k2 / 50; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00473/l2v5/index.heta b/latest/cases/00473/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00473/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00473/l2v5/json/output.json b/latest/cases/00473/l2v5/json/output.json new file mode 100644 index 000000000..4122fd82b --- /dev/null +++ b/latest/cases/00473/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00473/l3v2/heta-code/output.heta b/latest/cases/00473/l3v2/heta-code/output.heta new file mode 100644 index 000000000..955e16c1e --- /dev/null +++ b/latest/cases/00473/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k2 / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00473/l3v2/index.heta b/latest/cases/00473/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00473/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00473/l3v2/json/output.json b/latest/cases/00473/l3v2/json/output.json new file mode 100644 index 000000000..256b887c8 --- /dev/null +++ b/latest/cases/00473/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00473/model-sbml-l2v5.xml b/latest/cases/00473/model-sbml-l2v5.xml new file mode 100644 index 000000000..da679a67d --- /dev/null +++ b/latest/cases/00473/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k2 + 50 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00473/model-sbml-l3v2.xml b/latest/cases/00473/model-sbml-l3v2.xml new file mode 100644 index 000000000..9da389ec2 --- /dev/null +++ b/latest/cases/00473/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + 50 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00473/output.heta b/latest/cases/00473/output.heta new file mode 100644 index 000000000..4badade3f --- /dev/null +++ b/latest/cases/00473/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k2 / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00473/synopsis.txt b/latest/cases/00473/synopsis.txt new file mode 100644 index 000000000..fc5334418 --- /dev/null +++ b/latest/cases/00473/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00474/l2v5/heta-code/output.heta b/latest/cases/00474/l2v5/heta-code/output.heta new file mode 100644 index 000000000..449e9aabe --- /dev/null +++ b/latest/cases/00474/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.00125; + diff --git a/latest/cases/00474/l2v5/index.heta b/latest/cases/00474/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00474/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00474/l2v5/json/output.json b/latest/cases/00474/l2v5/json/output.json new file mode 100644 index 000000000..dc4d6e0d5 --- /dev/null +++ b/latest/cases/00474/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.00125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00474/l3v2/heta-code/output.heta b/latest/cases/00474/l3v2/heta-code/output.heta new file mode 100644 index 000000000..48a75925e --- /dev/null +++ b/latest/cases/00474/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00474/l3v2/index.heta b/latest/cases/00474/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00474/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00474/l3v2/json/output.json b/latest/cases/00474/l3v2/json/output.json new file mode 100644 index 000000000..68ff61cd9 --- /dev/null +++ b/latest/cases/00474/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.00125 + } +] \ No newline at end of file diff --git a/latest/cases/00474/model-sbml-l2v5.xml b/latest/cases/00474/model-sbml-l2v5.xml new file mode 100644 index 000000000..651e15a82 --- /dev/null +++ b/latest/cases/00474/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00474/model-sbml-l3v2.xml b/latest/cases/00474/model-sbml-l3v2.xml new file mode 100644 index 000000000..2dd5cdb5c --- /dev/null +++ b/latest/cases/00474/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00474/output.heta b/latest/cases/00474/output.heta new file mode 100644 index 000000000..a1995dbf4 --- /dev/null +++ b/latest/cases/00474/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00474/synopsis.txt b/latest/cases/00474/synopsis.txt new file mode 100644 index 000000000..4c5ed36ff --- /dev/null +++ b/latest/cases/00474/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00475/l2v5/heta-code/output.heta b/latest/cases/00475/l2v5/heta-code/output.heta new file mode 100644 index 000000000..459b62bde --- /dev/null +++ b/latest/cases/00475/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 1.25e-5; + diff --git a/latest/cases/00475/l2v5/index.heta b/latest/cases/00475/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00475/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00475/l2v5/json/output.json b/latest/cases/00475/l2v5/json/output.json new file mode 100644 index 000000000..7d96e6df2 --- /dev/null +++ b/latest/cases/00475/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00475/l3v2/heta-code/output.heta b/latest/cases/00475/l3v2/heta-code/output.heta new file mode 100644 index 000000000..25057a509 --- /dev/null +++ b/latest/cases/00475/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00475/l3v2/index.heta b/latest/cases/00475/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00475/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00475/l3v2/json/output.json b/latest/cases/00475/l3v2/json/output.json new file mode 100644 index 000000000..ed09b1c65 --- /dev/null +++ b/latest/cases/00475/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0000125 + } +] \ No newline at end of file diff --git a/latest/cases/00475/model-sbml-l2v5.xml b/latest/cases/00475/model-sbml-l2v5.xml new file mode 100644 index 000000000..a21164131 --- /dev/null +++ b/latest/cases/00475/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00475/model-sbml-l3v2.xml b/latest/cases/00475/model-sbml-l3v2.xml new file mode 100644 index 000000000..97d03d4d7 --- /dev/null +++ b/latest/cases/00475/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00475/output.heta b/latest/cases/00475/output.heta new file mode 100644 index 000000000..b44f159bd --- /dev/null +++ b/latest/cases/00475/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00475/synopsis.txt b/latest/cases/00475/synopsis.txt new file mode 100644 index 000000000..4433b9efd --- /dev/null +++ b/latest/cases/00475/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00476/l2v5/heta-code/output.heta b/latest/cases/00476/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5ab278da6 --- /dev/null +++ b/latest/cases/00476/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.0125; + diff --git a/latest/cases/00476/l2v5/index.heta b/latest/cases/00476/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00476/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00476/l2v5/json/output.json b/latest/cases/00476/l2v5/json/output.json new file mode 100644 index 000000000..ac636c4ec --- /dev/null +++ b/latest/cases/00476/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.0125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00476/l3v2/heta-code/output.heta b/latest/cases/00476/l3v2/heta-code/output.heta new file mode 100644 index 000000000..70dbab65b --- /dev/null +++ b/latest/cases/00476/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0125; + diff --git a/latest/cases/00476/l3v2/index.heta b/latest/cases/00476/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00476/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00476/l3v2/json/output.json b/latest/cases/00476/l3v2/json/output.json new file mode 100644 index 000000000..b4a9f4e4d --- /dev/null +++ b/latest/cases/00476/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0125 + } +] \ No newline at end of file diff --git a/latest/cases/00476/model-sbml-l2v5.xml b/latest/cases/00476/model-sbml-l2v5.xml new file mode 100644 index 000000000..b79e069aa --- /dev/null +++ b/latest/cases/00476/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00476/model-sbml-l3v2.xml b/latest/cases/00476/model-sbml-l3v2.xml new file mode 100644 index 000000000..d3bebc0ea --- /dev/null +++ b/latest/cases/00476/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00476/output.heta b/latest/cases/00476/output.heta new file mode 100644 index 000000000..0ac33c67f --- /dev/null +++ b/latest/cases/00476/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-2$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0125; + diff --git a/latest/cases/00476/synopsis.txt b/latest/cases/00476/synopsis.txt new file mode 100644 index 000000000..ee3e501e3 --- /dev/null +++ b/latest/cases/00476/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-2$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00477/l2v5/heta-code/output.heta b/latest/cases/00477/l2v5/heta-code/output.heta new file mode 100644 index 000000000..16e449900 --- /dev/null +++ b/latest/cases/00477/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2 * p1; +p1 @Record 'p1' { } .= 0.125; + diff --git a/latest/cases/00477/l2v5/index.heta b/latest/cases/00477/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00477/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00477/l2v5/json/output.json b/latest/cases/00477/l2v5/json/output.json new file mode 100644 index 000000000..be6974eb6 --- /dev/null +++ b/latest/cases/00477/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00477/l3v2/heta-code/output.heta b/latest/cases/00477/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d7b950ddb --- /dev/null +++ b/latest/cases/00477/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k2 @Record 'k2' { } .= 2 * p1; + +k1 @Const 'k1' { } = 0.75; +p1 @Const 'p1' { } = 0.125; + diff --git a/latest/cases/00477/l3v2/index.heta b/latest/cases/00477/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00477/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00477/l3v2/json/output.json b/latest/cases/00477/l3v2/json/output.json new file mode 100644 index 000000000..1d0a97be4 --- /dev/null +++ b/latest/cases/00477/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.125 + } +] \ No newline at end of file diff --git a/latest/cases/00477/model-sbml-l2v5.xml b/latest/cases/00477/model-sbml-l2v5.xml new file mode 100644 index 000000000..63ce06b05 --- /dev/null +++ b/latest/cases/00477/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00477/model-sbml-l3v2.xml b/latest/cases/00477/model-sbml-l3v2.xml new file mode 100644 index 000000000..00cb20413 --- /dev/null +++ b/latest/cases/00477/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00477/output.heta b/latest/cases/00477/output.heta new file mode 100644 index 000000000..43d158a1c --- /dev/null +++ b/latest/cases/00477/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k2 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k2 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter p1 |$0.125$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k2 @Record 'k2' { } .= 2 * p1; + +k1 @Const 'k1' { } = 0.75; +p1 @Const 'p1' { } = 0.125; + diff --git a/latest/cases/00477/synopsis.txt b/latest/cases/00477/synopsis.txt new file mode 100644 index 000000000..f9e18fb45 --- /dev/null +++ b/latest/cases/00477/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k2 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k2 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter p1 |$0.125$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00478/l2v5/heta-code/output.heta b/latest/cases/00478/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3f9eb71b1 --- /dev/null +++ b/latest/cases/00478/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2 * p1; +p1 @Record 'p1' { } .= 0.125; + diff --git a/latest/cases/00478/l2v5/index.heta b/latest/cases/00478/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00478/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00478/l2v5/json/output.json b/latest/cases/00478/l2v5/json/output.json new file mode 100644 index 000000000..101837c6b --- /dev/null +++ b/latest/cases/00478/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00478/l3v2/heta-code/output.heta b/latest/cases/00478/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5b0426c31 --- /dev/null +++ b/latest/cases/00478/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k2 @Record 'k2' { } .= 2 * p1; + +k1 @Const 'k1' { } = 0.75; +p1 @Const 'p1' { } = 0.125; + diff --git a/latest/cases/00478/l3v2/index.heta b/latest/cases/00478/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00478/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00478/l3v2/json/output.json b/latest/cases/00478/l3v2/json/output.json new file mode 100644 index 000000000..cc7764f36 --- /dev/null +++ b/latest/cases/00478/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.125 + } +] \ No newline at end of file diff --git a/latest/cases/00478/model-sbml-l2v5.xml b/latest/cases/00478/model-sbml-l2v5.xml new file mode 100644 index 000000000..8109bc306 --- /dev/null +++ b/latest/cases/00478/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00478/model-sbml-l3v2.xml b/latest/cases/00478/model-sbml-l3v2.xml new file mode 100644 index 000000000..90e83e4e9 --- /dev/null +++ b/latest/cases/00478/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00478/output.heta b/latest/cases/00478/output.heta new file mode 100644 index 000000000..10310fb28 --- /dev/null +++ b/latest/cases/00478/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k2 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for parameter k2 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$1.0$ |second^-1^ | +|Value of parameter p1 |$0.125$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k2 @Record 'k2' { } .= 2 * p1; + +k1 @Const 'k1' { } = 0.75; +p1 @Const 'p1' { } = 0.125; + diff --git a/latest/cases/00478/synopsis.txt b/latest/cases/00478/synopsis.txt new file mode 100644 index 000000000..ce40089d9 --- /dev/null +++ b/latest/cases/00478/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k2 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for parameter k2 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$1.0$ |second^-1^ | +|Value of parameter p1 |$0.125$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00479/l2v5/heta-code/output.heta b/latest/cases/00479/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1163a7796 --- /dev/null +++ b/latest/cases/00479/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2 * p1; +p1 @Record 'p1' { } .= 0.125; + diff --git a/latest/cases/00479/l2v5/index.heta b/latest/cases/00479/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00479/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00479/l2v5/json/output.json b/latest/cases/00479/l2v5/json/output.json new file mode 100644 index 000000000..a14d31b67 --- /dev/null +++ b/latest/cases/00479/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00479/l3v2/heta-code/output.heta b/latest/cases/00479/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b544f77f9 --- /dev/null +++ b/latest/cases/00479/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k2 @Record 'k2' { } .= 2 * p1; + +k1 @Const 'k1' { } = 0.75; +p1 @Const 'p1' { } = 0.125; + diff --git a/latest/cases/00479/l3v2/index.heta b/latest/cases/00479/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00479/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00479/l3v2/json/output.json b/latest/cases/00479/l3v2/json/output.json new file mode 100644 index 000000000..1f42c2ecd --- /dev/null +++ b/latest/cases/00479/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.125 + } +] \ No newline at end of file diff --git a/latest/cases/00479/model-sbml-l2v5.xml b/latest/cases/00479/model-sbml-l2v5.xml new file mode 100644 index 000000000..94170e417 --- /dev/null +++ b/latest/cases/00479/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00479/model-sbml-l3v2.xml b/latest/cases/00479/model-sbml-l3v2.xml new file mode 100644 index 000000000..2f9475d5d --- /dev/null +++ b/latest/cases/00479/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00479/output.heta b/latest/cases/00479/output.heta new file mode 100644 index 000000000..1a3102f95 --- /dev/null +++ b/latest/cases/00479/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k2 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for parameter k2 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.125$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k2 @Record 'k2' { } .= 2 * p1; + +k1 @Const 'k1' { } = 0.75; +p1 @Const 'p1' { } = 0.125; + diff --git a/latest/cases/00479/synopsis.txt b/latest/cases/00479/synopsis.txt new file mode 100644 index 000000000..0ae2f4d36 --- /dev/null +++ b/latest/cases/00479/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k2 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for parameter k2 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.125$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00480/l2v5/heta-code/output.heta b/latest/cases/00480/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6574e0cee --- /dev/null +++ b/latest/cases/00480/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00480/l2v5/index.heta b/latest/cases/00480/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00480/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00480/l2v5/json/output.json b/latest/cases/00480/l2v5/json/output.json new file mode 100644 index 000000000..3e476fefb --- /dev/null +++ b/latest/cases/00480/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00480/l3v2/heta-code/output.heta b/latest/cases/00480/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e86b773c0 --- /dev/null +++ b/latest/cases/00480/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00480/l3v2/index.heta b/latest/cases/00480/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00480/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00480/l3v2/json/output.json b/latest/cases/00480/l3v2/json/output.json new file mode 100644 index 000000000..871b3c85e --- /dev/null +++ b/latest/cases/00480/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00480/model-sbml-l2v5.xml b/latest/cases/00480/model-sbml-l2v5.xml new file mode 100644 index 000000000..cb6f74fc9 --- /dev/null +++ b/latest/cases/00480/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00480/model-sbml-l3v2.xml b/latest/cases/00480/model-sbml-l3v2.xml new file mode 100644 index 000000000..d35c8fc2e --- /dev/null +++ b/latest/cases/00480/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00480/output.heta b/latest/cases/00480/output.heta new file mode 100644 index 000000000..bf6744ba6 --- /dev/null +++ b/latest/cases/00480/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |litre | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00480/synopsis.txt b/latest/cases/00480/synopsis.txt new file mode 100644 index 000000000..a54b7d3f8 --- /dev/null +++ b/latest/cases/00480/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |litre | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00481/l2v5/heta-code/output.heta b/latest/cases/00481/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e6ffab474 --- /dev/null +++ b/latest/cases/00481/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00481/l2v5/index.heta b/latest/cases/00481/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00481/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00481/l2v5/json/output.json b/latest/cases/00481/l2v5/json/output.json new file mode 100644 index 000000000..eae8362cd --- /dev/null +++ b/latest/cases/00481/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00481/l3v2/heta-code/output.heta b/latest/cases/00481/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1e230537b --- /dev/null +++ b/latest/cases/00481/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00481/l3v2/index.heta b/latest/cases/00481/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00481/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00481/l3v2/json/output.json b/latest/cases/00481/l3v2/json/output.json new file mode 100644 index 000000000..8b5a81917 --- /dev/null +++ b/latest/cases/00481/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00481/model-sbml-l2v5.xml b/latest/cases/00481/model-sbml-l2v5.xml new file mode 100644 index 000000000..607ff7914 --- /dev/null +++ b/latest/cases/00481/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00481/model-sbml-l3v2.xml b/latest/cases/00481/model-sbml-l3v2.xml new file mode 100644 index 000000000..b3fac88eb --- /dev/null +++ b/latest/cases/00481/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00481/output.heta b/latest/cases/00481/output.heta new file mode 100644 index 000000000..f7c017f0d --- /dev/null +++ b/latest/cases/00481/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |litre | +|Volume of compartment C |$3.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00481/synopsis.txt b/latest/cases/00481/synopsis.txt new file mode 100644 index 000000000..be4657ead --- /dev/null +++ b/latest/cases/00481/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |litre | +|Volume of compartment C |$3.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00482/l2v5/heta-code/output.heta b/latest/cases/00482/l2v5/heta-code/output.heta new file mode 100644 index 000000000..278b7538e --- /dev/null +++ b/latest/cases/00482/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00482/l2v5/index.heta b/latest/cases/00482/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00482/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00482/l2v5/json/output.json b/latest/cases/00482/l2v5/json/output.json new file mode 100644 index 000000000..cfa5429c3 --- /dev/null +++ b/latest/cases/00482/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00482/l3v2/heta-code/output.heta b/latest/cases/00482/l3v2/heta-code/output.heta new file mode 100644 index 000000000..50d1a7050 --- /dev/null +++ b/latest/cases/00482/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00482/l3v2/index.heta b/latest/cases/00482/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00482/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00482/l3v2/json/output.json b/latest/cases/00482/l3v2/json/output.json new file mode 100644 index 000000000..1c80830da --- /dev/null +++ b/latest/cases/00482/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00482/model-sbml-l2v5.xml b/latest/cases/00482/model-sbml-l2v5.xml new file mode 100644 index 000000000..f1e8a0bea --- /dev/null +++ b/latest/cases/00482/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00482/model-sbml-l3v2.xml b/latest/cases/00482/model-sbml-l3v2.xml new file mode 100644 index 000000000..99752d948 --- /dev/null +++ b/latest/cases/00482/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00482/output.heta b/latest/cases/00482/output.heta new file mode 100644 index 000000000..6e3607182 --- /dev/null +++ b/latest/cases/00482/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00482/synopsis.txt b/latest/cases/00482/synopsis.txt new file mode 100644 index 000000000..ee49fbccf --- /dev/null +++ b/latest/cases/00482/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00483/l2v5/heta-code/output.heta b/latest/cases/00483/l2v5/heta-code/output.heta new file mode 100644 index 000000000..df27d5788 --- /dev/null +++ b/latest/cases/00483/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: area, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/area, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: substance/area, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: substance/area, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 2.5; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00483/l2v5/index.heta b/latest/cases/00483/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00483/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00483/l2v5/json/output.json b/latest/cases/00483/l2v5/json/output.json new file mode 100644 index 000000000..48061627c --- /dev/null +++ b/latest/cases/00483/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "area", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00483/l3v2/heta-code/output.heta b/latest/cases/00483/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a5d3121cc --- /dev/null +++ b/latest/cases/00483/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00483/l3v2/index.heta b/latest/cases/00483/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00483/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00483/l3v2/json/output.json b/latest/cases/00483/l3v2/json/output.json new file mode 100644 index 000000000..0ec5a34aa --- /dev/null +++ b/latest/cases/00483/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre^2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00483/model-sbml-l2v5.xml b/latest/cases/00483/model-sbml-l2v5.xml new file mode 100644 index 000000000..45dab82b5 --- /dev/null +++ b/latest/cases/00483/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00483/model-sbml-l3v2.xml b/latest/cases/00483/model-sbml-l3v2.xml new file mode 100644 index 000000000..02aa0c356 --- /dev/null +++ b/latest/cases/00483/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00483/output.heta b/latest/cases/00483/output.heta new file mode 100644 index 000000000..bdb15a10e --- /dev/null +++ b/latest/cases/00483/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a 2D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$7.5$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$2.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre^2^ | +|Area of compartment C |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00483/synopsis.txt b/latest/cases/00483/synopsis.txt new file mode 100644 index 000000000..8d1c22cb1 --- /dev/null +++ b/latest/cases/00483/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a 2D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$7.5$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$2.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre^2^ | +|Area of compartment C |$1$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00484/l2v5/heta-code/output.heta b/latest/cases/00484/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a3cd8e3ab --- /dev/null +++ b/latest/cases/00484/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: area, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/area, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: substance/area, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: substance/area, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 2.5; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00484/l2v5/index.heta b/latest/cases/00484/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00484/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00484/l2v5/json/output.json b/latest/cases/00484/l2v5/json/output.json new file mode 100644 index 000000000..17bc1a17c --- /dev/null +++ b/latest/cases/00484/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "area", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00484/l3v2/heta-code/output.heta b/latest/cases/00484/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6e7ade4ab --- /dev/null +++ b/latest/cases/00484/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00484/l3v2/index.heta b/latest/cases/00484/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00484/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00484/l3v2/json/output.json b/latest/cases/00484/l3v2/json/output.json new file mode 100644 index 000000000..5b951bd16 --- /dev/null +++ b/latest/cases/00484/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre^2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00484/model-sbml-l2v5.xml b/latest/cases/00484/model-sbml-l2v5.xml new file mode 100644 index 000000000..30d42071a --- /dev/null +++ b/latest/cases/00484/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00484/model-sbml-l3v2.xml b/latest/cases/00484/model-sbml-l3v2.xml new file mode 100644 index 000000000..e2a109faa --- /dev/null +++ b/latest/cases/00484/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00484/output.heta b/latest/cases/00484/output.heta new file mode 100644 index 000000000..b021994aa --- /dev/null +++ b/latest/cases/00484/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a 2D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$7.5$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$2.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre^2^ | +|Area of compartment C |$3.5$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00484/synopsis.txt b/latest/cases/00484/synopsis.txt new file mode 100644 index 000000000..0a929797a --- /dev/null +++ b/latest/cases/00484/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a 2D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$7.5$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$2.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre^2^ | +|Area of compartment C |$3.5$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00485/l2v5/heta-code/output.heta b/latest/cases/00485/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1817c3b97 --- /dev/null +++ b/latest/cases/00485/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: area, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/area, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: substance/area, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: substance/area, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 2.5; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00485/l2v5/index.heta b/latest/cases/00485/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00485/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00485/l2v5/json/output.json b/latest/cases/00485/l2v5/json/output.json new file mode 100644 index 000000000..b5f58f3b4 --- /dev/null +++ b/latest/cases/00485/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "area", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00485/l3v2/heta-code/output.heta b/latest/cases/00485/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2a0fea238 --- /dev/null +++ b/latest/cases/00485/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00485/l3v2/index.heta b/latest/cases/00485/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00485/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00485/l3v2/json/output.json b/latest/cases/00485/l3v2/json/output.json new file mode 100644 index 000000000..ce237c759 --- /dev/null +++ b/latest/cases/00485/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre^2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00485/model-sbml-l2v5.xml b/latest/cases/00485/model-sbml-l2v5.xml new file mode 100644 index 000000000..6e76423d8 --- /dev/null +++ b/latest/cases/00485/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00485/model-sbml-l3v2.xml b/latest/cases/00485/model-sbml-l3v2.xml new file mode 100644 index 000000000..416fa4f18 --- /dev/null +++ b/latest/cases/00485/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00485/output.heta b/latest/cases/00485/output.heta new file mode 100644 index 000000000..e66c1a113 --- /dev/null +++ b/latest/cases/00485/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a 2D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$7.5$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$2.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre^2^ | +|Area of compartment C |$undeclared$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00485/synopsis.txt b/latest/cases/00485/synopsis.txt new file mode 100644 index 000000000..ad4a9ad86 --- /dev/null +++ b/latest/cases/00485/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a 2D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$7.5$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$2.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre^2^ | +|Area of compartment C |$undeclared$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00486/l2v5/heta-code/output.heta b/latest/cases/00486/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2c3cd8c95 --- /dev/null +++ b/latest/cases/00486/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: length, boundary: true, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/length, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/length, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/length, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 3.5; +k2 @Record 'k2' { } .= 1.5; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00486/l2v5/index.heta b/latest/cases/00486/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00486/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00486/l2v5/json/output.json b/latest/cases/00486/l2v5/json/output.json new file mode 100644 index 000000000..801ae6fbe --- /dev/null +++ b/latest/cases/00486/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "length", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "3.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00486/l3v2/heta-code/output.heta b/latest/cases/00486/l3v2/heta-code/output.heta new file mode 100644 index 000000000..be170e539 --- /dev/null +++ b/latest/cases/00486/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 3.5; +k2 @Const 'k2' { } = 1.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00486/l3v2/index.heta b/latest/cases/00486/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00486/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00486/l3v2/json/output.json b/latest/cases/00486/l3v2/json/output.json new file mode 100644 index 000000000..ec495682d --- /dev/null +++ b/latest/cases/00486/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 3.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00486/model-sbml-l2v5.xml b/latest/cases/00486/model-sbml-l2v5.xml new file mode 100644 index 000000000..9747c3608 --- /dev/null +++ b/latest/cases/00486/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00486/model-sbml-l3v2.xml b/latest/cases/00486/model-sbml-l3v2.xml new file mode 100644 index 000000000..deacd3790 --- /dev/null +++ b/latest/cases/00486/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00486/output.heta b/latest/cases/00486/output.heta new file mode 100644 index 000000000..4ed1927e5 --- /dev/null +++ b/latest/cases/00486/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a 1D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$3.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$1.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 3.5; +k2 @Const 'k2' { } = 1.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00486/synopsis.txt b/latest/cases/00486/synopsis.txt new file mode 100644 index 000000000..ff2ac72b3 --- /dev/null +++ b/latest/cases/00486/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a 1D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$3.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$1.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre | +|Length of compartment C |$1$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00487/l2v5/heta-code/output.heta b/latest/cases/00487/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2c3cd8c95 --- /dev/null +++ b/latest/cases/00487/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: length, boundary: true, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/length, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/length, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/length, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 3.5; +k2 @Record 'k2' { } .= 1.5; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00487/l2v5/index.heta b/latest/cases/00487/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00487/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00487/l2v5/json/output.json b/latest/cases/00487/l2v5/json/output.json new file mode 100644 index 000000000..801ae6fbe --- /dev/null +++ b/latest/cases/00487/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "length", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "3.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00487/l3v2/heta-code/output.heta b/latest/cases/00487/l3v2/heta-code/output.heta new file mode 100644 index 000000000..be170e539 --- /dev/null +++ b/latest/cases/00487/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 3.5; +k2 @Const 'k2' { } = 1.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00487/l3v2/index.heta b/latest/cases/00487/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00487/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00487/l3v2/json/output.json b/latest/cases/00487/l3v2/json/output.json new file mode 100644 index 000000000..ec495682d --- /dev/null +++ b/latest/cases/00487/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 3.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00487/model-sbml-l2v5.xml b/latest/cases/00487/model-sbml-l2v5.xml new file mode 100644 index 000000000..241a04037 --- /dev/null +++ b/latest/cases/00487/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00487/model-sbml-l3v2.xml b/latest/cases/00487/model-sbml-l3v2.xml new file mode 100644 index 000000000..6b7b7f39d --- /dev/null +++ b/latest/cases/00487/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00487/output.heta b/latest/cases/00487/output.heta new file mode 100644 index 000000000..9344a995e --- /dev/null +++ b/latest/cases/00487/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a 1D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$3.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$1.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre | +|Length of compartment C |$3.5$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 3.5; +k2 @Const 'k2' { } = 1.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00487/synopsis.txt b/latest/cases/00487/synopsis.txt new file mode 100644 index 000000000..b1bf4da9a --- /dev/null +++ b/latest/cases/00487/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a 1D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$3.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$1.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre | +|Length of compartment C |$3.5$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00488/l2v5/heta-code/output.heta b/latest/cases/00488/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2c3cd8c95 --- /dev/null +++ b/latest/cases/00488/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: length, boundary: true, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/length, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/length, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/length, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 3.5; +k2 @Record 'k2' { } .= 1.5; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00488/l2v5/index.heta b/latest/cases/00488/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00488/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00488/l2v5/json/output.json b/latest/cases/00488/l2v5/json/output.json new file mode 100644 index 000000000..801ae6fbe --- /dev/null +++ b/latest/cases/00488/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "length", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "3.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00488/l3v2/heta-code/output.heta b/latest/cases/00488/l3v2/heta-code/output.heta new file mode 100644 index 000000000..be170e539 --- /dev/null +++ b/latest/cases/00488/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 3.5; +k2 @Const 'k2' { } = 1.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00488/l3v2/index.heta b/latest/cases/00488/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00488/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00488/l3v2/json/output.json b/latest/cases/00488/l3v2/json/output.json new file mode 100644 index 000000000..ec495682d --- /dev/null +++ b/latest/cases/00488/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 3.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00488/model-sbml-l2v5.xml b/latest/cases/00488/model-sbml-l2v5.xml new file mode 100644 index 000000000..b1c018a6c --- /dev/null +++ b/latest/cases/00488/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00488/model-sbml-l3v2.xml b/latest/cases/00488/model-sbml-l3v2.xml new file mode 100644 index 000000000..ba7d4d648 --- /dev/null +++ b/latest/cases/00488/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00488/output.heta b/latest/cases/00488/output.heta new file mode 100644 index 000000000..bfc128bc1 --- /dev/null +++ b/latest/cases/00488/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a 1D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$3.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$1.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre | +|Length of compartment C |$undeclared$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 3.5; +k2 @Const 'k2' { } = 1.5; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00488/synopsis.txt b/latest/cases/00488/synopsis.txt new file mode 100644 index 000000000..21c298a27 --- /dev/null +++ b/latest/cases/00488/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a 1D compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$3.5$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$1.5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |metre | +|Length of compartment C |$undeclared$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00489/l2v5/heta-code/output.heta b/latest/cases/00489/l2v5/heta-code/output.heta new file mode 100644 index 000000000..180fa43c1 --- /dev/null +++ b/latest/cases/00489/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: C, isAmount: true, } .= 2 * p1; +S2 @Species 'S2' { units: substance, compartment: C, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: substance, compartment: C, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.00125; + diff --git a/latest/cases/00489/l2v5/index.heta b/latest/cases/00489/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00489/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00489/l2v5/json/output.json b/latest/cases/00489/l2v5/json/output.json new file mode 100644 index 000000000..778c735ae --- /dev/null +++ b/latest/cases/00489/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.02" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.00125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00489/l3v2/heta-code/output.heta b/latest/cases/00489/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a5c11f9ca --- /dev/null +++ b/latest/cases/00489/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 2 * p1; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00489/l3v2/index.heta b/latest/cases/00489/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00489/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00489/l3v2/json/output.json b/latest/cases/00489/l3v2/json/output.json new file mode 100644 index 000000000..31980624f --- /dev/null +++ b/latest/cases/00489/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.02" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.00125 + } +] \ No newline at end of file diff --git a/latest/cases/00489/model-sbml-l2v5.xml b/latest/cases/00489/model-sbml-l2v5.xml new file mode 100644 index 000000000..04b8aaa69 --- /dev/null +++ b/latest/cases/00489/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00489/model-sbml-l3v2.xml b/latest/cases/00489/model-sbml-l3v2.xml new file mode 100644 index 000000000..c835eb540 --- /dev/null +++ b/latest/cases/00489/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00489/output.heta b/latest/cases/00489/output.heta new file mode 100644 index 000000000..72c449915 --- /dev/null +++ b/latest/cases/00489/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a 0D compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, 0D-Compartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole |] + +In this example, the compartment has its spatialDimensions attribute set to +zero, i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 2 * p1; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00489/synopsis.txt b/latest/cases/00489/synopsis.txt new file mode 100644 index 000000000..7da16c065 --- /dev/null +++ b/latest/cases/00489/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in a 0D compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, 0D-Compartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole |] + +In this example, the compartment has its spatialDimensions attribute set to +zero, i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00490/l2v5/heta-code/output.heta b/latest/cases/00490/l2v5/heta-code/output.heta new file mode 100644 index 000000000..823b0aee0 --- /dev/null +++ b/latest/cases/00490/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: C, isAmount: true, } .= 2 * p1; +S2 @Species 'S2' { units: substance, compartment: C, isAmount: true, } .= 2e-4; +S3 @Species 'S3' { units: substance, compartment: C, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 1.25e-5; + diff --git a/latest/cases/00490/l2v5/index.heta b/latest/cases/00490/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00490/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00490/l2v5/json/output.json b/latest/cases/00490/l2v5/json/output.json new file mode 100644 index 000000000..13b54728a --- /dev/null +++ b/latest/cases/00490/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00490/l3v2/heta-code/output.heta b/latest/cases/00490/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5401ed8e3 --- /dev/null +++ b/latest/cases/00490/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 2 * p1; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2e-4; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00490/l3v2/index.heta b/latest/cases/00490/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00490/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00490/l3v2/json/output.json b/latest/cases/00490/l3v2/json/output.json new file mode 100644 index 000000000..03cab6351 --- /dev/null +++ b/latest/cases/00490/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0000125 + } +] \ No newline at end of file diff --git a/latest/cases/00490/model-sbml-l2v5.xml b/latest/cases/00490/model-sbml-l2v5.xml new file mode 100644 index 000000000..40f00a2c1 --- /dev/null +++ b/latest/cases/00490/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00490/model-sbml-l3v2.xml b/latest/cases/00490/model-sbml-l3v2.xml new file mode 100644 index 000000000..fbbc711d9 --- /dev/null +++ b/latest/cases/00490/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00490/output.heta b/latest/cases/00490/output.heta new file mode 100644 index 000000000..59cddcd67 --- /dev/null +++ b/latest/cases/00490/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a 0D compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole |] + +In this example, the compartment has its spatialDimensions attribute set to +zero, i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 2 * p1; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2e-4; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00490/synopsis.txt b/latest/cases/00490/synopsis.txt new file mode 100644 index 000000000..0e577896a --- /dev/null +++ b/latest/cases/00490/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in a 0D compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole |] + +In this example, the compartment has its spatialDimensions attribute set to +zero, i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00491/l2v5/heta-code/output.heta b/latest/cases/00491/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b9c6f99cf --- /dev/null +++ b/latest/cases/00491/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: substance, compartment: C, isAmount: true, } .= 2 * p1; +S2 @Species 'S2' { units: substance, compartment: C, isAmount: true, } .= 0.2; +S3 @Species 'S3' { units: substance, compartment: C, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.0125; + diff --git a/latest/cases/00491/l2v5/index.heta b/latest/cases/00491/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00491/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00491/l2v5/json/output.json b/latest/cases/00491/l2v5/json/output.json new file mode 100644 index 000000000..8b96fa950 --- /dev/null +++ b/latest/cases/00491/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.0125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00491/l3v2/heta-code/output.heta b/latest/cases/00491/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c295c2877 --- /dev/null +++ b/latest/cases/00491/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 2 * p1; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 0.2; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0125; + diff --git a/latest/cases/00491/l3v2/index.heta b/latest/cases/00491/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00491/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00491/l3v2/json/output.json b/latest/cases/00491/l3v2/json/output.json new file mode 100644 index 000000000..363772c13 --- /dev/null +++ b/latest/cases/00491/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0125 + } +] \ No newline at end of file diff --git a/latest/cases/00491/model-sbml-l2v5.xml b/latest/cases/00491/model-sbml-l2v5.xml new file mode 100644 index 000000000..2b1070a4d --- /dev/null +++ b/latest/cases/00491/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00491/model-sbml-l3v2.xml b/latest/cases/00491/model-sbml-l3v2.xml new file mode 100644 index 000000000..0ceba19fa --- /dev/null +++ b/latest/cases/00491/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00491/output.heta b/latest/cases/00491/output.heta new file mode 100644 index 000000000..86709f9c4 --- /dev/null +++ b/latest/cases/00491/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a 0D compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, 0D-Compartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 $ | +| S3 -> S1 + S2 | $k2 * S3$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-2$ |mole |] + +In this example, the compartment has its spatialDimensions attribute set to +zero, i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { boundary: true, } .= 0; + +S1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 2 * p1; +S2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 0.2; +S3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0125; + diff --git a/latest/cases/00491/synopsis.txt b/latest/cases/00491/synopsis.txt new file mode 100644 index 000000000..42a61092a --- /dev/null +++ b/latest/cases/00491/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in a 0D compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, 0D-Compartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is +0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 $ | +| S3 -> S1 + S2 | $k2 * S3$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-2$ |mole |] + +In this example, the compartment has its spatialDimensions attribute set to +zero, i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00492/l2v5/heta-code/output.heta b/latest/cases/00492/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bbd467fac --- /dev/null +++ b/latest/cases/00492/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= k2 / 9; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00492/l2v5/index.heta b/latest/cases/00492/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00492/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00492/l2v5/json/output.json b/latest/cases/00492/l2v5/json/output.json new file mode 100644 index 000000000..9651004c2 --- /dev/null +++ b/latest/cases/00492/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 / 9" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00492/l3v2/heta-code/output.heta b/latest/cases/00492/l3v2/heta-code/output.heta new file mode 100644 index 000000000..586c2be81 --- /dev/null +++ b/latest/cases/00492/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 / 9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00492/l3v2/index.heta b/latest/cases/00492/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00492/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00492/l3v2/json/output.json b/latest/cases/00492/l3v2/json/output.json new file mode 100644 index 000000000..cd81fb6d6 --- /dev/null +++ b/latest/cases/00492/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 / 9" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00492/model-sbml-l2v5.xml b/latest/cases/00492/model-sbml-l2v5.xml new file mode 100644 index 000000000..32bb35d73 --- /dev/null +++ b/latest/cases/00492/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k2 + 9 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00492/model-sbml-l3v2.xml b/latest/cases/00492/model-sbml-l3v2.xml new file mode 100644 index 000000000..895c14f3d --- /dev/null +++ b/latest/cases/00492/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + 9 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00492/output.heta b/latest/cases/00492/output.heta new file mode 100644 index 000000000..09f38d650 --- /dev/null +++ b/latest/cases/00492/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 9$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5.4$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 / 9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00492/synopsis.txt b/latest/cases/00492/synopsis.txt new file mode 100644 index 000000000..838fc5cf7 --- /dev/null +++ b/latest/cases/00492/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 9$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5.4$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00493/l2v5/heta-code/output.heta b/latest/cases/00493/l2v5/heta-code/output.heta new file mode 100644 index 000000000..75bfd3475 --- /dev/null +++ b/latest/cases/00493/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= k2 / 10; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00493/l2v5/index.heta b/latest/cases/00493/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00493/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00493/l2v5/json/output.json b/latest/cases/00493/l2v5/json/output.json new file mode 100644 index 000000000..01dab0ac1 --- /dev/null +++ b/latest/cases/00493/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 / 10" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00493/l3v2/heta-code/output.heta b/latest/cases/00493/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c27a11b07 --- /dev/null +++ b/latest/cases/00493/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 / 10; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00493/l3v2/index.heta b/latest/cases/00493/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00493/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00493/l3v2/json/output.json b/latest/cases/00493/l3v2/json/output.json new file mode 100644 index 000000000..f187a677c --- /dev/null +++ b/latest/cases/00493/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 / 10" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00493/model-sbml-l2v5.xml b/latest/cases/00493/model-sbml-l2v5.xml new file mode 100644 index 000000000..67fea23ed --- /dev/null +++ b/latest/cases/00493/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k2 + 10 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00493/model-sbml-l3v2.xml b/latest/cases/00493/model-sbml-l3v2.xml new file mode 100644 index 000000000..39690315c --- /dev/null +++ b/latest/cases/00493/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + 10 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00493/output.heta b/latest/cases/00493/output.heta new file mode 100644 index 000000000..916acfd4b --- /dev/null +++ b/latest/cases/00493/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 10$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 / 10; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00493/synopsis.txt b/latest/cases/00493/synopsis.txt new file mode 100644 index 000000000..888464b7b --- /dev/null +++ b/latest/cases/00493/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 10$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00494/l2v5/heta-code/output.heta b/latest/cases/00494/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bbd467fac --- /dev/null +++ b/latest/cases/00494/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= k2 / 9; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00494/l2v5/index.heta b/latest/cases/00494/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00494/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00494/l2v5/json/output.json b/latest/cases/00494/l2v5/json/output.json new file mode 100644 index 000000000..9651004c2 --- /dev/null +++ b/latest/cases/00494/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 / 9" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00494/l3v2/heta-code/output.heta b/latest/cases/00494/l3v2/heta-code/output.heta new file mode 100644 index 000000000..586c2be81 --- /dev/null +++ b/latest/cases/00494/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 / 9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00494/l3v2/index.heta b/latest/cases/00494/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00494/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00494/l3v2/json/output.json b/latest/cases/00494/l3v2/json/output.json new file mode 100644 index 000000000..cd81fb6d6 --- /dev/null +++ b/latest/cases/00494/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 / 9" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00494/model-sbml-l2v5.xml b/latest/cases/00494/model-sbml-l2v5.xml new file mode 100644 index 000000000..3b14f8d00 --- /dev/null +++ b/latest/cases/00494/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k2 + 9 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00494/model-sbml-l3v2.xml b/latest/cases/00494/model-sbml-l3v2.xml new file mode 100644 index 000000000..c06d4499e --- /dev/null +++ b/latest/cases/00494/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + 9 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00494/output.heta b/latest/cases/00494/output.heta new file mode 100644 index 000000000..5f1d7c687 --- /dev/null +++ b/latest/cases/00494/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 9$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 / 9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00494/synopsis.txt b/latest/cases/00494/synopsis.txt new file mode 100644 index 000000000..5777e992c --- /dev/null +++ b/latest/cases/00494/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 9$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00495/l2v5/heta-code/output.heta b/latest/cases/00495/l2v5/heta-code/output.heta new file mode 100644 index 000000000..10c4affef --- /dev/null +++ b/latest/cases/00495/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.25; + diff --git a/latest/cases/00495/l2v5/index.heta b/latest/cases/00495/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00495/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00495/l2v5/json/output.json b/latest/cases/00495/l2v5/json/output.json new file mode 100644 index 000000000..3881809d9 --- /dev/null +++ b/latest/cases/00495/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00495/l3v2/heta-code/output.heta b/latest/cases/00495/l3v2/heta-code/output.heta new file mode 100644 index 000000000..edbb7d0b5 --- /dev/null +++ b/latest/cases/00495/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00495/l3v2/index.heta b/latest/cases/00495/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00495/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00495/l3v2/json/output.json b/latest/cases/00495/l3v2/json/output.json new file mode 100644 index 000000000..7ba23f1ea --- /dev/null +++ b/latest/cases/00495/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00495/model-sbml-l2v5.xml b/latest/cases/00495/model-sbml-l2v5.xml new file mode 100644 index 000000000..13cc1cb32 --- /dev/null +++ b/latest/cases/00495/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00495/model-sbml-l3v2.xml b/latest/cases/00495/model-sbml-l3v2.xml new file mode 100644 index 000000000..0a366ec5b --- /dev/null +++ b/latest/cases/00495/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00495/output.heta b/latest/cases/00495/output.heta new file mode 100644 index 000000000..ab4e2aa6f --- /dev/null +++ b/latest/cases/00495/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$0.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00495/synopsis.txt b/latest/cases/00495/synopsis.txt new file mode 100644 index 000000000..a4a5e76e8 --- /dev/null +++ b/latest/cases/00495/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$0.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00496/l2v5/heta-code/output.heta b/latest/cases/00496/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e4a762b12 --- /dev/null +++ b/latest/cases/00496/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.25; + diff --git a/latest/cases/00496/l2v5/index.heta b/latest/cases/00496/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00496/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00496/l2v5/json/output.json b/latest/cases/00496/l2v5/json/output.json new file mode 100644 index 000000000..b403e7260 --- /dev/null +++ b/latest/cases/00496/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00496/l3v2/heta-code/output.heta b/latest/cases/00496/l3v2/heta-code/output.heta new file mode 100644 index 000000000..29a39d64e --- /dev/null +++ b/latest/cases/00496/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00496/l3v2/index.heta b/latest/cases/00496/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00496/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00496/l3v2/json/output.json b/latest/cases/00496/l3v2/json/output.json new file mode 100644 index 000000000..6439c6892 --- /dev/null +++ b/latest/cases/00496/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00496/model-sbml-l2v5.xml b/latest/cases/00496/model-sbml-l2v5.xml new file mode 100644 index 000000000..c9892b591 --- /dev/null +++ b/latest/cases/00496/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00496/model-sbml-l3v2.xml b/latest/cases/00496/model-sbml-l3v2.xml new file mode 100644 index 000000000..bd1125226 --- /dev/null +++ b/latest/cases/00496/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00496/output.heta b/latest/cases/00496/output.heta new file mode 100644 index 000000000..cf072bbaf --- /dev/null +++ b/latest/cases/00496/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$3.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00496/synopsis.txt b/latest/cases/00496/synopsis.txt new file mode 100644 index 000000000..10591ca91 --- /dev/null +++ b/latest/cases/00496/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$3.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00497/l2v5/heta-code/output.heta b/latest/cases/00497/l2v5/heta-code/output.heta new file mode 100644 index 000000000..50f5bccc5 --- /dev/null +++ b/latest/cases/00497/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.25; + diff --git a/latest/cases/00497/l2v5/index.heta b/latest/cases/00497/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00497/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00497/l2v5/json/output.json b/latest/cases/00497/l2v5/json/output.json new file mode 100644 index 000000000..9d6b25e8f --- /dev/null +++ b/latest/cases/00497/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00497/l3v2/heta-code/output.heta b/latest/cases/00497/l3v2/heta-code/output.heta new file mode 100644 index 000000000..910d3f96d --- /dev/null +++ b/latest/cases/00497/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00497/l3v2/index.heta b/latest/cases/00497/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00497/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00497/l3v2/json/output.json b/latest/cases/00497/l3v2/json/output.json new file mode 100644 index 000000000..3009a9bb6 --- /dev/null +++ b/latest/cases/00497/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00497/model-sbml-l2v5.xml b/latest/cases/00497/model-sbml-l2v5.xml new file mode 100644 index 000000000..48df284cb --- /dev/null +++ b/latest/cases/00497/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00497/model-sbml-l3v2.xml b/latest/cases/00497/model-sbml-l3v2.xml new file mode 100644 index 000000000..42ca3c860 --- /dev/null +++ b/latest/cases/00497/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00497/output.heta b/latest/cases/00497/output.heta new file mode 100644 index 000000000..564255a31 --- /dev/null +++ b/latest/cases/00497/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00497/synopsis.txt b/latest/cases/00497/synopsis.txt new file mode 100644 index 000000000..7c397e6f9 --- /dev/null +++ b/latest/cases/00497/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00498/l2v5/heta-code/output.heta b/latest/cases/00498/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0eb94a4a9 --- /dev/null +++ b/latest/cases/00498/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00498/l2v5/index.heta b/latest/cases/00498/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00498/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00498/l2v5/json/output.json b/latest/cases/00498/l2v5/json/output.json new file mode 100644 index 000000000..8e07a0e3b --- /dev/null +++ b/latest/cases/00498/l2v5/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00498/l3v2/heta-code/output.heta b/latest/cases/00498/l3v2/heta-code/output.heta new file mode 100644 index 000000000..37c2ed1f0 --- /dev/null +++ b/latest/cases/00498/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00498/l3v2/index.heta b/latest/cases/00498/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00498/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00498/l3v2/json/output.json b/latest/cases/00498/l3v2/json/output.json new file mode 100644 index 000000000..e674ef61d --- /dev/null +++ b/latest/cases/00498/l3v2/json/output.json @@ -0,0 +1,68 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00498/model-sbml-l2v5.xml b/latest/cases/00498/model-sbml-l2v5.xml new file mode 100644 index 000000000..a44d6cee7 --- /dev/null +++ b/latest/cases/00498/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00498/model-sbml-l3v2.xml b/latest/cases/00498/model-sbml-l3v2.xml new file mode 100644 index 000000000..bd82d2955 --- /dev/null +++ b/latest/cases/00498/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00498/output.heta b/latest/cases/00498/output.heta new file mode 100644 index 000000000..928c4e7b8 --- /dev/null +++ b/latest/cases/00498/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. Species S1 is +labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00498/synopsis.txt b/latest/cases/00498/synopsis.txt new file mode 100644 index 000000000..c078f15f8 --- /dev/null +++ b/latest/cases/00498/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. Species S1 is +labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00499/l2v5/heta-code/output.heta b/latest/cases/00499/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0eb94a4a9 --- /dev/null +++ b/latest/cases/00499/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00499/l2v5/index.heta b/latest/cases/00499/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00499/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00499/l2v5/json/output.json b/latest/cases/00499/l2v5/json/output.json new file mode 100644 index 000000000..8e07a0e3b --- /dev/null +++ b/latest/cases/00499/l2v5/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00499/l3v2/heta-code/output.heta b/latest/cases/00499/l3v2/heta-code/output.heta new file mode 100644 index 000000000..37c2ed1f0 --- /dev/null +++ b/latest/cases/00499/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00499/l3v2/index.heta b/latest/cases/00499/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00499/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00499/l3v2/json/output.json b/latest/cases/00499/l3v2/json/output.json new file mode 100644 index 000000000..e674ef61d --- /dev/null +++ b/latest/cases/00499/l3v2/json/output.json @@ -0,0 +1,68 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00499/model-sbml-l2v5.xml b/latest/cases/00499/model-sbml-l2v5.xml new file mode 100644 index 000000000..ac14f6476 --- /dev/null +++ b/latest/cases/00499/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00499/model-sbml-l3v2.xml b/latest/cases/00499/model-sbml-l3v2.xml new file mode 100644 index 000000000..de2fd2478 --- /dev/null +++ b/latest/cases/00499/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00499/output.heta b/latest/cases/00499/output.heta new file mode 100644 index 000000000..c8146b200 --- /dev/null +++ b/latest/cases/00499/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. Species S1 is +labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$30$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00499/synopsis.txt b/latest/cases/00499/synopsis.txt new file mode 100644 index 000000000..475decdeb --- /dev/null +++ b/latest/cases/00499/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. Species S1 is +labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$30$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00500/l2v5/heta-code/output.heta b/latest/cases/00500/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0eb94a4a9 --- /dev/null +++ b/latest/cases/00500/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00500/l2v5/index.heta b/latest/cases/00500/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00500/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00500/l2v5/json/output.json b/latest/cases/00500/l2v5/json/output.json new file mode 100644 index 000000000..8e07a0e3b --- /dev/null +++ b/latest/cases/00500/l2v5/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00500/l3v2/heta-code/output.heta b/latest/cases/00500/l3v2/heta-code/output.heta new file mode 100644 index 000000000..37c2ed1f0 --- /dev/null +++ b/latest/cases/00500/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00500/l3v2/index.heta b/latest/cases/00500/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00500/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00500/l3v2/json/output.json b/latest/cases/00500/l3v2/json/output.json new file mode 100644 index 000000000..e674ef61d --- /dev/null +++ b/latest/cases/00500/l3v2/json/output.json @@ -0,0 +1,68 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00500/model-sbml-l2v5.xml b/latest/cases/00500/model-sbml-l2v5.xml new file mode 100644 index 000000000..c212c1863 --- /dev/null +++ b/latest/cases/00500/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00500/model-sbml-l3v2.xml b/latest/cases/00500/model-sbml-l3v2.xml new file mode 100644 index 000000000..9ee414034 --- /dev/null +++ b/latest/cases/00500/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00500/output.heta b/latest/cases/00500/output.heta new file mode 100644 index 000000000..574405d87 --- /dev/null +++ b/latest/cases/00500/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. Species S1 is +labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.125$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00500/synopsis.txt b/latest/cases/00500/synopsis.txt new file mode 100644 index 000000000..9355037d1 --- /dev/null +++ b/latest/cases/00500/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. Species S1 is +labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.125$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00501/l2v5/heta-code/output.heta b/latest/cases/00501/l2v5/heta-code/output.heta new file mode 100644 index 000000000..dd55cf4b7 --- /dev/null +++ b/latest/cases/00501/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 1.25e-4; + diff --git a/latest/cases/00501/l2v5/index.heta b/latest/cases/00501/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00501/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00501/l2v5/json/output.json b/latest/cases/00501/l2v5/json/output.json new file mode 100644 index 000000000..d79e17445 --- /dev/null +++ b/latest/cases/00501/l2v5/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-4" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00501/l3v2/heta-code/output.heta b/latest/cases/00501/l3v2/heta-code/output.heta new file mode 100644 index 000000000..654e6d08c --- /dev/null +++ b/latest/cases/00501/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.000125; + diff --git a/latest/cases/00501/l3v2/index.heta b/latest/cases/00501/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00501/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00501/l3v2/json/output.json b/latest/cases/00501/l3v2/json/output.json new file mode 100644 index 000000000..80d95f662 --- /dev/null +++ b/latest/cases/00501/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.000125 + } +] \ No newline at end of file diff --git a/latest/cases/00501/model-sbml-l2v5.xml b/latest/cases/00501/model-sbml-l2v5.xml new file mode 100644 index 000000000..2c5e55581 --- /dev/null +++ b/latest/cases/00501/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00501/model-sbml-l3v2.xml b/latest/cases/00501/model-sbml-l3v2.xml new file mode 100644 index 000000000..704852aa5 --- /dev/null +++ b/latest/cases/00501/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00501/output.heta b/latest/cases/00501/output.heta new file mode 100644 index 000000000..a98c9e762 --- /dev/null +++ b/latest/cases/00501/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Species S1 is labeled +as an SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-4$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.000125; + diff --git a/latest/cases/00501/synopsis.txt b/latest/cases/00501/synopsis.txt new file mode 100644 index 000000000..fd80c5f39 --- /dev/null +++ b/latest/cases/00501/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Species S1 is labeled +as an SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-4$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00502/l2v5/heta-code/output.heta b/latest/cases/00502/l2v5/heta-code/output.heta new file mode 100644 index 000000000..afbf166ce --- /dev/null +++ b/latest/cases/00502/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.00125; + diff --git a/latest/cases/00502/l2v5/index.heta b/latest/cases/00502/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00502/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00502/l2v5/json/output.json b/latest/cases/00502/l2v5/json/output.json new file mode 100644 index 000000000..bcbfad7ef --- /dev/null +++ b/latest/cases/00502/l2v5/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.00125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00502/l3v2/heta-code/output.heta b/latest/cases/00502/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e6d68790b --- /dev/null +++ b/latest/cases/00502/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00502/l3v2/index.heta b/latest/cases/00502/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00502/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00502/l3v2/json/output.json b/latest/cases/00502/l3v2/json/output.json new file mode 100644 index 000000000..7b5c7941b --- /dev/null +++ b/latest/cases/00502/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.00125 + } +] \ No newline at end of file diff --git a/latest/cases/00502/model-sbml-l2v5.xml b/latest/cases/00502/model-sbml-l2v5.xml new file mode 100644 index 000000000..67083ff43 --- /dev/null +++ b/latest/cases/00502/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00502/model-sbml-l3v2.xml b/latest/cases/00502/model-sbml-l3v2.xml new file mode 100644 index 000000000..959739d1a --- /dev/null +++ b/latest/cases/00502/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00502/output.heta b/latest/cases/00502/output.heta new file mode 100644 index 000000000..bfc9d0b5f --- /dev/null +++ b/latest/cases/00502/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Species S1 is labeled +as an SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00502/synopsis.txt b/latest/cases/00502/synopsis.txt new file mode 100644 index 000000000..fa6d86643 --- /dev/null +++ b/latest/cases/00502/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Species S1 is labeled +as an SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00503/l2v5/heta-code/output.heta b/latest/cases/00503/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7aa175e9c --- /dev/null +++ b/latest/cases/00503/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 1.25e-5; + diff --git a/latest/cases/00503/l2v5/index.heta b/latest/cases/00503/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00503/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00503/l2v5/json/output.json b/latest/cases/00503/l2v5/json/output.json new file mode 100644 index 000000000..29a404ce6 --- /dev/null +++ b/latest/cases/00503/l2v5/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00503/l3v2/heta-code/output.heta b/latest/cases/00503/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d22f822d9 --- /dev/null +++ b/latest/cases/00503/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00503/l3v2/index.heta b/latest/cases/00503/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00503/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00503/l3v2/json/output.json b/latest/cases/00503/l3v2/json/output.json new file mode 100644 index 000000000..1e0b82cf6 --- /dev/null +++ b/latest/cases/00503/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0000125 + } +] \ No newline at end of file diff --git a/latest/cases/00503/model-sbml-l2v5.xml b/latest/cases/00503/model-sbml-l2v5.xml new file mode 100644 index 000000000..d3e8132d4 --- /dev/null +++ b/latest/cases/00503/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00503/model-sbml-l3v2.xml b/latest/cases/00503/model-sbml-l3v2.xml new file mode 100644 index 000000000..4f95dccb2 --- /dev/null +++ b/latest/cases/00503/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00503/output.heta b/latest/cases/00503/output.heta new file mode 100644 index 000000000..0a428e69b --- /dev/null +++ b/latest/cases/00503/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Species S1 is labeled +as an SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00503/synopsis.txt b/latest/cases/00503/synopsis.txt new file mode 100644 index 000000000..deb1523ca --- /dev/null +++ b/latest/cases/00503/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. Species S1 is labeled +as an SBML boundary species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00504/l2v5/heta-code/output.heta b/latest/cases/00504/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b329bd19a --- /dev/null +++ b/latest/cases/00504/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.025 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.1 / C; +S4 @Species 'S4' { boundary: true, compartment: C, } .= 2 * p1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, }; +reaction1 := C * k1 * S1 * S4; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.05; + diff --git a/latest/cases/00504/l2v5/index.heta b/latest/cases/00504/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00504/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00504/l2v5/json/output.json b/latest/cases/00504/l2v5/json/output.json new file mode 100644 index 000000000..5f2fc899b --- /dev/null +++ b/latest/cases/00504/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.025 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.05" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00504/l3v2/heta-code/output.heta b/latest/cases/00504/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5f01d2717 --- /dev/null +++ b/latest/cases/00504/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.025 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, }; +reaction1 := C * k1 * S1 * S4; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.05; + diff --git a/latest/cases/00504/l3v2/index.heta b/latest/cases/00504/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00504/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00504/l3v2/json/output.json b/latest/cases/00504/l3v2/json/output.json new file mode 100644 index 000000000..8172d2ac7 --- /dev/null +++ b/latest/cases/00504/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.025 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.05 + } +] \ No newline at end of file diff --git a/latest/cases/00504/model-sbml-l2v5.xml b/latest/cases/00504/model-sbml-l2v5.xml new file mode 100644 index 000000000..87479d21c --- /dev/null +++ b/latest/cases/00504/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S4 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00504/model-sbml-l3v2.xml b/latest/cases/00504/model-sbml-l3v2.xml new file mode 100644 index 000000000..fecb130bb --- /dev/null +++ b/latest/cases/00504/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S4 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00504/output.heta b/latest/cases/00504/output.heta new file mode 100644 index 000000000..dbe9f1d5d --- /dev/null +++ b/latest/cases/00504/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled +as a constant species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S4 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S4 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S4 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Initial amount of S4 |$undeclared$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$5 \x 10^-2$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.025 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, }; +reaction1 := C * k1 * S1 * S4; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.05; + diff --git a/latest/cases/00504/synopsis.txt b/latest/cases/00504/synopsis.txt new file mode 100644 index 000000000..b968d93e6 --- /dev/null +++ b/latest/cases/00504/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled +as a constant species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S4 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S4 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S4 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Initial amount of S4 |$undeclared$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$5 \x 10^-2$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00505/l2v5/heta-code/output.heta b/latest/cases/00505/l2v5/heta-code/output.heta new file mode 100644 index 000000000..57e30b35f --- /dev/null +++ b/latest/cases/00505/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2.5e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001 / C; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: C, } .= 2 * p1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, }; +reaction1 := C * k1 * S1 * S4; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 5e-4; + diff --git a/latest/cases/00505/l2v5/index.heta b/latest/cases/00505/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00505/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00505/l2v5/json/output.json b/latest/cases/00505/l2v5/json/output.json new file mode 100644 index 000000000..05a50b61f --- /dev/null +++ b/latest/cases/00505/l2v5/json/output.json @@ -0,0 +1,156 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "5e-4" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00505/l3v2/heta-code/output.heta b/latest/cases/00505/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0d8cf845d --- /dev/null +++ b/latest/cases/00505/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, }; +reaction1 := C * k1 * S1 * S4; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0005; + diff --git a/latest/cases/00505/l3v2/index.heta b/latest/cases/00505/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00505/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00505/l3v2/json/output.json b/latest/cases/00505/l3v2/json/output.json new file mode 100644 index 000000000..1b1a5e40d --- /dev/null +++ b/latest/cases/00505/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0005 + } +] \ No newline at end of file diff --git a/latest/cases/00505/model-sbml-l2v5.xml b/latest/cases/00505/model-sbml-l2v5.xml new file mode 100644 index 000000000..0806d563f --- /dev/null +++ b/latest/cases/00505/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S4 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00505/model-sbml-l3v2.xml b/latest/cases/00505/model-sbml-l3v2.xml new file mode 100644 index 000000000..47b68ef67 --- /dev/null +++ b/latest/cases/00505/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S4 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00505/output.heta b/latest/cases/00505/output.heta new file mode 100644 index 000000000..65bbc9ef2 --- /dev/null +++ b/latest/cases/00505/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled +as a constant species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S4 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S4 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S4 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$5 \x 10^-4$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, }; +reaction1 := C * k1 * S1 * S4; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0005; + diff --git a/latest/cases/00505/synopsis.txt b/latest/cases/00505/synopsis.txt new file mode 100644 index 000000000..69bee79a2 --- /dev/null +++ b/latest/cases/00505/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled +as a constant species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S4 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S4 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S4 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$5 \x 10^-4$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00506/l2v5/heta-code/output.heta b/latest/cases/00506/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2a2c3d0e6 --- /dev/null +++ b/latest/cases/00506/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.0025 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01 / C; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: C, } .= 2 * p1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, }; +reaction1 := C * k1 * S1 * S4; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.005; + diff --git a/latest/cases/00506/l2v5/index.heta b/latest/cases/00506/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00506/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00506/l2v5/json/output.json b/latest/cases/00506/l2v5/json/output.json new file mode 100644 index 000000000..d2b68fcea --- /dev/null +++ b/latest/cases/00506/l2v5/json/output.json @@ -0,0 +1,156 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0025 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.005" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00506/l3v2/heta-code/output.heta b/latest/cases/00506/l3v2/heta-code/output.heta new file mode 100644 index 000000000..86a4d10eb --- /dev/null +++ b/latest/cases/00506/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0025 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, }; +reaction1 := C * k1 * S1 * S4; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.005; + diff --git a/latest/cases/00506/l3v2/index.heta b/latest/cases/00506/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00506/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00506/l3v2/json/output.json b/latest/cases/00506/l3v2/json/output.json new file mode 100644 index 000000000..4c3552755 --- /dev/null +++ b/latest/cases/00506/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0025 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.005 + } +] \ No newline at end of file diff --git a/latest/cases/00506/model-sbml-l2v5.xml b/latest/cases/00506/model-sbml-l2v5.xml new file mode 100644 index 000000000..82e4113fe --- /dev/null +++ b/latest/cases/00506/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S4 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00506/model-sbml-l3v2.xml b/latest/cases/00506/model-sbml-l3v2.xml new file mode 100644 index 000000000..869800620 --- /dev/null +++ b/latest/cases/00506/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S4 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00506/output.heta b/latest/cases/00506/output.heta new file mode 100644 index 000000000..58169d841 --- /dev/null +++ b/latest/cases/00506/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled +as a constant species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S4 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S4 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S4 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Initial amount of S4 |$5.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$5 \x 10^-3$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0025 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, }; +reaction1 := C * k1 * S1 * S4; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.005; + diff --git a/latest/cases/00506/synopsis.txt b/latest/cases/00506/synopsis.txt new file mode 100644 index 000000000..5411b7349 --- /dev/null +++ b/latest/cases/00506/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled +as a constant species. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S4 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S4 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S4 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Initial amount of S4 |$5.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$5 \x 10^-3$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00507/l2v5/heta-code/output.heta b/latest/cases/00507/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8f3085604 --- /dev/null +++ b/latest/cases/00507/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k2 * S1 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2.7; + diff --git a/latest/cases/00507/l2v5/index.heta b/latest/cases/00507/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00507/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00507/l2v5/json/output.json b/latest/cases/00507/l2v5/json/output.json new file mode 100644 index 000000000..7f02f36af --- /dev/null +++ b/latest/cases/00507/l2v5/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00507/l3v2/heta-code/output.heta b/latest/cases/00507/l3v2/heta-code/output.heta new file mode 100644 index 000000000..08babebd5 --- /dev/null +++ b/latest/cases/00507/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k2 * S1 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.7; + diff --git a/latest/cases/00507/l3v2/index.heta b/latest/cases/00507/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00507/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00507/l3v2/json/output.json b/latest/cases/00507/l3v2/json/output.json new file mode 100644 index 000000000..46e3bd757 --- /dev/null +++ b/latest/cases/00507/l3v2/json/output.json @@ -0,0 +1,83 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.7 + } +] \ No newline at end of file diff --git a/latest/cases/00507/model-sbml-l2v5.xml b/latest/cases/00507/model-sbml-l2v5.xml new file mode 100644 index 000000000..287d08ead --- /dev/null +++ b/latest/cases/00507/model-sbml-l2v5.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S1 + S3 + + + + + + + diff --git a/latest/cases/00507/model-sbml-l3v2.xml b/latest/cases/00507/model-sbml-l3v2.xml new file mode 100644 index 000000000..c05094317 --- /dev/null +++ b/latest/cases/00507/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S1 + S3 + + + + + + + diff --git a/latest/cases/00507/output.heta b/latest/cases/00507/output.heta new file mode 100644 index 000000000..050050bee --- /dev/null +++ b/latest/cases/00507/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled a constant species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S3 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S3 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Initial amount of S3 |$1.125$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$2.7$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k2 * S1 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.7; + diff --git a/latest/cases/00507/synopsis.txt b/latest/cases/00507/synopsis.txt new file mode 100644 index 000000000..c33f785ae --- /dev/null +++ b/latest/cases/00507/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled a constant species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S3 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S3 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Initial amount of S3 |$1.125$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$2.7$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00508/l2v5/heta-code/output.heta b/latest/cases/00508/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8f3085604 --- /dev/null +++ b/latest/cases/00508/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k2 * S1 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2.7; + diff --git a/latest/cases/00508/l2v5/index.heta b/latest/cases/00508/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00508/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00508/l2v5/json/output.json b/latest/cases/00508/l2v5/json/output.json new file mode 100644 index 000000000..7f02f36af --- /dev/null +++ b/latest/cases/00508/l2v5/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00508/l3v2/heta-code/output.heta b/latest/cases/00508/l3v2/heta-code/output.heta new file mode 100644 index 000000000..08babebd5 --- /dev/null +++ b/latest/cases/00508/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k2 * S1 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.7; + diff --git a/latest/cases/00508/l3v2/index.heta b/latest/cases/00508/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00508/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00508/l3v2/json/output.json b/latest/cases/00508/l3v2/json/output.json new file mode 100644 index 000000000..46e3bd757 --- /dev/null +++ b/latest/cases/00508/l3v2/json/output.json @@ -0,0 +1,83 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.7 + } +] \ No newline at end of file diff --git a/latest/cases/00508/model-sbml-l2v5.xml b/latest/cases/00508/model-sbml-l2v5.xml new file mode 100644 index 000000000..90eeb7516 --- /dev/null +++ b/latest/cases/00508/model-sbml-l2v5.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S1 + S3 + + + + + + + diff --git a/latest/cases/00508/model-sbml-l3v2.xml b/latest/cases/00508/model-sbml-l3v2.xml new file mode 100644 index 000000000..a8db581bc --- /dev/null +++ b/latest/cases/00508/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S1 + S3 + + + + + + + diff --git a/latest/cases/00508/output.heta b/latest/cases/00508/output.heta new file mode 100644 index 000000000..ab3e39b2f --- /dev/null +++ b/latest/cases/00508/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled a constant species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S3 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S3 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Initial amount of S3 |$5.7$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$2.7$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k2 * S1 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.7; + diff --git a/latest/cases/00508/synopsis.txt b/latest/cases/00508/synopsis.txt new file mode 100644 index 000000000..5688e1d53 --- /dev/null +++ b/latest/cases/00508/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled a constant species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S3 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S3 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Initial amount of S3 |$5.7$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$2.7$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00509/l2v5/heta-code/output.heta b/latest/cases/00509/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8f3085604 --- /dev/null +++ b/latest/cases/00509/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k2 * S1 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2.7; + diff --git a/latest/cases/00509/l2v5/index.heta b/latest/cases/00509/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00509/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00509/l2v5/json/output.json b/latest/cases/00509/l2v5/json/output.json new file mode 100644 index 000000000..7f02f36af --- /dev/null +++ b/latest/cases/00509/l2v5/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00509/l3v2/heta-code/output.heta b/latest/cases/00509/l3v2/heta-code/output.heta new file mode 100644 index 000000000..08babebd5 --- /dev/null +++ b/latest/cases/00509/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k2 * S1 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.7; + diff --git a/latest/cases/00509/l3v2/index.heta b/latest/cases/00509/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00509/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00509/l3v2/json/output.json b/latest/cases/00509/l3v2/json/output.json new file mode 100644 index 000000000..46e3bd757 --- /dev/null +++ b/latest/cases/00509/l3v2/json/output.json @@ -0,0 +1,83 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.7 + } +] \ No newline at end of file diff --git a/latest/cases/00509/model-sbml-l2v5.xml b/latest/cases/00509/model-sbml-l2v5.xml new file mode 100644 index 000000000..8233e0f0d --- /dev/null +++ b/latest/cases/00509/model-sbml-l2v5.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S1 + S3 + + + + + + + diff --git a/latest/cases/00509/model-sbml-l3v2.xml b/latest/cases/00509/model-sbml-l3v2.xml new file mode 100644 index 000000000..efc6868c0 --- /dev/null +++ b/latest/cases/00509/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S1 + S3 + + + + + + + diff --git a/latest/cases/00509/output.heta b/latest/cases/00509/output.heta new file mode 100644 index 000000000..96fe82365 --- /dev/null +++ b/latest/cases/00509/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled a constant species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S3 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S3 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Initial amount of S3 |$undeclared$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$2.7$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k2 * S1 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.7; + diff --git a/latest/cases/00509/synopsis.txt b/latest/cases/00509/synopsis.txt new file mode 100644 index 000000000..cb726166c --- /dev/null +++ b/latest/cases/00509/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ConstantSpecies, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is +labeled a constant species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1 * S3$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S3 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S3 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Initial amount of S3 |$undeclared$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$2.7$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00510/l2v5/heta-code/output.heta b/latest/cases/00510/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b32435d5e --- /dev/null +++ b/latest/cases/00510/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00510/l2v5/index.heta b/latest/cases/00510/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00510/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00510/l2v5/json/output.json b/latest/cases/00510/l2v5/json/output.json new file mode 100644 index 000000000..1c8da8504 --- /dev/null +++ b/latest/cases/00510/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00510/l3v2/heta-code/output.heta b/latest/cases/00510/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2e1da5cd3 --- /dev/null +++ b/latest/cases/00510/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00510/l3v2/index.heta b/latest/cases/00510/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00510/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00510/l3v2/json/output.json b/latest/cases/00510/l3v2/json/output.json new file mode 100644 index 000000000..84a7af048 --- /dev/null +++ b/latest/cases/00510/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/00510/model-sbml-l2v5.xml b/latest/cases/00510/model-sbml-l2v5.xml new file mode 100644 index 000000000..3788063ab --- /dev/null +++ b/latest/cases/00510/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00510/model-sbml-l3v2.xml b/latest/cases/00510/model-sbml-l3v2.xml new file mode 100644 index 000000000..4a4e0937c --- /dev/null +++ b/latest/cases/00510/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00510/output.heta b/latest/cases/00510/output.heta new file mode 100644 index 000000000..a9e6c2b4a --- /dev/null +++ b/latest/cases/00510/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00510/synopsis.txt b/latest/cases/00510/synopsis.txt new file mode 100644 index 000000000..83a0bd82e --- /dev/null +++ b/latest/cases/00510/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00511/l2v5/heta-code/output.heta b/latest/cases/00511/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b32435d5e --- /dev/null +++ b/latest/cases/00511/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00511/l2v5/index.heta b/latest/cases/00511/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00511/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00511/l2v5/json/output.json b/latest/cases/00511/l2v5/json/output.json new file mode 100644 index 000000000..1c8da8504 --- /dev/null +++ b/latest/cases/00511/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00511/l3v2/heta-code/output.heta b/latest/cases/00511/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2e1da5cd3 --- /dev/null +++ b/latest/cases/00511/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00511/l3v2/index.heta b/latest/cases/00511/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00511/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00511/l3v2/json/output.json b/latest/cases/00511/l3v2/json/output.json new file mode 100644 index 000000000..84a7af048 --- /dev/null +++ b/latest/cases/00511/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/00511/model-sbml-l2v5.xml b/latest/cases/00511/model-sbml-l2v5.xml new file mode 100644 index 000000000..4523298ce --- /dev/null +++ b/latest/cases/00511/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00511/model-sbml-l3v2.xml b/latest/cases/00511/model-sbml-l3v2.xml new file mode 100644 index 000000000..12978742b --- /dev/null +++ b/latest/cases/00511/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00511/output.heta b/latest/cases/00511/output.heta new file mode 100644 index 000000000..4377c2594 --- /dev/null +++ b/latest/cases/00511/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$3.2$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00511/synopsis.txt b/latest/cases/00511/synopsis.txt new file mode 100644 index 000000000..86784c5ea --- /dev/null +++ b/latest/cases/00511/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$3.2$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00512/l2v5/heta-code/output.heta b/latest/cases/00512/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b32435d5e --- /dev/null +++ b/latest/cases/00512/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00512/l2v5/index.heta b/latest/cases/00512/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00512/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00512/l2v5/json/output.json b/latest/cases/00512/l2v5/json/output.json new file mode 100644 index 000000000..1c8da8504 --- /dev/null +++ b/latest/cases/00512/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00512/l3v2/heta-code/output.heta b/latest/cases/00512/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2e1da5cd3 --- /dev/null +++ b/latest/cases/00512/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00512/l3v2/index.heta b/latest/cases/00512/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00512/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00512/l3v2/json/output.json b/latest/cases/00512/l3v2/json/output.json new file mode 100644 index 000000000..84a7af048 --- /dev/null +++ b/latest/cases/00512/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/00512/model-sbml-l2v5.xml b/latest/cases/00512/model-sbml-l2v5.xml new file mode 100644 index 000000000..d3a17d6a9 --- /dev/null +++ b/latest/cases/00512/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00512/model-sbml-l3v2.xml b/latest/cases/00512/model-sbml-l3v2.xml new file mode 100644 index 000000000..8b2518bd0 --- /dev/null +++ b/latest/cases/00512/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00512/output.heta b/latest/cases/00512/output.heta new file mode 100644 index 000000000..87b1e8541 --- /dev/null +++ b/latest/cases/00512/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.125$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= k1 * S2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00512/synopsis.txt b/latest/cases/00512/synopsis.txt new file mode 100644 index 000000000..0df548a0f --- /dev/null +++ b/latest/cases/00512/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.125$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00513/l2v5/heta-code/output.heta b/latest/cases/00513/l2v5/heta-code/output.heta new file mode 100644 index 000000000..fa76fa8ff --- /dev/null +++ b/latest/cases/00513/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 1.25e-5; + diff --git a/latest/cases/00513/l2v5/index.heta b/latest/cases/00513/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00513/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00513/l2v5/json/output.json b/latest/cases/00513/l2v5/json/output.json new file mode 100644 index 000000000..456409fea --- /dev/null +++ b/latest/cases/00513/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00513/l3v2/heta-code/output.heta b/latest/cases/00513/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5071244d8 --- /dev/null +++ b/latest/cases/00513/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00513/l3v2/index.heta b/latest/cases/00513/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00513/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00513/l3v2/json/output.json b/latest/cases/00513/l3v2/json/output.json new file mode 100644 index 000000000..a3352517d --- /dev/null +++ b/latest/cases/00513/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0000125 + } +] \ No newline at end of file diff --git a/latest/cases/00513/model-sbml-l2v5.xml b/latest/cases/00513/model-sbml-l2v5.xml new file mode 100644 index 000000000..6446b5799 --- /dev/null +++ b/latest/cases/00513/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00513/model-sbml-l3v2.xml b/latest/cases/00513/model-sbml-l3v2.xml new file mode 100644 index 000000000..e38bc9c1c --- /dev/null +++ b/latest/cases/00513/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00513/output.heta b/latest/cases/00513/output.heta new file mode 100644 index 000000000..148649fc5 --- /dev/null +++ b/latest/cases/00513/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> 2S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00513/synopsis.txt b/latest/cases/00513/synopsis.txt new file mode 100644 index 000000000..04f00d4f0 --- /dev/null +++ b/latest/cases/00513/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> 2S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00514/l2v5/heta-code/output.heta b/latest/cases/00514/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bab0a2cd6 --- /dev/null +++ b/latest/cases/00514/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.0125; + diff --git a/latest/cases/00514/l2v5/index.heta b/latest/cases/00514/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00514/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00514/l2v5/json/output.json b/latest/cases/00514/l2v5/json/output.json new file mode 100644 index 000000000..7a09245a5 --- /dev/null +++ b/latest/cases/00514/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.0125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00514/l3v2/heta-code/output.heta b/latest/cases/00514/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4602e0252 --- /dev/null +++ b/latest/cases/00514/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0125; + diff --git a/latest/cases/00514/l3v2/index.heta b/latest/cases/00514/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00514/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00514/l3v2/json/output.json b/latest/cases/00514/l3v2/json/output.json new file mode 100644 index 000000000..3f673018b --- /dev/null +++ b/latest/cases/00514/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0125 + } +] \ No newline at end of file diff --git a/latest/cases/00514/model-sbml-l2v5.xml b/latest/cases/00514/model-sbml-l2v5.xml new file mode 100644 index 000000000..5232aeb71 --- /dev/null +++ b/latest/cases/00514/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00514/model-sbml-l3v2.xml b/latest/cases/00514/model-sbml-l3v2.xml new file mode 100644 index 000000000..87bdccdd4 --- /dev/null +++ b/latest/cases/00514/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00514/output.heta b/latest/cases/00514/output.heta new file mode 100644 index 000000000..6309d8990 --- /dev/null +++ b/latest/cases/00514/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> 2S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.5 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-2$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0125; + diff --git a/latest/cases/00514/synopsis.txt b/latest/cases/00514/synopsis.txt new file mode 100644 index 000000000..60a607cbf --- /dev/null +++ b/latest/cases/00514/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> 2S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.5 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-2$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00515/l2v5/heta-code/output.heta b/latest/cases/00515/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8e6f5e48d --- /dev/null +++ b/latest/cases/00515/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 1.25e-4; + diff --git a/latest/cases/00515/l2v5/index.heta b/latest/cases/00515/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00515/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00515/l2v5/json/output.json b/latest/cases/00515/l2v5/json/output.json new file mode 100644 index 000000000..f0cb857ca --- /dev/null +++ b/latest/cases/00515/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-4" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00515/l3v2/heta-code/output.heta b/latest/cases/00515/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e3d2a2220 --- /dev/null +++ b/latest/cases/00515/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.000125; + diff --git a/latest/cases/00515/l3v2/index.heta b/latest/cases/00515/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00515/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00515/l3v2/json/output.json b/latest/cases/00515/l3v2/json/output.json new file mode 100644 index 000000000..1919b3464 --- /dev/null +++ b/latest/cases/00515/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.000125 + } +] \ No newline at end of file diff --git a/latest/cases/00515/model-sbml-l2v5.xml b/latest/cases/00515/model-sbml-l2v5.xml new file mode 100644 index 000000000..cfe79d6e3 --- /dev/null +++ b/latest/cases/00515/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00515/model-sbml-l3v2.xml b/latest/cases/00515/model-sbml-l3v2.xml new file mode 100644 index 000000000..5a32014f8 --- /dev/null +++ b/latest/cases/00515/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00515/output.heta b/latest/cases/00515/output.heta new file mode 100644 index 000000000..52a824d1a --- /dev/null +++ b/latest/cases/00515/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> 2S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-4$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.000125; + diff --git a/latest/cases/00515/synopsis.txt b/latest/cases/00515/synopsis.txt new file mode 100644 index 000000000..6bc4a1ae7 --- /dev/null +++ b/latest/cases/00515/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> 2S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-4$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00516/l2v5/build.log b/latest/cases/00516/l2v5/build.log new file mode 100644 index 000000000..5711a9334 --- /dev/null +++ b/latest/cases/00516/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00516/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00516/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00516/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00516/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00516/l2v5/index.heta b/latest/cases/00516/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00516/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00516/l3v2/index.heta b/latest/cases/00516/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00516/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00516/model-sbml-l2v5.xml b/latest/cases/00516/model-sbml-l2v5.xml new file mode 100644 index 000000000..73e00e8a7 --- /dev/null +++ b/latest/cases/00516/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00516/synopsis.txt b/latest/cases/00516/synopsis.txt new file mode 100644 index 000000000..3540e5c90 --- /dev/null +++ b/latest/cases/00516/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, k2 and p1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00517/l2v5/build.log b/latest/cases/00517/l2v5/build.log new file mode 100644 index 000000000..1510564d0 --- /dev/null +++ b/latest/cases/00517/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00517/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00517/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00517/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00517/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00517/l2v5/index.heta b/latest/cases/00517/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00517/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00517/l3v2/index.heta b/latest/cases/00517/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00517/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00517/model-sbml-l2v5.xml b/latest/cases/00517/model-sbml-l2v5.xml new file mode 100644 index 000000000..092a82b12 --- /dev/null +++ b/latest/cases/00517/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00517/synopsis.txt b/latest/cases/00517/synopsis.txt new file mode 100644 index 000000000..c2cf9d902 --- /dev/null +++ b/latest/cases/00517/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, k2 and p1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$5$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00518/l2v5/build.log b/latest/cases/00518/l2v5/build.log new file mode 100644 index 000000000..522bed710 --- /dev/null +++ b/latest/cases/00518/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00518/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00518/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00518/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00518/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00518/l2v5/index.heta b/latest/cases/00518/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00518/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00518/l3v2/index.heta b/latest/cases/00518/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00518/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00518/model-sbml-l2v5.xml b/latest/cases/00518/model-sbml-l2v5.xml new file mode 100644 index 000000000..b96efde59 --- /dev/null +++ b/latest/cases/00518/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00518/synopsis.txt b/latest/cases/00518/synopsis.txt new file mode 100644 index 000000000..c0d2b0067 --- /dev/null +++ b/latest/cases/00518/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, k2 and p1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.125$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00519/l2v5/build.log b/latest/cases/00519/l2v5/build.log new file mode 100644 index 000000000..0e98af46d --- /dev/null +++ b/latest/cases/00519/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00519/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00519/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00519/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00519/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00519/l2v5/index.heta b/latest/cases/00519/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00519/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00519/l3v2/index.heta b/latest/cases/00519/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00519/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00519/model-sbml-l2v5.xml b/latest/cases/00519/model-sbml-l2v5.xml new file mode 100644 index 000000000..8318dc6cf --- /dev/null +++ b/latest/cases/00519/model-sbml-l2v5.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00519/synopsis.txt b/latest/cases/00519/synopsis.txt new file mode 100644 index 000000000..eb62bdaaf --- /dev/null +++ b/latest/cases/00519/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p2)S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Value of parameter p2 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00520/l2v5/build.log b/latest/cases/00520/l2v5/build.log new file mode 100644 index 000000000..299396af5 --- /dev/null +++ b/latest/cases/00520/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00520/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00520/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00520/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00520/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00520/l2v5/index.heta b/latest/cases/00520/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00520/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00520/l3v2/index.heta b/latest/cases/00520/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00520/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00520/model-sbml-l2v5.xml b/latest/cases/00520/model-sbml-l2v5.xml new file mode 100644 index 000000000..99b25f730 --- /dev/null +++ b/latest/cases/00520/model-sbml-l2v5.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00520/synopsis.txt b/latest/cases/00520/synopsis.txt new file mode 100644 index 000000000..a1309ee1c --- /dev/null +++ b/latest/cases/00520/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p2)S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Value of parameter p2 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00521/l2v5/build.log b/latest/cases/00521/l2v5/build.log new file mode 100644 index 000000000..d6459b625 --- /dev/null +++ b/latest/cases/00521/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00521/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00521/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00521/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00521/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00521/l2v5/index.heta b/latest/cases/00521/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00521/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00521/l3v2/index.heta b/latest/cases/00521/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00521/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00521/model-sbml-l2v5.xml b/latest/cases/00521/model-sbml-l2v5.xml new file mode 100644 index 000000000..7d1407979 --- /dev/null +++ b/latest/cases/00521/model-sbml-l2v5.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00521/synopsis.txt b/latest/cases/00521/synopsis.txt new file mode 100644 index 000000000..6598c25a1 --- /dev/null +++ b/latest/cases/00521/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p2)S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-2$ |mole | +|Value of parameter p2 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00522/l2v5/heta-code/output.heta b/latest/cases/00522/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4fb085567 --- /dev/null +++ b/latest/cases/00522/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +p1 @Record 'p1' { } .= 1.25e-4; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; + diff --git a/latest/cases/00522/l2v5/index.heta b/latest/cases/00522/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00522/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00522/l2v5/json/output.json b/latest/cases/00522/l2v5/json/output.json new file mode 100644 index 000000000..d5e2fb011 --- /dev/null +++ b/latest/cases/00522/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-4" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00522/l3v2/heta-code/output.heta b/latest/cases/00522/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d7b64dbec --- /dev/null +++ b/latest/cases/00522/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; +p1 @Const 'p1' { } = 0.000125; + diff --git a/latest/cases/00522/l3v2/index.heta b/latest/cases/00522/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00522/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00522/l3v2/json/output.json b/latest/cases/00522/l3v2/json/output.json new file mode 100644 index 000000000..784753daa --- /dev/null +++ b/latest/cases/00522/l3v2/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.000125 + } +] \ No newline at end of file diff --git a/latest/cases/00522/model-sbml-l2v5.xml b/latest/cases/00522/model-sbml-l2v5.xml new file mode 100644 index 000000000..78da4b49f --- /dev/null +++ b/latest/cases/00522/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00522/model-sbml-l3v2.xml b/latest/cases/00522/model-sbml-l3v2.xml new file mode 100644 index 000000000..ab2f4387f --- /dev/null +++ b/latest/cases/00522/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00522/output.heta b/latest/cases/00522/output.heta new file mode 100644 index 000000000..c2c0c2707 --- /dev/null +++ b/latest/cases/00522/output.heta @@ -0,0 +1,68 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameters called p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1 ++ S2$ defines another (different) local parameter k. Note that these +parameters have a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter p1 |$1.25 \x 10^-4$ |mole | +|Value of parameter local k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter local k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; +p1 @Const 'p1' { } = 0.000125; + diff --git a/latest/cases/00522/synopsis.txt b/latest/cases/00522/synopsis.txt new file mode 100644 index 000000000..606ba5ebf --- /dev/null +++ b/latest/cases/00522/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameters called p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1 ++ S2$ defines another (different) local parameter k. Note that these +parameters have a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter p1 |$1.25 \x 10^-4$ |mole | +|Value of parameter local k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter local k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00523/l2v5/heta-code/output.heta b/latest/cases/00523/l2v5/heta-code/output.heta new file mode 100644 index 000000000..adfa8e6ad --- /dev/null +++ b/latest/cases/00523/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +p1 @Record 'p1' { } .= 0.00125; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; + diff --git a/latest/cases/00523/l2v5/index.heta b/latest/cases/00523/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00523/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00523/l2v5/json/output.json b/latest/cases/00523/l2v5/json/output.json new file mode 100644 index 000000000..efc671b9f --- /dev/null +++ b/latest/cases/00523/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.00125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00523/l3v2/heta-code/output.heta b/latest/cases/00523/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f23a70a40 --- /dev/null +++ b/latest/cases/00523/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00523/l3v2/index.heta b/latest/cases/00523/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00523/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00523/l3v2/json/output.json b/latest/cases/00523/l3v2/json/output.json new file mode 100644 index 000000000..52ac5a93e --- /dev/null +++ b/latest/cases/00523/l3v2/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.00125 + } +] \ No newline at end of file diff --git a/latest/cases/00523/model-sbml-l2v5.xml b/latest/cases/00523/model-sbml-l2v5.xml new file mode 100644 index 000000000..ddc92fe5e --- /dev/null +++ b/latest/cases/00523/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00523/model-sbml-l3v2.xml b/latest/cases/00523/model-sbml-l3v2.xml new file mode 100644 index 000000000..5d5de919e --- /dev/null +++ b/latest/cases/00523/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00523/output.heta b/latest/cases/00523/output.heta new file mode 100644 index 000000000..4be1b8393 --- /dev/null +++ b/latest/cases/00523/output.heta @@ -0,0 +1,68 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameters called p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1 ++ S2$ defines another (different) local parameter k. Note that these +parameters have a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Value of parameter local k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter local k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00523/synopsis.txt b/latest/cases/00523/synopsis.txt new file mode 100644 index 000000000..e920cd030 --- /dev/null +++ b/latest/cases/00523/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameters called p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1 ++ S2$ defines another (different) local parameter k. Note that these +parameters have a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Value of parameter local k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter local k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00524/l2v5/heta-code/output.heta b/latest/cases/00524/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9f4dc9a8a --- /dev/null +++ b/latest/cases/00524/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +p1 @Record 'p1' { } .= 1.25e-5; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; + diff --git a/latest/cases/00524/l2v5/index.heta b/latest/cases/00524/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00524/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00524/l2v5/json/output.json b/latest/cases/00524/l2v5/json/output.json new file mode 100644 index 000000000..05624ebc0 --- /dev/null +++ b/latest/cases/00524/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00524/l3v2/heta-code/output.heta b/latest/cases/00524/l3v2/heta-code/output.heta new file mode 100644 index 000000000..434bb276f --- /dev/null +++ b/latest/cases/00524/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00524/l3v2/index.heta b/latest/cases/00524/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00524/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00524/l3v2/json/output.json b/latest/cases/00524/l3v2/json/output.json new file mode 100644 index 000000000..53d6757d9 --- /dev/null +++ b/latest/cases/00524/l3v2/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.25 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0000125 + } +] \ No newline at end of file diff --git a/latest/cases/00524/model-sbml-l2v5.xml b/latest/cases/00524/model-sbml-l2v5.xml new file mode 100644 index 000000000..e3146306a --- /dev/null +++ b/latest/cases/00524/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00524/model-sbml-l3v2.xml b/latest/cases/00524/model-sbml-l3v2.xml new file mode 100644 index 000000000..6c7c854a4 --- /dev/null +++ b/latest/cases/00524/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00524/output.heta b/latest/cases/00524/output.heta new file mode 100644 index 000000000..df9f570ac --- /dev/null +++ b/latest/cases/00524/output.heta @@ -0,0 +1,68 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameters called p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1 ++ S2$ defines another (different) local parameter k. Note that these +parameters have a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Value of parameter local k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter local k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 0.75; +k__reaction2_local @Const { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00524/synopsis.txt b/latest/cases/00524/synopsis.txt new file mode 100644 index 000000000..c6d60881b --- /dev/null +++ b/latest/cases/00524/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameters called p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1 ++ S2$ defines another (different) local parameter k. Note that these +parameters have a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Value of parameter local k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter local k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00525/l2v5/heta-code/output.heta b/latest/cases/00525/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7d0c2ab2b --- /dev/null +++ b/latest/cases/00525/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= k / 50; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k @Record 'k' { } .= 50; + +k__reaction1_local @Const { } = 0.5; + diff --git a/latest/cases/00525/l2v5/index.heta b/latest/cases/00525/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00525/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00525/l2v5/json/output.json b/latest/cases/00525/l2v5/json/output.json new file mode 100644 index 000000000..0533e7f5c --- /dev/null +++ b/latest/cases/00525/l2v5/json/output.json @@ -0,0 +1,92 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00525/l3v2/heta-code/output.heta b/latest/cases/00525/l3v2/heta-code/output.heta new file mode 100644 index 000000000..73b25bc0d --- /dev/null +++ b/latest/cases/00525/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 0.5; +k @Const 'k' { } = 50; + diff --git a/latest/cases/00525/l3v2/index.heta b/latest/cases/00525/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00525/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00525/l3v2/json/output.json b/latest/cases/00525/l3v2/json/output.json new file mode 100644 index 000000000..6f7248ad6 --- /dev/null +++ b/latest/cases/00525/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00525/model-sbml-l2v5.xml b/latest/cases/00525/model-sbml-l2v5.xml new file mode 100644 index 000000000..9421b8660 --- /dev/null +++ b/latest/cases/00525/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + k + 50 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00525/model-sbml-l3v2.xml b/latest/cases/00525/model-sbml-l3v2.xml new file mode 100644 index 000000000..63a35d394 --- /dev/null +++ b/latest/cases/00525/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k + 50 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00525/output.heta b/latest/cases/00525/output.heta new file mode 100644 index 000000000..9ce6dbf25 --- /dev/null +++ b/latest/cases/00525/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction $S1 -> S2$ defines one local parameter k. Note that this +parameter has a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k |$50$ |litre | +|Value of local parameter k |$0.5$ |second^-1^ | +|Volume of compartment C |$5.4$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 0.5; +k @Const 'k' { } = 50; + diff --git a/latest/cases/00525/synopsis.txt b/latest/cases/00525/synopsis.txt new file mode 100644 index 000000000..02a2f63c9 --- /dev/null +++ b/latest/cases/00525/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction $S1 -> S2$ defines one local parameter k. Note that this +parameter has a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k |$50$ |litre | +|Value of local parameter k |$0.5$ |second^-1^ | +|Volume of compartment C |$5.4$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00526/l2v5/heta-code/output.heta b/latest/cases/00526/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7d0c2ab2b --- /dev/null +++ b/latest/cases/00526/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= k / 50; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k @Record 'k' { } .= 50; + +k__reaction1_local @Const { } = 0.5; + diff --git a/latest/cases/00526/l2v5/index.heta b/latest/cases/00526/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00526/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00526/l2v5/json/output.json b/latest/cases/00526/l2v5/json/output.json new file mode 100644 index 000000000..0533e7f5c --- /dev/null +++ b/latest/cases/00526/l2v5/json/output.json @@ -0,0 +1,92 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00526/l3v2/heta-code/output.heta b/latest/cases/00526/l3v2/heta-code/output.heta new file mode 100644 index 000000000..73b25bc0d --- /dev/null +++ b/latest/cases/00526/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 0.5; +k @Const 'k' { } = 50; + diff --git a/latest/cases/00526/l3v2/index.heta b/latest/cases/00526/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00526/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00526/l3v2/json/output.json b/latest/cases/00526/l3v2/json/output.json new file mode 100644 index 000000000..6f7248ad6 --- /dev/null +++ b/latest/cases/00526/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00526/model-sbml-l2v5.xml b/latest/cases/00526/model-sbml-l2v5.xml new file mode 100644 index 000000000..428af6e13 --- /dev/null +++ b/latest/cases/00526/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + k + 50 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00526/model-sbml-l3v2.xml b/latest/cases/00526/model-sbml-l3v2.xml new file mode 100644 index 000000000..7c623900e --- /dev/null +++ b/latest/cases/00526/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k + 50 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00526/output.heta b/latest/cases/00526/output.heta new file mode 100644 index 000000000..427e59f5d --- /dev/null +++ b/latest/cases/00526/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction $S1 -> S2$ defines one local parameter k. Note that this +parameter has a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k |$50$ |litre | +|Value of local parameter k |$0.5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 0.5; +k @Const 'k' { } = 50; + diff --git a/latest/cases/00526/synopsis.txt b/latest/cases/00526/synopsis.txt new file mode 100644 index 000000000..36dc1f9ee --- /dev/null +++ b/latest/cases/00526/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction $S1 -> S2$ defines one local parameter k. Note that this +parameter has a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k |$50$ |litre | +|Value of local parameter k |$0.5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00527/l2v5/heta-code/output.heta b/latest/cases/00527/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7d0c2ab2b --- /dev/null +++ b/latest/cases/00527/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= k / 50; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k @Record 'k' { } .= 50; + +k__reaction1_local @Const { } = 0.5; + diff --git a/latest/cases/00527/l2v5/index.heta b/latest/cases/00527/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00527/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00527/l2v5/json/output.json b/latest/cases/00527/l2v5/json/output.json new file mode 100644 index 000000000..0533e7f5c --- /dev/null +++ b/latest/cases/00527/l2v5/json/output.json @@ -0,0 +1,92 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00527/l3v2/heta-code/output.heta b/latest/cases/00527/l3v2/heta-code/output.heta new file mode 100644 index 000000000..73b25bc0d --- /dev/null +++ b/latest/cases/00527/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 0.5; +k @Const 'k' { } = 50; + diff --git a/latest/cases/00527/l3v2/index.heta b/latest/cases/00527/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00527/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00527/l3v2/json/output.json b/latest/cases/00527/l3v2/json/output.json new file mode 100644 index 000000000..6f7248ad6 --- /dev/null +++ b/latest/cases/00527/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k / 50" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00527/model-sbml-l2v5.xml b/latest/cases/00527/model-sbml-l2v5.xml new file mode 100644 index 000000000..cf6b38f04 --- /dev/null +++ b/latest/cases/00527/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + k + 50 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00527/model-sbml-l3v2.xml b/latest/cases/00527/model-sbml-l3v2.xml new file mode 100644 index 000000000..fec216107 --- /dev/null +++ b/latest/cases/00527/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k + 50 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00527/output.heta b/latest/cases/00527/output.heta new file mode 100644 index 000000000..93b01a950 --- /dev/null +++ b/latest/cases/00527/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction $S1 -> S2$ defines one local parameter k. Note that this +parameter has a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k |$50$ |litre | +|Value of local parameter k |$0.5$ |second^-1^ | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= k / 50; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 0.5; +k @Const 'k' { } = 50; + diff --git a/latest/cases/00527/synopsis.txt b/latest/cases/00527/synopsis.txt new file mode 100644 index 000000000..eedacc47e --- /dev/null +++ b/latest/cases/00527/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction $S1 -> S2$ defines one local parameter k. Note that this +parameter has a scope local to the defining reaction. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k / 50$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k |$50$ |litre | +|Value of local parameter k |$0.5$ |second^-1^ | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00528/l2v5/heta-code/output.heta b/latest/cases/00528/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7f1b62e87 --- /dev/null +++ b/latest/cases/00528/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +division #defineFunction { arguments: [x, y], math: x / y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= division(k2, 100); +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00528/l2v5/index.heta b/latest/cases/00528/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00528/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00528/l2v5/json/output.json b/latest/cases/00528/l2v5/json/output.json new file mode 100644 index 000000000..06c64bab0 --- /dev/null +++ b/latest/cases/00528/l2v5/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "division(k2, 100)" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "division", + "arguments": [ + "x", + "y" + ], + "math": "x / y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00528/l3v2/heta-code/output.heta b/latest/cases/00528/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5027f124a --- /dev/null +++ b/latest/cases/00528/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + +division #defineFunction { arguments: [x, y], math: x / y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= division(k2, 100); + +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00528/l3v2/index.heta b/latest/cases/00528/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00528/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00528/l3v2/json/output.json b/latest/cases/00528/l3v2/json/output.json new file mode 100644 index 000000000..1377471e7 --- /dev/null +++ b/latest/cases/00528/l3v2/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "division(k2, 100)" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "id": "division", + "arguments": [ + "x", + "y" + ], + "math": "x / y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00528/model-sbml-l2v5.xml b/latest/cases/00528/model-sbml-l2v5.xml new file mode 100644 index 000000000..35abce9a4 --- /dev/null +++ b/latest/cases/00528/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + division + k2 + 100 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00528/model-sbml-l3v2.xml b/latest/cases/00528/model-sbml-l3v2.xml new file mode 100644 index 000000000..2025c50ad --- /dev/null +++ b/latest/cases/00528/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + division + k2 + 100 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00528/output.heta b/latest/cases/00528/output.heta new file mode 100644 index 000000000..dcdcbda14 --- /dev/null +++ b/latest/cases/00528/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $division(k2, 100)$ |] + +The initialAssignment uses a functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | division | x, y | $x / y$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k1 has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +*/ + + +division #defineFunction { arguments: [x, y], math: x / y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= division(k2, 100); + +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00528/synopsis.txt b/latest/cases/00528/synopsis.txt new file mode 100644 index 000000000..5a6b7a577 --- /dev/null +++ b/latest/cases/00528/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $division(k2, 100)$ |] + +The initialAssignment uses a functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | division | x, y | $x / y$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k1 has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/00529/l2v5/heta-code/output.heta b/latest/cases/00529/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7d5e93500 --- /dev/null +++ b/latest/cases/00529/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= multiply(k1, S2); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.0015 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00529/l2v5/index.heta b/latest/cases/00529/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00529/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00529/l2v5/json/output.json b/latest/cases/00529/l2v5/json/output.json new file mode 100644 index 000000000..a2ccde0f3 --- /dev/null +++ b/latest/cases/00529/l2v5/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00529/l3v2/heta-code/output.heta b/latest/cases/00529/l3v2/heta-code/output.heta new file mode 100644 index 000000000..40fbf515a --- /dev/null +++ b/latest/cases/00529/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= multiply(k1, S2); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0015 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00529/l3v2/index.heta b/latest/cases/00529/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00529/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00529/l3v2/json/output.json b/latest/cases/00529/l3v2/json/output.json new file mode 100644 index 000000000..79578737d --- /dev/null +++ b/latest/cases/00529/l3v2/json/output.json @@ -0,0 +1,76 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00529/model-sbml-l2v5.xml b/latest/cases/00529/model-sbml-l2v5.xml new file mode 100644 index 000000000..be8b7c695 --- /dev/null +++ b/latest/cases/00529/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00529/model-sbml-l3v2.xml b/latest/cases/00529/model-sbml-l3v2.xml new file mode 100644 index 000000000..7f1b2a46b --- /dev/null +++ b/latest/cases/00529/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00529/output.heta b/latest/cases/00529/output.heta new file mode 100644 index 000000000..741a66637 --- /dev/null +++ b/latest/cases/00529/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $multiply(k1, S2)$ |] + +The initialAssignment uses a functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= multiply(k1, S2); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0015 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00529/synopsis.txt b/latest/cases/00529/synopsis.txt new file mode 100644 index 000000000..4e0095c23 --- /dev/null +++ b/latest/cases/00529/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $multiply(k1, S2)$ |] + +The initialAssignment uses a functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ $ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00530/l2v5/heta-code/output.heta b/latest/cases/00530/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a0023d136 --- /dev/null +++ b/latest/cases/00530/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +division #defineFunction { arguments: [x, y], math: x / y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= division(k2, 50); + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00530/l2v5/index.heta b/latest/cases/00530/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00530/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00530/l2v5/json/output.json b/latest/cases/00530/l2v5/json/output.json new file mode 100644 index 000000000..c26606289 --- /dev/null +++ b/latest/cases/00530/l2v5/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "division(k2, 50)" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "division", + "arguments": [ + "x", + "y" + ], + "math": "x / y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00530/l3v2/heta-code/output.heta b/latest/cases/00530/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c9efe496a --- /dev/null +++ b/latest/cases/00530/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + +division #defineFunction { arguments: [x, y], math: x / y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= division(k2, 50); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00530/l3v2/index.heta b/latest/cases/00530/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00530/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00530/l3v2/json/output.json b/latest/cases/00530/l3v2/json/output.json new file mode 100644 index 000000000..203b0bece --- /dev/null +++ b/latest/cases/00530/l3v2/json/output.json @@ -0,0 +1,76 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "division(k2, 50)" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "id": "division", + "arguments": [ + "x", + "y" + ], + "math": "x / y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00530/model-sbml-l2v5.xml b/latest/cases/00530/model-sbml-l2v5.xml new file mode 100644 index 000000000..907fe8ecb --- /dev/null +++ b/latest/cases/00530/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + division + k2 + 50 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00530/model-sbml-l3v2.xml b/latest/cases/00530/model-sbml-l3v2.xml new file mode 100644 index 000000000..64871d77d --- /dev/null +++ b/latest/cases/00530/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + division + k2 + 50 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00530/output.heta b/latest/cases/00530/output.heta new file mode 100644 index 000000000..ad2427b40 --- /dev/null +++ b/latest/cases/00530/output.heta @@ -0,0 +1,71 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $division(k2, 50)$ |] + +The initialAssignment uses a functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | division | x, y | $x / y$ |] + + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +division #defineFunction { arguments: [x, y], math: x / y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= division(k2, 50); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00530/synopsis.txt b/latest/cases/00530/synopsis.txt new file mode 100644 index 000000000..b4051c9b0 --- /dev/null +++ b/latest/cases/00530/synopsis.txt @@ -0,0 +1,53 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $division(k2, 50)$ |] + +The initialAssignment uses a functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | division | x, y | $x / y$ |] + + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00531/l2v5/build.log b/latest/cases/00531/l2v5/build.log new file mode 100644 index 000000000..ebd2d1de5 --- /dev/null +++ b/latest/cases/00531/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00531/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00531/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00531/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00531/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00531/l2v5/index.heta b/latest/cases/00531/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00531/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00531/l3v2/build.log b/latest/cases/00531/l3v2/build.log new file mode 100644 index 000000000..3f448cd79 --- /dev/null +++ b/latest/cases/00531/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00531/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00531/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00531/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00531/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00531/l3v2/index.heta b/latest/cases/00531/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00531/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00531/model-sbml-l2v5.xml b/latest/cases/00531/model-sbml-l2v5.xml new file mode 100644 index 000000000..6be45216d --- /dev/null +++ b/latest/cases/00531/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + T + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00531/model-sbml-l3v2.xml b/latest/cases/00531/model-sbml-l3v2.xml new file mode 100644 index 000000000..4dd9af92c --- /dev/null +++ b/latest/cases/00531/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + T + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00531/synopsis.txt b/latest/cases/00531/synopsis.txt new file mode 100644 index 000000000..fc301baf7 --- /dev/null +++ b/latest/cases/00531/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00532/l2v5/build.log b/latest/cases/00532/l2v5/build.log new file mode 100644 index 000000000..f5d4f0e51 --- /dev/null +++ b/latest/cases/00532/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00532/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00532/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00532/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00532/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00532/l2v5/index.heta b/latest/cases/00532/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00532/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00532/l3v2/build.log b/latest/cases/00532/l3v2/build.log new file mode 100644 index 000000000..eef092e9a --- /dev/null +++ b/latest/cases/00532/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00532/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00532/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00532/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00532/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00532/l3v2/index.heta b/latest/cases/00532/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00532/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00532/model-sbml-l2v5.xml b/latest/cases/00532/model-sbml-l2v5.xml new file mode 100644 index 000000000..07afaf3d4 --- /dev/null +++ b/latest/cases/00532/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00532/model-sbml-l3v2.xml b/latest/cases/00532/model-sbml-l3v2.xml new file mode 100644 index 000000000..f867c0c3e --- /dev/null +++ b/latest/cases/00532/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00532/synopsis.txt b/latest/cases/00532/synopsis.txt new file mode 100644 index 000000000..e1e2c7b8d --- /dev/null +++ b/latest/cases/00532/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $X0 + X1 + T - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1.25$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Initial amount of S1 |$3.75$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00533/l2v5/build.log b/latest/cases/00533/l2v5/build.log new file mode 100644 index 000000000..1a6375489 --- /dev/null +++ b/latest/cases/00533/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00533/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00533/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00533/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00533/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00533/l2v5/index.heta b/latest/cases/00533/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00533/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00533/l3v2/build.log b/latest/cases/00533/l3v2/build.log new file mode 100644 index 000000000..594e9d07d --- /dev/null +++ b/latest/cases/00533/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00533/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00533/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00533/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00533/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00533/l3v2/index.heta b/latest/cases/00533/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00533/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00533/model-sbml-l2v5.xml b/latest/cases/00533/model-sbml-l2v5.xml new file mode 100644 index 000000000..ffb0263fb --- /dev/null +++ b/latest/cases/00533/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + k2 + -0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00533/model-sbml-l3v2.xml b/latest/cases/00533/model-sbml-l3v2.xml new file mode 100644 index 000000000..903600d6c --- /dev/null +++ b/latest/cases/00533/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + -0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00533/synopsis.txt b/latest/cases/00533/synopsis.txt new file mode 100644 index 000000000..060594817 --- /dev/null +++ b/latest/cases/00533/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Three reactions with four species in one compartment, +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $k2 - 0.9$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00534/l2v5/build.log b/latest/cases/00534/l2v5/build.log new file mode 100644 index 000000000..6411bba57 --- /dev/null +++ b/latest/cases/00534/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00534/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00534/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00534/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00534/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00534/l2v5/index.heta b/latest/cases/00534/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00534/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00534/l3v2/build.log b/latest/cases/00534/l3v2/build.log new file mode 100644 index 000000000..7fd75ef6c --- /dev/null +++ b/latest/cases/00534/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00534/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00534/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00534/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00534/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00534/l3v2/index.heta b/latest/cases/00534/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00534/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00534/model-sbml-l2v5.xml b/latest/cases/00534/model-sbml-l2v5.xml new file mode 100644 index 000000000..17755d7a9 --- /dev/null +++ b/latest/cases/00534/model-sbml-l2v5.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + k2 + + + -1 + k3 + + -0.2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00534/model-sbml-l3v2.xml b/latest/cases/00534/model-sbml-l3v2.xml new file mode 100644 index 000000000..f7d569c66 --- /dev/null +++ b/latest/cases/00534/model-sbml-l3v2.xml @@ -0,0 +1,112 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + -1 + k3 + + -0.2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00534/synopsis.txt b/latest/cases/00534/synopsis.txt new file mode 100644 index 000000000..14caf84a5 --- /dev/null +++ b/latest/cases/00534/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Three reactions with four species in one compartment, +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $k2 - k3 - 0.2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00535/l2v5/build.log b/latest/cases/00535/l2v5/build.log new file mode 100644 index 000000000..41dc72132 --- /dev/null +++ b/latest/cases/00535/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00535/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00535/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00535/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00535/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00535/l2v5/index.heta b/latest/cases/00535/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00535/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00535/l3v2/build.log b/latest/cases/00535/l3v2/build.log new file mode 100644 index 000000000..68aa40b9a --- /dev/null +++ b/latest/cases/00535/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00535/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00535/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00535/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00535/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00535/l3v2/index.heta b/latest/cases/00535/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00535/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00535/model-sbml-l2v5.xml b/latest/cases/00535/model-sbml-l2v5.xml new file mode 100644 index 000000000..f0c5ece78 --- /dev/null +++ b/latest/cases/00535/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00535/model-sbml-l3v2.xml b/latest/cases/00535/model-sbml-l3v2.xml new file mode 100644 index 000000000..7c35286e0 --- /dev/null +++ b/latest/cases/00535/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00535/synopsis.txt b/latest/cases/00535/synopsis.txt new file mode 100644 index 000000000..7ec1c6dac --- /dev/null +++ b/latest/cases/00535/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00536/l2v5/build.log b/latest/cases/00536/l2v5/build.log new file mode 100644 index 000000000..6447aded2 --- /dev/null +++ b/latest/cases/00536/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00536/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00536/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00536/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00536/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00536/l2v5/index.heta b/latest/cases/00536/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00536/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00536/l3v2/build.log b/latest/cases/00536/l3v2/build.log new file mode 100644 index 000000000..51bfef111 --- /dev/null +++ b/latest/cases/00536/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00536/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00536/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00536/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00536/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00536/l3v2/index.heta b/latest/cases/00536/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00536/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00536/model-sbml-l2v5.xml b/latest/cases/00536/model-sbml-l2v5.xml new file mode 100644 index 000000000..eade3b018 --- /dev/null +++ b/latest/cases/00536/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + k1 + -0.1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00536/model-sbml-l3v2.xml b/latest/cases/00536/model-sbml-l3v2.xml new file mode 100644 index 000000000..01dd5cff8 --- /dev/null +++ b/latest/cases/00536/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + -0.1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00536/synopsis.txt b/latest/cases/00536/synopsis.txt new file mode 100644 index 000000000..01c985679 --- /dev/null +++ b/latest/cases/00536/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions with three species in one compartment, +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called X0, X1 and T and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule which must be used to determine the value of +parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $k1 - 0.1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00537/l2v5/build.log b/latest/cases/00537/l2v5/build.log new file mode 100644 index 000000000..0254041af --- /dev/null +++ b/latest/cases/00537/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00537/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00537/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00537/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00537/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00537/l2v5/index.heta b/latest/cases/00537/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00537/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00537/l3v2/build.log b/latest/cases/00537/l3v2/build.log new file mode 100644 index 000000000..9c2e5a993 --- /dev/null +++ b/latest/cases/00537/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00537/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00537/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00537/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00537/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00537/l3v2/index.heta b/latest/cases/00537/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00537/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00537/model-sbml-l2v5.xml b/latest/cases/00537/model-sbml-l2v5.xml new file mode 100644 index 000000000..0d97e0579 --- /dev/null +++ b/latest/cases/00537/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + k2 + -0.2 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00537/model-sbml-l3v2.xml b/latest/cases/00537/model-sbml-l3v2.xml new file mode 100644 index 000000000..34e6160f1 --- /dev/null +++ b/latest/cases/00537/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + -0.2 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00537/synopsis.txt b/latest/cases/00537/synopsis.txt new file mode 100644 index 000000000..502c83ec9 --- /dev/null +++ b/latest/cases/00537/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions with three species in one compartment, +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called X0, X1 and T and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule which must be used to determine the value of +parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $k2 - 0.2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1.25$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00538/l2v5/build.log b/latest/cases/00538/l2v5/build.log new file mode 100644 index 000000000..e727f8963 --- /dev/null +++ b/latest/cases/00538/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00538/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00538/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00538/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00538/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00538/l2v5/index.heta b/latest/cases/00538/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00538/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00538/l3v2/build.log b/latest/cases/00538/l3v2/build.log new file mode 100644 index 000000000..3fa19c64e --- /dev/null +++ b/latest/cases/00538/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00538/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00538/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00538/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00538/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00538/l3v2/index.heta b/latest/cases/00538/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00538/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00538/model-sbml-l2v5.xml b/latest/cases/00538/model-sbml-l2v5.xml new file mode 100644 index 000000000..778a0eca0 --- /dev/null +++ b/latest/cases/00538/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + k2 + -0.25 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00538/model-sbml-l3v2.xml b/latest/cases/00538/model-sbml-l3v2.xml new file mode 100644 index 000000000..873264a9f --- /dev/null +++ b/latest/cases/00538/model-sbml-l3v2.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + -0.25 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00538/synopsis.txt b/latest/cases/00538/synopsis.txt new file mode 100644 index 000000000..caac0c33b --- /dev/null +++ b/latest/cases/00538/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment with +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $k2 - 0.25$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00539/l2v5/build.log b/latest/cases/00539/l2v5/build.log new file mode 100644 index 000000000..5244c26b7 --- /dev/null +++ b/latest/cases/00539/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00539/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00539/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00539/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00539/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00539/l2v5/index.heta b/latest/cases/00539/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00539/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00539/l3v2/build.log b/latest/cases/00539/l3v2/build.log new file mode 100644 index 000000000..d6ee66d9e --- /dev/null +++ b/latest/cases/00539/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00539/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00539/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00539/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00539/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00539/l3v2/index.heta b/latest/cases/00539/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00539/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00539/model-sbml-l2v5.xml b/latest/cases/00539/model-sbml-l2v5.xml new file mode 100644 index 000000000..07bcb2a7a --- /dev/null +++ b/latest/cases/00539/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00539/model-sbml-l3v2.xml b/latest/cases/00539/model-sbml-l3v2.xml new file mode 100644 index 000000000..dbfeed581 --- /dev/null +++ b/latest/cases/00539/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00539/synopsis.txt b/latest/cases/00539/synopsis.txt new file mode 100644 index 000000000..d4ab5bc3f --- /dev/null +++ b/latest/cases/00539/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions with three species in one compartment, +with an algebraic rule used to determine value of the compartment size. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called X0, X1 and T and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule which must be used to determine the value of +compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $C - 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00540/l2v5/build.log b/latest/cases/00540/l2v5/build.log new file mode 100644 index 000000000..d702e8e9d --- /dev/null +++ b/latest/cases/00540/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00540/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00540/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00540/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00540/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00540/l2v5/index.heta b/latest/cases/00540/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00540/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00540/l3v2/build.log b/latest/cases/00540/l3v2/build.log new file mode 100644 index 000000000..71ade2425 --- /dev/null +++ b/latest/cases/00540/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00540/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00540/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00540/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00540/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00540/l3v2/index.heta b/latest/cases/00540/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00540/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00540/model-sbml-l2v5.xml b/latest/cases/00540/model-sbml-l2v5.xml new file mode 100644 index 000000000..0e2d65025 --- /dev/null +++ b/latest/cases/00540/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00540/model-sbml-l3v2.xml b/latest/cases/00540/model-sbml-l3v2.xml new file mode 100644 index 000000000..a82059800 --- /dev/null +++ b/latest/cases/00540/model-sbml-l3v2.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00540/synopsis.txt b/latest/cases/00540/synopsis.txt new file mode 100644 index 000000000..425a09d3e --- /dev/null +++ b/latest/cases/00540/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment with +with an algebraic rule used to determine value of the compartment size. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $C - 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00541/l2v5/build.log b/latest/cases/00541/l2v5/build.log new file mode 100644 index 000000000..8e9aa6062 --- /dev/null +++ b/latest/cases/00541/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00541/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00541/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00541/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00541/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00541/l2v5/index.heta b/latest/cases/00541/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00541/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00541/l3v2/build.log b/latest/cases/00541/l3v2/build.log new file mode 100644 index 000000000..452181f74 --- /dev/null +++ b/latest/cases/00541/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00541/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00541/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00541/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00541/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00541/l3v2/index.heta b/latest/cases/00541/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00541/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00541/model-sbml-l2v5.xml b/latest/cases/00541/model-sbml-l2v5.xml new file mode 100644 index 000000000..4d136077c --- /dev/null +++ b/latest/cases/00541/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00541/model-sbml-l3v2.xml b/latest/cases/00541/model-sbml-l3v2.xml new file mode 100644 index 000000000..e54799c64 --- /dev/null +++ b/latest/cases/00541/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00541/synopsis.txt b/latest/cases/00541/synopsis.txt new file mode 100644 index 000000000..34d750860 --- /dev/null +++ b/latest/cases/00541/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions with three species in one 2D compartment, +with an algebraic rule used to determine value of the compartment size. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called X0, X1 and T and two parameters called k1 and k2. Compartment +C is 2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule which must be used to determine the value of +compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $C - 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Area of compartment C |$undeclared$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00542/l2v5/build.log b/latest/cases/00542/l2v5/build.log new file mode 100644 index 000000000..173491919 --- /dev/null +++ b/latest/cases/00542/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00542/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00542/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00542/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00542/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00542/l2v5/index.heta b/latest/cases/00542/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00542/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00542/l3v2/build.log b/latest/cases/00542/l3v2/build.log new file mode 100644 index 000000000..856841102 --- /dev/null +++ b/latest/cases/00542/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00542/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00542/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00542/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00542/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00542/l3v2/index.heta b/latest/cases/00542/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00542/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00542/model-sbml-l2v5.xml b/latest/cases/00542/model-sbml-l2v5.xml new file mode 100644 index 000000000..5c492e3c3 --- /dev/null +++ b/latest/cases/00542/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00542/model-sbml-l3v2.xml b/latest/cases/00542/model-sbml-l3v2.xml new file mode 100644 index 000000000..12e1738a3 --- /dev/null +++ b/latest/cases/00542/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00542/synopsis.txt b/latest/cases/00542/synopsis.txt new file mode 100644 index 000000000..c4f1cbc72 --- /dev/null +++ b/latest/cases/00542/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions with three species in one 1D compartment, +with an algebraic rule used to determine value of the compartment size. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called X0, X1 and T and two parameters called k1 and k2. Compartment +C is 1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule which must be used to determine the value of +compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $C - 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Length of compartment C |$undeclared$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00543/l2v5/build.log b/latest/cases/00543/l2v5/build.log new file mode 100644 index 000000000..a6c8c4394 --- /dev/null +++ b/latest/cases/00543/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00543/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00543/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00543/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00543/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00543/l2v5/index.heta b/latest/cases/00543/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00543/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00543/l3v2/build.log b/latest/cases/00543/l3v2/build.log new file mode 100644 index 000000000..a684c9a91 --- /dev/null +++ b/latest/cases/00543/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00543/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00543/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00543/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00543/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00543/l3v2/index.heta b/latest/cases/00543/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00543/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00543/model-sbml-l2v5.xml b/latest/cases/00543/model-sbml-l2v5.xml new file mode 100644 index 000000000..cc58b47b2 --- /dev/null +++ b/latest/cases/00543/model-sbml-l2v5.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + k1 + X0 + + + + + + + + + + + + + + + + + + + k2 + S1 + + + + + + + diff --git a/latest/cases/00543/model-sbml-l3v2.xml b/latest/cases/00543/model-sbml-l3v2.xml new file mode 100644 index 000000000..7e2206d75 --- /dev/null +++ b/latest/cases/00543/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + k1 + X0 + + + + + + + + + + + + + + + + + + + k2 + S1 + + + + + + + diff --git a/latest/cases/00543/synopsis.txt b/latest/cases/00543/synopsis.txt new file mode 100644 index 000000000..7828c2e90 --- /dev/null +++ b/latest/cases/00543/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. +Compartment C is 0-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $k1 * X0$ | +| T -> X1 | $k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00544/l2v5/build.log b/latest/cases/00544/l2v5/build.log new file mode 100644 index 000000000..c7f7eb8f8 --- /dev/null +++ b/latest/cases/00544/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00544/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00544/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00544/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00544/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00544/l2v5/index.heta b/latest/cases/00544/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00544/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00544/l3v2/build.log b/latest/cases/00544/l3v2/build.log new file mode 100644 index 000000000..1574a5ea5 --- /dev/null +++ b/latest/cases/00544/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00544/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00544/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00544/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00544/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00544/l3v2/index.heta b/latest/cases/00544/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00544/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00544/model-sbml-l2v5.xml b/latest/cases/00544/model-sbml-l2v5.xml new file mode 100644 index 000000000..767464ef6 --- /dev/null +++ b/latest/cases/00544/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00544/model-sbml-l3v2.xml b/latest/cases/00544/model-sbml-l3v2.xml new file mode 100644 index 000000000..8afb859df --- /dev/null +++ b/latest/cases/00544/model-sbml-l3v2.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00544/synopsis.txt b/latest/cases/00544/synopsis.txt new file mode 100644 index 000000000..592d3a756 --- /dev/null +++ b/latest/cases/00544/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 2D compartment with +with an algebraic rule used to determine value of the compartment size. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Compartment +C is 2-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $C - 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Area of compartment C |$undeclared$ |metre^2^ |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00545/l2v5/build.log b/latest/cases/00545/l2v5/build.log new file mode 100644 index 000000000..e3f652a30 --- /dev/null +++ b/latest/cases/00545/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00545/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00545/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00545/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00545/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00545/l2v5/index.heta b/latest/cases/00545/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00545/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00545/l3v2/build.log b/latest/cases/00545/l3v2/build.log new file mode 100644 index 000000000..cf7bb3a79 --- /dev/null +++ b/latest/cases/00545/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00545/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00545/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00545/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00545/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00545/l3v2/index.heta b/latest/cases/00545/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00545/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00545/model-sbml-l2v5.xml b/latest/cases/00545/model-sbml-l2v5.xml new file mode 100644 index 000000000..bdc4d8297 --- /dev/null +++ b/latest/cases/00545/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00545/model-sbml-l3v2.xml b/latest/cases/00545/model-sbml-l3v2.xml new file mode 100644 index 000000000..520d20ae1 --- /dev/null +++ b/latest/cases/00545/model-sbml-l3v2.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00545/synopsis.txt b/latest/cases/00545/synopsis.txt new file mode 100644 index 000000000..6d43f55a6 --- /dev/null +++ b/latest/cases/00545/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one 1D compartment with +with an algebraic rule used to determine value of the compartment size. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Compartment +C is 1-dimensional. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $C - 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Length of compartment C |$undeclared$ |metre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00546/l2v5/build.log b/latest/cases/00546/l2v5/build.log new file mode 100644 index 000000000..9744c6aef --- /dev/null +++ b/latest/cases/00546/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00546/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00546/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00546/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00546/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00546/l2v5/index.heta b/latest/cases/00546/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00546/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00546/l3v2/build.log b/latest/cases/00546/l3v2/build.log new file mode 100644 index 000000000..76b743f90 --- /dev/null +++ b/latest/cases/00546/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00546/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00546/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00546/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00546/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00546/l3v2/index.heta b/latest/cases/00546/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00546/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00546/model-sbml-l2v5.xml b/latest/cases/00546/model-sbml-l2v5.xml new file mode 100644 index 000000000..42a4ab890 --- /dev/null +++ b/latest/cases/00546/model-sbml-l2v5.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00546/model-sbml-l3v2.xml b/latest/cases/00546/model-sbml-l3v2.xml new file mode 100644 index 000000000..74c0e14ec --- /dev/null +++ b/latest/cases/00546/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/00546/synopsis.txt b/latest/cases/00546/synopsis.txt new file mode 100644 index 000000000..1a86984af --- /dev/null +++ b/latest/cases/00546/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with four species in one 0D compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, 0D-Compartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Compartment C is 0-dimensional. The model contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + +In this example the compartment has its spatialDimensions attribute set to +zero; i.e., it represents a point and therefore cannot have size or units. +The species values must be treated as amounts and not concentrations. + diff --git a/latest/cases/00547/l2v5/build.log b/latest/cases/00547/l2v5/build.log new file mode 100644 index 000000000..3439d5f33 --- /dev/null +++ b/latest/cases/00547/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00547/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00547/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00547/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00547/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00547/l2v5/index.heta b/latest/cases/00547/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00547/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00547/l3v2/build.log b/latest/cases/00547/l3v2/build.log new file mode 100644 index 000000000..662588971 --- /dev/null +++ b/latest/cases/00547/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00547/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00547/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00547/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00547/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00547/l3v2/index.heta b/latest/cases/00547/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00547/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00547/model-sbml-l2v5.xml b/latest/cases/00547/model-sbml-l2v5.xml new file mode 100644 index 000000000..34ab20313 --- /dev/null +++ b/latest/cases/00547/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + C + -2.5 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00547/model-sbml-l3v2.xml b/latest/cases/00547/model-sbml-l3v2.xml new file mode 100644 index 000000000..a2698ab34 --- /dev/null +++ b/latest/cases/00547/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + -2.5 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00547/synopsis.txt b/latest/cases/00547/synopsis.txt new file mode 100644 index 000000000..3e93b8423 --- /dev/null +++ b/latest/cases/00547/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions with three species in one compartment, +with an algebraic rule used to determine value of the compartment size. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called X0, X1 and T and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule which must be used to determine the value of +compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $C - 2.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00548/l2v5/build.log b/latest/cases/00548/l2v5/build.log new file mode 100644 index 000000000..b60a7353e --- /dev/null +++ b/latest/cases/00548/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00548/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00548/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00548/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00548/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00548/l2v5/index.heta b/latest/cases/00548/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00548/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00548/l3v2/build.log b/latest/cases/00548/l3v2/build.log new file mode 100644 index 000000000..f0145b72f --- /dev/null +++ b/latest/cases/00548/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00548/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00548/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00548/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00548/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00548/l3v2/index.heta b/latest/cases/00548/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00548/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00548/model-sbml-l2v5.xml b/latest/cases/00548/model-sbml-l2v5.xml new file mode 100644 index 000000000..0bcac8917 --- /dev/null +++ b/latest/cases/00548/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + C + -0.75 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00548/model-sbml-l3v2.xml b/latest/cases/00548/model-sbml-l3v2.xml new file mode 100644 index 000000000..d73faeb3b --- /dev/null +++ b/latest/cases/00548/model-sbml-l3v2.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + -0.75 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00548/synopsis.txt b/latest/cases/00548/synopsis.txt new file mode 100644 index 000000000..1d14dbe99 --- /dev/null +++ b/latest/cases/00548/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment with +with an algebraic rule used to determine value of the compartment size. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $C - 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$7.5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$undeclared$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00549/l2v5/build.log b/latest/cases/00549/l2v5/build.log new file mode 100644 index 000000000..1642cd3a8 --- /dev/null +++ b/latest/cases/00549/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00549/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00549/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00549/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00549/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00549/l2v5/index.heta b/latest/cases/00549/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00549/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00549/l3v2/build.log b/latest/cases/00549/l3v2/build.log new file mode 100644 index 000000000..76b7c2c97 --- /dev/null +++ b/latest/cases/00549/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00549/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00549/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00549/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00549/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00549/l3v2/index.heta b/latest/cases/00549/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00549/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00549/model-sbml-l2v5.xml b/latest/cases/00549/model-sbml-l2v5.xml new file mode 100644 index 000000000..d2d28d70a --- /dev/null +++ b/latest/cases/00549/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00549/model-sbml-l3v2.xml b/latest/cases/00549/model-sbml-l3v2.xml new file mode 100644 index 000000000..9f73e1ca3 --- /dev/null +++ b/latest/cases/00549/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00549/synopsis.txt b/latest/cases/00549/synopsis.txt new file mode 100644 index 000000000..c0aa4b347 --- /dev/null +++ b/latest/cases/00549/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. +Species X0 is labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00550/l2v5/build.log b/latest/cases/00550/l2v5/build.log new file mode 100644 index 000000000..6833c71a1 --- /dev/null +++ b/latest/cases/00550/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00550/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00550/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00550/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00550/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00550/l2v5/index.heta b/latest/cases/00550/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00550/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00550/l3v2/build.log b/latest/cases/00550/l3v2/build.log new file mode 100644 index 000000000..e4eec7d95 --- /dev/null +++ b/latest/cases/00550/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00550/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00550/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00550/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00550/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00550/l3v2/index.heta b/latest/cases/00550/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00550/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00550/model-sbml-l2v5.xml b/latest/cases/00550/model-sbml-l2v5.xml new file mode 100644 index 000000000..1751037ac --- /dev/null +++ b/latest/cases/00550/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00550/model-sbml-l3v2.xml b/latest/cases/00550/model-sbml-l3v2.xml new file mode 100644 index 000000000..2f90730fb --- /dev/null +++ b/latest/cases/00550/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00550/synopsis.txt b/latest/cases/00550/synopsis.txt new file mode 100644 index 000000000..6fb4c999c --- /dev/null +++ b/latest/cases/00550/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. +Species X1 is labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00551/l2v5/build.log b/latest/cases/00551/l2v5/build.log new file mode 100644 index 000000000..1065f5eab --- /dev/null +++ b/latest/cases/00551/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00551/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00551/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00551/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00551/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00551/l2v5/index.heta b/latest/cases/00551/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00551/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00551/l3v2/build.log b/latest/cases/00551/l3v2/build.log new file mode 100644 index 000000000..c28894854 --- /dev/null +++ b/latest/cases/00551/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00551/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00551/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00551/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00551/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00551/l3v2/index.heta b/latest/cases/00551/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00551/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00551/model-sbml-l2v5.xml b/latest/cases/00551/model-sbml-l2v5.xml new file mode 100644 index 000000000..2849146a1 --- /dev/null +++ b/latest/cases/00551/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00551/model-sbml-l3v2.xml b/latest/cases/00551/model-sbml-l3v2.xml new file mode 100644 index 000000000..d4e237f77 --- /dev/null +++ b/latest/cases/00551/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00551/synopsis.txt b/latest/cases/00551/synopsis.txt new file mode 100644 index 000000000..6f8d15dd8 --- /dev/null +++ b/latest/cases/00551/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00552/l2v5/build.log b/latest/cases/00552/l2v5/build.log new file mode 100644 index 000000000..8a7c30a7e --- /dev/null +++ b/latest/cases/00552/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00552/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00552/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00552/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00552/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00552/l2v5/index.heta b/latest/cases/00552/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00552/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00552/l3v2/build.log b/latest/cases/00552/l3v2/build.log new file mode 100644 index 000000000..e0f00be0d --- /dev/null +++ b/latest/cases/00552/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00552/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00552/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00552/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00552/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00552/l3v2/index.heta b/latest/cases/00552/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00552/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00552/model-sbml-l2v5.xml b/latest/cases/00552/model-sbml-l2v5.xml new file mode 100644 index 000000000..451809c3a --- /dev/null +++ b/latest/cases/00552/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00552/model-sbml-l3v2.xml b/latest/cases/00552/model-sbml-l3v2.xml new file mode 100644 index 000000000..2644de25c --- /dev/null +++ b/latest/cases/00552/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00552/synopsis.txt b/latest/cases/00552/synopsis.txt new file mode 100644 index 000000000..9b602f5b6 --- /dev/null +++ b/latest/cases/00552/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Species S2 is labeled as an SBML boundary species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00553/l2v5/build.log b/latest/cases/00553/l2v5/build.log new file mode 100644 index 000000000..3a10b07c2 --- /dev/null +++ b/latest/cases/00553/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00553/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00553/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00553/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00553/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00553/l2v5/index.heta b/latest/cases/00553/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00553/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00553/l3v2/build.log b/latest/cases/00553/l3v2/build.log new file mode 100644 index 000000000..779b4d0c0 --- /dev/null +++ b/latest/cases/00553/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00553/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00553/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00553/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00553/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00553/l3v2/index.heta b/latest/cases/00553/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00553/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00553/model-sbml-l2v5.xml b/latest/cases/00553/model-sbml-l2v5.xml new file mode 100644 index 000000000..40d5377c2 --- /dev/null +++ b/latest/cases/00553/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00553/model-sbml-l3v2.xml b/latest/cases/00553/model-sbml-l3v2.xml new file mode 100644 index 000000000..af44a17c9 --- /dev/null +++ b/latest/cases/00553/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00553/synopsis.txt b/latest/cases/00553/synopsis.txt new file mode 100644 index 000000000..89034ce28 --- /dev/null +++ b/latest/cases/00553/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Species S3 is labeled as an SBML boundary species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00554/l2v5/build.log b/latest/cases/00554/l2v5/build.log new file mode 100644 index 000000000..a0feb032d --- /dev/null +++ b/latest/cases/00554/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00554/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00554/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00554/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00554/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00554/l2v5/index.heta b/latest/cases/00554/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00554/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00554/l3v2/build.log b/latest/cases/00554/l3v2/build.log new file mode 100644 index 000000000..18d7176fd --- /dev/null +++ b/latest/cases/00554/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00554/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00554/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00554/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00554/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00554/l3v2/index.heta b/latest/cases/00554/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00554/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00554/model-sbml-l2v5.xml b/latest/cases/00554/model-sbml-l2v5.xml new file mode 100644 index 000000000..15eac6220 --- /dev/null +++ b/latest/cases/00554/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00554/model-sbml-l3v2.xml b/latest/cases/00554/model-sbml-l3v2.xml new file mode 100644 index 000000000..9f6f2a83c --- /dev/null +++ b/latest/cases/00554/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00554/synopsis.txt b/latest/cases/00554/synopsis.txt new file mode 100644 index 000000000..9656c8603 --- /dev/null +++ b/latest/cases/00554/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Species S4 is labeled as an SBML boundary species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00555/l2v5/build.log b/latest/cases/00555/l2v5/build.log new file mode 100644 index 000000000..94de40a17 --- /dev/null +++ b/latest/cases/00555/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00555/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00555/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00555/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00555/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00555/l2v5/index.heta b/latest/cases/00555/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00555/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00555/l3v2/build.log b/latest/cases/00555/l3v2/build.log new file mode 100644 index 000000000..dac4c4ac0 --- /dev/null +++ b/latest/cases/00555/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00555/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00555/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00555/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00555/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00555/l3v2/index.heta b/latest/cases/00555/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00555/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00555/model-sbml-l2v5.xml b/latest/cases/00555/model-sbml-l2v5.xml new file mode 100644 index 000000000..9af952edb --- /dev/null +++ b/latest/cases/00555/model-sbml-l2v5.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + S2 + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00555/model-sbml-l3v2.xml b/latest/cases/00555/model-sbml-l3v2.xml new file mode 100644 index 000000000..70f76afb4 --- /dev/null +++ b/latest/cases/00555/model-sbml-l3v2.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + S2 + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00555/synopsis.txt b/latest/cases/00555/synopsis.txt new file mode 100644 index 000000000..265c49d4e --- /dev/null +++ b/latest/cases/00555/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are five +species called X0, X1, T, S1 and S2 and three parameters called k1, k2 and k3. +Species S2 is labeled as a constant. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T + S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00556/l2v5/build.log b/latest/cases/00556/l2v5/build.log new file mode 100644 index 000000000..7a8ae6bcf --- /dev/null +++ b/latest/cases/00556/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00556/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00556/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00556/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00556/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00556/l2v5/index.heta b/latest/cases/00556/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00556/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00556/l3v2/build.log b/latest/cases/00556/l3v2/build.log new file mode 100644 index 000000000..b17ea8624 --- /dev/null +++ b/latest/cases/00556/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00556/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00556/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00556/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00556/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00556/l3v2/index.heta b/latest/cases/00556/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00556/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00556/model-sbml-l2v5.xml b/latest/cases/00556/model-sbml-l2v5.xml new file mode 100644 index 000000000..58abf7095 --- /dev/null +++ b/latest/cases/00556/model-sbml-l2v5.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + S4 + + + -1 + S5 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00556/model-sbml-l3v2.xml b/latest/cases/00556/model-sbml-l3v2.xml new file mode 100644 index 000000000..718475f24 --- /dev/null +++ b/latest/cases/00556/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + S4 + + + -1 + S5 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00556/synopsis.txt b/latest/cases/00556/synopsis.txt new file mode 100644 index 000000000..e474e778d --- /dev/null +++ b/latest/cases/00556/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with five species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are five +species called S1, S2, S3, S4 and S5 and two parameters called k1 and k2. +Species S5 is labeled as a constant species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1 - S5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$5.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Initial amount of S5 |$5.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00557/l2v5/build.log b/latest/cases/00557/l2v5/build.log new file mode 100644 index 000000000..f8505be13 --- /dev/null +++ b/latest/cases/00557/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00557/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00557/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00557/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00557/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00557/l2v5/index.heta b/latest/cases/00557/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00557/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00557/l3v2/build.log b/latest/cases/00557/l3v2/build.log new file mode 100644 index 000000000..bcfee9821 --- /dev/null +++ b/latest/cases/00557/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00557/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00557/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00557/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00557/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00557/l3v2/index.heta b/latest/cases/00557/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00557/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00557/model-sbml-l2v5.xml b/latest/cases/00557/model-sbml-l2v5.xml new file mode 100644 index 000000000..9c5d69c89 --- /dev/null +++ b/latest/cases/00557/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00557/model-sbml-l3v2.xml b/latest/cases/00557/model-sbml-l3v2.xml new file mode 100644 index 000000000..a4d67fca1 --- /dev/null +++ b/latest/cases/00557/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00557/synopsis.txt b/latest/cases/00557/synopsis.txt new file mode 100644 index 000000000..d3d4e4fef --- /dev/null +++ b/latest/cases/00557/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. +Species X0 is labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> 2T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00558/l2v5/build.log b/latest/cases/00558/l2v5/build.log new file mode 100644 index 000000000..e1a176ced --- /dev/null +++ b/latest/cases/00558/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00558/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00558/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00558/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00558/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00558/l2v5/index.heta b/latest/cases/00558/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00558/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00558/l3v2/build.log b/latest/cases/00558/l3v2/build.log new file mode 100644 index 000000000..83a620c92 --- /dev/null +++ b/latest/cases/00558/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00558/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00558/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00558/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00558/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00558/l3v2/index.heta b/latest/cases/00558/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00558/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00558/model-sbml-l2v5.xml b/latest/cases/00558/model-sbml-l2v5.xml new file mode 100644 index 000000000..ea8a47fa2 --- /dev/null +++ b/latest/cases/00558/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00558/model-sbml-l3v2.xml b/latest/cases/00558/model-sbml-l3v2.xml new file mode 100644 index 000000000..8fc3e48b0 --- /dev/null +++ b/latest/cases/00558/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00558/synopsis.txt b/latest/cases/00558/synopsis.txt new file mode 100644 index 000000000..43de4cb22 --- /dev/null +++ b/latest/cases/00558/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. +Species X0 is labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$0.5$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00559/l2v5/build.log b/latest/cases/00559/l2v5/build.log new file mode 100644 index 000000000..b67eadaf3 --- /dev/null +++ b/latest/cases/00559/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00559/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00559/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00559/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00559/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00559/l2v5/index.heta b/latest/cases/00559/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00559/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00559/l3v2/build.log b/latest/cases/00559/l3v2/build.log new file mode 100644 index 000000000..41af217db --- /dev/null +++ b/latest/cases/00559/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00559/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00559/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00559/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00559/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00559/l3v2/index.heta b/latest/cases/00559/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00559/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00559/model-sbml-l2v5.xml b/latest/cases/00559/model-sbml-l2v5.xml new file mode 100644 index 000000000..4757d4b0b --- /dev/null +++ b/latest/cases/00559/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00559/model-sbml-l3v2.xml b/latest/cases/00559/model-sbml-l3v2.xml new file mode 100644 index 000000000..b165069b4 --- /dev/null +++ b/latest/cases/00559/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00559/synopsis.txt b/latest/cases/00559/synopsis.txt new file mode 100644 index 000000000..42269ef5d --- /dev/null +++ b/latest/cases/00559/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Species S3 is labeled as an SBML boundary species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00560/l2v5/build.log b/latest/cases/00560/l2v5/build.log new file mode 100644 index 000000000..8842b40c0 --- /dev/null +++ b/latest/cases/00560/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00560/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00560/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00560/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00560/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00560/l2v5/index.heta b/latest/cases/00560/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00560/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00560/l3v2/build.log b/latest/cases/00560/l3v2/build.log new file mode 100644 index 000000000..4866fa535 --- /dev/null +++ b/latest/cases/00560/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00560/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00560/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00560/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00560/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00560/l3v2/index.heta b/latest/cases/00560/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00560/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00560/model-sbml-l2v5.xml b/latest/cases/00560/model-sbml-l2v5.xml new file mode 100644 index 000000000..15e6b9d98 --- /dev/null +++ b/latest/cases/00560/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00560/model-sbml-l3v2.xml b/latest/cases/00560/model-sbml-l3v2.xml new file mode 100644 index 000000000..6ef0db991 --- /dev/null +++ b/latest/cases/00560/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00560/synopsis.txt b/latest/cases/00560/synopsis.txt new file mode 100644 index 000000000..299aae5ee --- /dev/null +++ b/latest/cases/00560/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Species S3 is labeled as an SBML boundary species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| 2S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00561/l2v5/build.log b/latest/cases/00561/l2v5/build.log new file mode 100644 index 000000000..e1c325b54 --- /dev/null +++ b/latest/cases/00561/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00561/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00561/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00561/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00561/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00561/l2v5/index.heta b/latest/cases/00561/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00561/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00561/l3v2/index.heta b/latest/cases/00561/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00561/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00561/model-sbml-l2v5.xml b/latest/cases/00561/model-sbml-l2v5.xml new file mode 100644 index 000000000..df5bb4922 --- /dev/null +++ b/latest/cases/00561/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00561/synopsis.txt b/latest/cases/00561/synopsis.txt new file mode 100644 index 000000000..3fcdce6ba --- /dev/null +++ b/latest/cases/00561/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and four parameters called k1, k2, k3 and p1. +Species X0 is labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> (4 * p1)T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00562/l2v5/build.log b/latest/cases/00562/l2v5/build.log new file mode 100644 index 000000000..6213d1a63 --- /dev/null +++ b/latest/cases/00562/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00562/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00562/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00562/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00562/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00562/l2v5/index.heta b/latest/cases/00562/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00562/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00562/l3v2/index.heta b/latest/cases/00562/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00562/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00562/model-sbml-l2v5.xml b/latest/cases/00562/model-sbml-l2v5.xml new file mode 100644 index 000000000..01e1b960a --- /dev/null +++ b/latest/cases/00562/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00562/synopsis.txt b/latest/cases/00562/synopsis.txt new file mode 100644 index 000000000..b10141ca0 --- /dev/null +++ b/latest/cases/00562/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and four parameters called k1, k2, k3 and p1. +Species X0 is labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| (4 * p1)X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$0.5$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00563/l2v5/build.log b/latest/cases/00563/l2v5/build.log new file mode 100644 index 000000000..001e19a82 --- /dev/null +++ b/latest/cases/00563/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00563/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00563/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00563/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00563/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00563/l2v5/index.heta b/latest/cases/00563/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00563/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00563/l3v2/index.heta b/latest/cases/00563/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00563/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00563/model-sbml-l2v5.xml b/latest/cases/00563/model-sbml-l2v5.xml new file mode 100644 index 000000000..6483adefc --- /dev/null +++ b/latest/cases/00563/model-sbml-l2v5.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00563/synopsis.txt b/latest/cases/00563/synopsis.txt new file mode 100644 index 000000000..e6ec6d334 --- /dev/null +++ b/latest/cases/00563/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +Species S3 is labeled as an SBML boundary species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00564/l2v5/build.log b/latest/cases/00564/l2v5/build.log new file mode 100644 index 000000000..1fa4cedb1 --- /dev/null +++ b/latest/cases/00564/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00564/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00564/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00564/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00564/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00564/l2v5/index.heta b/latest/cases/00564/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00564/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00564/l3v2/index.heta b/latest/cases/00564/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00564/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00564/model-sbml-l2v5.xml b/latest/cases/00564/model-sbml-l2v5.xml new file mode 100644 index 000000000..3a0d594c7 --- /dev/null +++ b/latest/cases/00564/model-sbml-l2v5.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00564/synopsis.txt b/latest/cases/00564/synopsis.txt new file mode 100644 index 000000000..38ac4c8a7 --- /dev/null +++ b/latest/cases/00564/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +Species S3 is labeled as an SBML boundary species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| (4 * p1)S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00565/l2v5/build.log b/latest/cases/00565/l2v5/build.log new file mode 100644 index 000000000..6499e7173 --- /dev/null +++ b/latest/cases/00565/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00565/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00565/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00565/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00565/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00565/l2v5/index.heta b/latest/cases/00565/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00565/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00565/l3v2/build.log b/latest/cases/00565/l3v2/build.log new file mode 100644 index 000000000..f3e99667c --- /dev/null +++ b/latest/cases/00565/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00565/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00565/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00565/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00565/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00565/l3v2/index.heta b/latest/cases/00565/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00565/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00565/model-sbml-l2v5.xml b/latest/cases/00565/model-sbml-l2v5.xml new file mode 100644 index 000000000..8e6fd8ed0 --- /dev/null +++ b/latest/cases/00565/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k + X0 + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00565/model-sbml-l3v2.xml b/latest/cases/00565/model-sbml-l3v2.xml new file mode 100644 index 000000000..18d3b1547 --- /dev/null +++ b/latest/cases/00565/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k + X0 + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00565/synopsis.txt b/latest/cases/00565/synopsis.txt new file mode 100644 index 000000000..790222d0c --- /dev/null +++ b/latest/cases/00565/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and one parameter k. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k * X0$ | +| T -> X1 | $C * k * S1$ |] + +Reaction X0 -> T defines one local parameter k. Reaction T -> X1 defines another +local parameter k. Note that these parameters have a +scope local to the defining reaction. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k |$2.5$ |dimensionless | +|Value of local parameter k |$0.1$ |second^-1^ | +|Value of local parameter k |$0.375$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00566/l2v5/build.log b/latest/cases/00566/l2v5/build.log new file mode 100644 index 000000000..f3d0771ad --- /dev/null +++ b/latest/cases/00566/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00566/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00566/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00566/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00566/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00566/l2v5/index.heta b/latest/cases/00566/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00566/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00566/l3v2/build.log b/latest/cases/00566/l3v2/build.log new file mode 100644 index 000000000..27e59dcd2 --- /dev/null +++ b/latest/cases/00566/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00566/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00566/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00566/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00566/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00566/l3v2/index.heta b/latest/cases/00566/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00566/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00566/model-sbml-l2v5.xml b/latest/cases/00566/model-sbml-l2v5.xml new file mode 100644 index 000000000..edc3953d0 --- /dev/null +++ b/latest/cases/00566/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00566/model-sbml-l3v2.xml b/latest/cases/00566/model-sbml-l3v2.xml new file mode 100644 index 000000000..5dd31720c --- /dev/null +++ b/latest/cases/00566/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00566/synopsis.txt b/latest/cases/00566/synopsis.txt new file mode 100644 index 000000000..d454eee32 --- /dev/null +++ b/latest/cases/00566/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, AlgebraicRule +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + + +Reaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 + +S2 defines another local parameter k. Note that these parameters have a +scope local to the defining reaction. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of local parameter k |$0.75$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00567/l2v5/build.log b/latest/cases/00567/l2v5/build.log new file mode 100644 index 000000000..d46dcce55 --- /dev/null +++ b/latest/cases/00567/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00567/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00567/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00567/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00567/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00567/l2v5/index.heta b/latest/cases/00567/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00567/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00567/l3v2/build.log b/latest/cases/00567/l3v2/build.log new file mode 100644 index 000000000..269c538bf --- /dev/null +++ b/latest/cases/00567/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00567/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00567/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00567/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00567/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00567/l3v2/index.heta b/latest/cases/00567/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00567/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00567/model-sbml-l2v5.xml b/latest/cases/00567/model-sbml-l2v5.xml new file mode 100644 index 000000000..ea9881242 --- /dev/null +++ b/latest/cases/00567/model-sbml-l2v5.xml @@ -0,0 +1,102 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00567/model-sbml-l3v2.xml b/latest/cases/00567/model-sbml-l3v2.xml new file mode 100644 index 000000000..7cf1ad815 --- /dev/null +++ b/latest/cases/00567/model-sbml-l3v2.xml @@ -0,0 +1,119 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00567/synopsis.txt b/latest/cases/00567/synopsis.txt new file mode 100644 index 000000000..926aeed6e --- /dev/null +++ b/latest/cases/00567/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $multiply((1 + k3), S1) - T$ |] + +The rule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00568/l2v5/build.log b/latest/cases/00568/l2v5/build.log new file mode 100644 index 000000000..960daef0b --- /dev/null +++ b/latest/cases/00568/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00568/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00568/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00568/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00568/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00568/l2v5/index.heta b/latest/cases/00568/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00568/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00568/l3v2/build.log b/latest/cases/00568/l3v2/build.log new file mode 100644 index 000000000..6786c7dc4 --- /dev/null +++ b/latest/cases/00568/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00568/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00568/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00568/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00568/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00568/l3v2/index.heta b/latest/cases/00568/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00568/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00568/model-sbml-l2v5.xml b/latest/cases/00568/model-sbml-l2v5.xml new file mode 100644 index 000000000..470d8caba --- /dev/null +++ b/latest/cases/00568/model-sbml-l2v5.xml @@ -0,0 +1,95 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + + add + X0 + X1 + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00568/model-sbml-l3v2.xml b/latest/cases/00568/model-sbml-l3v2.xml new file mode 100644 index 000000000..0944427d9 --- /dev/null +++ b/latest/cases/00568/model-sbml-l3v2.xml @@ -0,0 +1,112 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + + add + X0 + X1 + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00568/synopsis.txt b/latest/cases/00568/synopsis.txt new file mode 100644 index 000000000..5ca4d902d --- /dev/null +++ b/latest/cases/00568/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $add(X0, X1) + T - S1$ |] + +The rule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1.25$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Initial amount of S1 |$3.75$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00569/l2v5/build.log b/latest/cases/00569/l2v5/build.log new file mode 100644 index 000000000..8d3a6c6ff --- /dev/null +++ b/latest/cases/00569/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00569/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00569/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00569/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00569/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00569/l2v5/index.heta b/latest/cases/00569/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00569/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00569/l3v2/build.log b/latest/cases/00569/l3v2/build.log new file mode 100644 index 000000000..33849789d --- /dev/null +++ b/latest/cases/00569/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00569/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00569/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00569/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00569/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00569/l3v2/index.heta b/latest/cases/00569/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00569/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00569/model-sbml-l2v5.xml b/latest/cases/00569/model-sbml-l2v5.xml new file mode 100644 index 000000000..f67608f22 --- /dev/null +++ b/latest/cases/00569/model-sbml-l2v5.xml @@ -0,0 +1,113 @@ + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + subtract + k2 + 0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00569/model-sbml-l3v2.xml b/latest/cases/00569/model-sbml-l3v2.xml new file mode 100644 index 000000000..682ba7321 --- /dev/null +++ b/latest/cases/00569/model-sbml-l3v2.xml @@ -0,0 +1,130 @@ + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subtract + k2 + 0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00569/synopsis.txt b/latest/cases/00569/synopsis.txt new file mode 100644 index 000000000..4948e45dc --- /dev/null +++ b/latest/cases/00569/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Three reactions with four species in one compartment, +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $subtract(k2, 0.9)$ |] + +The rule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | subtract | x, y | $x - y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00570/l2v5/build.log b/latest/cases/00570/l2v5/build.log new file mode 100644 index 000000000..1a2fc359d --- /dev/null +++ b/latest/cases/00570/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00570/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00570/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00570/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00570/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00570/l2v5/index.heta b/latest/cases/00570/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00570/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00570/l3v2/build.log b/latest/cases/00570/l3v2/build.log new file mode 100644 index 000000000..9c3f82434 --- /dev/null +++ b/latest/cases/00570/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00570/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00570/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00570/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00570/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00570/l3v2/index.heta b/latest/cases/00570/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00570/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00570/model-sbml-l2v5.xml b/latest/cases/00570/model-sbml-l2v5.xml new file mode 100644 index 000000000..cb7723b3c --- /dev/null +++ b/latest/cases/00570/model-sbml-l2v5.xml @@ -0,0 +1,117 @@ + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + + + subtract + k2 + k3 + + -0.2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00570/model-sbml-l3v2.xml b/latest/cases/00570/model-sbml-l3v2.xml new file mode 100644 index 000000000..dbe642dfc --- /dev/null +++ b/latest/cases/00570/model-sbml-l3v2.xml @@ -0,0 +1,134 @@ + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subtract + k2 + k3 + + -0.2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00570/synopsis.txt b/latest/cases/00570/synopsis.txt new file mode 100644 index 000000000..63e577d5a --- /dev/null +++ b/latest/cases/00570/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Three reactions with four species in one compartment, +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $subtract(k2, k3) - 0.2$ |] + +The rule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | subtract | x, y | $x - y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00571/l2v5/build.log b/latest/cases/00571/l2v5/build.log new file mode 100644 index 000000000..ec471a72b --- /dev/null +++ b/latest/cases/00571/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00571/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00571/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00571/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00571/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00571/l2v5/index.heta b/latest/cases/00571/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00571/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00571/l3v2/build.log b/latest/cases/00571/l3v2/build.log new file mode 100644 index 000000000..d730b01ef --- /dev/null +++ b/latest/cases/00571/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00571/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00571/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00571/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00571/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00571/l3v2/index.heta b/latest/cases/00571/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00571/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00571/model-sbml-l2v5.xml b/latest/cases/00571/model-sbml-l2v5.xml new file mode 100644 index 000000000..82e913fa1 --- /dev/null +++ b/latest/cases/00571/model-sbml-l2v5.xml @@ -0,0 +1,119 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + subtract + + multiply + + + k3 + 1 + + S1 + + T + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00571/model-sbml-l3v2.xml b/latest/cases/00571/model-sbml-l3v2.xml new file mode 100644 index 000000000..e2e8cf774 --- /dev/null +++ b/latest/cases/00571/model-sbml-l3v2.xml @@ -0,0 +1,136 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subtract + + multiply + + + k3 + 1 + + S1 + + T + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00571/synopsis.txt b/latest/cases/00571/synopsis.txt new file mode 100644 index 000000000..3859ccbc3 --- /dev/null +++ b/latest/cases/00571/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $subtract(multiply((1 + k3), S1), T)$ |] + +The rule applies both the functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | subtract | x, y | $x - y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00572/l2v5/build.log b/latest/cases/00572/l2v5/build.log new file mode 100644 index 000000000..e9eb6edac --- /dev/null +++ b/latest/cases/00572/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00572/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00572/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00572/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00572/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00572/l2v5/index.heta b/latest/cases/00572/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00572/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00572/l3v2/build.log b/latest/cases/00572/l3v2/build.log new file mode 100644 index 000000000..f38f43185 --- /dev/null +++ b/latest/cases/00572/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00572/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00572/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00572/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00572/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00572/l3v2/index.heta b/latest/cases/00572/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00572/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00572/model-sbml-l2v5.xml b/latest/cases/00572/model-sbml-l2v5.xml new file mode 100644 index 000000000..d733661d0 --- /dev/null +++ b/latest/cases/00572/model-sbml-l2v5.xml @@ -0,0 +1,98 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + add + + add + X0 + X1 + + T + + + + -1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00572/model-sbml-l3v2.xml b/latest/cases/00572/model-sbml-l3v2.xml new file mode 100644 index 000000000..76cdbc686 --- /dev/null +++ b/latest/cases/00572/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + add + + add + X0 + X1 + + T + + + + -1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + diff --git a/latest/cases/00572/synopsis.txt b/latest/cases/00572/synopsis.txt new file mode 100644 index 000000000..4e65a8536 --- /dev/null +++ b/latest/cases/00572/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $add(add(X0, X1), T) - S1$ |] + +The rule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1.25$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Initial amount of S1 |$3.75$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00573/l2v5/build.log b/latest/cases/00573/l2v5/build.log new file mode 100644 index 000000000..49d89b1bd --- /dev/null +++ b/latest/cases/00573/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00573/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00573/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00573/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00573/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00573/l2v5/index.heta b/latest/cases/00573/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00573/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00573/l3v2/build.log b/latest/cases/00573/l3v2/build.log new file mode 100644 index 000000000..cdf8d5da2 --- /dev/null +++ b/latest/cases/00573/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00573/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00573/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00573/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00573/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00573/l3v2/index.heta b/latest/cases/00573/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00573/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00573/model-sbml-l2v5.xml b/latest/cases/00573/model-sbml-l2v5.xml new file mode 100644 index 000000000..4abded618 --- /dev/null +++ b/latest/cases/00573/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + p4 + + + + -1 + p3 + + + + + + + + + -1 + k1 + p1 + + + + + + + + + + k1 + p1 + + + + -1 + k2 + p4 + + + + + + + + + k2 + p4 + + + + + + diff --git a/latest/cases/00573/model-sbml-l3v2.xml b/latest/cases/00573/model-sbml-l3v2.xml new file mode 100644 index 000000000..b743c7810 --- /dev/null +++ b/latest/cases/00573/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + p4 + + + + -1 + p3 + + + + + + + + + -1 + k1 + p1 + + + + + + + + + + k1 + p1 + + + + -1 + k2 + p4 + + + + + + + + + k2 + p4 + + + + + + diff --git a/latest/cases/00573/synopsis.txt b/latest/cases/00573/synopsis.txt new file mode 100644 index 000000000..92c5b29fd --- /dev/null +++ b/latest/cases/00573/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Model using parameters and rules only with an algebraic rule. +componentTags: Parameter, RateRule, AlgebraicRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four variable parameters called p1, p2, p3 and p4 +and three constant parameters called k1, k2 and k3. The model contains +four rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * p4 - p3$ | + | Rate | p1 | $-p1 * k1$ | + | Rate | p2 | $p4 * k2$ | + | Rate | p3 | $p1 * k1 - k2 * p4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto} | |*Value* |*Units* | +|Initial value of parameter p1 |$1$ |any | +|Initial value of parameter p2 |$0$ |same as p1 | +|Initial value of parameter p3 |$0$ |same as p1 | +|Initial value of parameter p4 |$0$ |same as p1 | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless |] + + diff --git a/latest/cases/00574/l2v5/build.log b/latest/cases/00574/l2v5/build.log new file mode 100644 index 000000000..34d2153fb --- /dev/null +++ b/latest/cases/00574/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00574/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00574/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00574/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00574/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00574/l2v5/index.heta b/latest/cases/00574/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00574/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00574/l3v2/build.log b/latest/cases/00574/l3v2/build.log new file mode 100644 index 000000000..15d1bd8f4 --- /dev/null +++ b/latest/cases/00574/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00574/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00574/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00574/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00574/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00574/l3v2/index.heta b/latest/cases/00574/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00574/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00574/model-sbml-l2v5.xml b/latest/cases/00574/model-sbml-l2v5.xml new file mode 100644 index 000000000..f04ab834a --- /dev/null +++ b/latest/cases/00574/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + p1 + p2 + p3 + + + -1 + p4 + + + + + + + + + -1 + k1 + p1 + + + + + + + + + + k1 + p1 + + + + -1 + k2 + p3 + + + + + + + + + k2 + p3 + + + + + + diff --git a/latest/cases/00574/model-sbml-l3v2.xml b/latest/cases/00574/model-sbml-l3v2.xml new file mode 100644 index 000000000..acc9b20df --- /dev/null +++ b/latest/cases/00574/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + p1 + p2 + p3 + + + -1 + p4 + + + + + + + + + -1 + k1 + p1 + + + + + + + + + + k1 + p1 + + + + -1 + k2 + p3 + + + + + + + + + k2 + p3 + + + + + + diff --git a/latest/cases/00574/synopsis.txt b/latest/cases/00574/synopsis.txt new file mode 100644 index 000000000..c25ef60c8 --- /dev/null +++ b/latest/cases/00574/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Model using parameters and rules only with an algebraic rule. +componentTags: Parameter, RateRule, AlgebraicRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four variable parameters called p1, p2, p3 and p4 +and two constant parameters called k1 and k2. The model contains +four rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $p1 + p2 + p3 - p4$ | + | Rate | p1 | $-p1 * k1$ | + | Rate | p2 | $p3 * k2$ | + | Rate | p3 | $p1 * k1 - k2 * p3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial value of parameter p1 |$1.25$ |any | +|Initial value of parameter p2 |$1.5$ |same as p1 | +|Initial value of parameter p3 |$1$ |same as p1 | +|Initial value of parameter p4 |$3.75$ |same as p1 | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ |] + diff --git a/latest/cases/00575/l2v5/build.log b/latest/cases/00575/l2v5/build.log new file mode 100644 index 000000000..e47b2edd8 --- /dev/null +++ b/latest/cases/00575/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00575/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00575/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00575/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00575/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00575/l2v5/index.heta b/latest/cases/00575/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00575/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00575/l3v2/build.log b/latest/cases/00575/l3v2/build.log new file mode 100644 index 000000000..bd58f5fc3 --- /dev/null +++ b/latest/cases/00575/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00575/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00575/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00575/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00575/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00575/l3v2/index.heta b/latest/cases/00575/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00575/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00575/model-sbml-l2v5.xml b/latest/cases/00575/model-sbml-l2v5.xml new file mode 100644 index 000000000..508c774a2 --- /dev/null +++ b/latest/cases/00575/model-sbml-l2v5.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + k2 + -0.9 + + + + + + + + + + -1 + k1 + p1 + p2 + + + + k2 + p3 + + + + k3 + p3 + + + + + + + + + + + k2 + p3 + + + + -1 + k1 + p1 + p2 + + + + + + + + + + + k1 + p1 + p2 + + + + -1 + k2 + p3 + + + + -1 + k3 + p3 + + + + + + + + + k3 + p3 + + + + + + diff --git a/latest/cases/00575/model-sbml-l3v2.xml b/latest/cases/00575/model-sbml-l3v2.xml new file mode 100644 index 000000000..9d89edfe7 --- /dev/null +++ b/latest/cases/00575/model-sbml-l3v2.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + -0.9 + + + + + + + + + + -1 + k1 + p1 + p2 + + + + k2 + p3 + + + + k3 + p3 + + + + + + + + + + + k2 + p3 + + + + -1 + k1 + p1 + p2 + + + + + + + + + + + k1 + p1 + p2 + + + + -1 + k2 + p3 + + + + -1 + k3 + p3 + + + + + + + + + k3 + p3 + + + + + + diff --git a/latest/cases/00575/synopsis.txt b/latest/cases/00575/synopsis.txt new file mode 100644 index 000000000..ae24d11fd --- /dev/null +++ b/latest/cases/00575/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Model using parameters and rules only with an algebraic rule. +componentTags: Parameter, RateRule, AlgebraicRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four variable parameters called p1, p2, p3 and p4 +and three constant parameters called k1, k2 and k3. The model contains +five rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $k2 - 0.9$ |] + | Rate | p1 | $-k1 * p1 * p2 + k2 * p3 + k3 * p3$ | + | Rate | p2 | $-k1 * p1 * p2 + k2 * p3$ | + | Rate | p3 | $k1 * p1 * p2 - k2 * p3 - k3 * p3$ | + | Rate | p4 | $k3 * p3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial value of parameter p1 |$2.0 \x 10^-4$ |any | +|Initial value of parameter p2 |$2.0 \x 10^-4$ |same as p1 | +|Initial value of parameter p3 |$0$ |same as p1 | +|Initial value of parameter p4 |$0$ |same as p1 | +|Value of parameter k1 |$1.0 \x 10^4$ |(units of p1)^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ |] + diff --git a/latest/cases/00576/l2v5/build.log b/latest/cases/00576/l2v5/build.log new file mode 100644 index 000000000..3f7f6cf34 --- /dev/null +++ b/latest/cases/00576/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00576/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00576/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00576/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00576/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00576/l2v5/index.heta b/latest/cases/00576/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00576/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00576/l3v2/build.log b/latest/cases/00576/l3v2/build.log new file mode 100644 index 000000000..1feda8581 --- /dev/null +++ b/latest/cases/00576/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00576/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00576/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00576/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00576/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00576/l3v2/index.heta b/latest/cases/00576/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00576/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00576/model-sbml-l2v5.xml b/latest/cases/00576/model-sbml-l2v5.xml new file mode 100644 index 000000000..88c1ccc67 --- /dev/null +++ b/latest/cases/00576/model-sbml-l2v5.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + p4 + + + -1 + p1 + + + + + + + + + + + k2 + p3 + + + + -1 + k1 + p1 + p2 + + + + + + + + + + + k2 + p3 + + + + -1 + k1 + p1 + p2 + + + + + + + + + + + k1 + p1 + p2 + + + + -1 + k2 + p3 + + + + + + + diff --git a/latest/cases/00576/model-sbml-l3v2.xml b/latest/cases/00576/model-sbml-l3v2.xml new file mode 100644 index 000000000..bd2e6edaa --- /dev/null +++ b/latest/cases/00576/model-sbml-l3v2.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + p4 + + + -1 + p1 + + + + + + + + + + + k2 + p3 + + + + -1 + k1 + p1 + p2 + + + + + + + + + + + k2 + p3 + + + + -1 + k1 + p1 + p2 + + + + + + + + + + + k1 + p1 + p2 + + + + -1 + k2 + p3 + + + + + + + diff --git a/latest/cases/00576/synopsis.txt b/latest/cases/00576/synopsis.txt new file mode 100644 index 000000000..4568ffd8a --- /dev/null +++ b/latest/cases/00576/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Model using parameters and rules only with an algebraic rule. +componentTags: Parameter, RateRule, AlgebraicRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains four variable parameters called p1, p2, p3 and p4 +and two constant parameters called k1 and k2. The model contains +four rules defined as: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $p4 + -1 * p1$ | + | Rate | p1 | $-k1 * p1 * p2 + k2 * p3$ | + | Rate | p2 | $-k1 * p1 * p2 + k2 * p3$ | + | Rate | p3 | $k1 * p1 * p2 - k2 * p3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial value of parameter p1 |$1.0 \x 10^-3$ |any | +|Initial value of parameter p2 |$2.0 \x 10^-3$ |same as p1 | +|Initial value of parameter p3 |$1.0 \x 10^-3$ |same as p1 | +|Initial value of parameter p4 |$1.0 \x 10^-3$ |same as p1 | +|Value of parameter k1 |$0.75$ |(units of p1)^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ |] + diff --git a/latest/cases/00577/l2v5/heta-code/output.heta b/latest/cases/00577/l2v5/heta-code/output.heta new file mode 100644 index 000000000..651e21292 --- /dev/null +++ b/latest/cases/00577/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00577/l2v5/index.heta b/latest/cases/00577/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00577/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00577/l2v5/json/output.json b/latest/cases/00577/l2v5/json/output.json new file mode 100644 index 000000000..561fb753a --- /dev/null +++ b/latest/cases/00577/l2v5/json/output.json @@ -0,0 +1,133 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00577/l3v2/heta-code/output.heta b/latest/cases/00577/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ddcfe4e18 --- /dev/null +++ b/latest/cases/00577/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00577/l3v2/index.heta b/latest/cases/00577/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00577/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00577/l3v2/json/output.json b/latest/cases/00577/l3v2/json/output.json new file mode 100644 index 000000000..34e69fb22 --- /dev/null +++ b/latest/cases/00577/l3v2/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00577/model-sbml-l2v5.xml b/latest/cases/00577/model-sbml-l2v5.xml new file mode 100644 index 000000000..a0c8a5578 --- /dev/null +++ b/latest/cases/00577/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00577/model-sbml-l3v2.xml b/latest/cases/00577/model-sbml-l3v2.xml new file mode 100644 index 000000000..4d7c0e84f --- /dev/null +++ b/latest/cases/00577/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00577/output.heta b/latest/cases/00577/output.heta new file mode 100644 index 000000000..777a748be --- /dev/null +++ b/latest/cases/00577/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment, + and one species labeled as a boundary condition +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S1 +is labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto} | |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00577/synopsis.txt b/latest/cases/00577/synopsis.txt new file mode 100644 index 000000000..2e79f65aa --- /dev/null +++ b/latest/cases/00577/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment, + and one species labeled as a boundary condition +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S1 +is labeled as an SBML boundary species. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto} | |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00578/l2v5/heta-code/output.heta b/latest/cases/00578/l2v5/heta-code/output.heta new file mode 100644 index 000000000..31f105ec9 --- /dev/null +++ b/latest/cases/00578/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00578/l2v5/index.heta b/latest/cases/00578/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00578/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00578/l2v5/json/output.json b/latest/cases/00578/l2v5/json/output.json new file mode 100644 index 000000000..fdb38a889 --- /dev/null +++ b/latest/cases/00578/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00578/l3v2/heta-code/output.heta b/latest/cases/00578/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a152bbf03 --- /dev/null +++ b/latest/cases/00578/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00578/l3v2/index.heta b/latest/cases/00578/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00578/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00578/l3v2/json/output.json b/latest/cases/00578/l3v2/json/output.json new file mode 100644 index 000000000..b3dead5ad --- /dev/null +++ b/latest/cases/00578/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00578/model-sbml-l2v5.xml b/latest/cases/00578/model-sbml-l2v5.xml new file mode 100644 index 000000000..cdfac8fdf --- /dev/null +++ b/latest/cases/00578/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00578/model-sbml-l3v2.xml b/latest/cases/00578/model-sbml-l3v2.xml new file mode 100644 index 000000000..e2f89af70 --- /dev/null +++ b/latest/cases/00578/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00578/output.heta b/latest/cases/00578/output.heta new file mode 100644 index 000000000..e4fc38d38 --- /dev/null +++ b/latest/cases/00578/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment, + and two species labeled as a boundary condition +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S1 +and S2 are labeled as SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00578/synopsis.txt b/latest/cases/00578/synopsis.txt new file mode 100644 index 000000000..e559cba52 --- /dev/null +++ b/latest/cases/00578/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment, + and two species labeled as a boundary condition +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S1 +and S2 are labeled as SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00579/l2v5/heta-code/output.heta b/latest/cases/00579/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0427b6615 --- /dev/null +++ b/latest/cases/00579/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00579/l2v5/index.heta b/latest/cases/00579/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00579/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00579/l2v5/json/output.json b/latest/cases/00579/l2v5/json/output.json new file mode 100644 index 000000000..f7f158d8c --- /dev/null +++ b/latest/cases/00579/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00579/l3v2/heta-code/output.heta b/latest/cases/00579/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a3fd4c307 --- /dev/null +++ b/latest/cases/00579/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00579/l3v2/index.heta b/latest/cases/00579/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00579/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00579/l3v2/json/output.json b/latest/cases/00579/l3v2/json/output.json new file mode 100644 index 000000000..3fd373116 --- /dev/null +++ b/latest/cases/00579/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00579/model-sbml-l2v5.xml b/latest/cases/00579/model-sbml-l2v5.xml new file mode 100644 index 000000000..7265e4448 --- /dev/null +++ b/latest/cases/00579/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00579/model-sbml-l3v2.xml b/latest/cases/00579/model-sbml-l3v2.xml new file mode 100644 index 000000000..de145c295 --- /dev/null +++ b/latest/cases/00579/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00579/output.heta b/latest/cases/00579/output.heta new file mode 100644 index 000000000..69f597e96 --- /dev/null +++ b/latest/cases/00579/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment, + and all species labeled as a boundary condition +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. All three +species S1, S2 and S3 are labeled as SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00579/synopsis.txt b/latest/cases/00579/synopsis.txt new file mode 100644 index 000000000..0512f04a2 --- /dev/null +++ b/latest/cases/00579/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment, + and all species labeled as a boundary condition +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. All three +species S1, S2 and S3 are labeled as SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00580/l2v5/heta-code/output.heta b/latest/cases/00580/l2v5/heta-code/output.heta new file mode 100644 index 000000000..57d725d8e --- /dev/null +++ b/latest/cases/00580/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 1000; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00580/l2v5/index.heta b/latest/cases/00580/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00580/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00580/l2v5/json/output.json b/latest/cases/00580/l2v5/json/output.json new file mode 100644 index 000000000..ef6d39c70 --- /dev/null +++ b/latest/cases/00580/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1000" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00580/l3v2/heta-code/output.heta b/latest/cases/00580/l3v2/heta-code/output.heta new file mode 100644 index 000000000..36aa7ac7e --- /dev/null +++ b/latest/cases/00580/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 1000; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00580/l3v2/index.heta b/latest/cases/00580/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00580/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00580/l3v2/json/output.json b/latest/cases/00580/l3v2/json/output.json new file mode 100644 index 000000000..5406234ac --- /dev/null +++ b/latest/cases/00580/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 2 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00580/model-sbml-l2v5.xml b/latest/cases/00580/model-sbml-l2v5.xml new file mode 100644 index 000000000..1edc45642 --- /dev/null +++ b/latest/cases/00580/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + + + S1 + 2 + + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00580/model-sbml-l3v2.xml b/latest/cases/00580/model-sbml-l3v2.xml new file mode 100644 index 000000000..266387067 --- /dev/null +++ b/latest/cases/00580/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + + + S1 + 2 + + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00580/output.heta b/latest/cases/00580/output.heta new file mode 100644 index 000000000..186c1ce38 --- /dev/null +++ b/latest/cases/00580/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment, + with one species having a stoichiometry of 2 +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2 * C$ | +| S3 -> 2S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$1.0 \x 10^3$ |litre^2^ mole^-2^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * pow(S1, 2) * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 1000; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00580/synopsis.txt b/latest/cases/00580/synopsis.txt new file mode 100644 index 000000000..e9cd84c40 --- /dev/null +++ b/latest/cases/00580/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment, + with one species having a stoichiometry of 2 +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2 * C$ | +| S3 -> 2S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$1.0 \x 10^3$ |litre^2^ mole^-2^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00581/l2v5/heta-code/output.heta b/latest/cases/00581/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e172b74ac --- /dev/null +++ b/latest/cases/00581/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.2; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 2.5; + diff --git a/latest/cases/00581/l2v5/index.heta b/latest/cases/00581/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00581/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00581/l2v5/json/output.json b/latest/cases/00581/l2v5/json/output.json new file mode 100644 index 000000000..ab647f73d --- /dev/null +++ b/latest/cases/00581/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00581/l3v2/heta-code/output.heta b/latest/cases/00581/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ecceb99c8 --- /dev/null +++ b/latest/cases/00581/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00581/l3v2/index.heta b/latest/cases/00581/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00581/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00581/l3v2/json/output.json b/latest/cases/00581/l3v2/json/output.json new file mode 100644 index 000000000..6043d5d44 --- /dev/null +++ b/latest/cases/00581/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + } +] \ No newline at end of file diff --git a/latest/cases/00581/model-sbml-l2v5.xml b/latest/cases/00581/model-sbml-l2v5.xml new file mode 100644 index 000000000..828fbb81b --- /dev/null +++ b/latest/cases/00581/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00581/model-sbml-l3v2.xml b/latest/cases/00581/model-sbml-l3v2.xml new file mode 100644 index 000000000..add1751ca --- /dev/null +++ b/latest/cases/00581/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00581/output.heta b/latest/cases/00581/output.heta new file mode 100644 index 000000000..3fa624b12 --- /dev/null +++ b/latest/cases/00581/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00581/synopsis.txt b/latest/cases/00581/synopsis.txt new file mode 100644 index 000000000..a8de0b5d2 --- /dev/null +++ b/latest/cases/00581/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00582/l2v5/heta-code/output.heta b/latest/cases/00582/l2v5/heta-code/output.heta new file mode 100644 index 000000000..908ea56c4 --- /dev/null +++ b/latest/cases/00582/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.01; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.02; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 25; + diff --git a/latest/cases/00582/l2v5/index.heta b/latest/cases/00582/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00582/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00582/l2v5/json/output.json b/latest/cases/00582/l2v5/json/output.json new file mode 100644 index 000000000..f2ee0295c --- /dev/null +++ b/latest/cases/00582/l2v5/json/output.json @@ -0,0 +1,151 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00582/l3v2/heta-code/output.heta b/latest/cases/00582/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0871ce838 --- /dev/null +++ b/latest/cases/00582/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.01; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00582/l3v2/index.heta b/latest/cases/00582/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00582/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00582/l3v2/json/output.json b/latest/cases/00582/l3v2/json/output.json new file mode 100644 index 000000000..f8a6640f5 --- /dev/null +++ b/latest/cases/00582/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + } +] \ No newline at end of file diff --git a/latest/cases/00582/model-sbml-l2v5.xml b/latest/cases/00582/model-sbml-l2v5.xml new file mode 100644 index 000000000..ac8559bf2 --- /dev/null +++ b/latest/cases/00582/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00582/model-sbml-l3v2.xml b/latest/cases/00582/model-sbml-l3v2.xml new file mode 100644 index 000000000..00c18da74 --- /dev/null +++ b/latest/cases/00582/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00582/output.heta b/latest/cases/00582/output.heta new file mode 100644 index 000000000..e08d0c65c --- /dev/null +++ b/latest/cases/00582/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment, + with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Species S4 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.01; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/00582/synopsis.txt b/latest/cases/00582/synopsis.txt new file mode 100644 index 000000000..71542161c --- /dev/null +++ b/latest/cases/00582/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment, + with one species acting as a boundary condition. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Species S4 is labeled as an SBML boundary species. The model contains two +reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00583/l2v5/heta-code/output.heta b/latest/cases/00583/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ca73b2615 --- /dev/null +++ b/latest/cases/00583/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1e-4; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00583/l2v5/index.heta b/latest/cases/00583/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00583/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00583/l2v5/json/output.json b/latest/cases/00583/l2v5/json/output.json new file mode 100644 index 000000000..848ea53c6 --- /dev/null +++ b/latest/cases/00583/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00583/l3v2/heta-code/output.heta b/latest/cases/00583/l3v2/heta-code/output.heta new file mode 100644 index 000000000..84ada0789 --- /dev/null +++ b/latest/cases/00583/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00583/l3v2/index.heta b/latest/cases/00583/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00583/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00583/l3v2/json/output.json b/latest/cases/00583/l3v2/json/output.json new file mode 100644 index 000000000..99e1be04e --- /dev/null +++ b/latest/cases/00583/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + } +] \ No newline at end of file diff --git a/latest/cases/00583/model-sbml-l2v5.xml b/latest/cases/00583/model-sbml-l2v5.xml new file mode 100644 index 000000000..eabc8e979 --- /dev/null +++ b/latest/cases/00583/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00583/model-sbml-l3v2.xml b/latest/cases/00583/model-sbml-l3v2.xml new file mode 100644 index 000000000..67f3a04e2 --- /dev/null +++ b/latest/cases/00583/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00583/output.heta b/latest/cases/00583/output.heta new file mode 100644 index 000000000..c3b418592 --- /dev/null +++ b/latest/cases/00583/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment, + with non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00583/synopsis.txt b/latest/cases/00583/synopsis.txt new file mode 100644 index 000000000..8d1e57600 --- /dev/null +++ b/latest/cases/00583/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment, + with non-unity stoichiometry. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00584/l2v5/heta-code/output.heta b/latest/cases/00584/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8b17a6dc1 --- /dev/null +++ b/latest/cases/00584/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.002; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Record 'k1' { } .= 1000; +k2 @Record 'k2' { } .= 0.9; +k3 @Record 'k3' { } .= 0.7; + diff --git a/latest/cases/00584/l2v5/index.heta b/latest/cases/00584/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00584/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00584/l2v5/json/output.json b/latest/cases/00584/l2v5/json/output.json new file mode 100644 index 000000000..373aaf8d8 --- /dev/null +++ b/latest/cases/00584/l2v5/json/output.json @@ -0,0 +1,173 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1000" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00584/l3v2/heta-code/output.heta b/latest/cases/00584/l3v2/heta-code/output.heta new file mode 100644 index 000000000..18ed2fcc0 --- /dev/null +++ b/latest/cases/00584/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.002; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 1000; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00584/l3v2/index.heta b/latest/cases/00584/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00584/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00584/l3v2/json/output.json b/latest/cases/00584/l3v2/json/output.json new file mode 100644 index 000000000..c5b177d8c --- /dev/null +++ b/latest/cases/00584/l3v2/json/output.json @@ -0,0 +1,143 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.9 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00584/model-sbml-l2v5.xml b/latest/cases/00584/model-sbml-l2v5.xml new file mode 100644 index 000000000..88a2a6da1 --- /dev/null +++ b/latest/cases/00584/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00584/model-sbml-l3v2.xml b/latest/cases/00584/model-sbml-l3v2.xml new file mode 100644 index 000000000..82bea881d --- /dev/null +++ b/latest/cases/00584/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00584/output.heta b/latest/cases/00584/output.heta new file mode 100644 index 000000000..b112326ac --- /dev/null +++ b/latest/cases/00584/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Three reactions with four species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1.0 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.9$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.002; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 1000; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00584/synopsis.txt b/latest/cases/00584/synopsis.txt new file mode 100644 index 000000000..a471bfe66 --- /dev/null +++ b/latest/cases/00584/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Three reactions with four species in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1.0 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.9$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00585/l2v5/heta-code/output.heta b/latest/cases/00585/l2v5/heta-code/output.heta new file mode 100644 index 000000000..58aa67cfc --- /dev/null +++ b/latest/cases/00585/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00585/l2v5/index.heta b/latest/cases/00585/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00585/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00585/l2v5/json/output.json b/latest/cases/00585/l2v5/json/output.json new file mode 100644 index 000000000..47b5207eb --- /dev/null +++ b/latest/cases/00585/l2v5/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00585/l3v2/heta-code/output.heta b/latest/cases/00585/l3v2/heta-code/output.heta new file mode 100644 index 000000000..83cfa2f98 --- /dev/null +++ b/latest/cases/00585/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00585/l3v2/index.heta b/latest/cases/00585/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00585/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00585/l3v2/json/output.json b/latest/cases/00585/l3v2/json/output.json new file mode 100644 index 000000000..3f412e0cb --- /dev/null +++ b/latest/cases/00585/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00585/model-sbml-l2v5.xml b/latest/cases/00585/model-sbml-l2v5.xml new file mode 100644 index 000000000..502e5f4db --- /dev/null +++ b/latest/cases/00585/model-sbml-l2v5.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00585/model-sbml-l3v2.xml b/latest/cases/00585/model-sbml-l3v2.xml new file mode 100644 index 000000000..e0cc38a0c --- /dev/null +++ b/latest/cases/00585/model-sbml-l3v2.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00585/output.heta b/latest/cases/00585/output.heta new file mode 100644 index 000000000..a73ebd0c6 --- /dev/null +++ b/latest/cases/00585/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S4 | $k3 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$0.7$ |second^-1^ | +|Value of parameter k2 |$0.5$ |second^-1^ | +|Value of parameter k3 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00585/synopsis.txt b/latest/cases/00585/synopsis.txt new file mode 100644 index 000000000..c05196ff8 --- /dev/null +++ b/latest/cases/00585/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S4 | $k3 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$0.7$ |second^-1^ | +|Value of parameter k2 |$0.5$ |second^-1^ | +|Value of parameter k3 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00586/l2v5/heta-code/output.heta b/latest/cases/00586/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5c5941ac5 --- /dev/null +++ b/latest/cases/00586/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00586/l2v5/index.heta b/latest/cases/00586/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00586/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00586/l2v5/json/output.json b/latest/cases/00586/l2v5/json/output.json new file mode 100644 index 000000000..b2d18ad69 --- /dev/null +++ b/latest/cases/00586/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00586/l3v2/heta-code/output.heta b/latest/cases/00586/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b6fb8002a --- /dev/null +++ b/latest/cases/00586/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00586/l3v2/index.heta b/latest/cases/00586/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00586/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00586/l3v2/json/output.json b/latest/cases/00586/l3v2/json/output.json new file mode 100644 index 000000000..077874bae --- /dev/null +++ b/latest/cases/00586/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00586/model-sbml-l2v5.xml b/latest/cases/00586/model-sbml-l2v5.xml new file mode 100644 index 000000000..b5cc1118f --- /dev/null +++ b/latest/cases/00586/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00586/model-sbml-l3v2.xml b/latest/cases/00586/model-sbml-l3v2.xml new file mode 100644 index 000000000..887b2c9f0 --- /dev/null +++ b/latest/cases/00586/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00586/output.heta b/latest/cases/00586/output.heta new file mode 100644 index 000000000..51b2bdb87 --- /dev/null +++ b/latest/cases/00586/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1.5$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00586/synopsis.txt b/latest/cases/00586/synopsis.txt new file mode 100644 index 000000000..ca1a0cd56 --- /dev/null +++ b/latest/cases/00586/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1.5$ |litre |] + diff --git a/latest/cases/00587/l2v5/heta-code/output.heta b/latest/cases/00587/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2bb6b3976 --- /dev/null +++ b/latest/cases/00587/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.7; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 0.0025; + diff --git a/latest/cases/00587/l2v5/index.heta b/latest/cases/00587/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00587/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00587/l2v5/json/output.json b/latest/cases/00587/l2v5/json/output.json new file mode 100644 index 000000000..cb2a51310 --- /dev/null +++ b/latest/cases/00587/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.7" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0025" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00587/l3v2/heta-code/output.heta b/latest/cases/00587/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9031374e --- /dev/null +++ b/latest/cases/00587/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.7; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0.0025; + diff --git a/latest/cases/00587/l3v2/index.heta b/latest/cases/00587/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00587/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00587/l3v2/json/output.json b/latest/cases/00587/l3v2/json/output.json new file mode 100644 index 000000000..32756b2f2 --- /dev/null +++ b/latest/cases/00587/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.7" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0025 + } +] \ No newline at end of file diff --git a/latest/cases/00587/model-sbml-l2v5.xml b/latest/cases/00587/model-sbml-l2v5.xml new file mode 100644 index 000000000..4dd05f512 --- /dev/null +++ b/latest/cases/00587/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00587/model-sbml-l3v2.xml b/latest/cases/00587/model-sbml-l3v2.xml new file mode 100644 index 000000000..7a88934c4 --- /dev/null +++ b/latest/cases/00587/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00587/output.heta b/latest/cases/00587/output.heta new file mode 100644 index 000000000..5ee8761fd --- /dev/null +++ b/latest/cases/00587/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic reaction with two species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 0.7$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.7; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0.0025; + diff --git a/latest/cases/00587/synopsis.txt b/latest/cases/00587/synopsis.txt new file mode 100644 index 000000000..093e69a63 --- /dev/null +++ b/latest/cases/00587/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic reaction with two species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 0.7$ |litre |] + diff --git a/latest/cases/00588/l2v5/heta-code/output.heta b/latest/cases/00588/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0cbb69874 --- /dev/null +++ b/latest/cases/00588/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.3; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.7; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00588/l2v5/index.heta b/latest/cases/00588/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00588/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00588/l2v5/json/output.json b/latest/cases/00588/l2v5/json/output.json new file mode 100644 index 000000000..45c8b9d6b --- /dev/null +++ b/latest/cases/00588/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.7" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00588/l3v2/heta-code/output.heta b/latest/cases/00588/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dad49d7b3 --- /dev/null +++ b/latest/cases/00588/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.7; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00588/l3v2/index.heta b/latest/cases/00588/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00588/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00588/l3v2/json/output.json b/latest/cases/00588/l3v2/json/output.json new file mode 100644 index 000000000..a590bad80 --- /dev/null +++ b/latest/cases/00588/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.7" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00588/model-sbml-l2v5.xml b/latest/cases/00588/model-sbml-l2v5.xml new file mode 100644 index 000000000..594761870 --- /dev/null +++ b/latest/cases/00588/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00588/model-sbml-l3v2.xml b/latest/cases/00588/model-sbml-l3v2.xml new file mode 100644 index 000000000..ce6963c4d --- /dev/null +++ b/latest/cases/00588/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00588/output.heta b/latest/cases/00588/output.heta new file mode 100644 index 000000000..90ca6cebb --- /dev/null +++ b/latest/cases/00588/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.7$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S4 |$ 1.0$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 0.3$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.7; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00588/synopsis.txt b/latest/cases/00588/synopsis.txt new file mode 100644 index 000000000..c49a313dc --- /dev/null +++ b/latest/cases/00588/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.7$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S4 |$ 1.0$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 0.3$ |litre |] + diff --git a/latest/cases/00589/l2v5/heta-code/output.heta b/latest/cases/00589/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c2f98391b --- /dev/null +++ b/latest/cases/00589/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: C, } .= 0.015; +S2 @Species 'S2' { units: substance/area, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00589/l2v5/index.heta b/latest/cases/00589/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00589/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00589/l2v5/json/output.json b/latest/cases/00589/l2v5/json/output.json new file mode 100644 index 000000000..f0bae5223 --- /dev/null +++ b/latest/cases/00589/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00589/l3v2/heta-code/output.heta b/latest/cases/00589/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1edd75ec3 --- /dev/null +++ b/latest/cases/00589/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.015; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00589/l3v2/index.heta b/latest/cases/00589/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00589/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00589/l3v2/json/output.json b/latest/cases/00589/l3v2/json/output.json new file mode 100644 index 000000000..39929c0e0 --- /dev/null +++ b/latest/cases/00589/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00589/model-sbml-l2v5.xml b/latest/cases/00589/model-sbml-l2v5.xml new file mode 100644 index 000000000..7ec0a42e2 --- /dev/null +++ b/latest/cases/00589/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00589/model-sbml-l3v2.xml b/latest/cases/00589/model-sbml-l3v2.xml new file mode 100644 index 000000000..e4a86ddc0 --- /dev/null +++ b/latest/cases/00589/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00589/output.heta b/latest/cases/00589/output.heta new file mode 100644 index 000000000..ab3f8f0e7 --- /dev/null +++ b/latest/cases/00589/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment. +componentTags: Compartment, Species, Reaction, Parameter, +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Compartment +C is two-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-2$ |mole metre^-2^ | +|Initial concentration of S2 |$ 0$ |mole metre^-2^ | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment C |$1$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.015; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00589/synopsis.txt b/latest/cases/00589/synopsis.txt new file mode 100644 index 000000000..3d7b66b9e --- /dev/null +++ b/latest/cases/00589/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +compartment. +componentTags: Compartment, Species, Reaction, Parameter, +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Compartment +C is two-dimensional. The model contains one reaction defined +as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-2$ |mole metre^-2^ | +|Initial concentration of S2 |$ 0$ |mole metre^-2^ | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment C |$1$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00590/l2v5/heta-code/output.heta b/latest/cases/00590/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4aef6a061 --- /dev/null +++ b/latest/cases/00590/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: substance/area, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: substance/area, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00590/l2v5/index.heta b/latest/cases/00590/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00590/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00590/l2v5/json/output.json b/latest/cases/00590/l2v5/json/output.json new file mode 100644 index 000000000..a0e985f99 --- /dev/null +++ b/latest/cases/00590/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00590/l3v2/heta-code/output.heta b/latest/cases/00590/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c3d91f33b --- /dev/null +++ b/latest/cases/00590/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00590/l3v2/index.heta b/latest/cases/00590/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00590/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00590/l3v2/json/output.json b/latest/cases/00590/l3v2/json/output.json new file mode 100644 index 000000000..68bdf9a9a --- /dev/null +++ b/latest/cases/00590/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00590/model-sbml-l2v5.xml b/latest/cases/00590/model-sbml-l2v5.xml new file mode 100644 index 000000000..f20dbf3bc --- /dev/null +++ b/latest/cases/00590/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00590/model-sbml-l3v2.xml b/latest/cases/00590/model-sbml-l3v2.xml new file mode 100644 index 000000000..17dcb9ba4 --- /dev/null +++ b/latest/cases/00590/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00590/output.heta b/latest/cases/00590/output.heta new file mode 100644 index 000000000..c4f682e30 --- /dev/null +++ b/latest/cases/00590/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic reaction with two species in a 2-dimensional compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Compartment C is 2-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole metre^-2^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole metre^-2^ | +|Initial concentration of S3 |$1.0 \x 10^-4$ |mole metre^-2^ | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment C |$ 1$ |metre^2^ |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00590/synopsis.txt b/latest/cases/00590/synopsis.txt new file mode 100644 index 000000000..15885a205 --- /dev/null +++ b/latest/cases/00590/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic reaction with two species in a 2-dimensional compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Compartment C is 2-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole metre^-2^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole metre^-2^ | +|Initial concentration of S3 |$1.0 \x 10^-4$ |mole metre^-2^ | +|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Area of compartment C |$ 1$ |metre^2^ |] + diff --git a/latest/cases/00591/l2v5/heta-code/output.heta b/latest/cases/00591/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a415ac6a3 --- /dev/null +++ b/latest/cases/00591/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: area, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/area, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: substance/area, compartment: C, } .= 0.001; +S3 @Species 'S3' { units: substance/area, compartment: C, } .= 0.002; +S4 @Species 'S4' { units: substance/area, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 750; +k2 @Record 'k2' { } .= 250; + diff --git a/latest/cases/00591/l2v5/index.heta b/latest/cases/00591/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00591/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00591/l2v5/json/output.json b/latest/cases/00591/l2v5/json/output.json new file mode 100644 index 000000000..6aa32b694 --- /dev/null +++ b/latest/cases/00591/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "area", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/area", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/area", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/area", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/area", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "750" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "250" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00591/l3v2/heta-code/output.heta b/latest/cases/00591/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f975877ec --- /dev/null +++ b/latest/cases/00591/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0.001; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 0.002; +S4 @Species 'S4' { units: mole/metre^2, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00591/l3v2/index.heta b/latest/cases/00591/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00591/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00591/l3v2/json/output.json b/latest/cases/00591/l3v2/json/output.json new file mode 100644 index 000000000..ac438581b --- /dev/null +++ b/latest/cases/00591/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre^2", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre^2", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre^2", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 250 + } +] \ No newline at end of file diff --git a/latest/cases/00591/model-sbml-l2v5.xml b/latest/cases/00591/model-sbml-l2v5.xml new file mode 100644 index 000000000..d4b90fc60 --- /dev/null +++ b/latest/cases/00591/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00591/model-sbml-l3v2.xml b/latest/cases/00591/model-sbml-l3v2.xml new file mode 100644 index 000000000..24986061b --- /dev/null +++ b/latest/cases/00591/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00591/output.heta b/latest/cases/00591/output.heta new file mode 100644 index 000000000..5c14767dd --- /dev/null +++ b/latest/cases/00591/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Compartment C is 2-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-3$ |mole metre^-2^ | +|Initial concentration of S2 |$1.0 \x 10^-3$ |mole metre^-2^ | +|Initial concentration of S3 |$2.0 \x 10^-3$ |mole metre^-2^ | +|Initial concentration of S4 |$1.0 \x 10^-3$ |mole metre^-2^ | +|Value of parameter k1 |$0.75 \x 10^3$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment C |$ 1$ |metre^2^ |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre^2, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0.001; +S3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 0.002; +S4 @Species 'S4' { units: mole/metre^2, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00591/synopsis.txt b/latest/cases/00591/synopsis.txt new file mode 100644 index 000000000..1fe8b4d40 --- /dev/null +++ b/latest/cases/00591/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Compartment C is 2-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-3$ |mole metre^-2^ | +|Initial concentration of S2 |$1.0 \x 10^-3$ |mole metre^-2^ | +|Initial concentration of S3 |$2.0 \x 10^-3$ |mole metre^-2^ | +|Initial concentration of S4 |$1.0 \x 10^-3$ |mole metre^-2^ | +|Value of parameter k1 |$0.75 \x 10^3$ |metre^2^ mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |metre^2^ mole^-1^ second^-1^ | +|Area of compartment C |$ 1$ |metre^2^ |] + diff --git a/latest/cases/00592/l2v5/heta-code/output.heta b/latest/cases/00592/l2v5/heta-code/output.heta new file mode 100644 index 000000000..589c34287 --- /dev/null +++ b/latest/cases/00592/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: C, } .= 0.15; +S2 @Species 'S2' { units: substance/length, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00592/l2v5/index.heta b/latest/cases/00592/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00592/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00592/l2v5/json/output.json b/latest/cases/00592/l2v5/json/output.json new file mode 100644 index 000000000..5fffb450f --- /dev/null +++ b/latest/cases/00592/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00592/l3v2/heta-code/output.heta b/latest/cases/00592/l3v2/heta-code/output.heta new file mode 100644 index 000000000..45d80724c --- /dev/null +++ b/latest/cases/00592/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 0.15; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00592/l3v2/index.heta b/latest/cases/00592/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00592/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00592/l3v2/json/output.json b/latest/cases/00592/l3v2/json/output.json new file mode 100644 index 000000000..aaca485a6 --- /dev/null +++ b/latest/cases/00592/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00592/model-sbml-l2v5.xml b/latest/cases/00592/model-sbml-l2v5.xml new file mode 100644 index 000000000..64d35a8e1 --- /dev/null +++ b/latest/cases/00592/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00592/model-sbml-l3v2.xml b/latest/cases/00592/model-sbml-l3v2.xml new file mode 100644 index 000000000..e84411c02 --- /dev/null +++ b/latest/cases/00592/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00592/output.heta b/latest/cases/00592/output.heta new file mode 100644 index 000000000..2aa338c0a --- /dev/null +++ b/latest/cases/00592/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Compartment +C is 1-dimensional. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-1$ |mole metre^-1^ | +|Initial concentration of S2 |$ 0$ |mole metre^-1^ | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Length of compartment C |$ 1$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 0.15; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00592/synopsis.txt b/latest/cases/00592/synopsis.txt new file mode 100644 index 000000000..aae15b5f6 --- /dev/null +++ b/latest/cases/00592/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Compartment +C is 1-dimensional. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-1$ |mole metre^-1^ | +|Initial concentration of S2 |$ 0$ |mole metre^-1^ | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Length of compartment C |$ 1$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00593/l2v5/heta-code/output.heta b/latest/cases/00593/l2v5/heta-code/output.heta new file mode 100644 index 000000000..50cc544db --- /dev/null +++ b/latest/cases/00593/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: substance/length, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: substance/length, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00593/l2v5/index.heta b/latest/cases/00593/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00593/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00593/l2v5/json/output.json b/latest/cases/00593/l2v5/json/output.json new file mode 100644 index 000000000..02533d621 --- /dev/null +++ b/latest/cases/00593/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00593/l3v2/heta-code/output.heta b/latest/cases/00593/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b32932883 --- /dev/null +++ b/latest/cases/00593/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00593/l3v2/index.heta b/latest/cases/00593/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00593/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00593/l3v2/json/output.json b/latest/cases/00593/l3v2/json/output.json new file mode 100644 index 000000000..6f0100e32 --- /dev/null +++ b/latest/cases/00593/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00593/model-sbml-l2v5.xml b/latest/cases/00593/model-sbml-l2v5.xml new file mode 100644 index 000000000..391188c1c --- /dev/null +++ b/latest/cases/00593/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00593/model-sbml-l3v2.xml b/latest/cases/00593/model-sbml-l3v2.xml new file mode 100644 index 000000000..3cf845734 --- /dev/null +++ b/latest/cases/00593/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00593/output.heta b/latest/cases/00593/output.heta new file mode 100644 index 000000000..3f143b781 --- /dev/null +++ b/latest/cases/00593/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic reaction with two species in a 1-dimensional compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Compartment C is 1-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole metre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole metre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole metre^-1^ | +|Value of parameter k1 |$ 0.75$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Length of compartment C |$ 1$ |metre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00593/synopsis.txt b/latest/cases/00593/synopsis.txt new file mode 100644 index 000000000..39b201681 --- /dev/null +++ b/latest/cases/00593/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic reaction with two species in a 1-dimensional compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Compartment C is 1-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole metre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole metre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole metre^-1^ | +|Value of parameter k1 |$ 0.75$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Length of compartment C |$ 1$ |metre |] + diff --git a/latest/cases/00594/l2v5/heta-code/output.heta b/latest/cases/00594/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b131403ff --- /dev/null +++ b/latest/cases/00594/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: length, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/length, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: substance/length, compartment: C, } .= 1e-4; +S3 @Species 'S3' { units: substance/length, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: substance/length, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + diff --git a/latest/cases/00594/l2v5/index.heta b/latest/cases/00594/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00594/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00594/l2v5/json/output.json b/latest/cases/00594/l2v5/json/output.json new file mode 100644 index 000000000..2beb1a4df --- /dev/null +++ b/latest/cases/00594/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "length", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/length", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/length", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/length", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/length", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00594/l3v2/heta-code/output.heta b/latest/cases/00594/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a0bb1849b --- /dev/null +++ b/latest/cases/00594/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 1e-4; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: mole/metre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00594/l3v2/index.heta b/latest/cases/00594/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00594/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00594/l3v2/json/output.json b/latest/cases/00594/l3v2/json/output.json new file mode 100644 index 000000000..8b4abed94 --- /dev/null +++ b/latest/cases/00594/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "metre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/metre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/metre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/metre", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/metre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + } +] \ No newline at end of file diff --git a/latest/cases/00594/model-sbml-l2v5.xml b/latest/cases/00594/model-sbml-l2v5.xml new file mode 100644 index 000000000..a37662489 --- /dev/null +++ b/latest/cases/00594/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00594/model-sbml-l3v2.xml b/latest/cases/00594/model-sbml-l3v2.xml new file mode 100644 index 000000000..343fe18f5 --- /dev/null +++ b/latest/cases/00594/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00594/output.heta b/latest/cases/00594/output.heta new file mode 100644 index 000000000..9f2082c78 --- /dev/null +++ b/latest/cases/00594/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Compartment C is 1-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole metre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-4$ |mole metre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-4$ |mole metre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-4$ |mole metre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre mole^-1^ second^-1^ | +|Length of compartment C |$ 1$ |metre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: metre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1e-4; +S2 @Species 'S2' { units: mole/metre, compartment: C, } .= 1e-4; +S3 @Species 'S3' { units: mole/metre, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: mole/metre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + diff --git a/latest/cases/00594/synopsis.txt b/latest/cases/00594/synopsis.txt new file mode 100644 index 000000000..32f82d8d7 --- /dev/null +++ b/latest/cases/00594/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional +compartment. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Compartment C is 1-dimensional. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole metre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-4$ |mole metre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-4$ |mole metre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-4$ |mole metre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |metre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |metre mole^-1^ second^-1^ | +|Length of compartment C |$ 1$ |metre |] + diff --git a/latest/cases/00595/l2v5/heta-code/output.heta b/latest/cases/00595/l2v5/heta-code/output.heta new file mode 100644 index 000000000..79ac96833 --- /dev/null +++ b/latest/cases/00595/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.003; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k__reaction2_local * S2; + +k__reaction1_local @Const { } = 1; +k__reaction2_local @Const { } = 2; + diff --git a/latest/cases/00595/l2v5/index.heta b/latest/cases/00595/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00595/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00595/l2v5/json/output.json b/latest/cases/00595/l2v5/json/output.json new file mode 100644 index 000000000..1afae832a --- /dev/null +++ b/latest/cases/00595/l2v5/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.003" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00595/l3v2/heta-code/output.heta b/latest/cases/00595/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cc1ee292e --- /dev/null +++ b/latest/cases/00595/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.003; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k__reaction2_local * S2; + +k__reaction1_local @Const { } = 1; +k__reaction2_local @Const { } = 2; + diff --git a/latest/cases/00595/l3v2/index.heta b/latest/cases/00595/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00595/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00595/l3v2/json/output.json b/latest/cases/00595/l3v2/json/output.json new file mode 100644 index 000000000..f98435df9 --- /dev/null +++ b/latest/cases/00595/l3v2/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.003" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + } +] \ No newline at end of file diff --git a/latest/cases/00595/model-sbml-l2v5.xml b/latest/cases/00595/model-sbml-l2v5.xml new file mode 100644 index 000000000..9c3366c7e --- /dev/null +++ b/latest/cases/00595/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + + + + + C + k + S2 + + + + + + + + + + diff --git a/latest/cases/00595/model-sbml-l3v2.xml b/latest/cases/00595/model-sbml-l3v2.xml new file mode 100644 index 000000000..f147b535a --- /dev/null +++ b/latest/cases/00595/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + + + + + C + k + S2 + + + + + + + + + + diff --git a/latest/cases/00595/output.heta b/latest/cases/00595/output.heta new file mode 100644 index 000000000..9e80c4b46 --- /dev/null +++ b/latest/cases/00595/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Basic two reactions with three species and parameters local to + reactions. +componentTags: Compartment, Species, Reaction +testTags: Concentration, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * C,$ | +| S2 -> S3 | $k * S2 * C,$ |] + +Reaction S1 -> S2 defines one local parameter k. Reaction S2 -> S3 also +defines one (different) local parameter k. Both of these parameters have a +scope local to the defining reaction. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$3.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Value of local parameter k |$ 1$ |second^-1^ | +|Value of local parameter k |$ 2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.003; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k__reaction2_local * S2; + +k__reaction1_local @Const { } = 1; +k__reaction2_local @Const { } = 2; + diff --git a/latest/cases/00595/synopsis.txt b/latest/cases/00595/synopsis.txt new file mode 100644 index 000000000..c73f5e00a --- /dev/null +++ b/latest/cases/00595/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Basic two reactions with three species and parameters local to + reactions. +componentTags: Compartment, Species, Reaction +testTags: Concentration, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * C,$ | +| S2 -> S3 | $k * S2 * C,$ |] + +Reaction S1 -> S2 defines one local parameter k. Reaction S2 -> S3 also +defines one (different) local parameter k. Both of these parameters have a +scope local to the defining reaction. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$3.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Value of local parameter k |$ 1$ |second^-1^ | +|Value of local parameter k |$ 2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + diff --git a/latest/cases/00596/l2v5/heta-code/output.heta b/latest/cases/00596/l2v5/heta-code/output.heta new file mode 100644 index 000000000..75f24cdf2 --- /dev/null +++ b/latest/cases/00596/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.3; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k__reaction2_local * S2; + +k @Record 'k' { } .= 1; + +k__reaction2_local @Const { } = 2; + diff --git a/latest/cases/00596/l2v5/index.heta b/latest/cases/00596/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00596/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00596/l2v5/json/output.json b/latest/cases/00596/l2v5/json/output.json new file mode 100644 index 000000000..520a235a4 --- /dev/null +++ b/latest/cases/00596/l2v5/json/output.json @@ -0,0 +1,121 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00596/l3v2/heta-code/output.heta b/latest/cases/00596/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4eff5306e --- /dev/null +++ b/latest/cases/00596/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.3; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k__reaction2_local * S2; + +k__reaction2_local @Const { } = 2; +k @Const 'k' { } = 1; + diff --git a/latest/cases/00596/l3v2/index.heta b/latest/cases/00596/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00596/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00596/l3v2/json/output.json b/latest/cases/00596/l3v2/json/output.json new file mode 100644 index 000000000..7e7aa0279 --- /dev/null +++ b/latest/cases/00596/l3v2/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00596/model-sbml-l2v5.xml b/latest/cases/00596/model-sbml-l2v5.xml new file mode 100644 index 000000000..3122c257c --- /dev/null +++ b/latest/cases/00596/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + + C + k + S2 + + + + + + + + + + diff --git a/latest/cases/00596/model-sbml-l3v2.xml b/latest/cases/00596/model-sbml-l3v2.xml new file mode 100644 index 000000000..2f092f2b0 --- /dev/null +++ b/latest/cases/00596/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + + C + k + S2 + + + + + + + + + + diff --git a/latest/cases/00596/output.heta b/latest/cases/00596/output.heta new file mode 100644 index 000000000..2b145860e --- /dev/null +++ b/latest/cases/00596/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic two reactions with three species and parameters both global + and local to reactions. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one global parameter called k. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * C$ | +| S2 -> S3 | $k * S2 * C$ |] + +Reaction S2 -> S3 defines one local parameter k. + +Note that the id of the local parameter k shadows the global parameter k. +Within the defining reaction, the value of the locally-defined parameter k +must be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$3.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Value of parameter k |$ 1$ |second^-1^ | +|Value of local parameter k |$ 2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.3; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k__reaction2_local * S2; + +k__reaction2_local @Const { } = 2; +k @Const 'k' { } = 1; + diff --git a/latest/cases/00596/synopsis.txt b/latest/cases/00596/synopsis.txt new file mode 100644 index 000000000..d05f60eff --- /dev/null +++ b/latest/cases/00596/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with three species and parameters both global + and local to reactions. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one global parameter called k. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * C$ | +| S2 -> S3 | $k * S2 * C$ |] + +Reaction S2 -> S3 defines one local parameter k. + +Note that the id of the local parameter k shadows the global parameter k. +Within the defining reaction, the value of the locally-defined parameter k +must be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$3.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Value of parameter k |$ 1$ |second^-1^ | +|Value of local parameter k |$ 2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + diff --git a/latest/cases/00597/l2v5/heta-code/output.heta b/latest/cases/00597/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f74c9a245 --- /dev/null +++ b/latest/cases/00597/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.03; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, modifiers: [S1], reversible: false, }; +reaction2 := C * S1__reaction2_local * S2; + +k @Record 'k' { } .= 2; + +S1__reaction2_local @Const { } = 1; + diff --git a/latest/cases/00597/l2v5/index.heta b/latest/cases/00597/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00597/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00597/l2v5/json/output.json b/latest/cases/00597/l2v5/json/output.json new file mode 100644 index 000000000..074e11668 --- /dev/null +++ b/latest/cases/00597/l2v5/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.03" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "S1__reaction2_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * S1__reaction2_local * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S1" + } + ] + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00597/l3v2/index.heta b/latest/cases/00597/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00597/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00597/model-sbml-l2v5.xml b/latest/cases/00597/model-sbml-l2v5.xml new file mode 100644 index 000000000..5ad0e6583 --- /dev/null +++ b/latest/cases/00597/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + + + + + C + S1 + S2 + + + + + + + + + + diff --git a/latest/cases/00597/output.heta b/latest/cases/00597/output.heta new file mode 100644 index 000000000..ae1e35b25 --- /dev/null +++ b/latest/cases/00597/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic two reactions with three species and parameters both global + and local to reactions. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one global parameter called k. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * C$ | +| S2 -> S3 | $S1 * S2 * C$ |] + +Reaction S2 -> S3 defines one local parameter S1. + +Note that the id of the local parameter S1 shadows the species S1. Within +the defining reaction, the value of the locally-defined symbol S1 must be +used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$3.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Value of parameter k |$ 2$ |second^-1^ | +|Value of local parameter S1 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.03; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, modifiers: [S1], reversible: false, }; +reaction2 := C * S1__reaction2_local * S2; + +k @Record 'k' { } .= 2; + +S1__reaction2_local @Const { } = 1; + diff --git a/latest/cases/00597/synopsis.txt b/latest/cases/00597/synopsis.txt new file mode 100644 index 000000000..eb24402cf --- /dev/null +++ b/latest/cases/00597/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with three species and parameters both global + and local to reactions. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one global parameter called k. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * C$ | +| S2 -> S3 | $S1 * S2 * C$ |] + +Reaction S2 -> S3 defines one local parameter S1. + +Note that the id of the local parameter S1 shadows the species S1. Within +the defining reaction, the value of the locally-defined symbol S1 must be +used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$3.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Value of parameter k |$ 2$ |second^-1^ | +|Value of local parameter S1 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + diff --git a/latest/cases/00598/l2v5/heta-code/output.heta b/latest/cases/00598/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7df747576 --- /dev/null +++ b/latest/cases/00598/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k1 * S1 * S3; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00598/l2v5/index.heta b/latest/cases/00598/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00598/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00598/l2v5/json/output.json b/latest/cases/00598/l2v5/json/output.json new file mode 100644 index 000000000..5f3dfc8e6 --- /dev/null +++ b/latest/cases/00598/l2v5/json/output.json @@ -0,0 +1,103 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00598/l3v2/heta-code/output.heta b/latest/cases/00598/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9c0a9c2af --- /dev/null +++ b/latest/cases/00598/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00598/l3v2/index.heta b/latest/cases/00598/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00598/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00598/l3v2/json/output.json b/latest/cases/00598/l3v2/json/output.json new file mode 100644 index 000000000..b870da506 --- /dev/null +++ b/latest/cases/00598/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S3" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00598/model-sbml-l2v5.xml b/latest/cases/00598/model-sbml-l2v5.xml new file mode 100644 index 000000000..b92ecf6e8 --- /dev/null +++ b/latest/cases/00598/model-sbml-l2v5.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00598/model-sbml-l3v2.xml b/latest/cases/00598/model-sbml-l3v2.xml new file mode 100644 index 000000000..d08a1d4eb --- /dev/null +++ b/latest/cases/00598/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S3 + + + + + + + diff --git a/latest/cases/00598/output.heta b/latest/cases/00598/output.heta new file mode 100644 index 000000000..1e96dded8 --- /dev/null +++ b/latest/cases/00598/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k1. Species S3 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, }; +reaction1 := C * k1 * S1 * S3; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00598/synopsis.txt b/latest/cases/00598/synopsis.txt new file mode 100644 index 000000000..f95a38c30 --- /dev/null +++ b/latest/cases/00598/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Basic single forward reaction with three species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k1. Species S3 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00599/l2v5/heta-code/output.heta b/latest/cases/00599/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d89a3d04b --- /dev/null +++ b/latest/cases/00599/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 1.7; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00599/l2v5/index.heta b/latest/cases/00599/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00599/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00599/l2v5/json/output.json b/latest/cases/00599/l2v5/json/output.json new file mode 100644 index 000000000..ce42451f2 --- /dev/null +++ b/latest/cases/00599/l2v5/json/output.json @@ -0,0 +1,148 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00599/l3v2/heta-code/output.heta b/latest/cases/00599/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1a0690627 --- /dev/null +++ b/latest/cases/00599/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 1.7; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00599/l3v2/index.heta b/latest/cases/00599/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00599/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00599/l3v2/json/output.json b/latest/cases/00599/l3v2/json/output.json new file mode 100644 index 000000000..abb03ed2a --- /dev/null +++ b/latest/cases/00599/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S4" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00599/model-sbml-l2v5.xml b/latest/cases/00599/model-sbml-l2v5.xml new file mode 100644 index 000000000..0d4fd0363 --- /dev/null +++ b/latest/cases/00599/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00599/model-sbml-l3v2.xml b/latest/cases/00599/model-sbml-l3v2.xml new file mode 100644 index 000000000..adebc04c9 --- /dev/null +++ b/latest/cases/00599/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00599/output.heta b/latest/cases/00599/output.heta new file mode 100644 index 000000000..5c2d07592 --- /dev/null +++ b/latest/cases/00599/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Basic reactions with four species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Species S4 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1.0$ |mole litre^-1^ | +|Initial concentration of S4 |$ 1.5$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 1.7; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00599/synopsis.txt b/latest/cases/00599/synopsis.txt new file mode 100644 index 000000000..07b220de4 --- /dev/null +++ b/latest/cases/00599/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Basic reactions with four species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. +Species S4 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1.0$ |mole litre^-1^ | +|Initial concentration of S4 |$ 1.5$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + diff --git a/latest/cases/00600/l2v5/heta-code/output.heta b/latest/cases/00600/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f3cf8b3bc --- /dev/null +++ b/latest/cases/00600/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-6; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-6; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2e-6; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5e-7; +S5 @Species 'S5' { units: substance/volume, boundary: true, compartment: C, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := C * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Record 'k1' { } .= 1.3e+6; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00600/l2v5/index.heta b/latest/cases/00600/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00600/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00600/l2v5/json/output.json b/latest/cases/00600/l2v5/json/output.json new file mode 100644 index 000000000..18fd01e12 --- /dev/null +++ b/latest/cases/00600/l2v5/json/output.json @@ -0,0 +1,166 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5e-7" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "1e-6" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.3e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00600/l3v2/heta-code/output.heta b/latest/cases/00600/l3v2/heta-code/output.heta new file mode 100644 index 000000000..db8f82b52 --- /dev/null +++ b/latest/cases/00600/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-6; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-6; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-6; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-7; +S5 @Species 'S5' { units: mole/litre, boundary: true, compartment: C, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := C * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00600/l3v2/index.heta b/latest/cases/00600/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00600/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00600/l3v2/json/output.json b/latest/cases/00600/l3v2/json/output.json new file mode 100644 index 000000000..1872a17bf --- /dev/null +++ b/latest/cases/00600/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5e-7" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "1e-6" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4 * pow(S5, (-1))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1300000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00600/model-sbml-l2v5.xml b/latest/cases/00600/model-sbml-l2v5.xml new file mode 100644 index 000000000..caf0ef345 --- /dev/null +++ b/latest/cases/00600/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00600/model-sbml-l3v2.xml b/latest/cases/00600/model-sbml-l3v2.xml new file mode 100644 index 000000000..2fc9c2c1d --- /dev/null +++ b/latest/cases/00600/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + S5 + -1 + + + + + + + + diff --git a/latest/cases/00600/output.heta b/latest/cases/00600/output.heta new file mode 100644 index 000000000..2b2e78505 --- /dev/null +++ b/latest/cases/00600/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic two reactions with five species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are five +species called S1, S2, S3, S4 and S5 and two parameters called k1 and k2. +Species S5 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C / S5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2.0 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S4 |$ 0.5 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S5 |$ 1.0 \x 10^-6$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-6; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-6; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-6; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-7; +S5 @Species 'S5' { units: mole/litre, boundary: true, compartment: C, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, }; +reaction2 := C * k2 * S3 * S4 * pow(S5, (-1)); + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00600/synopsis.txt b/latest/cases/00600/synopsis.txt new file mode 100644 index 000000000..dae0c20cc --- /dev/null +++ b/latest/cases/00600/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Basic two reactions with five species in a compartment + where one species is constant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are five +species called S1, S2, S3, S4 and S5 and two parameters called k1 and k2. +Species S5 is labeled as constant and therefore cannot be changed by rules +or reactions. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C / S5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2.0 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S4 |$ 0.5 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S5 |$ 1.0 \x 10^-6$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + diff --git a/latest/cases/00601/l2v5/heta-code/output.heta b/latest/cases/00601/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5c5941ac5 --- /dev/null +++ b/latest/cases/00601/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00601/l2v5/index.heta b/latest/cases/00601/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00601/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00601/l2v5/json/output.json b/latest/cases/00601/l2v5/json/output.json new file mode 100644 index 000000000..b2d18ad69 --- /dev/null +++ b/latest/cases/00601/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00601/l3v2/heta-code/output.heta b/latest/cases/00601/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b6fb8002a --- /dev/null +++ b/latest/cases/00601/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00601/l3v2/index.heta b/latest/cases/00601/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00601/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00601/l3v2/json/output.json b/latest/cases/00601/l3v2/json/output.json new file mode 100644 index 000000000..077874bae --- /dev/null +++ b/latest/cases/00601/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00601/model-sbml-l2v5.xml b/latest/cases/00601/model-sbml-l2v5.xml new file mode 100644 index 000000000..424a872ce --- /dev/null +++ b/latest/cases/00601/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00601/model-sbml-l3v2.xml b/latest/cases/00601/model-sbml-l3v2.xml new file mode 100644 index 000000000..de9abc65b --- /dev/null +++ b/latest/cases/00601/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00601/output.heta b/latest/cases/00601/output.heta new file mode 100644 index 000000000..e7211cc8e --- /dev/null +++ b/latest/cases/00601/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1.5$ |litre |] + + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00601/synopsis.txt b/latest/cases/00601/synopsis.txt new file mode 100644 index 000000000..bcb7ea766 --- /dev/null +++ b/latest/cases/00601/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1.5$ |litre |] + + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00602/l2v5/heta-code/output.heta b/latest/cases/00602/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8c9d18b90 --- /dev/null +++ b/latest/cases/00602/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.7; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.015; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 0.025; + diff --git a/latest/cases/00602/l2v5/index.heta b/latest/cases/00602/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00602/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00602/l2v5/json/output.json b/latest/cases/00602/l2v5/json/output.json new file mode 100644 index 000000000..73d24c3da --- /dev/null +++ b/latest/cases/00602/l2v5/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.7" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.015" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.025" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00602/l3v2/heta-code/output.heta b/latest/cases/00602/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a2ad0a5d4 --- /dev/null +++ b/latest/cases/00602/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.7; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.015; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 0.025; + diff --git a/latest/cases/00602/l3v2/index.heta b/latest/cases/00602/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00602/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00602/l3v2/json/output.json b/latest/cases/00602/l3v2/json/output.json new file mode 100644 index 000000000..8d41c8a57 --- /dev/null +++ b/latest/cases/00602/l3v2/json/output.json @@ -0,0 +1,104 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.7" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.015" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.025 + } +] \ No newline at end of file diff --git a/latest/cases/00602/model-sbml-l2v5.xml b/latest/cases/00602/model-sbml-l2v5.xml new file mode 100644 index 000000000..1d7f46cc6 --- /dev/null +++ b/latest/cases/00602/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00602/model-sbml-l3v2.xml b/latest/cases/00602/model-sbml-l3v2.xml new file mode 100644 index 000000000..dbc477592 --- /dev/null +++ b/latest/cases/00602/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00602/output.heta b/latest/cases/00602/output.heta new file mode 100644 index 000000000..454507722 --- /dev/null +++ b/latest/cases/00602/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Basic reaction with two species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.5 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Volume of compartment C |$ 0.7$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.7; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.015; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 0.025; + diff --git a/latest/cases/00602/synopsis.txt b/latest/cases/00602/synopsis.txt new file mode 100644 index 000000000..9fbe29180 --- /dev/null +++ b/latest/cases/00602/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Basic reaction with two species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.5 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Volume of compartment C |$ 0.7$ |litre |] + diff --git a/latest/cases/00603/l2v5/heta-code/output.heta b/latest/cases/00603/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0cbb69874 --- /dev/null +++ b/latest/cases/00603/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.3; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.7; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00603/l2v5/index.heta b/latest/cases/00603/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00603/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00603/l2v5/json/output.json b/latest/cases/00603/l2v5/json/output.json new file mode 100644 index 000000000..45c8b9d6b --- /dev/null +++ b/latest/cases/00603/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.7" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00603/l3v2/heta-code/output.heta b/latest/cases/00603/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dad49d7b3 --- /dev/null +++ b/latest/cases/00603/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.7; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00603/l3v2/index.heta b/latest/cases/00603/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00603/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00603/l3v2/json/output.json b/latest/cases/00603/l3v2/json/output.json new file mode 100644 index 000000000..a590bad80 --- /dev/null +++ b/latest/cases/00603/l3v2/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.7" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00603/model-sbml-l2v5.xml b/latest/cases/00603/model-sbml-l2v5.xml new file mode 100644 index 000000000..f355f2984 --- /dev/null +++ b/latest/cases/00603/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00603/model-sbml-l3v2.xml b/latest/cases/00603/model-sbml-l3v2.xml new file mode 100644 index 000000000..4f7b1966e --- /dev/null +++ b/latest/cases/00603/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00603/output.heta b/latest/cases/00603/output.heta new file mode 100644 index 000000000..90ca6cebb --- /dev/null +++ b/latest/cases/00603/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.7$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S4 |$ 1.0$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 0.3$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.7; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00603/synopsis.txt b/latest/cases/00603/synopsis.txt new file mode 100644 index 000000000..c49a313dc --- /dev/null +++ b/latest/cases/00603/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Basic two reactions with four species in a compartment + of non-unity volume. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.7$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S4 |$ 1.0$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 0.3$ |litre |] + diff --git a/latest/cases/00604/l2v5/heta-code/output.heta b/latest/cases/00604/l2v5/heta-code/output.heta new file mode 100644 index 000000000..738634312 --- /dev/null +++ b/latest/cases/00604/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.0015; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * multiply(k1, S1); + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00604/l2v5/index.heta b/latest/cases/00604/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00604/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00604/l2v5/json/output.json b/latest/cases/00604/l2v5/json/output.json new file mode 100644 index 000000000..a0a08c5c3 --- /dev/null +++ b/latest/cases/00604/l2v5/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00604/l3v2/heta-code/output.heta b/latest/cases/00604/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ef325073a --- /dev/null +++ b/latest/cases/00604/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0015; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * multiply(k1, S1); + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00604/l3v2/index.heta b/latest/cases/00604/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00604/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00604/l3v2/json/output.json b/latest/cases/00604/l3v2/json/output.json new file mode 100644 index 000000000..7700f564c --- /dev/null +++ b/latest/cases/00604/l3v2/json/output.json @@ -0,0 +1,70 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00604/model-sbml-l2v5.xml b/latest/cases/00604/model-sbml-l2v5.xml new file mode 100644 index 000000000..d3c6ea249 --- /dev/null +++ b/latest/cases/00604/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00604/model-sbml-l3v2.xml b/latest/cases/00604/model-sbml-l3v2.xml new file mode 100644 index 000000000..13440ab6a --- /dev/null +++ b/latest/cases/00604/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + + + + + + + + diff --git a/latest/cases/00604/output.heta b/latest/cases/00604/output.heta new file mode 100644 index 000000000..c6724d0a2 --- /dev/null +++ b/latest/cases/00604/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment of non-unity size using a function to apply +the kinetic law. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 2.3$ |litre |] + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0015; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * multiply(k1, S1); + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00604/synopsis.txt b/latest/cases/00604/synopsis.txt new file mode 100644 index 000000000..506ef87fb --- /dev/null +++ b/latest/cases/00604/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment of non-unity size using a function to apply +the kinetic law. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 2.3$ |litre |] + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00605/l2v5/heta-code/output.heta b/latest/cases/00605/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8b17c2af2 --- /dev/null +++ b/latest/cases/00605/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2.5; + diff --git a/latest/cases/00605/l2v5/index.heta b/latest/cases/00605/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00605/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00605/l2v5/json/output.json b/latest/cases/00605/l2v5/json/output.json new file mode 100644 index 000000000..eb8bf7cb8 --- /dev/null +++ b/latest/cases/00605/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00605/l3v2/heta-code/output.heta b/latest/cases/00605/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6910a6aeb --- /dev/null +++ b/latest/cases/00605/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00605/l3v2/index.heta b/latest/cases/00605/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00605/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00605/l3v2/json/output.json b/latest/cases/00605/l3v2/json/output.json new file mode 100644 index 000000000..2598c36c5 --- /dev/null +++ b/latest/cases/00605/l3v2/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00605/model-sbml-l2v5.xml b/latest/cases/00605/model-sbml-l2v5.xml new file mode 100644 index 000000000..88d2caaf5 --- /dev/null +++ b/latest/cases/00605/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00605/model-sbml-l3v2.xml b/latest/cases/00605/model-sbml-l3v2.xml new file mode 100644 index 000000000..a14597255 --- /dev/null +++ b/latest/cases/00605/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00605/output.heta b/latest/cases/00605/output.heta new file mode 100644 index 000000000..a93aa270e --- /dev/null +++ b/latest/cases/00605/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + of non-unity size using a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. +There are three species called S1, S2 and S3 and two parameters called k1 and k2. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 | $ 0.75$ | litre mole^-1^ second^-1^ | +|Value of parameter k2 | $ 2.5$ | second^-1^ | +|Volume of compartment C |$ 2.3$ |litre |] + + +*/ + + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * multiply(k1, S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00605/synopsis.txt b/latest/cases/00605/synopsis.txt new file mode 100644 index 000000000..4cf84c509 --- /dev/null +++ b/latest/cases/00605/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + of non-unity size using a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. +There are three species called S1, S2 and S3 and two parameters called k1 and k2. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $multiply(k1, S1, S2) * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 | $ 0.75$ | litre mole^-1^ second^-1^ | +|Value of parameter k2 | $ 2.5$ | second^-1^ | +|Volume of compartment C |$ 2.3$ |litre |] + + diff --git a/latest/cases/00606/l2v5/heta-code/output.heta b/latest/cases/00606/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cd4369402 --- /dev/null +++ b/latest/cases/00606/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 12.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 5e-4; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.001; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.002; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.0015; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 250; + diff --git a/latest/cases/00606/l2v5/index.heta b/latest/cases/00606/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00606/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00606/l2v5/json/output.json b/latest/cases/00606/l2v5/json/output.json new file mode 100644 index 000000000..d696f2d6d --- /dev/null +++ b/latest/cases/00606/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "12.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "250" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00606/l3v2/heta-code/output.heta b/latest/cases/00606/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fd1d13c96 --- /dev/null +++ b/latest/cases/00606/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 12.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 5e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.001; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.002; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.0015; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00606/l3v2/index.heta b/latest/cases/00606/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00606/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00606/l3v2/json/output.json b/latest/cases/00606/l3v2/json/output.json new file mode 100644 index 000000000..9c20b8674 --- /dev/null +++ b/latest/cases/00606/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "12.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, multiply(S1, S2))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 250 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00606/model-sbml-l2v5.xml b/latest/cases/00606/model-sbml-l2v5.xml new file mode 100644 index 000000000..588cf80c4 --- /dev/null +++ b/latest/cases/00606/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00606/model-sbml-l3v2.xml b/latest/cases/00606/model-sbml-l3v2.xml new file mode 100644 index 000000000..4de2a5e93 --- /dev/null +++ b/latest/cases/00606/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00606/output.heta b/latest/cases/00606/output.heta new file mode 100644 index 000000000..68d8d2f8e --- /dev/null +++ b/latest/cases/00606/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one varying compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$0.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S4 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 12.5$ |litre |] + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 12.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 5e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.001; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.002; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.0015; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * multiply(k1, multiply(S1, S2)); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/00606/synopsis.txt b/latest/cases/00606/synopsis.txt new file mode 100644 index 000000000..2d3ccdc5b --- /dev/null +++ b/latest/cases/00606/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic two reactions with four species in one varying compartment + and one functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$0.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S4 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$ 12.5$ |litre |] + diff --git a/latest/cases/00607/l2v5/heta-code/output.heta b/latest/cases/00607/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cdedb4f37 --- /dev/null +++ b/latest/cases/00607/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00607/l2v5/index.heta b/latest/cases/00607/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00607/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00607/l2v5/json/output.json b/latest/cases/00607/l2v5/json/output.json new file mode 100644 index 000000000..1ed78ee28 --- /dev/null +++ b/latest/cases/00607/l2v5/json/output.json @@ -0,0 +1,150 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00607/l3v2/heta-code/output.heta b/latest/cases/00607/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0f1e5f9be --- /dev/null +++ b/latest/cases/00607/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00607/l3v2/index.heta b/latest/cases/00607/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00607/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00607/l3v2/json/output.json b/latest/cases/00607/l3v2/json/output.json new file mode 100644 index 000000000..7b5f07c45 --- /dev/null +++ b/latest/cases/00607/l3v2/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k3 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00607/model-sbml-l2v5.xml b/latest/cases/00607/model-sbml-l2v5.xml new file mode 100644 index 000000000..3b738b93b --- /dev/null +++ b/latest/cases/00607/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00607/model-sbml-l3v2.xml b/latest/cases/00607/model-sbml-l3v2.xml new file mode 100644 index 000000000..d516df5ab --- /dev/null +++ b/latest/cases/00607/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00607/output.heta b/latest/cases/00607/output.heta new file mode 100644 index 000000000..5f5f00e01 --- /dev/null +++ b/latest/cases/00607/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S4 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 0.1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00607/synopsis.txt b/latest/cases/00607/synopsis.txt new file mode 100644 index 000000000..350d8c355 --- /dev/null +++ b/latest/cases/00607/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + +In this case there is no initial value declared for species S4 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S4 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 0.1$ |litre |] + diff --git a/latest/cases/00608/l2v5/heta-code/output.heta b/latest/cases/00608/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ff5752367 --- /dev/null +++ b/latest/cases/00608/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.08; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-4; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00608/l2v5/index.heta b/latest/cases/00608/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00608/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00608/l2v5/json/output.json b/latest/cases/00608/l2v5/json/output.json new file mode 100644 index 000000000..7ed3fac1a --- /dev/null +++ b/latest/cases/00608/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.08" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00608/l3v2/heta-code/output.heta b/latest/cases/00608/l3v2/heta-code/output.heta new file mode 100644 index 000000000..940b1d3a2 --- /dev/null +++ b/latest/cases/00608/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.08; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00608/l3v2/index.heta b/latest/cases/00608/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00608/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00608/l3v2/json/output.json b/latest/cases/00608/l3v2/json/output.json new file mode 100644 index 000000000..801ff4e5f --- /dev/null +++ b/latest/cases/00608/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.08" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/00608/model-sbml-l2v5.xml b/latest/cases/00608/model-sbml-l2v5.xml new file mode 100644 index 000000000..c4dfcdea1 --- /dev/null +++ b/latest/cases/00608/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00608/model-sbml-l3v2.xml b/latest/cases/00608/model-sbml-l3v2.xml new file mode 100644 index 000000000..0559853c2 --- /dev/null +++ b/latest/cases/00608/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00608/output.heta b/latest/cases/00608/output.heta new file mode 100644 index 000000000..b1280bae9 --- /dev/null +++ b/latest/cases/00608/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 0.08$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.08; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00608/synopsis.txt b/latest/cases/00608/synopsis.txt new file mode 100644 index 000000000..c2134bf68 --- /dev/null +++ b/latest/cases/00608/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3 and thus it +must be calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 0.08$ |litre |] + diff --git a/latest/cases/00609/l2v5/build.log b/latest/cases/00609/l2v5/build.log new file mode 100644 index 000000000..4c8db7c33 --- /dev/null +++ b/latest/cases/00609/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00609/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00609/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00609/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00609/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00609/l2v5/index.heta b/latest/cases/00609/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00609/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00609/l3v2/index.heta b/latest/cases/00609/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00609/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00609/model-sbml-l2v5.xml b/latest/cases/00609/model-sbml-l2v5.xml new file mode 100644 index 000000000..19bac2c97 --- /dev/null +++ b/latest/cases/00609/model-sbml-l2v5.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00609/synopsis.txt b/latest/cases/00609/synopsis.txt new file mode 100644 index 000000000..02a79e7a8 --- /dev/null +++ b/latest/cases/00609/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$ 1$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter p1 |$ 0.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00610/l2v5/build.log b/latest/cases/00610/l2v5/build.log new file mode 100644 index 000000000..e77c31489 --- /dev/null +++ b/latest/cases/00610/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00610/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00610/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00610/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00610/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00610/l2v5/index.heta b/latest/cases/00610/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00610/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00610/l3v2/index.heta b/latest/cases/00610/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00610/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00610/model-sbml-l2v5.xml b/latest/cases/00610/model-sbml-l2v5.xml new file mode 100644 index 000000000..a4019993e --- /dev/null +++ b/latest/cases/00610/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00610/synopsis.txt b/latest/cases/00610/synopsis.txt new file mode 100644 index 000000000..b508f677b --- /dev/null +++ b/latest/cases/00610/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $3 * S2$ |] + +Note that in this case the initial value of species S4 has not been declared and must be +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5 |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$ 0.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00611/l2v5/heta-code/output.heta b/latest/cases/00611/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6f5296496 --- /dev/null +++ b/latest/cases/00611/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; +S3 := k * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k @Record 'k' { } .= 0.75; + +k__reaction1_local @Const { } = 5; + diff --git a/latest/cases/00611/l2v5/index.heta b/latest/cases/00611/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00611/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00611/l2v5/json/output.json b/latest/cases/00611/l2v5/json/output.json new file mode 100644 index 000000000..d787e2ac3 --- /dev/null +++ b/latest/cases/00611/l2v5/json/output.json @@ -0,0 +1,103 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "ode_": "k * S2" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00611/l3v2/heta-code/output.heta b/latest/cases/00611/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9157ab2aa --- /dev/null +++ b/latest/cases/00611/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S3 := k * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 5; +k @Const 'k' { } = 0.75; + diff --git a/latest/cases/00611/l3v2/index.heta b/latest/cases/00611/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00611/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00611/l3v2/json/output.json b/latest/cases/00611/l3v2/json/output.json new file mode 100644 index 000000000..6348aba19 --- /dev/null +++ b/latest/cases/00611/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "ode_": "k * S2" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 0.75 + } +] \ No newline at end of file diff --git a/latest/cases/00611/model-sbml-l2v5.xml b/latest/cases/00611/model-sbml-l2v5.xml new file mode 100644 index 000000000..f01549768 --- /dev/null +++ b/latest/cases/00611/model-sbml-l2v5.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + k + S2 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00611/model-sbml-l3v2.xml b/latest/cases/00611/model-sbml-l3v2.xml new file mode 100644 index 000000000..7b9dbd189 --- /dev/null +++ b/latest/cases/00611/model-sbml-l3v2.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k + S2 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00611/output.heta b/latest/cases/00611/output.heta new file mode 100644 index 000000000..ba498a350 --- /dev/null +++ b/latest/cases/00611/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameters called k. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S$ |] + +Reaction S1 -> S2 defines one local parameter k which has a +scope local to the defining reaction. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$1$ |mole | +|Value of parameter k |$0.75$ |dimensionless | +|Value of local parameter k |$5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S3 := k * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 5; +k @Const 'k' { } = 0.75; + diff --git a/latest/cases/00611/synopsis.txt b/latest/cases/00611/synopsis.txt new file mode 100644 index 000000000..de4710515 --- /dev/null +++ b/latest/cases/00611/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameters called k. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S$ |] + +Reaction S1 -> S2 defines one local parameter k which has a +scope local to the defining reaction. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$1$ |mole | +|Value of parameter k |$0.75$ |dimensionless | +|Value of local parameter k |$5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00612/l2v5/heta-code/output.heta b/latest/cases/00612/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4f47f8ea3 --- /dev/null +++ b/latest/cases/00612/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := k * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k @Record 'k' { } .= 1.5; + +k__reaction1_local @Const { } = 15000; +k__reaction2_local @Const { } = 5; + diff --git a/latest/cases/00612/l2v5/index.heta b/latest/cases/00612/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00612/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00612/l2v5/json/output.json b/latest/cases/00612/l2v5/json/output.json new file mode 100644 index 000000000..9dcde3f70 --- /dev/null +++ b/latest/cases/00612/l2v5/json/output.json @@ -0,0 +1,144 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k * S2" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 15000 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 5 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00612/l3v2/heta-code/output.heta b/latest/cases/00612/l3v2/heta-code/output.heta new file mode 100644 index 000000000..18c803f9e --- /dev/null +++ b/latest/cases/00612/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 15000; +k__reaction2_local @Const { } = 5; +k @Const 'k' { } = 1.5; + diff --git a/latest/cases/00612/l3v2/index.heta b/latest/cases/00612/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00612/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00612/l3v2/json/output.json b/latest/cases/00612/l3v2/json/output.json new file mode 100644 index 000000000..eda199a03 --- /dev/null +++ b/latest/cases/00612/l3v2/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k * S2" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 15000 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 5 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00612/model-sbml-l2v5.xml b/latest/cases/00612/model-sbml-l2v5.xml new file mode 100644 index 000000000..67a2e4890 --- /dev/null +++ b/latest/cases/00612/model-sbml-l2v5.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + k + S2 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00612/model-sbml-l3v2.xml b/latest/cases/00612/model-sbml-l3v2.xml new file mode 100644 index 000000000..ca32f514d --- /dev/null +++ b/latest/cases/00612/model-sbml-l3v2.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k + S2 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00612/output.heta b/latest/cases/00612/output.heta new file mode 100644 index 000000000..93b192f28 --- /dev/null +++ b/latest/cases/00612/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and one parameter called k. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 + S2 also +defines one (different) local parameter k. Both of these parameters have a +scope local to the defining reaction. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k * S2$ |] + +Note that in this case the initial value of species S4 has not been declared and must be +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5 |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k |$ 1.5$ |dimensionless | +|Value of local parameter k |$ 1.5 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 15000; +k__reaction2_local @Const { } = 5; +k @Const 'k' { } = 1.5; + diff --git a/latest/cases/00612/synopsis.txt b/latest/cases/00612/synopsis.txt new file mode 100644 index 000000000..b20438450 --- /dev/null +++ b/latest/cases/00612/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and one parameter called k. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 + S2 also +defines one (different) local parameter k. Both of these parameters have a +scope local to the defining reaction. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k * S2$ |] + +Note that in this case the initial value of species S4 has not been declared and must be +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5 |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k |$ 1.5$ |dimensionless | +|Value of local parameter k |$ 1.5 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of local parameter k |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00613/l2v5/build.log b/latest/cases/00613/l2v5/build.log new file mode 100644 index 000000000..9d55a00f1 --- /dev/null +++ b/latest/cases/00613/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00613/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00613/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00613/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00613/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00613/l2v5/index.heta b/latest/cases/00613/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00613/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00613/l3v2/build.log b/latest/cases/00613/l3v2/build.log new file mode 100644 index 000000000..a66846902 --- /dev/null +++ b/latest/cases/00613/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00613/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00613/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00613/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00613/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00613/l3v2/index.heta b/latest/cases/00613/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00613/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00613/model-sbml-l2v5.xml b/latest/cases/00613/model-sbml-l2v5.xml new file mode 100644 index 000000000..b50d2086d --- /dev/null +++ b/latest/cases/00613/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00613/model-sbml-l3v2.xml b/latest/cases/00613/model-sbml-l3v2.xml new file mode 100644 index 000000000..5f9986db9 --- /dev/null +++ b/latest/cases/00613/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00613/synopsis.txt b/latest/cases/00613/synopsis.txt new file mode 100644 index 000000000..753776154 --- /dev/null +++ b/latest/cases/00613/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $0.1$ |] + +The assignment rule assigns a value to parameter k1 which is consistent with the value +attributed to the parameter by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00614/l2v5/build.log b/latest/cases/00614/l2v5/build.log new file mode 100644 index 000000000..85c57f260 --- /dev/null +++ b/latest/cases/00614/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00614/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00614/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00614/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00614/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00614/l2v5/index.heta b/latest/cases/00614/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00614/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00614/l3v2/build.log b/latest/cases/00614/l3v2/build.log new file mode 100644 index 000000000..888f19c3e --- /dev/null +++ b/latest/cases/00614/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00614/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00614/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00614/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00614/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00614/l3v2/index.heta b/latest/cases/00614/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00614/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00614/model-sbml-l2v5.xml b/latest/cases/00614/model-sbml-l2v5.xml new file mode 100644 index 000000000..d4a3ca231 --- /dev/null +++ b/latest/cases/00614/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00614/model-sbml-l3v2.xml b/latest/cases/00614/model-sbml-l3v2.xml new file mode 100644 index 000000000..12537cc3f --- /dev/null +++ b/latest/cases/00614/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00614/synopsis.txt b/latest/cases/00614/synopsis.txt new file mode 100644 index 000000000..e0f2f6b36 --- /dev/null +++ b/latest/cases/00614/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $0.1$ |] + +The assignment rule assigns a value to parameter k1 which is inconsistent with the value +attributed to the parameter by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$2$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00615/l2v5/build.log b/latest/cases/00615/l2v5/build.log new file mode 100644 index 000000000..9cc41d017 --- /dev/null +++ b/latest/cases/00615/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00615/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00615/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00615/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00615/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00615/l2v5/index.heta b/latest/cases/00615/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00615/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00615/l3v2/build.log b/latest/cases/00615/l3v2/build.log new file mode 100644 index 000000000..f8182e06c --- /dev/null +++ b/latest/cases/00615/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00615/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00615/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00615/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00615/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00615/l3v2/index.heta b/latest/cases/00615/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00615/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00615/model-sbml-l2v5.xml b/latest/cases/00615/model-sbml-l2v5.xml new file mode 100644 index 000000000..e60265536 --- /dev/null +++ b/latest/cases/00615/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00615/model-sbml-l3v2.xml b/latest/cases/00615/model-sbml-l3v2.xml new file mode 100644 index 000000000..0c77fe517 --- /dev/null +++ b/latest/cases/00615/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00615/synopsis.txt b/latest/cases/00615/synopsis.txt new file mode 100644 index 000000000..60c563cc2 --- /dev/null +++ b/latest/cases/00615/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $0.1$ |] + +The assignment rule assigns a value to parameter k1 which has no value +attributed to it by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00616/l2v5/heta-code/output.heta b/latest/cases/00616/l2v5/heta-code/output.heta new file mode 100644 index 000000000..22667bc13 --- /dev/null +++ b/latest/cases/00616/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00616/l2v5/index.heta b/latest/cases/00616/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00616/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00616/l2v5/json/output.json b/latest/cases/00616/l2v5/json/output.json new file mode 100644 index 000000000..5fe5a5c3b --- /dev/null +++ b/latest/cases/00616/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00616/l3v2/heta-code/output.heta b/latest/cases/00616/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5015fde8b --- /dev/null +++ b/latest/cases/00616/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00616/l3v2/index.heta b/latest/cases/00616/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00616/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00616/l3v2/json/output.json b/latest/cases/00616/l3v2/json/output.json new file mode 100644 index 000000000..0e8d13569 --- /dev/null +++ b/latest/cases/00616/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00616/model-sbml-l2v5.xml b/latest/cases/00616/model-sbml-l2v5.xml new file mode 100644 index 000000000..632c1544a --- /dev/null +++ b/latest/cases/00616/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00616/model-sbml-l3v2.xml b/latest/cases/00616/model-sbml-l3v2.xml new file mode 100644 index 000000000..e73c6e535 --- /dev/null +++ b/latest/cases/00616/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00616/output.heta b/latest/cases/00616/output.heta new file mode 100644 index 000000000..e31121633 --- /dev/null +++ b/latest/cases/00616/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00616/synopsis.txt b/latest/cases/00616/synopsis.txt new file mode 100644 index 000000000..f4b4220da --- /dev/null +++ b/latest/cases/00616/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00617/l2v5/heta-code/output.heta b/latest/cases/00617/l2v5/heta-code/output.heta new file mode 100644 index 000000000..22667bc13 --- /dev/null +++ b/latest/cases/00617/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00617/l2v5/index.heta b/latest/cases/00617/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00617/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00617/l2v5/json/output.json b/latest/cases/00617/l2v5/json/output.json new file mode 100644 index 000000000..5fe5a5c3b --- /dev/null +++ b/latest/cases/00617/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00617/l3v2/heta-code/output.heta b/latest/cases/00617/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5015fde8b --- /dev/null +++ b/latest/cases/00617/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00617/l3v2/index.heta b/latest/cases/00617/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00617/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00617/l3v2/json/output.json b/latest/cases/00617/l3v2/json/output.json new file mode 100644 index 000000000..0e8d13569 --- /dev/null +++ b/latest/cases/00617/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00617/model-sbml-l2v5.xml b/latest/cases/00617/model-sbml-l2v5.xml new file mode 100644 index 000000000..b17b747fe --- /dev/null +++ b/latest/cases/00617/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00617/model-sbml-l3v2.xml b/latest/cases/00617/model-sbml-l3v2.xml new file mode 100644 index 000000000..b9c09c3e9 --- /dev/null +++ b/latest/cases/00617/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00617/output.heta b/latest/cases/00617/output.heta new file mode 100644 index 000000000..ff2139b27 --- /dev/null +++ b/latest/cases/00617/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$10$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00617/synopsis.txt b/latest/cases/00617/synopsis.txt new file mode 100644 index 000000000..88a8a02bf --- /dev/null +++ b/latest/cases/00617/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$10$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00618/l2v5/heta-code/output.heta b/latest/cases/00618/l2v5/heta-code/output.heta new file mode 100644 index 000000000..22667bc13 --- /dev/null +++ b/latest/cases/00618/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00618/l2v5/index.heta b/latest/cases/00618/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00618/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00618/l2v5/json/output.json b/latest/cases/00618/l2v5/json/output.json new file mode 100644 index 000000000..5fe5a5c3b --- /dev/null +++ b/latest/cases/00618/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00618/l3v2/heta-code/output.heta b/latest/cases/00618/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5015fde8b --- /dev/null +++ b/latest/cases/00618/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00618/l3v2/index.heta b/latest/cases/00618/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00618/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00618/l3v2/json/output.json b/latest/cases/00618/l3v2/json/output.json new file mode 100644 index 000000000..0e8d13569 --- /dev/null +++ b/latest/cases/00618/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00618/model-sbml-l2v5.xml b/latest/cases/00618/model-sbml-l2v5.xml new file mode 100644 index 000000000..355f9b528 --- /dev/null +++ b/latest/cases/00618/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00618/model-sbml-l3v2.xml b/latest/cases/00618/model-sbml-l3v2.xml new file mode 100644 index 000000000..b1a410e81 --- /dev/null +++ b/latest/cases/00618/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00618/output.heta b/latest/cases/00618/output.heta new file mode 100644 index 000000000..739aed6fd --- /dev/null +++ b/latest/cases/00618/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is consisent with the value declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00618/synopsis.txt b/latest/cases/00618/synopsis.txt new file mode 100644 index 000000000..47ff15ae8 --- /dev/null +++ b/latest/cases/00618/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is consisent with the value declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00619/l2v5/heta-code/output.heta b/latest/cases/00619/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e75fb3293 --- /dev/null +++ b/latest/cases/00619/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00619/l2v5/index.heta b/latest/cases/00619/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00619/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00619/l2v5/json/output.json b/latest/cases/00619/l2v5/json/output.json new file mode 100644 index 000000000..40d24a642 --- /dev/null +++ b/latest/cases/00619/l2v5/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00619/l3v2/heta-code/output.heta b/latest/cases/00619/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1625428bb --- /dev/null +++ b/latest/cases/00619/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00619/l3v2/index.heta b/latest/cases/00619/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00619/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00619/l3v2/json/output.json b/latest/cases/00619/l3v2/json/output.json new file mode 100644 index 000000000..f13d2b19e --- /dev/null +++ b/latest/cases/00619/l3v2/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + } +] \ No newline at end of file diff --git a/latest/cases/00619/model-sbml-l2v5.xml b/latest/cases/00619/model-sbml-l2v5.xml new file mode 100644 index 000000000..529938a78 --- /dev/null +++ b/latest/cases/00619/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00619/model-sbml-l3v2.xml b/latest/cases/00619/model-sbml-l3v2.xml new file mode 100644 index 000000000..74e7ffb7b --- /dev/null +++ b/latest/cases/00619/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00619/output.heta b/latest/cases/00619/output.heta new file mode 100644 index 000000000..339e839a1 --- /dev/null +++ b/latest/cases/00619/output.heta @@ -0,0 +1,68 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00619/synopsis.txt b/latest/cases/00619/synopsis.txt new file mode 100644 index 000000000..991cc31f4 --- /dev/null +++ b/latest/cases/00619/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00620/l2v5/heta-code/output.heta b/latest/cases/00620/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1f2daadb7 --- /dev/null +++ b/latest/cases/00620/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.375 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00620/l2v5/index.heta b/latest/cases/00620/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00620/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00620/l2v5/json/output.json b/latest/cases/00620/l2v5/json/output.json new file mode 100644 index 000000000..91e43b107 --- /dev/null +++ b/latest/cases/00620/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.375 / C", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00620/l3v2/heta-code/output.heta b/latest/cases/00620/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f3c81f622 --- /dev/null +++ b/latest/cases/00620/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00620/l3v2/index.heta b/latest/cases/00620/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00620/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00620/l3v2/json/output.json b/latest/cases/00620/l3v2/json/output.json new file mode 100644 index 000000000..3b1d2f334 --- /dev/null +++ b/latest/cases/00620/l3v2/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.375 / C", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + } +] \ No newline at end of file diff --git a/latest/cases/00620/model-sbml-l2v5.xml b/latest/cases/00620/model-sbml-l2v5.xml new file mode 100644 index 000000000..ddc94bf6a --- /dev/null +++ b/latest/cases/00620/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00620/model-sbml-l3v2.xml b/latest/cases/00620/model-sbml-l3v2.xml new file mode 100644 index 000000000..260904088 --- /dev/null +++ b/latest/cases/00620/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00620/output.heta b/latest/cases/00620/output.heta new file mode 100644 index 000000000..6d717d3cd --- /dev/null +++ b/latest/cases/00620/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00620/synopsis.txt b/latest/cases/00620/synopsis.txt new file mode 100644 index 000000000..1e783f429 --- /dev/null +++ b/latest/cases/00620/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00621/l2v5/heta-code/output.heta b/latest/cases/00621/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8e9d81037 --- /dev/null +++ b/latest/cases/00621/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 3.75 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00621/l2v5/index.heta b/latest/cases/00621/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00621/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00621/l2v5/json/output.json b/latest/cases/00621/l2v5/json/output.json new file mode 100644 index 000000000..70c186dd4 --- /dev/null +++ b/latest/cases/00621/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "3.75 / C", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00621/l3v2/heta-code/output.heta b/latest/cases/00621/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c81f68d7d --- /dev/null +++ b/latest/cases/00621/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00621/l3v2/index.heta b/latest/cases/00621/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00621/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00621/l3v2/json/output.json b/latest/cases/00621/l3v2/json/output.json new file mode 100644 index 000000000..89c83c372 --- /dev/null +++ b/latest/cases/00621/l3v2/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "3.75 / C", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + } +] \ No newline at end of file diff --git a/latest/cases/00621/model-sbml-l2v5.xml b/latest/cases/00621/model-sbml-l2v5.xml new file mode 100644 index 000000000..cf91e808d --- /dev/null +++ b/latest/cases/00621/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00621/model-sbml-l3v2.xml b/latest/cases/00621/model-sbml-l3v2.xml new file mode 100644 index 000000000..dee7db681 --- /dev/null +++ b/latest/cases/00621/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00621/output.heta b/latest/cases/00621/output.heta new file mode 100644 index 000000000..7c14d522d --- /dev/null +++ b/latest/cases/00621/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00621/synopsis.txt b/latest/cases/00621/synopsis.txt new file mode 100644 index 000000000..73b420fde --- /dev/null +++ b/latest/cases/00621/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00622/l2v5/build.log b/latest/cases/00622/l2v5/build.log new file mode 100644 index 000000000..78531d971 --- /dev/null +++ b/latest/cases/00622/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00622/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00622/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00622/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00622/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00622/l2v5/index.heta b/latest/cases/00622/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00622/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00622/l3v2/build.log b/latest/cases/00622/l3v2/build.log new file mode 100644 index 000000000..ef9e624c2 --- /dev/null +++ b/latest/cases/00622/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00622/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00622/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00622/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00622/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00622/l3v2/index.heta b/latest/cases/00622/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00622/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00622/model-sbml-l2v5.xml b/latest/cases/00622/model-sbml-l2v5.xml new file mode 100644 index 000000000..068396657 --- /dev/null +++ b/latest/cases/00622/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00622/model-sbml-l3v2.xml b/latest/cases/00622/model-sbml-l3v2.xml new file mode 100644 index 000000000..959b0e694 --- /dev/null +++ b/latest/cases/00622/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00622/synopsis.txt b/latest/cases/00622/synopsis.txt new file mode 100644 index 000000000..b2e396194 --- /dev/null +++ b/latest/cases/00622/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00623/l2v5/build.log b/latest/cases/00623/l2v5/build.log new file mode 100644 index 000000000..8f377bde7 --- /dev/null +++ b/latest/cases/00623/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00623/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00623/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00623/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00623/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00623/l2v5/index.heta b/latest/cases/00623/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00623/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00623/l3v2/build.log b/latest/cases/00623/l3v2/build.log new file mode 100644 index 000000000..d503cbcc6 --- /dev/null +++ b/latest/cases/00623/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00623/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00623/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00623/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00623/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00623/l3v2/index.heta b/latest/cases/00623/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00623/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00623/model-sbml-l2v5.xml b/latest/cases/00623/model-sbml-l2v5.xml new file mode 100644 index 000000000..0b04cc0bc --- /dev/null +++ b/latest/cases/00623/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1.5 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00623/model-sbml-l3v2.xml b/latest/cases/00623/model-sbml-l3v2.xml new file mode 100644 index 000000000..33651bb27 --- /dev/null +++ b/latest/cases/00623/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1.5 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00623/synopsis.txt b/latest/cases/00623/synopsis.txt new file mode 100644 index 000000000..efcb69da2 --- /dev/null +++ b/latest/cases/00623/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1.5$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00624/l2v5/build.log b/latest/cases/00624/l2v5/build.log new file mode 100644 index 000000000..1a6e3da3a --- /dev/null +++ b/latest/cases/00624/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00624/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00624/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00624/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00624/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00624/l2v5/index.heta b/latest/cases/00624/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00624/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00624/l3v2/build.log b/latest/cases/00624/l3v2/build.log new file mode 100644 index 000000000..1e976c5ad --- /dev/null +++ b/latest/cases/00624/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00624/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00624/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00624/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00624/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00624/l3v2/index.heta b/latest/cases/00624/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00624/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00624/model-sbml-l2v5.xml b/latest/cases/00624/model-sbml-l2v5.xml new file mode 100644 index 000000000..05f50bdd3 --- /dev/null +++ b/latest/cases/00624/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00624/model-sbml-l3v2.xml b/latest/cases/00624/model-sbml-l3v2.xml new file mode 100644 index 000000000..9eabc3167 --- /dev/null +++ b/latest/cases/00624/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00624/synopsis.txt b/latest/cases/00624/synopsis.txt new file mode 100644 index 000000000..38d646759 --- /dev/null +++ b/latest/cases/00624/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $0.5$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00625/l2v5/heta-code/output.heta b/latest/cases/00625/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3d9e3dfa0 --- /dev/null +++ b/latest/cases/00625/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 2.25 / C; +S4 := multiply(k3, S1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00625/l2v5/index.heta b/latest/cases/00625/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00625/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00625/l2v5/json/output.json b/latest/cases/00625/l2v5/json/output.json new file mode 100644 index 000000000..f74d2548b --- /dev/null +++ b/latest/cases/00625/l2v5/json/output.json @@ -0,0 +1,168 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25 / C", + "ode_": "multiply(k3, S1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00625/l3v2/heta-code/output.heta b/latest/cases/00625/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d2d4c5ad3 --- /dev/null +++ b/latest/cases/00625/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C; +S4 := multiply(k3, S1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00625/l3v2/index.heta b/latest/cases/00625/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00625/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00625/l3v2/json/output.json b/latest/cases/00625/l3v2/json/output.json new file mode 100644 index 000000000..bc033be46 --- /dev/null +++ b/latest/cases/00625/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25 / C", + "ode_": "multiply(k3, S1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00625/model-sbml-l2v5.xml b/latest/cases/00625/model-sbml-l2v5.xml new file mode 100644 index 000000000..d663ae971 --- /dev/null +++ b/latest/cases/00625/model-sbml-l2v5.xml @@ -0,0 +1,105 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + multiply + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00625/model-sbml-l3v2.xml b/latest/cases/00625/model-sbml-l3v2.xml new file mode 100644 index 000000000..30cc7d367 --- /dev/null +++ b/latest/cases/00625/model-sbml-l3v2.xml @@ -0,0 +1,122 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00625/output.heta b/latest/cases/00625/output.heta new file mode 100644 index 000000000..09fb92ee8 --- /dev/null +++ b/latest/cases/00625/output.heta @@ -0,0 +1,76 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(k3, S1)$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C; +S4 := multiply(k3, S1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00625/synopsis.txt b/latest/cases/00625/synopsis.txt new file mode 100644 index 000000000..e8bf31804 --- /dev/null +++ b/latest/cases/00625/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(k3, S1)$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00626/l2v5/heta-code/output.heta b/latest/cases/00626/l2v5/heta-code/output.heta new file mode 100644 index 000000000..566bff08a --- /dev/null +++ b/latest/cases/00626/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := multiply(k3, S1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00626/l2v5/index.heta b/latest/cases/00626/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00626/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00626/l2v5/json/output.json b/latest/cases/00626/l2v5/json/output.json new file mode 100644 index 000000000..239f3679d --- /dev/null +++ b/latest/cases/00626/l2v5/json/output.json @@ -0,0 +1,167 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "multiply(k3, S1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00626/l3v2/heta-code/output.heta b/latest/cases/00626/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0b41c46ff --- /dev/null +++ b/latest/cases/00626/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := multiply(k3, S1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00626/l3v2/index.heta b/latest/cases/00626/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00626/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00626/l3v2/json/output.json b/latest/cases/00626/l3v2/json/output.json new file mode 100644 index 000000000..6a75f6577 --- /dev/null +++ b/latest/cases/00626/l3v2/json/output.json @@ -0,0 +1,137 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "multiply(k3, S1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00626/model-sbml-l2v5.xml b/latest/cases/00626/model-sbml-l2v5.xml new file mode 100644 index 000000000..31e1c26df --- /dev/null +++ b/latest/cases/00626/model-sbml-l2v5.xml @@ -0,0 +1,105 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + multiply + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00626/model-sbml-l3v2.xml b/latest/cases/00626/model-sbml-l3v2.xml new file mode 100644 index 000000000..0185724e2 --- /dev/null +++ b/latest/cases/00626/model-sbml-l3v2.xml @@ -0,0 +1,122 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00626/output.heta b/latest/cases/00626/output.heta new file mode 100644 index 000000000..6dc892708 --- /dev/null +++ b/latest/cases/00626/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(k3, S1)$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := multiply(k3, S1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00626/synopsis.txt b/latest/cases/00626/synopsis.txt new file mode 100644 index 000000000..a323b539a --- /dev/null +++ b/latest/cases/00626/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(k3, S1)$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00627/l2v5/heta-code/output.heta b/latest/cases/00627/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3f931b82c --- /dev/null +++ b/latest/cases/00627/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S4 := multiply(k3, S1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00627/l2v5/index.heta b/latest/cases/00627/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00627/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00627/l2v5/json/output.json b/latest/cases/00627/l2v5/json/output.json new file mode 100644 index 000000000..7c4bb44e1 --- /dev/null +++ b/latest/cases/00627/l2v5/json/output.json @@ -0,0 +1,168 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C", + "ode_": "multiply(k3, S1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00627/l3v2/heta-code/output.heta b/latest/cases/00627/l3v2/heta-code/output.heta new file mode 100644 index 000000000..427d45ef1 --- /dev/null +++ b/latest/cases/00627/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S4 := multiply(k3, S1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00627/l3v2/index.heta b/latest/cases/00627/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00627/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00627/l3v2/json/output.json b/latest/cases/00627/l3v2/json/output.json new file mode 100644 index 000000000..e02b07d31 --- /dev/null +++ b/latest/cases/00627/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C", + "ode_": "multiply(k3, S1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00627/model-sbml-l2v5.xml b/latest/cases/00627/model-sbml-l2v5.xml new file mode 100644 index 000000000..eb09efd5e --- /dev/null +++ b/latest/cases/00627/model-sbml-l2v5.xml @@ -0,0 +1,105 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + multiply + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00627/model-sbml-l3v2.xml b/latest/cases/00627/model-sbml-l3v2.xml new file mode 100644 index 000000000..f6a865110 --- /dev/null +++ b/latest/cases/00627/model-sbml-l3v2.xml @@ -0,0 +1,122 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00627/output.heta b/latest/cases/00627/output.heta new file mode 100644 index 000000000..5eb1a1f14 --- /dev/null +++ b/latest/cases/00627/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(k3, S1)$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value declared for species S4 is consistent +with the value calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 1.5 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S4 := multiply(k3, S1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00627/synopsis.txt b/latest/cases/00627/synopsis.txt new file mode 100644 index 000000000..60daf3d0c --- /dev/null +++ b/latest/cases/00627/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(k3, S1)$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value declared for species S4 is consistent +with the value calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 1.5 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00628/l2v5/build.log b/latest/cases/00628/l2v5/build.log new file mode 100644 index 000000000..8a77741a0 --- /dev/null +++ b/latest/cases/00628/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00628/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00628/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00628/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00628/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00628/l2v5/index.heta b/latest/cases/00628/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00628/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00628/l3v2/build.log b/latest/cases/00628/l3v2/build.log new file mode 100644 index 000000000..a9872c5ad --- /dev/null +++ b/latest/cases/00628/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00628/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00628/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00628/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00628/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00628/l3v2/index.heta b/latest/cases/00628/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00628/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00628/model-sbml-l2v5.xml b/latest/cases/00628/model-sbml-l2v5.xml new file mode 100644 index 000000000..36dee2b7f --- /dev/null +++ b/latest/cases/00628/model-sbml-l2v5.xml @@ -0,0 +1,113 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00628/model-sbml-l3v2.xml b/latest/cases/00628/model-sbml-l3v2.xml new file mode 100644 index 000000000..46ebbd61c --- /dev/null +++ b/latest/cases/00628/model-sbml-l3v2.xml @@ -0,0 +1,130 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00628/synopsis.txt b/latest/cases/00628/synopsis.txt new file mode 100644 index 000000000..018f876b9 --- /dev/null +++ b/latest/cases/00628/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and five parameters called k1, k2 +k3, p1 and p2. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $multiply(p1, p2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The assignment rule assigns a value to parameter k1 which is consistent with the value +attributed to the parameter by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Value of parameter p1 |$10$ |dimensionless | +|Value of parameter p2 |$0.01$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00629/l2v5/build.log b/latest/cases/00629/l2v5/build.log new file mode 100644 index 000000000..1ae01b456 --- /dev/null +++ b/latest/cases/00629/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00629/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00629/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00629/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00629/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00629/l2v5/index.heta b/latest/cases/00629/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00629/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00629/l3v2/build.log b/latest/cases/00629/l3v2/build.log new file mode 100644 index 000000000..bcf272eeb --- /dev/null +++ b/latest/cases/00629/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00629/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00629/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00629/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00629/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00629/l3v2/index.heta b/latest/cases/00629/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00629/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00629/model-sbml-l2v5.xml b/latest/cases/00629/model-sbml-l2v5.xml new file mode 100644 index 000000000..1103593ca --- /dev/null +++ b/latest/cases/00629/model-sbml-l2v5.xml @@ -0,0 +1,113 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00629/model-sbml-l3v2.xml b/latest/cases/00629/model-sbml-l3v2.xml new file mode 100644 index 000000000..ebd54a1f5 --- /dev/null +++ b/latest/cases/00629/model-sbml-l3v2.xml @@ -0,0 +1,130 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00629/synopsis.txt b/latest/cases/00629/synopsis.txt new file mode 100644 index 000000000..4745e9e4a --- /dev/null +++ b/latest/cases/00629/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and five parameters called k1, k2 +k3, p1 and p2. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $multiply(p1, p2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The assignment rule assigns a value to parameter k1 which is inconsistent with the value +attributed to the parameter by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$2$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Value of parameter p1 |$10$ |dimensionless | +|Value of parameter p2 |$0.01$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00630/l2v5/build.log b/latest/cases/00630/l2v5/build.log new file mode 100644 index 000000000..6a69b9b1a --- /dev/null +++ b/latest/cases/00630/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00630/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00630/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00630/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00630/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00630/l2v5/index.heta b/latest/cases/00630/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00630/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00630/l3v2/build.log b/latest/cases/00630/l3v2/build.log new file mode 100644 index 000000000..5d54f07ef --- /dev/null +++ b/latest/cases/00630/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00630/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00630/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00630/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00630/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00630/l3v2/index.heta b/latest/cases/00630/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00630/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00630/model-sbml-l2v5.xml b/latest/cases/00630/model-sbml-l2v5.xml new file mode 100644 index 000000000..a3cc16d05 --- /dev/null +++ b/latest/cases/00630/model-sbml-l2v5.xml @@ -0,0 +1,113 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00630/model-sbml-l3v2.xml b/latest/cases/00630/model-sbml-l3v2.xml new file mode 100644 index 000000000..3446fefd8 --- /dev/null +++ b/latest/cases/00630/model-sbml-l3v2.xml @@ -0,0 +1,130 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00630/synopsis.txt b/latest/cases/00630/synopsis.txt new file mode 100644 index 000000000..ebd53ab9a --- /dev/null +++ b/latest/cases/00630/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and five parameters called k1, k2 +k3, p1 and p2. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $multiply(p1, p2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The assignment rule assigns a value to parameter k1 which has no value +attributed to it by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Value of parameter p1 |$10$ |dimensionless | +|Value of parameter p2 |$0.01$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00631/l2v5/heta-code/output.heta b/latest/cases/00631/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1096b506b --- /dev/null +++ b/latest/cases/00631/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := multiply(p1, p2); +p1 @Record 'p1' { } .= 75; +p2 @Record 'p2' { } .= 0.01; + diff --git a/latest/cases/00631/l2v5/index.heta b/latest/cases/00631/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00631/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00631/l2v5/json/output.json b/latest/cases/00631/l2v5/json/output.json new file mode 100644 index 000000000..1184fe378 --- /dev/null +++ b/latest/cases/00631/l2v5/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "multiply(p1, p2)" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.01" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00631/l3v2/heta-code/output.heta b/latest/cases/00631/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6f349d89f --- /dev/null +++ b/latest/cases/00631/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := multiply(p1, p2); + +p1 @Const 'p1' { } = 75; +p2 @Const 'p2' { } = 0.01; + diff --git a/latest/cases/00631/l3v2/index.heta b/latest/cases/00631/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00631/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00631/l3v2/json/output.json b/latest/cases/00631/l3v2/json/output.json new file mode 100644 index 000000000..aa17a67df --- /dev/null +++ b/latest/cases/00631/l3v2/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "multiply(p1, p2)" + } + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 75 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.01 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00631/model-sbml-l2v5.xml b/latest/cases/00631/model-sbml-l2v5.xml new file mode 100644 index 000000000..84af71899 --- /dev/null +++ b/latest/cases/00631/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00631/model-sbml-l3v2.xml b/latest/cases/00631/model-sbml-l3v2.xml new file mode 100644 index 000000000..b59fbbda6 --- /dev/null +++ b/latest/cases/00631/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00631/output.heta b/latest/cases/00631/output.heta new file mode 100644 index 000000000..88685efc3 --- /dev/null +++ b/latest/cases/00631/output.heta @@ -0,0 +1,73 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $multiply(p1, p2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := multiply(p1, p2); + +p1 @Const 'p1' { } = 75; +p2 @Const 'p2' { } = 0.01; + diff --git a/latest/cases/00631/synopsis.txt b/latest/cases/00631/synopsis.txt new file mode 100644 index 000000000..3a709e7bf --- /dev/null +++ b/latest/cases/00631/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $multiply(p1, p2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00632/l2v5/heta-code/output.heta b/latest/cases/00632/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1096b506b --- /dev/null +++ b/latest/cases/00632/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := multiply(p1, p2); +p1 @Record 'p1' { } .= 75; +p2 @Record 'p2' { } .= 0.01; + diff --git a/latest/cases/00632/l2v5/index.heta b/latest/cases/00632/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00632/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00632/l2v5/json/output.json b/latest/cases/00632/l2v5/json/output.json new file mode 100644 index 000000000..1184fe378 --- /dev/null +++ b/latest/cases/00632/l2v5/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "multiply(p1, p2)" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.01" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00632/l3v2/heta-code/output.heta b/latest/cases/00632/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6f349d89f --- /dev/null +++ b/latest/cases/00632/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := multiply(p1, p2); + +p1 @Const 'p1' { } = 75; +p2 @Const 'p2' { } = 0.01; + diff --git a/latest/cases/00632/l3v2/index.heta b/latest/cases/00632/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00632/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00632/l3v2/json/output.json b/latest/cases/00632/l3v2/json/output.json new file mode 100644 index 000000000..aa17a67df --- /dev/null +++ b/latest/cases/00632/l3v2/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "multiply(p1, p2)" + } + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 75 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.01 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00632/model-sbml-l2v5.xml b/latest/cases/00632/model-sbml-l2v5.xml new file mode 100644 index 000000000..4d29a3d84 --- /dev/null +++ b/latest/cases/00632/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00632/model-sbml-l3v2.xml b/latest/cases/00632/model-sbml-l3v2.xml new file mode 100644 index 000000000..3fc300f4e --- /dev/null +++ b/latest/cases/00632/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00632/output.heta b/latest/cases/00632/output.heta new file mode 100644 index 000000000..b73b757e6 --- /dev/null +++ b/latest/cases/00632/output.heta @@ -0,0 +1,73 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $multiply(p1, p2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$10$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := multiply(p1, p2); + +p1 @Const 'p1' { } = 75; +p2 @Const 'p2' { } = 0.01; + diff --git a/latest/cases/00632/synopsis.txt b/latest/cases/00632/synopsis.txt new file mode 100644 index 000000000..27f70aae3 --- /dev/null +++ b/latest/cases/00632/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $multiply(p1, p2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$10$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00633/l2v5/heta-code/output.heta b/latest/cases/00633/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1096b506b --- /dev/null +++ b/latest/cases/00633/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := multiply(p1, p2); +p1 @Record 'p1' { } .= 75; +p2 @Record 'p2' { } .= 0.01; + diff --git a/latest/cases/00633/l2v5/index.heta b/latest/cases/00633/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00633/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00633/l2v5/json/output.json b/latest/cases/00633/l2v5/json/output.json new file mode 100644 index 000000000..1184fe378 --- /dev/null +++ b/latest/cases/00633/l2v5/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "multiply(p1, p2)" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0.01" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00633/l3v2/heta-code/output.heta b/latest/cases/00633/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6f349d89f --- /dev/null +++ b/latest/cases/00633/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := multiply(p1, p2); + +p1 @Const 'p1' { } = 75; +p2 @Const 'p2' { } = 0.01; + diff --git a/latest/cases/00633/l3v2/index.heta b/latest/cases/00633/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00633/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00633/l3v2/json/output.json b/latest/cases/00633/l3v2/json/output.json new file mode 100644 index 000000000..aa17a67df --- /dev/null +++ b/latest/cases/00633/l3v2/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "multiply(p1, p2)" + } + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 75 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 0.01 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00633/model-sbml-l2v5.xml b/latest/cases/00633/model-sbml-l2v5.xml new file mode 100644 index 000000000..e58106263 --- /dev/null +++ b/latest/cases/00633/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00633/model-sbml-l3v2.xml b/latest/cases/00633/model-sbml-l3v2.xml new file mode 100644 index 000000000..7f3b2a16c --- /dev/null +++ b/latest/cases/00633/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + + multiply + p1 + p2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00633/output.heta b/latest/cases/00633/output.heta new file mode 100644 index 000000000..52457b329 --- /dev/null +++ b/latest/cases/00633/output.heta @@ -0,0 +1,72 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $multiply(p1, p2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is consisent with the value declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := multiply(p1, p2); + +p1 @Const 'p1' { } = 75; +p2 @Const 'p2' { } = 0.01; + diff --git a/latest/cases/00633/synopsis.txt b/latest/cases/00633/synopsis.txt new file mode 100644 index 000000000..e9b1f6c11 --- /dev/null +++ b/latest/cases/00633/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, p1 and p2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $multiply(p1, p2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is consisent with the value declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.1$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00634/l2v5/heta-code/output.heta b/latest/cases/00634/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2edcd7e34 --- /dev/null +++ b/latest/cases/00634/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00634/l2v5/index.heta b/latest/cases/00634/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00634/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00634/l2v5/json/output.json b/latest/cases/00634/l2v5/json/output.json new file mode 100644 index 000000000..8a29f1e55 --- /dev/null +++ b/latest/cases/00634/l2v5/json/output.json @@ -0,0 +1,121 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00634/l3v2/heta-code/output.heta b/latest/cases/00634/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8ed2a485c --- /dev/null +++ b/latest/cases/00634/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00634/l3v2/index.heta b/latest/cases/00634/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00634/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00634/l3v2/json/output.json b/latest/cases/00634/l3v2/json/output.json new file mode 100644 index 000000000..104737d38 --- /dev/null +++ b/latest/cases/00634/l3v2/json/output.json @@ -0,0 +1,93 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00634/model-sbml-l2v5.xml b/latest/cases/00634/model-sbml-l2v5.xml new file mode 100644 index 000000000..21b92b049 --- /dev/null +++ b/latest/cases/00634/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00634/model-sbml-l3v2.xml b/latest/cases/00634/model-sbml-l3v2.xml new file mode 100644 index 000000000..8df9c06cc --- /dev/null +++ b/latest/cases/00634/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00634/output.heta b/latest/cases/00634/output.heta new file mode 100644 index 000000000..06b9af889 --- /dev/null +++ b/latest/cases/00634/output.heta @@ -0,0 +1,74 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00634/synopsis.txt b/latest/cases/00634/synopsis.txt new file mode 100644 index 000000000..bc4ce76e1 --- /dev/null +++ b/latest/cases/00634/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00635/l2v5/heta-code/output.heta b/latest/cases/00635/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c83695b4a --- /dev/null +++ b/latest/cases/00635/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.375 / C; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00635/l2v5/index.heta b/latest/cases/00635/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00635/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00635/l2v5/json/output.json b/latest/cases/00635/l2v5/json/output.json new file mode 100644 index 000000000..5e02ab48b --- /dev/null +++ b/latest/cases/00635/l2v5/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.375 / C", + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00635/l3v2/heta-code/output.heta b/latest/cases/00635/l3v2/heta-code/output.heta new file mode 100644 index 000000000..026031387 --- /dev/null +++ b/latest/cases/00635/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00635/l3v2/index.heta b/latest/cases/00635/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00635/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00635/l3v2/json/output.json b/latest/cases/00635/l3v2/json/output.json new file mode 100644 index 000000000..9db55ffa9 --- /dev/null +++ b/latest/cases/00635/l3v2/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.375 / C", + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00635/model-sbml-l2v5.xml b/latest/cases/00635/model-sbml-l2v5.xml new file mode 100644 index 000000000..6e67be4d4 --- /dev/null +++ b/latest/cases/00635/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00635/model-sbml-l3v2.xml b/latest/cases/00635/model-sbml-l3v2.xml new file mode 100644 index 000000000..9037447ea --- /dev/null +++ b/latest/cases/00635/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00635/output.heta b/latest/cases/00635/output.heta new file mode 100644 index 000000000..83a2801b6 --- /dev/null +++ b/latest/cases/00635/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00635/synopsis.txt b/latest/cases/00635/synopsis.txt new file mode 100644 index 000000000..6e2da6f21 --- /dev/null +++ b/latest/cases/00635/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00636/l2v5/heta-code/output.heta b/latest/cases/00636/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9c0d738c1 --- /dev/null +++ b/latest/cases/00636/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 3.75 / C; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00636/l2v5/index.heta b/latest/cases/00636/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00636/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00636/l2v5/json/output.json b/latest/cases/00636/l2v5/json/output.json new file mode 100644 index 000000000..63933e1c9 --- /dev/null +++ b/latest/cases/00636/l2v5/json/output.json @@ -0,0 +1,122 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "3.75 / C", + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00636/l3v2/heta-code/output.heta b/latest/cases/00636/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4be03a03b --- /dev/null +++ b/latest/cases/00636/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75 / C; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00636/l3v2/index.heta b/latest/cases/00636/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00636/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00636/l3v2/json/output.json b/latest/cases/00636/l3v2/json/output.json new file mode 100644 index 000000000..23b2d4d85 --- /dev/null +++ b/latest/cases/00636/l3v2/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "3.75 / C", + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00636/model-sbml-l2v5.xml b/latest/cases/00636/model-sbml-l2v5.xml new file mode 100644 index 000000000..39327018d --- /dev/null +++ b/latest/cases/00636/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00636/model-sbml-l3v2.xml b/latest/cases/00636/model-sbml-l3v2.xml new file mode 100644 index 000000000..fea790bde --- /dev/null +++ b/latest/cases/00636/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00636/output.heta b/latest/cases/00636/output.heta new file mode 100644 index 000000000..7f595716e --- /dev/null +++ b/latest/cases/00636/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75 / C; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00636/synopsis.txt b/latest/cases/00636/synopsis.txt new file mode 100644 index 000000000..e6f9a718c --- /dev/null +++ b/latest/cases/00636/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00637/l2v5/build.log b/latest/cases/00637/l2v5/build.log new file mode 100644 index 000000000..f2c5d0077 --- /dev/null +++ b/latest/cases/00637/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00637/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00637/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00637/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00637/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00637/l2v5/index.heta b/latest/cases/00637/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00637/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00637/l3v2/build.log b/latest/cases/00637/l3v2/build.log new file mode 100644 index 000000000..d3ceb1947 --- /dev/null +++ b/latest/cases/00637/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00637/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00637/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00637/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00637/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00637/l3v2/index.heta b/latest/cases/00637/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00637/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00637/model-sbml-l2v5.xml b/latest/cases/00637/model-sbml-l2v5.xml new file mode 100644 index 000000000..c58ec2095 --- /dev/null +++ b/latest/cases/00637/model-sbml-l2v5.xml @@ -0,0 +1,92 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00637/model-sbml-l3v2.xml b/latest/cases/00637/model-sbml-l3v2.xml new file mode 100644 index 000000000..817e6c27f --- /dev/null +++ b/latest/cases/00637/model-sbml-l3v2.xml @@ -0,0 +1,109 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00637/synopsis.txt b/latest/cases/00637/synopsis.txt new file mode 100644 index 000000000..cf569bb08 --- /dev/null +++ b/latest/cases/00637/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00638/l2v5/build.log b/latest/cases/00638/l2v5/build.log new file mode 100644 index 000000000..f02a977ef --- /dev/null +++ b/latest/cases/00638/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00638/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00638/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00638/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00638/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00638/l2v5/index.heta b/latest/cases/00638/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00638/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00638/l3v2/build.log b/latest/cases/00638/l3v2/build.log new file mode 100644 index 000000000..62811a78a --- /dev/null +++ b/latest/cases/00638/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00638/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00638/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00638/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00638/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00638/l3v2/index.heta b/latest/cases/00638/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00638/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00638/model-sbml-l2v5.xml b/latest/cases/00638/model-sbml-l2v5.xml new file mode 100644 index 000000000..d36ba366c --- /dev/null +++ b/latest/cases/00638/model-sbml-l2v5.xml @@ -0,0 +1,92 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1.5 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00638/model-sbml-l3v2.xml b/latest/cases/00638/model-sbml-l3v2.xml new file mode 100644 index 000000000..ec3aa83cc --- /dev/null +++ b/latest/cases/00638/model-sbml-l3v2.xml @@ -0,0 +1,109 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1.5 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00638/synopsis.txt b/latest/cases/00638/synopsis.txt new file mode 100644 index 000000000..c6c85e0e7 --- /dev/null +++ b/latest/cases/00638/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1.5$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00639/l2v5/build.log b/latest/cases/00639/l2v5/build.log new file mode 100644 index 000000000..19694b9ac --- /dev/null +++ b/latest/cases/00639/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00639/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00639/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00639/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00639/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00639/l2v5/index.heta b/latest/cases/00639/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00639/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00639/l3v2/build.log b/latest/cases/00639/l3v2/build.log new file mode 100644 index 000000000..ad278939c --- /dev/null +++ b/latest/cases/00639/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00639/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00639/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00639/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00639/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00639/l3v2/index.heta b/latest/cases/00639/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00639/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00639/model-sbml-l2v5.xml b/latest/cases/00639/model-sbml-l2v5.xml new file mode 100644 index 000000000..76c21cace --- /dev/null +++ b/latest/cases/00639/model-sbml-l2v5.xml @@ -0,0 +1,92 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00639/model-sbml-l3v2.xml b/latest/cases/00639/model-sbml-l3v2.xml new file mode 100644 index 000000000..ac8084ff8 --- /dev/null +++ b/latest/cases/00639/model-sbml-l3v2.xml @@ -0,0 +1,109 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00639/synopsis.txt b/latest/cases/00639/synopsis.txt new file mode 100644 index 000000000..a935b3530 --- /dev/null +++ b/latest/cases/00639/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S2)$ |] + +The assignmentRule applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $0.5$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00640/l2v5/heta-code/output.heta b/latest/cases/00640/l2v5/heta-code/output.heta new file mode 100644 index 000000000..023e9b938 --- /dev/null +++ b/latest/cases/00640/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.75; + diff --git a/latest/cases/00640/l2v5/index.heta b/latest/cases/00640/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00640/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00640/l2v5/json/output.json b/latest/cases/00640/l2v5/json/output.json new file mode 100644 index 000000000..9e63a65bf --- /dev/null +++ b/latest/cases/00640/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00640/l3v2/heta-code/output.heta b/latest/cases/00640/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0862cf804 --- /dev/null +++ b/latest/cases/00640/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00640/l3v2/index.heta b/latest/cases/00640/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00640/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00640/l3v2/json/output.json b/latest/cases/00640/l3v2/json/output.json new file mode 100644 index 000000000..b103ce24c --- /dev/null +++ b/latest/cases/00640/l3v2/json/output.json @@ -0,0 +1,125 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.75 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00640/model-sbml-l2v5.xml b/latest/cases/00640/model-sbml-l2v5.xml new file mode 100644 index 000000000..06b19d29b --- /dev/null +++ b/latest/cases/00640/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00640/model-sbml-l3v2.xml b/latest/cases/00640/model-sbml-l3v2.xml new file mode 100644 index 000000000..5a8304d5b --- /dev/null +++ b/latest/cases/00640/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00640/output.heta b/latest/cases/00640/output.heta new file mode 100644 index 000000000..4d58f2ef5 --- /dev/null +++ b/latest/cases/00640/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 calculated by the initialAssignment is consisent with the value +declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p |$ 0.75$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00640/synopsis.txt b/latest/cases/00640/synopsis.txt new file mode 100644 index 000000000..9eb69d885 --- /dev/null +++ b/latest/cases/00640/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 calculated by the initialAssignment is consisent with the value +declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p |$ 0.75$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00641/l2v5/heta-code/output.heta b/latest/cases/00641/l2v5/heta-code/output.heta new file mode 100644 index 000000000..023e9b938 --- /dev/null +++ b/latest/cases/00641/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.75; + diff --git a/latest/cases/00641/l2v5/index.heta b/latest/cases/00641/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00641/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00641/l2v5/json/output.json b/latest/cases/00641/l2v5/json/output.json new file mode 100644 index 000000000..9e63a65bf --- /dev/null +++ b/latest/cases/00641/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00641/l3v2/heta-code/output.heta b/latest/cases/00641/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0862cf804 --- /dev/null +++ b/latest/cases/00641/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00641/l3v2/index.heta b/latest/cases/00641/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00641/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00641/l3v2/json/output.json b/latest/cases/00641/l3v2/json/output.json new file mode 100644 index 000000000..b103ce24c --- /dev/null +++ b/latest/cases/00641/l3v2/json/output.json @@ -0,0 +1,125 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.75 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00641/model-sbml-l2v5.xml b/latest/cases/00641/model-sbml-l2v5.xml new file mode 100644 index 000000000..66838c28f --- /dev/null +++ b/latest/cases/00641/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00641/model-sbml-l3v2.xml b/latest/cases/00641/model-sbml-l3v2.xml new file mode 100644 index 000000000..818ee5f52 --- /dev/null +++ b/latest/cases/00641/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00641/output.heta b/latest/cases/00641/output.heta new file mode 100644 index 000000000..324149248 --- /dev/null +++ b/latest/cases/00641/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 calculated by the initialAssignment is inconsisent with the value +declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p |$ 0.75$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00641/synopsis.txt b/latest/cases/00641/synopsis.txt new file mode 100644 index 000000000..e8a84ed12 --- /dev/null +++ b/latest/cases/00641/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 calculated by the initialAssignment is inconsisent with the value +declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p |$ 0.75$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00642/l2v5/heta-code/output.heta b/latest/cases/00642/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4c447f93e --- /dev/null +++ b/latest/cases/00642/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.5; +p1 @Record 'p1' { } .= 0.75; + diff --git a/latest/cases/00642/l2v5/index.heta b/latest/cases/00642/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00642/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00642/l2v5/json/output.json b/latest/cases/00642/l2v5/json/output.json new file mode 100644 index 000000000..93f41d26c --- /dev/null +++ b/latest/cases/00642/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00642/l3v2/heta-code/output.heta b/latest/cases/00642/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b647f46de --- /dev/null +++ b/latest/cases/00642/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.5; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00642/l3v2/index.heta b/latest/cases/00642/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00642/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00642/l3v2/json/output.json b/latest/cases/00642/l3v2/json/output.json new file mode 100644 index 000000000..64e1921fe --- /dev/null +++ b/latest/cases/00642/l3v2/json/output.json @@ -0,0 +1,125 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.75 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00642/model-sbml-l2v5.xml b/latest/cases/00642/model-sbml-l2v5.xml new file mode 100644 index 000000000..f0d8294d8 --- /dev/null +++ b/latest/cases/00642/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00642/model-sbml-l3v2.xml b/latest/cases/00642/model-sbml-l3v2.xml new file mode 100644 index 000000000..f50cc93dc --- /dev/null +++ b/latest/cases/00642/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00642/output.heta b/latest/cases/00642/output.heta new file mode 100644 index 000000000..e23a89f24 --- /dev/null +++ b/latest/cases/00642/output.heta @@ -0,0 +1,74 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter p |$ 0.75$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.5; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00642/synopsis.txt b/latest/cases/00642/synopsis.txt new file mode 100644 index 000000000..6f86690ce --- /dev/null +++ b/latest/cases/00642/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter p |$ 0.75$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00643/l2v5/heta-code/output.heta b/latest/cases/00643/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c4225ebde --- /dev/null +++ b/latest/cases/00643/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= p1 * pow(2000, (-1)); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; +p1 @Record 'p1' { } .= 0.02; + diff --git a/latest/cases/00643/l2v5/index.heta b/latest/cases/00643/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00643/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00643/l2v5/json/output.json b/latest/cases/00643/l2v5/json/output.json new file mode 100644 index 000000000..917fec24d --- /dev/null +++ b/latest/cases/00643/l2v5/json/output.json @@ -0,0 +1,167 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "p1 * pow(2000, (-1))" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00643/l3v2/heta-code/output.heta b/latest/cases/00643/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d9b239fd1 --- /dev/null +++ b/latest/cases/00643/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= p1 * pow(2000, (-1)); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; +p1 @Const 'p1' { } = 0.02; + diff --git a/latest/cases/00643/l3v2/index.heta b/latest/cases/00643/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00643/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00643/l3v2/json/output.json b/latest/cases/00643/l3v2/json/output.json new file mode 100644 index 000000000..f6a3415a8 --- /dev/null +++ b/latest/cases/00643/l3v2/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "p1 * pow(2000, (-1))" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.02 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00643/model-sbml-l2v5.xml b/latest/cases/00643/model-sbml-l2v5.xml new file mode 100644 index 000000000..f17959b02 --- /dev/null +++ b/latest/cases/00643/model-sbml-l2v5.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + + + + + + + p1 + + + 2000 + -1 + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00643/model-sbml-l3v2.xml b/latest/cases/00643/model-sbml-l3v2.xml new file mode 100644 index 000000000..f0a826887 --- /dev/null +++ b/latest/cases/00643/model-sbml-l3v2.xml @@ -0,0 +1,119 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + + 2000 + -1 + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00643/output.heta b/latest/cases/00643/output.heta new file mode 100644 index 000000000..29aff54d5 --- /dev/null +++ b/latest/cases/00643/output.heta @@ -0,0 +1,80 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 2000$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 calculated by the initialAssignment is consisent with the value +declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$ 2 \x 10^-2$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= p1 * pow(2000, (-1)); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; +p1 @Const 'p1' { } = 0.02; + diff --git a/latest/cases/00643/synopsis.txt b/latest/cases/00643/synopsis.txt new file mode 100644 index 000000000..e48f3dc03 --- /dev/null +++ b/latest/cases/00643/synopsis.txt @@ -0,0 +1,54 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 2000$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 calculated by the initialAssignment is consisent with the value +declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$ 2 \x 10^-2$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00644/l2v5/heta-code/output.heta b/latest/cases/00644/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c4225ebde --- /dev/null +++ b/latest/cases/00644/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= p1 * pow(2000, (-1)); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; +p1 @Record 'p1' { } .= 0.02; + diff --git a/latest/cases/00644/l2v5/index.heta b/latest/cases/00644/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00644/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00644/l2v5/json/output.json b/latest/cases/00644/l2v5/json/output.json new file mode 100644 index 000000000..917fec24d --- /dev/null +++ b/latest/cases/00644/l2v5/json/output.json @@ -0,0 +1,167 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "p1 * pow(2000, (-1))" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00644/l3v2/heta-code/output.heta b/latest/cases/00644/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d9b239fd1 --- /dev/null +++ b/latest/cases/00644/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= p1 * pow(2000, (-1)); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; +p1 @Const 'p1' { } = 0.02; + diff --git a/latest/cases/00644/l3v2/index.heta b/latest/cases/00644/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00644/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00644/l3v2/json/output.json b/latest/cases/00644/l3v2/json/output.json new file mode 100644 index 000000000..f6a3415a8 --- /dev/null +++ b/latest/cases/00644/l3v2/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "p1 * pow(2000, (-1))" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.02 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00644/model-sbml-l2v5.xml b/latest/cases/00644/model-sbml-l2v5.xml new file mode 100644 index 000000000..8c3fb762a --- /dev/null +++ b/latest/cases/00644/model-sbml-l2v5.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + + + + + + + p1 + + + 2000 + -1 + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00644/model-sbml-l3v2.xml b/latest/cases/00644/model-sbml-l3v2.xml new file mode 100644 index 000000000..99f1c7457 --- /dev/null +++ b/latest/cases/00644/model-sbml-l3v2.xml @@ -0,0 +1,119 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + + 2000 + -1 + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00644/output.heta b/latest/cases/00644/output.heta new file mode 100644 index 000000000..6f35c36fa --- /dev/null +++ b/latest/cases/00644/output.heta @@ -0,0 +1,80 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 2000$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 calculated by the initialAssignment is inconsisent with the value +declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$ 2 \x 10^-2$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= p1 * pow(2000, (-1)); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; +p1 @Const 'p1' { } = 0.02; + diff --git a/latest/cases/00644/synopsis.txt b/latest/cases/00644/synopsis.txt new file mode 100644 index 000000000..a8c747b26 --- /dev/null +++ b/latest/cases/00644/synopsis.txt @@ -0,0 +1,54 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 2000$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 calculated by the initialAssignment is inconsisent with the value +declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$ 2 \x 10^-2$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00645/l2v5/heta-code/output.heta b/latest/cases/00645/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c4225ebde --- /dev/null +++ b/latest/cases/00645/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= p1 * pow(2000, (-1)); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; +p1 @Record 'p1' { } .= 0.02; + diff --git a/latest/cases/00645/l2v5/index.heta b/latest/cases/00645/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00645/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00645/l2v5/json/output.json b/latest/cases/00645/l2v5/json/output.json new file mode 100644 index 000000000..917fec24d --- /dev/null +++ b/latest/cases/00645/l2v5/json/output.json @@ -0,0 +1,167 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "p1 * pow(2000, (-1))" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00645/l3v2/heta-code/output.heta b/latest/cases/00645/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d9b239fd1 --- /dev/null +++ b/latest/cases/00645/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= p1 * pow(2000, (-1)); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; +p1 @Const 'p1' { } = 0.02; + diff --git a/latest/cases/00645/l3v2/index.heta b/latest/cases/00645/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00645/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00645/l3v2/json/output.json b/latest/cases/00645/l3v2/json/output.json new file mode 100644 index 000000000..f6a3415a8 --- /dev/null +++ b/latest/cases/00645/l3v2/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "p1 * pow(2000, (-1))" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.02 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00645/model-sbml-l2v5.xml b/latest/cases/00645/model-sbml-l2v5.xml new file mode 100644 index 000000000..c63b60f8c --- /dev/null +++ b/latest/cases/00645/model-sbml-l2v5.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + + + + + + + p1 + + + 2000 + -1 + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00645/model-sbml-l3v2.xml b/latest/cases/00645/model-sbml-l3v2.xml new file mode 100644 index 000000000..93ab74974 --- /dev/null +++ b/latest/cases/00645/model-sbml-l3v2.xml @@ -0,0 +1,119 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + + 2000 + -1 + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00645/output.heta b/latest/cases/00645/output.heta new file mode 100644 index 000000000..75cf35baa --- /dev/null +++ b/latest/cases/00645/output.heta @@ -0,0 +1,79 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 2000$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$ 2 \x 10^-2$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= p1 * pow(2000, (-1)); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; +p1 @Const 'p1' { } = 0.02; + diff --git a/latest/cases/00645/synopsis.txt b/latest/cases/00645/synopsis.txt new file mode 100644 index 000000000..fd41add5f --- /dev/null +++ b/latest/cases/00645/synopsis.txt @@ -0,0 +1,53 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 2000$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$ 2 \x 10^-2$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00646/l2v5/heta-code/output.heta b/latest/cases/00646/l2v5/heta-code/output.heta new file mode 100644 index 000000000..747e549a2 --- /dev/null +++ b/latest/cases/00646/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Record 'k1' { } .= 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00646/l2v5/index.heta b/latest/cases/00646/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00646/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00646/l2v5/json/output.json b/latest/cases/00646/l2v5/json/output.json new file mode 100644 index 000000000..2f9313775 --- /dev/null +++ b/latest/cases/00646/l2v5/json/output.json @@ -0,0 +1,120 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00646/l3v2/heta-code/output.heta b/latest/cases/00646/l3v2/heta-code/output.heta new file mode 100644 index 000000000..56023c48c --- /dev/null +++ b/latest/cases/00646/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Const 'k1' { } = 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00646/l3v2/index.heta b/latest/cases/00646/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00646/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00646/l3v2/json/output.json b/latest/cases/00646/l3v2/json/output.json new file mode 100644 index 000000000..b8f003d4b --- /dev/null +++ b/latest/cases/00646/l3v2/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + } +] \ No newline at end of file diff --git a/latest/cases/00646/model-sbml-l2v5.xml b/latest/cases/00646/model-sbml-l2v5.xml new file mode 100644 index 000000000..b481deb87 --- /dev/null +++ b/latest/cases/00646/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00646/model-sbml-l3v2.xml b/latest/cases/00646/model-sbml-l3v2.xml new file mode 100644 index 000000000..f0b3d33bc --- /dev/null +++ b/latest/cases/00646/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00646/output.heta b/latest/cases/00646/output.heta new file mode 100644 index 000000000..704e4e835 --- /dev/null +++ b/latest/cases/00646/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Const 'k1' { } = 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00646/synopsis.txt b/latest/cases/00646/synopsis.txt new file mode 100644 index 000000000..666920d10 --- /dev/null +++ b/latest/cases/00646/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00647/l2v5/heta-code/output.heta b/latest/cases/00647/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8e0e7f03f --- /dev/null +++ b/latest/cases/00647/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2.5e-4; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00647/l2v5/index.heta b/latest/cases/00647/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00647/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00647/l2v5/json/output.json b/latest/cases/00647/l2v5/json/output.json new file mode 100644 index 000000000..9f13b8220 --- /dev/null +++ b/latest/cases/00647/l2v5/json/output.json @@ -0,0 +1,165 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5e-4" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00647/l3v2/heta-code/output.heta b/latest/cases/00647/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9a0aff60b --- /dev/null +++ b/latest/cases/00647/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.00025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00647/l3v2/index.heta b/latest/cases/00647/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00647/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00647/l3v2/json/output.json b/latest/cases/00647/l3v2/json/output.json new file mode 100644 index 000000000..4c0454d76 --- /dev/null +++ b/latest/cases/00647/l3v2/json/output.json @@ -0,0 +1,137 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.00025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + } +] \ No newline at end of file diff --git a/latest/cases/00647/model-sbml-l2v5.xml b/latest/cases/00647/model-sbml-l2v5.xml new file mode 100644 index 000000000..a00890d9c --- /dev/null +++ b/latest/cases/00647/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00647/model-sbml-l3v2.xml b/latest/cases/00647/model-sbml-l3v2.xml new file mode 100644 index 000000000..1bce87ae0 --- /dev/null +++ b/latest/cases/00647/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00647/output.heta b/latest/cases/00647/output.heta new file mode 100644 index 000000000..ac9b6fbc1 --- /dev/null +++ b/latest/cases/00647/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.5$ |mole | +|Initial amount of S4 |$ 1$ |mole | +|Value of parameter k1 |$0.$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.00025$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.00025; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00647/synopsis.txt b/latest/cases/00647/synopsis.txt new file mode 100644 index 000000000..860ca9232 --- /dev/null +++ b/latest/cases/00647/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.5$ |mole | +|Initial amount of S4 |$ 1$ |mole | +|Value of parameter k1 |$0.$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.00025$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00648/l2v5/heta-code/output.heta b/latest/cases/00648/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7cc753318 --- /dev/null +++ b/latest/cases/00648/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00648/l2v5/index.heta b/latest/cases/00648/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00648/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00648/l2v5/json/output.json b/latest/cases/00648/l2v5/json/output.json new file mode 100644 index 000000000..5542d5a30 --- /dev/null +++ b/latest/cases/00648/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00648/l3v2/heta-code/output.heta b/latest/cases/00648/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ffcda958f --- /dev/null +++ b/latest/cases/00648/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00648/l3v2/index.heta b/latest/cases/00648/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00648/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00648/l3v2/json/output.json b/latest/cases/00648/l3v2/json/output.json new file mode 100644 index 000000000..b1672e1ae --- /dev/null +++ b/latest/cases/00648/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + } +] \ No newline at end of file diff --git a/latest/cases/00648/model-sbml-l2v5.xml b/latest/cases/00648/model-sbml-l2v5.xml new file mode 100644 index 000000000..ad2bae744 --- /dev/null +++ b/latest/cases/00648/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00648/model-sbml-l3v2.xml b/latest/cases/00648/model-sbml-l3v2.xml new file mode 100644 index 000000000..f6e03ebdf --- /dev/null +++ b/latest/cases/00648/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00648/output.heta b/latest/cases/00648/output.heta new file mode 100644 index 000000000..5d4fb8233 --- /dev/null +++ b/latest/cases/00648/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00648/synopsis.txt b/latest/cases/00648/synopsis.txt new file mode 100644 index 000000000..597431cfb --- /dev/null +++ b/latest/cases/00648/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00649/l2v5/build.log b/latest/cases/00649/l2v5/build.log new file mode 100644 index 000000000..dce70d7f6 --- /dev/null +++ b/latest/cases/00649/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00649/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00649/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00649/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00649/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00649/l2v5/index.heta b/latest/cases/00649/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00649/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00649/l3v2/build.log b/latest/cases/00649/l3v2/build.log new file mode 100644 index 000000000..d8436c52c --- /dev/null +++ b/latest/cases/00649/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00649/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00649/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00649/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00649/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00649/l3v2/index.heta b/latest/cases/00649/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00649/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00649/model-sbml-l2v5.xml b/latest/cases/00649/model-sbml-l2v5.xml new file mode 100644 index 000000000..c21cfe842 --- /dev/null +++ b/latest/cases/00649/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.75 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00649/model-sbml-l3v2.xml b/latest/cases/00649/model-sbml-l3v2.xml new file mode 100644 index 000000000..a6308f446 --- /dev/null +++ b/latest/cases/00649/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.75 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00649/synopsis.txt b/latest/cases/00649/synopsis.txt new file mode 100644 index 000000000..9db71b0ee --- /dev/null +++ b/latest/cases/00649/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $0.75$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00650/l2v5/build.log b/latest/cases/00650/l2v5/build.log new file mode 100644 index 000000000..9b4d2f4b9 --- /dev/null +++ b/latest/cases/00650/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00650/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00650/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00650/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00650/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00650/l2v5/index.heta b/latest/cases/00650/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00650/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00650/l3v2/build.log b/latest/cases/00650/l3v2/build.log new file mode 100644 index 000000000..85e5d5565 --- /dev/null +++ b/latest/cases/00650/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00650/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00650/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00650/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00650/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00650/l3v2/index.heta b/latest/cases/00650/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00650/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00650/model-sbml-l2v5.xml b/latest/cases/00650/model-sbml-l2v5.xml new file mode 100644 index 000000000..7314ed671 --- /dev/null +++ b/latest/cases/00650/model-sbml-l2v5.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 2.5 + + + + + + 2 + + + + + + + diff --git a/latest/cases/00650/model-sbml-l3v2.xml b/latest/cases/00650/model-sbml-l3v2.xml new file mode 100644 index 000000000..aeadc11a6 --- /dev/null +++ b/latest/cases/00650/model-sbml-l3v2.xml @@ -0,0 +1,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 2.5 + + + + + + 2 + + + + + + + diff --git a/latest/cases/00650/synopsis.txt b/latest/cases/00650/synopsis.txt new file mode 100644 index 000000000..249d41ef2 --- /dev/null +++ b/latest/cases/00650/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $2.5$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.5$ |mole | +|Initial amount of S4 |$ 1$ |mole | +|Value of parameter k1 |$0.$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.00025$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00651/l2v5/build.log b/latest/cases/00651/l2v5/build.log new file mode 100644 index 000000000..2b6b25592 --- /dev/null +++ b/latest/cases/00651/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00651/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00651/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00651/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00651/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00651/l2v5/index.heta b/latest/cases/00651/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00651/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00651/l3v2/build.log b/latest/cases/00651/l3v2/build.log new file mode 100644 index 000000000..45061ad65 --- /dev/null +++ b/latest/cases/00651/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00651/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00651/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00651/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00651/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00651/l3v2/index.heta b/latest/cases/00651/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00651/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00651/model-sbml-l2v5.xml b/latest/cases/00651/model-sbml-l2v5.xml new file mode 100644 index 000000000..13bb5fd99 --- /dev/null +++ b/latest/cases/00651/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.5 + + + + + + 1.2 + + + + + + 2 + + + + + + + diff --git a/latest/cases/00651/model-sbml-l3v2.xml b/latest/cases/00651/model-sbml-l3v2.xml new file mode 100644 index 000000000..28173d40c --- /dev/null +++ b/latest/cases/00651/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.5 + + + + + + 1.2 + + + + + + 2 + + + + + + + diff --git a/latest/cases/00651/synopsis.txt b/latest/cases/00651/synopsis.txt new file mode 100644 index 000000000..0d26f9c67 --- /dev/null +++ b/latest/cases/00651/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $1.2$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00652/l2v5/heta-code/output.heta b/latest/cases/00652/l2v5/heta-code/output.heta new file mode 100644 index 000000000..94184ddb3 --- /dev/null +++ b/latest/cases/00652/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S3 [event1]= (1e-5); +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), }; + diff --git a/latest/cases/00652/l2v5/index.heta b/latest/cases/00652/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00652/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00652/l2v5/json/output.json b/latest/cases/00652/l2v5/json/output.json new file mode 100644 index 000000000..afc45783c --- /dev/null +++ b/latest/cases/00652/l2v5/json/output.json @@ -0,0 +1,166 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C", + "event1": "(1e-5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 > (1.5e-5)" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00652/l3v2/heta-code/output.heta b/latest/cases/00652/l3v2/heta-code/output.heta new file mode 100644 index 000000000..44a085bc2 --- /dev/null +++ b/latest/cases/00652/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S3 [event1]= (1e-5); +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), }; + diff --git a/latest/cases/00652/l3v2/index.heta b/latest/cases/00652/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00652/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00652/l3v2/json/output.json b/latest/cases/00652/l3v2/json/output.json new file mode 100644 index 000000000..0c6462911 --- /dev/null +++ b/latest/cases/00652/l3v2/json/output.json @@ -0,0 +1,136 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C", + "event1": "(1e-5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 > (1.5e-5)" + } +] \ No newline at end of file diff --git a/latest/cases/00652/model-sbml-l2v5.xml b/latest/cases/00652/model-sbml-l2v5.xml new file mode 100644 index 000000000..5ec67beba --- /dev/null +++ b/latest/cases/00652/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00652/model-sbml-l3v2.xml b/latest/cases/00652/model-sbml-l3v2.xml new file mode 100644 index 000000000..0e56c630f --- /dev/null +++ b/latest/cases/00652/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00652/output.heta b/latest/cases/00652/output.heta new file mode 100644 index 000000000..780e0c7f9 --- /dev/null +++ b/latest/cases/00652/output.heta @@ -0,0 +1,78 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventNoDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S3 [event1]= (1e-5); +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), }; + diff --git a/latest/cases/00652/synopsis.txt b/latest/cases/00652/synopsis.txt new file mode 100644 index 000000000..9f6843190 --- /dev/null +++ b/latest/cases/00652/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventNoDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00653/l2v5/heta-code/output.heta b/latest/cases/00653/l2v5/heta-code/output.heta new file mode 100644 index 000000000..002b592fa --- /dev/null +++ b/latest/cases/00653/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S3 [event1]= (1e-5); +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), }; + diff --git a/latest/cases/00653/l2v5/index.heta b/latest/cases/00653/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00653/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00653/l2v5/json/output.json b/latest/cases/00653/l2v5/json/output.json new file mode 100644 index 000000000..834f0ed3f --- /dev/null +++ b/latest/cases/00653/l2v5/json/output.json @@ -0,0 +1,165 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C", + "event1": "(1e-5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 > (1.5e-5)" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00653/l3v2/heta-code/output.heta b/latest/cases/00653/l3v2/heta-code/output.heta new file mode 100644 index 000000000..89d77b373 --- /dev/null +++ b/latest/cases/00653/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S3 [event1]= (1e-5); +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), }; + diff --git a/latest/cases/00653/l3v2/index.heta b/latest/cases/00653/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00653/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00653/l3v2/json/output.json b/latest/cases/00653/l3v2/json/output.json new file mode 100644 index 000000000..ec70391de --- /dev/null +++ b/latest/cases/00653/l3v2/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C", + "event1": "(1e-5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 > (1.5e-5)" + } +] \ No newline at end of file diff --git a/latest/cases/00653/model-sbml-l2v5.xml b/latest/cases/00653/model-sbml-l2v5.xml new file mode 100644 index 000000000..7eca5984e --- /dev/null +++ b/latest/cases/00653/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00653/model-sbml-l3v2.xml b/latest/cases/00653/model-sbml-l3v2.xml new file mode 100644 index 000000000..f23e2e06d --- /dev/null +++ b/latest/cases/00653/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00653/output.heta b/latest/cases/00653/output.heta new file mode 100644 index 000000000..f4fb53385 --- /dev/null +++ b/latest/cases/00653/output.heta @@ -0,0 +1,77 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventNoDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S3 [event1]= (1e-5); +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), }; + diff --git a/latest/cases/00653/synopsis.txt b/latest/cases/00653/synopsis.txt new file mode 100644 index 000000000..f5b881074 --- /dev/null +++ b/latest/cases/00653/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventNoDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00654/l2v5/heta-code/output.heta b/latest/cases/00654/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a89cb45f8 --- /dev/null +++ b/latest/cases/00654/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S3 [event1]= (1e-5); +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), }; + diff --git a/latest/cases/00654/l2v5/index.heta b/latest/cases/00654/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00654/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00654/l2v5/json/output.json b/latest/cases/00654/l2v5/json/output.json new file mode 100644 index 000000000..c210ef635 --- /dev/null +++ b/latest/cases/00654/l2v5/json/output.json @@ -0,0 +1,166 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C", + "event1": "(1e-5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 > (1.5e-5)" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00654/l3v2/heta-code/output.heta b/latest/cases/00654/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e1d718d15 --- /dev/null +++ b/latest/cases/00654/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S3 [event1]= (1e-5); +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), }; + diff --git a/latest/cases/00654/l3v2/index.heta b/latest/cases/00654/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00654/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00654/l3v2/json/output.json b/latest/cases/00654/l3v2/json/output.json new file mode 100644 index 000000000..673caf494 --- /dev/null +++ b/latest/cases/00654/l3v2/json/output.json @@ -0,0 +1,136 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C", + "event1": "(1e-5)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 > (1.5e-5)" + } +] \ No newline at end of file diff --git a/latest/cases/00654/model-sbml-l2v5.xml b/latest/cases/00654/model-sbml-l2v5.xml new file mode 100644 index 000000000..e7dff8f61 --- /dev/null +++ b/latest/cases/00654/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00654/model-sbml-l3v2.xml b/latest/cases/00654/model-sbml-l3v2.xml new file mode 100644 index 000000000..04f4bcbd0 --- /dev/null +++ b/latest/cases/00654/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00654/output.heta b/latest/cases/00654/output.heta new file mode 100644 index 000000000..ea05e6b6c --- /dev/null +++ b/latest/cases/00654/output.heta @@ -0,0 +1,77 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +consistent with the value calculated by the assignmentRule. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 1.5 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S3 [event1]= (1e-5); +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + +event1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), }; + diff --git a/latest/cases/00654/synopsis.txt b/latest/cases/00654/synopsis.txt new file mode 100644 index 000000000..605f010d2 --- /dev/null +++ b/latest/cases/00654/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +consistent with the value calculated by the assignmentRule. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 1.5 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00655/l2v5/build.log b/latest/cases/00655/l2v5/build.log new file mode 100644 index 000000000..bb6a1921f --- /dev/null +++ b/latest/cases/00655/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00655/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00655/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00655/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00655/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00655/l2v5/index.heta b/latest/cases/00655/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00655/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00655/l3v2/build.log b/latest/cases/00655/l3v2/build.log new file mode 100644 index 000000000..22187e81a --- /dev/null +++ b/latest/cases/00655/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00655/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00655/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00655/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00655/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00655/l3v2/index.heta b/latest/cases/00655/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00655/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00655/model-sbml-l2v5.xml b/latest/cases/00655/model-sbml-l2v5.xml new file mode 100644 index 000000000..c54f0fc31 --- /dev/null +++ b/latest/cases/00655/model-sbml-l2v5.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + 2 + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00655/model-sbml-l3v2.xml b/latest/cases/00655/model-sbml-l3v2.xml new file mode 100644 index 000000000..68a5e2d8d --- /dev/null +++ b/latest/cases/00655/model-sbml-l3v2.xml @@ -0,0 +1,128 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + 2 + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00655/synopsis.txt b/latest/cases/00655/synopsis.txt new file mode 100644 index 000000000..36bc7b1cc --- /dev/null +++ b/latest/cases/00655/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventWithDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 > 0.000015$ | $2$ | $S3 = 0.00001$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00656/l2v5/build.log b/latest/cases/00656/l2v5/build.log new file mode 100644 index 000000000..7a315ea72 --- /dev/null +++ b/latest/cases/00656/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00656/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00656/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00656/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00656/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00656/l2v5/index.heta b/latest/cases/00656/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00656/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00656/l3v2/build.log b/latest/cases/00656/l3v2/build.log new file mode 100644 index 000000000..b82d7b3fd --- /dev/null +++ b/latest/cases/00656/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00656/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00656/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00656/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00656/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00656/l3v2/index.heta b/latest/cases/00656/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00656/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00656/model-sbml-l2v5.xml b/latest/cases/00656/model-sbml-l2v5.xml new file mode 100644 index 000000000..e348d8677 --- /dev/null +++ b/latest/cases/00656/model-sbml-l2v5.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + 3.2 + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00656/model-sbml-l3v2.xml b/latest/cases/00656/model-sbml-l3v2.xml new file mode 100644 index 000000000..10bebbd34 --- /dev/null +++ b/latest/cases/00656/model-sbml-l3v2.xml @@ -0,0 +1,128 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + 3.2 + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00656/synopsis.txt b/latest/cases/00656/synopsis.txt new file mode 100644 index 000000000..362fd7d30 --- /dev/null +++ b/latest/cases/00656/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventWithDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 > 0.000015$ | $3.2$ | $S3 = 0.00001$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00657/l2v5/build.log b/latest/cases/00657/l2v5/build.log new file mode 100644 index 000000000..6665d14d7 --- /dev/null +++ b/latest/cases/00657/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00657/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00657/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00657/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00657/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00657/l2v5/index.heta b/latest/cases/00657/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00657/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00657/l3v2/build.log b/latest/cases/00657/l3v2/build.log new file mode 100644 index 000000000..fad2b1ae7 --- /dev/null +++ b/latest/cases/00657/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00657/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00657/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00657/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00657/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00657/l3v2/index.heta b/latest/cases/00657/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00657/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00657/model-sbml-l2v5.xml b/latest/cases/00657/model-sbml-l2v5.xml new file mode 100644 index 000000000..451f06e5e --- /dev/null +++ b/latest/cases/00657/model-sbml-l2v5.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + 1.2 + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00657/model-sbml-l3v2.xml b/latest/cases/00657/model-sbml-l3v2.xml new file mode 100644 index 000000000..c599637b6 --- /dev/null +++ b/latest/cases/00657/model-sbml-l3v2.xml @@ -0,0 +1,128 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 1.5 -5 + + + + + + 1.2 + + + + + + 1 -5 + + + + + + + diff --git a/latest/cases/00657/synopsis.txt b/latest/cases/00657/synopsis.txt new file mode 100644 index 000000000..ae5d0aa6c --- /dev/null +++ b/latest/cases/00657/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +consistent with the value calculated by the assignmentRule. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 1.5 \x 10^-5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00658/l2v5/build.log b/latest/cases/00658/l2v5/build.log new file mode 100644 index 000000000..386b203c7 --- /dev/null +++ b/latest/cases/00658/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00658/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00658/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00658/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00658/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00658/l2v5/index.heta b/latest/cases/00658/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00658/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00658/l3v2/build.log b/latest/cases/00658/l3v2/build.log new file mode 100644 index 000000000..17953bed9 --- /dev/null +++ b/latest/cases/00658/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00658/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00658/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00658/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00658/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00658/l3v2/index.heta b/latest/cases/00658/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00658/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00658/model-sbml-l2v5.xml b/latest/cases/00658/model-sbml-l2v5.xml new file mode 100644 index 000000000..a8a9a1215 --- /dev/null +++ b/latest/cases/00658/model-sbml-l2v5.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + -1 + k1 + + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + diff --git a/latest/cases/00658/model-sbml-l3v2.xml b/latest/cases/00658/model-sbml-l3v2.xml new file mode 100644 index 000000000..f00c0df99 --- /dev/null +++ b/latest/cases/00658/model-sbml-l3v2.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + -1 + k1 + + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + diff --git a/latest/cases/00658/synopsis.txt b/latest/cases/00658/synopsis.txt new file mode 100644 index 000000000..90b6e4bab --- /dev/null +++ b/latest/cases/00658/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| ->S1 | $C * k2 * S2$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S1 + S2-k1$ |] + +The model contains one initialAssignment that assigns the initial value for +parameter k1: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $1$ |] + +Note: InitialAssignments override any declared initial values. In this +case the value from the initialAssignment is consistent with the value +attributed to k1 by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Value of parameter k1 |$ 1.0$ |mole litre^-1^ | +|Value of parameter k2 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00659/l2v5/build.log b/latest/cases/00659/l2v5/build.log new file mode 100644 index 000000000..fb2accdde --- /dev/null +++ b/latest/cases/00659/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00659/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00659/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00659/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00659/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00659/l2v5/index.heta b/latest/cases/00659/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00659/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00659/l3v2/build.log b/latest/cases/00659/l3v2/build.log new file mode 100644 index 000000000..a9576479b --- /dev/null +++ b/latest/cases/00659/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00659/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00659/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00659/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00659/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00659/l3v2/index.heta b/latest/cases/00659/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00659/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00659/model-sbml-l2v5.xml b/latest/cases/00659/model-sbml-l2v5.xml new file mode 100644 index 000000000..5c3cccce1 --- /dev/null +++ b/latest/cases/00659/model-sbml-l2v5.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + -1 + k1 + + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + diff --git a/latest/cases/00659/model-sbml-l3v2.xml b/latest/cases/00659/model-sbml-l3v2.xml new file mode 100644 index 000000000..d6487481f --- /dev/null +++ b/latest/cases/00659/model-sbml-l3v2.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + -1 + k1 + + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + diff --git a/latest/cases/00659/synopsis.txt b/latest/cases/00659/synopsis.txt new file mode 100644 index 000000000..9d1195d44 --- /dev/null +++ b/latest/cases/00659/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| ->S1 | $C * k2 * S2$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S1 + S2-k1$ |] + +The model contains one initialAssignment that assigns the initial value for +parameter k1: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $1$ |] + +Note: InitialAssignments override any declared initial values. In this +case the value from the initialAssignment is inconsistent with the value +attributed to k1 by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Value of parameter k1 |$ 5.0$ |mole litre^-1^ | +|Value of parameter k2 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00660/l2v5/build.log b/latest/cases/00660/l2v5/build.log new file mode 100644 index 000000000..65bfeca76 --- /dev/null +++ b/latest/cases/00660/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00660/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00660/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00660/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00660/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00660/l2v5/index.heta b/latest/cases/00660/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00660/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00660/l3v2/build.log b/latest/cases/00660/l3v2/build.log new file mode 100644 index 000000000..477039bd0 --- /dev/null +++ b/latest/cases/00660/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00660/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00660/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00660/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00660/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00660/l3v2/index.heta b/latest/cases/00660/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00660/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00660/model-sbml-l2v5.xml b/latest/cases/00660/model-sbml-l2v5.xml new file mode 100644 index 000000000..ed50c0a16 --- /dev/null +++ b/latest/cases/00660/model-sbml-l2v5.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + -1 + k1 + + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + diff --git a/latest/cases/00660/model-sbml-l3v2.xml b/latest/cases/00660/model-sbml-l3v2.xml new file mode 100644 index 000000000..6e2e852b5 --- /dev/null +++ b/latest/cases/00660/model-sbml-l3v2.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + -1 + k1 + + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + diff --git a/latest/cases/00660/synopsis.txt b/latest/cases/00660/synopsis.txt new file mode 100644 index 000000000..74bdcc023 --- /dev/null +++ b/latest/cases/00660/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| ->S1 | $C * k2 * S2$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S1 + S2-k1$ |] + +The model contains one initialAssignment that assigns the initial value for +parameter k1: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $1$ |] + +Note: InitialAssignments override any declared initial values. In this +case there is no value attributed to k1 by the model definition. The +value calculated using the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 0.5$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Value of parameter k1 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k2 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00661/l2v5/build.log b/latest/cases/00661/l2v5/build.log new file mode 100644 index 000000000..43d52f72c --- /dev/null +++ b/latest/cases/00661/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00661/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00661/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00661/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00661/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00661/l2v5/index.heta b/latest/cases/00661/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00661/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00661/l3v2/build.log b/latest/cases/00661/l3v2/build.log new file mode 100644 index 000000000..942b25e84 --- /dev/null +++ b/latest/cases/00661/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00661/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00661/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00661/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00661/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00661/l3v2/index.heta b/latest/cases/00661/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00661/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00661/model-sbml-l2v5.xml b/latest/cases/00661/model-sbml-l2v5.xml new file mode 100644 index 000000000..33af2ff4b --- /dev/null +++ b/latest/cases/00661/model-sbml-l2v5.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00661/model-sbml-l3v2.xml b/latest/cases/00661/model-sbml-l3v2.xml new file mode 100644 index 000000000..7a9cd6bde --- /dev/null +++ b/latest/cases/00661/model-sbml-l3v2.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00661/synopsis.txt b/latest/cases/00661/synopsis.txt new file mode 100644 index 000000000..4f868c5ee --- /dev/null +++ b/latest/cases/00661/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $X0 + X1 + T - S1$ |] + +The model contains one event that assigns value to species X1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $X1 > 2$ | $-$ | $X1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1.25$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Initial amount of S1 |$3.75$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00662/l2v5/build.log b/latest/cases/00662/l2v5/build.log new file mode 100644 index 000000000..908cc9624 --- /dev/null +++ b/latest/cases/00662/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00662/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00662/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00662/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00662/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00662/l2v5/index.heta b/latest/cases/00662/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00662/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00662/l3v2/build.log b/latest/cases/00662/l3v2/build.log new file mode 100644 index 000000000..3a9a2c835 --- /dev/null +++ b/latest/cases/00662/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00662/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00662/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00662/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00662/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00662/l3v2/index.heta b/latest/cases/00662/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00662/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00662/model-sbml-l2v5.xml b/latest/cases/00662/model-sbml-l2v5.xml new file mode 100644 index 000000000..173506a7e --- /dev/null +++ b/latest/cases/00662/model-sbml-l2v5.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + X1 + 0.5 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00662/model-sbml-l3v2.xml b/latest/cases/00662/model-sbml-l3v2.xml new file mode 100644 index 000000000..1fc365511 --- /dev/null +++ b/latest/cases/00662/model-sbml-l3v2.xml @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + X1 + 0.5 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00662/synopsis.txt b/latest/cases/00662/synopsis.txt new file mode 100644 index 000000000..df0c08444 --- /dev/null +++ b/latest/cases/00662/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The model contains one event that assigns value to species X1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $X1 > 0.5$ | $-$ | $X1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00663/l2v5/build.log b/latest/cases/00663/l2v5/build.log new file mode 100644 index 000000000..01d8d690a --- /dev/null +++ b/latest/cases/00663/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00663/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00663/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00663/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00663/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00663/l2v5/index.heta b/latest/cases/00663/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00663/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00663/l3v2/build.log b/latest/cases/00663/l3v2/build.log new file mode 100644 index 000000000..4cbce7eca --- /dev/null +++ b/latest/cases/00663/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00663/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00663/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00663/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00663/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00663/l3v2/index.heta b/latest/cases/00663/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00663/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00663/model-sbml-l2v5.xml b/latest/cases/00663/model-sbml-l2v5.xml new file mode 100644 index 000000000..1f1c4d44b --- /dev/null +++ b/latest/cases/00663/model-sbml-l2v5.xml @@ -0,0 +1,114 @@ + + + + + + + + + + + + + + + + + + + + + + + k2 + -0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S4 + S3 + + + + + + + + + 2 + S4 + + + + + + + + diff --git a/latest/cases/00663/model-sbml-l3v2.xml b/latest/cases/00663/model-sbml-l3v2.xml new file mode 100644 index 000000000..75f99da18 --- /dev/null +++ b/latest/cases/00663/model-sbml-l3v2.xml @@ -0,0 +1,131 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + -0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S4 + S3 + + + + + + + + + 2 + S4 + + + + + + + + diff --git a/latest/cases/00663/synopsis.txt b/latest/cases/00663/synopsis.txt new file mode 100644 index 000000000..a0fd162ef --- /dev/null +++ b/latest/cases/00663/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Three reactions with four species in one compartment, +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventNoDelay +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $k2 - 0.9$ |] + +The model contains one event that assigns value to species S4 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S3$ | $-$ | $S4 = 2 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00664/l2v5/build.log b/latest/cases/00664/l2v5/build.log new file mode 100644 index 000000000..4df5d8bb9 --- /dev/null +++ b/latest/cases/00664/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00664/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00664/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00664/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00664/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00664/l2v5/index.heta b/latest/cases/00664/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00664/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00664/l3v2/build.log b/latest/cases/00664/l3v2/build.log new file mode 100644 index 000000000..38541765b --- /dev/null +++ b/latest/cases/00664/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00664/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00664/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00664/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00664/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00664/l3v2/index.heta b/latest/cases/00664/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00664/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00664/model-sbml-l2v5.xml b/latest/cases/00664/model-sbml-l2v5.xml new file mode 100644 index 000000000..5a426a4e0 --- /dev/null +++ b/latest/cases/00664/model-sbml-l2v5.xml @@ -0,0 +1,119 @@ + + + + + + + + + + + + + + + + + + + + + + + k2 + -0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S4 + S3 + + + + + + 2 + + + + + + + + 3 + S4 + + + + + + + + diff --git a/latest/cases/00664/model-sbml-l3v2.xml b/latest/cases/00664/model-sbml-l3v2.xml new file mode 100644 index 000000000..0ff55f1bf --- /dev/null +++ b/latest/cases/00664/model-sbml-l3v2.xml @@ -0,0 +1,136 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + -0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + + S4 + S3 + + + + + + 2 + + + + + + + + 3 + S4 + + + + + + + + diff --git a/latest/cases/00664/synopsis.txt b/latest/cases/00664/synopsis.txt new file mode 100644 index 000000000..7355c2f23 --- /dev/null +++ b/latest/cases/00664/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Three reactions with four species in one compartment, +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventWithDelay +testTags: Amount, EventUsesTriggerTimeValues, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $k2 - 0.9$ |] + +The model contains one event that assigns value to species S4 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S3$ | $2$ | $S4 = 2 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00665/l2v5/build.log b/latest/cases/00665/l2v5/build.log new file mode 100644 index 000000000..d49da92ed --- /dev/null +++ b/latest/cases/00665/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00665/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00665/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00665/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00665/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00665/l2v5/index.heta b/latest/cases/00665/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00665/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00665/l3v2/build.log b/latest/cases/00665/l3v2/build.log new file mode 100644 index 000000000..0dacf44f9 --- /dev/null +++ b/latest/cases/00665/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00665/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00665/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00665/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00665/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00665/l3v2/index.heta b/latest/cases/00665/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00665/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00665/model-sbml-l2v5.xml b/latest/cases/00665/model-sbml-l2v5.xml new file mode 100644 index 000000000..ec45ccb04 --- /dev/null +++ b/latest/cases/00665/model-sbml-l2v5.xml @@ -0,0 +1,98 @@ + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + 4.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00665/model-sbml-l3v2.xml b/latest/cases/00665/model-sbml-l3v2.xml new file mode 100644 index 000000000..509cd6bf3 --- /dev/null +++ b/latest/cases/00665/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + 4.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00665/synopsis.txt b/latest/cases/00665/synopsis.txt new file mode 100644 index 000000000..30032d24f --- /dev/null +++ b/latest/cases/00665/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $X0 + X1 + T - S1$ |] + +The model contains one event that assigns value to species X1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $X1 > 2$ | $4.3$ | $X1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1.25$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Initial amount of S1 |$3.75$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00666/l2v5/build.log b/latest/cases/00666/l2v5/build.log new file mode 100644 index 000000000..6fa0887e5 --- /dev/null +++ b/latest/cases/00666/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00666/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00666/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00666/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00666/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00666/l2v5/index.heta b/latest/cases/00666/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00666/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00666/l3v2/build.log b/latest/cases/00666/l3v2/build.log new file mode 100644 index 000000000..2012be5f7 --- /dev/null +++ b/latest/cases/00666/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00666/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00666/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00666/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00666/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00666/l3v2/index.heta b/latest/cases/00666/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00666/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00666/model-sbml-l2v5.xml b/latest/cases/00666/model-sbml-l2v5.xml new file mode 100644 index 000000000..e8b1296d8 --- /dev/null +++ b/latest/cases/00666/model-sbml-l2v5.xml @@ -0,0 +1,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + X1 + 0.5 + + + + + + 10 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00666/model-sbml-l3v2.xml b/latest/cases/00666/model-sbml-l3v2.xml new file mode 100644 index 000000000..a6666deff --- /dev/null +++ b/latest/cases/00666/model-sbml-l3v2.xml @@ -0,0 +1,125 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + X1 + 0.5 + + + + + + 10 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00666/synopsis.txt b/latest/cases/00666/synopsis.txt new file mode 100644 index 000000000..48aa2b412 --- /dev/null +++ b/latest/cases/00666/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The model contains one event that assigns value to species X1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $X1 > 0.5$ | $-$ | $X1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00667/l2v5/heta-code/output.heta b/latest/cases/00667/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a726bfb4e --- /dev/null +++ b/latest/cases/00667/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 1.5; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00667/l2v5/index.heta b/latest/cases/00667/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00667/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00667/l2v5/json/output.json b/latest/cases/00667/l2v5/json/output.json new file mode 100644 index 000000000..d8d09197d --- /dev/null +++ b/latest/cases/00667/l2v5/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00667/l3v2/heta-code/output.heta b/latest/cases/00667/l3v2/heta-code/output.heta new file mode 100644 index 000000000..776c69d17 --- /dev/null +++ b/latest/cases/00667/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 1.5; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00667/l3v2/index.heta b/latest/cases/00667/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00667/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00667/l3v2/json/output.json b/latest/cases/00667/l3v2/json/output.json new file mode 100644 index 000000000..6a9344ba0 --- /dev/null +++ b/latest/cases/00667/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00667/model-sbml-l2v5.xml b/latest/cases/00667/model-sbml-l2v5.xml new file mode 100644 index 000000000..139d221d9 --- /dev/null +++ b/latest/cases/00667/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00667/model-sbml-l3v2.xml b/latest/cases/00667/model-sbml-l3v2.xml new file mode 100644 index 000000000..9a2b588a3 --- /dev/null +++ b/latest/cases/00667/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00667/output.heta b/latest/cases/00667/output.heta new file mode 100644 index 000000000..7c1036e78 --- /dev/null +++ b/latest/cases/00667/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with a + functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S3 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 1.5; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00667/synopsis.txt b/latest/cases/00667/synopsis.txt new file mode 100644 index 000000000..a73f598aa --- /dev/null +++ b/latest/cases/00667/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with a + functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S3 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00668/l2v5/heta-code/output.heta b/latest/cases/00668/l2v5/heta-code/output.heta new file mode 100644 index 000000000..97644809e --- /dev/null +++ b/latest/cases/00668/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.86; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.015 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := multiply(p1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 0.025; +p1 @Record 'p1' { } .= 0.75; + diff --git a/latest/cases/00668/l2v5/index.heta b/latest/cases/00668/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00668/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00668/l2v5/json/output.json b/latest/cases/00668/l2v5/json/output.json new file mode 100644 index 000000000..0b38e04a1 --- /dev/null +++ b/latest/cases/00668/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.86" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "multiply(p1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.025" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00668/l3v2/heta-code/output.heta b/latest/cases/00668/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f1eca7962 --- /dev/null +++ b/latest/cases/00668/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.86; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.015 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := multiply(p1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 0.025; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00668/l3v2/index.heta b/latest/cases/00668/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00668/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00668/l3v2/json/output.json b/latest/cases/00668/l3v2/json/output.json new file mode 100644 index 000000000..a29448bf6 --- /dev/null +++ b/latest/cases/00668/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.86" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "multiply(p1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.025 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.75 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00668/model-sbml-l2v5.xml b/latest/cases/00668/model-sbml-l2v5.xml new file mode 100644 index 000000000..6d88e8641 --- /dev/null +++ b/latest/cases/00668/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + S2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00668/model-sbml-l3v2.xml b/latest/cases/00668/model-sbml-l3v2.xml new file mode 100644 index 000000000..889989fdf --- /dev/null +++ b/latest/cases/00668/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + S2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00668/output.heta b/latest/cases/00668/output.heta new file mode 100644 index 000000000..613b773ae --- /dev/null +++ b/latest/cases/00668/output.heta @@ -0,0 +1,72 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(p1, S2)$ |] + +The model contains one FunctionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S4 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.5 \x 10^-2$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Value of parameter p1 |$ 0.75$ |dimensionless | +|Volume of compartment C |$ 0.86$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.86; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.015 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := multiply(p1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 0.025; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00668/synopsis.txt b/latest/cases/00668/synopsis.txt new file mode 100644 index 000000000..da42ec183 --- /dev/null +++ b/latest/cases/00668/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(p1, S2)$ |] + +The model contains one FunctionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S4 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.5 \x 10^-2$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Value of parameter p1 |$ 0.75$ |dimensionless | +|Volume of compartment C |$ 0.86$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00669/l2v5/heta-code/output.heta b/latest/cases/00669/l2v5/heta-code/output.heta new file mode 100644 index 000000000..edaa034f9 --- /dev/null +++ b/latest/cases/00669/l2v5/heta-code/output.heta @@ -0,0 +1,30 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; +func1 #defineFunction { arguments: [x, y], math: x * pow(y + 1, (-1)), }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; +S4 := func1(S3, p1); +S5 @Species 'S5' { units: substance/volume, compartment: C, } .= 0 / C; +S5 := multiply(S4, p1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S2, modifiers: [S5], reversible: false, }; +reaction2 := C * k2 * S5; + +k1 @Record 'k1' { } .= 0.1; +k2 @Record 'k2' { } .= 0.15; +p1 @Record 'p1' { } .= 2.5; + diff --git a/latest/cases/00669/l2v5/index.heta b/latest/cases/00669/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00669/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00669/l2v5/json/output.json b/latest/cases/00669/l2v5/json/output.json new file mode 100644 index 000000000..68de2c1f2 --- /dev/null +++ b/latest/cases/00669/l2v5/json/output.json @@ -0,0 +1,177 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C", + "ode_": "func1(S3, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "0 / C", + "ode_": "multiply(S4, p1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S5" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "2.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + }, + { + "id": "func1", + "arguments": [ + "x", + "y" + ], + "math": "x * pow(y + 1, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00669/l3v2/heta-code/output.heta b/latest/cases/00669/l3v2/heta-code/output.heta new file mode 100644 index 000000000..72fe50598 --- /dev/null +++ b/latest/cases/00669/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; +func1 #defineFunction { arguments: [x, y], math: x * pow(y + 1, (-1)), }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; +S4 := func1(S3, p1); +S5 @Species 'S5' { units: mole/litre, compartment: C, } .= 0 / C; +S5 := multiply(S4, p1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S2, modifiers: [S5], reversible: false, }; +reaction2 := C * k2 * S5; + +k1 @Const 'k1' { } = 0.1; +k2 @Const 'k2' { } = 0.15; +p1 @Const 'p1' { } = 2.5; + diff --git a/latest/cases/00669/l3v2/index.heta b/latest/cases/00669/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00669/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00669/l3v2/json/output.json b/latest/cases/00669/l3v2/json/output.json new file mode 100644 index 000000000..9ea94e2d4 --- /dev/null +++ b/latest/cases/00669/l3v2/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "ode_": "func1(S3, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "ode_": "multiply(S4, p1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S5" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.15 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 2.5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + }, + { + "id": "func1", + "arguments": [ + "x", + "y" + ], + "math": "x * pow(y + 1, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00669/model-sbml-l2v5.xml b/latest/cases/00669/model-sbml-l2v5.xml new file mode 100644 index 000000000..7fca9d019 --- /dev/null +++ b/latest/cases/00669/model-sbml-l2v5.xml @@ -0,0 +1,125 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + + + y + 1 + + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + func1 + S3 + p1 + + + + + + + multiply + S4 + p1 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + + + + C + k2 + S5 + + + + + + + diff --git a/latest/cases/00669/model-sbml-l3v2.xml b/latest/cases/00669/model-sbml-l3v2.xml new file mode 100644 index 000000000..630e3afba --- /dev/null +++ b/latest/cases/00669/model-sbml-l3v2.xml @@ -0,0 +1,142 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + + + y + 1 + + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + func1 + S3 + p1 + + + + + + + multiply + S4 + p1 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + + + + C + k2 + S5 + + + + + + + diff --git a/latest/cases/00669/output.heta b/latest/cases/00669/output.heta new file mode 100644 index 000000000..4cd993b24 --- /dev/null +++ b/latest/cases/00669/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Two reactions with five species in one +compartment using an assignmentRules with functionDefinitions to vary two species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are five +species called S1, S2, S3, S4 and S5 and three parameters called k1, k2 and +p1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S2 | $k2 * S5 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $func1(S3, p1)$ | + | Assignment | S5 | $multiply(S4, p1)$ |] + +The model contains two functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | func1 | x, y | $x/(1 + y)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Initial amount of S5 |$ 0$ |mole | +|Value of parameter k1 |$ 0.1$ |second^-1^ | +|Value of parameter k2 |$ 0.15$ |second^-1^ | +|Value of parameter p1 |$ 2.5$ |dimensionless | +|Volume of compartment "compartment" |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; +func1 #defineFunction { arguments: [x, y], math: x * pow(y + 1, (-1)), }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; +S4 := func1(S3, p1); +S5 @Species 'S5' { units: mole/litre, compartment: C, } .= 0 / C; +S5 := multiply(S4, p1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S2, modifiers: [S5], reversible: false, }; +reaction2 := C * k2 * S5; + +k1 @Const 'k1' { } = 0.1; +k2 @Const 'k2' { } = 0.15; +p1 @Const 'p1' { } = 2.5; + diff --git a/latest/cases/00669/synopsis.txt b/latest/cases/00669/synopsis.txt new file mode 100644 index 000000000..028a7458d --- /dev/null +++ b/latest/cases/00669/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Two reactions with five species in one +compartment using an assignmentRules with functionDefinitions to vary two species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are five +species called S1, S2, S3, S4 and S5 and three parameters called k1, k2 and +p1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S2 | $k2 * S5 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $func1(S3, p1)$ | + | Assignment | S5 | $multiply(S4, p1)$ |] + +The model contains two functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | func1 | x, y | $x/(1 + y)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Initial amount of S4 |$ 0$ |mole | +|Initial amount of S5 |$ 0$ |mole | +|Value of parameter k1 |$ 0.1$ |second^-1^ | +|Value of parameter k2 |$ 0.15$ |second^-1^ | +|Value of parameter p1 |$ 2.5$ |dimensionless | +|Volume of compartment "compartment" |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00670/l2v5/heta-code/output.heta b/latest/cases/00670/l2v5/heta-code/output.heta new file mode 100644 index 000000000..24c6931f6 --- /dev/null +++ b/latest/cases/00670/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00670/l2v5/index.heta b/latest/cases/00670/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00670/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00670/l2v5/json/output.json b/latest/cases/00670/l2v5/json/output.json new file mode 100644 index 000000000..6559ac347 --- /dev/null +++ b/latest/cases/00670/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00670/l3v2/heta-code/output.heta b/latest/cases/00670/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e37f2f41a --- /dev/null +++ b/latest/cases/00670/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00670/l3v2/index.heta b/latest/cases/00670/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00670/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00670/l3v2/json/output.json b/latest/cases/00670/l3v2/json/output.json new file mode 100644 index 000000000..6d510890d --- /dev/null +++ b/latest/cases/00670/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00670/model-sbml-l2v5.xml b/latest/cases/00670/model-sbml-l2v5.xml new file mode 100644 index 000000000..9142080fc --- /dev/null +++ b/latest/cases/00670/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00670/model-sbml-l3v2.xml b/latest/cases/00670/model-sbml-l3v2.xml new file mode 100644 index 000000000..17b9c5871 --- /dev/null +++ b/latest/cases/00670/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00670/output.heta b/latest/cases/00670/output.heta new file mode 100644 index 000000000..bb0e9c489 --- /dev/null +++ b/latest/cases/00670/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00670/synopsis.txt b/latest/cases/00670/synopsis.txt new file mode 100644 index 000000000..cb805b909 --- /dev/null +++ b/latest/cases/00670/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00671/l2v5/heta-code/output.heta b/latest/cases/00671/l2v5/heta-code/output.heta new file mode 100644 index 000000000..fae75fb47 --- /dev/null +++ b/latest/cases/00671/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.76; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00671/l2v5/index.heta b/latest/cases/00671/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00671/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00671/l2v5/json/output.json b/latest/cases/00671/l2v5/json/output.json new file mode 100644 index 000000000..9b6f60fa3 --- /dev/null +++ b/latest/cases/00671/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.76" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00671/l3v2/heta-code/output.heta b/latest/cases/00671/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bddf6623f --- /dev/null +++ b/latest/cases/00671/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.76; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00671/l3v2/index.heta b/latest/cases/00671/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00671/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00671/l3v2/json/output.json b/latest/cases/00671/l3v2/json/output.json new file mode 100644 index 000000000..f88c8bd06 --- /dev/null +++ b/latest/cases/00671/l3v2/json/output.json @@ -0,0 +1,128 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.76" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00671/model-sbml-l2v5.xml b/latest/cases/00671/model-sbml-l2v5.xml new file mode 100644 index 000000000..d1cbdbca7 --- /dev/null +++ b/latest/cases/00671/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00671/model-sbml-l3v2.xml b/latest/cases/00671/model-sbml-l3v2.xml new file mode 100644 index 000000000..3277b2871 --- /dev/null +++ b/latest/cases/00671/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00671/output.heta b/latest/cases/00671/output.heta new file mode 100644 index 000000000..7415db9f6 --- /dev/null +++ b/latest/cases/00671/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 0.76$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.76; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00671/synopsis.txt b/latest/cases/00671/synopsis.txt new file mode 100644 index 000000000..a2e1ac482 --- /dev/null +++ b/latest/cases/00671/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 0.76$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00672/l2v5/heta-code/output.heta b/latest/cases/00672/l2v5/heta-code/output.heta new file mode 100644 index 000000000..23035160f --- /dev/null +++ b/latest/cases/00672/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.4; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00672/l2v5/index.heta b/latest/cases/00672/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00672/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00672/l2v5/json/output.json b/latest/cases/00672/l2v5/json/output.json new file mode 100644 index 000000000..160be638d --- /dev/null +++ b/latest/cases/00672/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.4" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00672/l3v2/heta-code/output.heta b/latest/cases/00672/l3v2/heta-code/output.heta new file mode 100644 index 000000000..deb57f49e --- /dev/null +++ b/latest/cases/00672/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.4; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00672/l3v2/index.heta b/latest/cases/00672/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00672/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00672/l3v2/json/output.json b/latest/cases/00672/l3v2/json/output.json new file mode 100644 index 000000000..8a15d037a --- /dev/null +++ b/latest/cases/00672/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.4" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00672/model-sbml-l2v5.xml b/latest/cases/00672/model-sbml-l2v5.xml new file mode 100644 index 000000000..b3ebe6153 --- /dev/null +++ b/latest/cases/00672/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00672/model-sbml-l3v2.xml b/latest/cases/00672/model-sbml-l3v2.xml new file mode 100644 index 000000000..d228f1b5d --- /dev/null +++ b/latest/cases/00672/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00672/output.heta b/latest/cases/00672/output.heta new file mode 100644 index 000000000..2d578e609 --- /dev/null +++ b/latest/cases/00672/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1.4$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.4; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00672/synopsis.txt b/latest/cases/00672/synopsis.txt new file mode 100644 index 000000000..7e27e4f15 --- /dev/null +++ b/latest/cases/00672/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 5$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1.4$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00673/l2v5/build.log b/latest/cases/00673/l2v5/build.log new file mode 100644 index 000000000..7b723eb75 --- /dev/null +++ b/latest/cases/00673/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00673/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00673/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00673/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00673/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00673/l2v5/index.heta b/latest/cases/00673/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00673/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00673/l3v2/build.log b/latest/cases/00673/l3v2/build.log new file mode 100644 index 000000000..b7ce87088 --- /dev/null +++ b/latest/cases/00673/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00673/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00673/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00673/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00673/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00673/l3v2/index.heta b/latest/cases/00673/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00673/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00673/model-sbml-l2v5.xml b/latest/cases/00673/model-sbml-l2v5.xml new file mode 100644 index 000000000..6254f7cde --- /dev/null +++ b/latest/cases/00673/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00673/model-sbml-l3v2.xml b/latest/cases/00673/model-sbml-l3v2.xml new file mode 100644 index 000000000..4e3e09883 --- /dev/null +++ b/latest/cases/00673/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00673/synopsis.txt b/latest/cases/00673/synopsis.txt new file mode 100644 index 000000000..aad01f90b --- /dev/null +++ b/latest/cases/00673/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $0.1$ |] + +The assignment rule assigns a value to parameter k1 which is consistent with the value +attributed to the parameter by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00674/l2v5/build.log b/latest/cases/00674/l2v5/build.log new file mode 100644 index 000000000..7d5f88626 --- /dev/null +++ b/latest/cases/00674/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00674/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00674/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00674/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00674/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00674/l2v5/index.heta b/latest/cases/00674/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00674/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00674/l3v2/build.log b/latest/cases/00674/l3v2/build.log new file mode 100644 index 000000000..cedbb26b0 --- /dev/null +++ b/latest/cases/00674/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00674/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00674/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00674/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00674/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00674/l3v2/index.heta b/latest/cases/00674/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00674/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00674/model-sbml-l2v5.xml b/latest/cases/00674/model-sbml-l2v5.xml new file mode 100644 index 000000000..3358d24aa --- /dev/null +++ b/latest/cases/00674/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00674/model-sbml-l3v2.xml b/latest/cases/00674/model-sbml-l3v2.xml new file mode 100644 index 000000000..f98464e5c --- /dev/null +++ b/latest/cases/00674/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00674/synopsis.txt b/latest/cases/00674/synopsis.txt new file mode 100644 index 000000000..b74bdb9c1 --- /dev/null +++ b/latest/cases/00674/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $0.1$ |] + +The assignment rule assigns a value to parameter k1 which is inconsistent with the value +attributed to the parameter by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$2$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$0.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00675/l2v5/build.log b/latest/cases/00675/l2v5/build.log new file mode 100644 index 000000000..0af50d7f2 --- /dev/null +++ b/latest/cases/00675/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00675/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00675/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00675/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00675/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00675/l2v5/index.heta b/latest/cases/00675/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00675/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00675/l3v2/build.log b/latest/cases/00675/l3v2/build.log new file mode 100644 index 000000000..180322e28 --- /dev/null +++ b/latest/cases/00675/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00675/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00675/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00675/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00675/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00675/l3v2/index.heta b/latest/cases/00675/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00675/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00675/model-sbml-l2v5.xml b/latest/cases/00675/model-sbml-l2v5.xml new file mode 100644 index 000000000..71a1dceeb --- /dev/null +++ b/latest/cases/00675/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00675/model-sbml-l3v2.xml b/latest/cases/00675/model-sbml-l3v2.xml new file mode 100644 index 000000000..b7f967f90 --- /dev/null +++ b/latest/cases/00675/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00675/synopsis.txt b/latest/cases/00675/synopsis.txt new file mode 100644 index 000000000..2ed47477f --- /dev/null +++ b/latest/cases/00675/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $0.1$ |] + +The assignment rule assigns a value to parameter k1 which has no value +attributed to it by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$9.8$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00676/l2v5/heta-code/output.heta b/latest/cases/00676/l2v5/heta-code/output.heta new file mode 100644 index 000000000..08c7f2bac --- /dev/null +++ b/latest/cases/00676/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00676/l2v5/index.heta b/latest/cases/00676/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00676/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00676/l2v5/json/output.json b/latest/cases/00676/l2v5/json/output.json new file mode 100644 index 000000000..bda322b24 --- /dev/null +++ b/latest/cases/00676/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00676/l3v2/heta-code/output.heta b/latest/cases/00676/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a5d445ec7 --- /dev/null +++ b/latest/cases/00676/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00676/l3v2/index.heta b/latest/cases/00676/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00676/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00676/l3v2/json/output.json b/latest/cases/00676/l3v2/json/output.json new file mode 100644 index 000000000..fa1ee89d9 --- /dev/null +++ b/latest/cases/00676/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00676/model-sbml-l2v5.xml b/latest/cases/00676/model-sbml-l2v5.xml new file mode 100644 index 000000000..840a9b2ce --- /dev/null +++ b/latest/cases/00676/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00676/model-sbml-l3v2.xml b/latest/cases/00676/model-sbml-l3v2.xml new file mode 100644 index 000000000..9da0bdc54 --- /dev/null +++ b/latest/cases/00676/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00676/output.heta b/latest/cases/00676/output.heta new file mode 100644 index 000000000..dee5c7357 --- /dev/null +++ b/latest/cases/00676/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00676/synopsis.txt b/latest/cases/00676/synopsis.txt new file mode 100644 index 000000000..adfc69d1f --- /dev/null +++ b/latest/cases/00676/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00677/l2v5/heta-code/output.heta b/latest/cases/00677/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f09b55c9b --- /dev/null +++ b/latest/cases/00677/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.47; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00677/l2v5/index.heta b/latest/cases/00677/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00677/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00677/l2v5/json/output.json b/latest/cases/00677/l2v5/json/output.json new file mode 100644 index 000000000..76dc340c6 --- /dev/null +++ b/latest/cases/00677/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.47" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00677/l3v2/heta-code/output.heta b/latest/cases/00677/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fe04c144c --- /dev/null +++ b/latest/cases/00677/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.47; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00677/l3v2/index.heta b/latest/cases/00677/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00677/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00677/l3v2/json/output.json b/latest/cases/00677/l3v2/json/output.json new file mode 100644 index 000000000..a5a102a37 --- /dev/null +++ b/latest/cases/00677/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.47" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00677/model-sbml-l2v5.xml b/latest/cases/00677/model-sbml-l2v5.xml new file mode 100644 index 000000000..fb04506d9 --- /dev/null +++ b/latest/cases/00677/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00677/model-sbml-l3v2.xml b/latest/cases/00677/model-sbml-l3v2.xml new file mode 100644 index 000000000..fa05fe9f6 --- /dev/null +++ b/latest/cases/00677/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00677/output.heta b/latest/cases/00677/output.heta new file mode 100644 index 000000000..78b337d23 --- /dev/null +++ b/latest/cases/00677/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$10$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 0.47$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.47; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00677/synopsis.txt b/latest/cases/00677/synopsis.txt new file mode 100644 index 000000000..8da3afa8d --- /dev/null +++ b/latest/cases/00677/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$10$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 0.47$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00678/l2v5/heta-code/output.heta b/latest/cases/00678/l2v5/heta-code/output.heta new file mode 100644 index 000000000..19d9f1163 --- /dev/null +++ b/latest/cases/00678/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 6.6; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00678/l2v5/index.heta b/latest/cases/00678/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00678/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00678/l2v5/json/output.json b/latest/cases/00678/l2v5/json/output.json new file mode 100644 index 000000000..e6e7d7893 --- /dev/null +++ b/latest/cases/00678/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "6.6" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00678/l3v2/heta-code/output.heta b/latest/cases/00678/l3v2/heta-code/output.heta new file mode 100644 index 000000000..604df7ede --- /dev/null +++ b/latest/cases/00678/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 6.6; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00678/l3v2/index.heta b/latest/cases/00678/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00678/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00678/l3v2/json/output.json b/latest/cases/00678/l3v2/json/output.json new file mode 100644 index 000000000..447c53553 --- /dev/null +++ b/latest/cases/00678/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "6.6" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00678/model-sbml-l2v5.xml b/latest/cases/00678/model-sbml-l2v5.xml new file mode 100644 index 000000000..0cca78e2e --- /dev/null +++ b/latest/cases/00678/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00678/model-sbml-l3v2.xml b/latest/cases/00678/model-sbml-l3v2.xml new file mode 100644 index 000000000..332a7a366 --- /dev/null +++ b/latest/cases/00678/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00678/output.heta b/latest/cases/00678/output.heta new file mode 100644 index 000000000..a57877765 --- /dev/null +++ b/latest/cases/00678/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is consisent with the value declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.66$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 6.6$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 6.6; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00678/synopsis.txt b/latest/cases/00678/synopsis.txt new file mode 100644 index 000000000..bb5e7c38b --- /dev/null +++ b/latest/cases/00678/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is consisent with the value declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.66$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 6.6$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00679/l2v5/heta-code/output.heta b/latest/cases/00679/l2v5/heta-code/output.heta new file mode 100644 index 000000000..441152d1f --- /dev/null +++ b/latest/cases/00679/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00679/l2v5/index.heta b/latest/cases/00679/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00679/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00679/l2v5/json/output.json b/latest/cases/00679/l2v5/json/output.json new file mode 100644 index 000000000..a5740507a --- /dev/null +++ b/latest/cases/00679/l2v5/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00679/l3v2/heta-code/output.heta b/latest/cases/00679/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dc7dcdd17 --- /dev/null +++ b/latest/cases/00679/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00679/l3v2/index.heta b/latest/cases/00679/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00679/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00679/l3v2/json/output.json b/latest/cases/00679/l3v2/json/output.json new file mode 100644 index 000000000..be3b50818 --- /dev/null +++ b/latest/cases/00679/l3v2/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + } +] \ No newline at end of file diff --git a/latest/cases/00679/model-sbml-l2v5.xml b/latest/cases/00679/model-sbml-l2v5.xml new file mode 100644 index 000000000..f9a98dba4 --- /dev/null +++ b/latest/cases/00679/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00679/model-sbml-l3v2.xml b/latest/cases/00679/model-sbml-l3v2.xml new file mode 100644 index 000000000..3959b3e62 --- /dev/null +++ b/latest/cases/00679/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00679/output.heta b/latest/cases/00679/output.heta new file mode 100644 index 000000000..56c71921d --- /dev/null +++ b/latest/cases/00679/output.heta @@ -0,0 +1,68 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00679/synopsis.txt b/latest/cases/00679/synopsis.txt new file mode 100644 index 000000000..dc12e07af --- /dev/null +++ b/latest/cases/00679/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00680/l2v5/heta-code/output.heta b/latest/cases/00680/l2v5/heta-code/output.heta new file mode 100644 index 000000000..24c8976c1 --- /dev/null +++ b/latest/cases/00680/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.79; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.375 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00680/l2v5/index.heta b/latest/cases/00680/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00680/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00680/l2v5/json/output.json b/latest/cases/00680/l2v5/json/output.json new file mode 100644 index 000000000..962faaa81 --- /dev/null +++ b/latest/cases/00680/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.79" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.375 / C", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00680/l3v2/heta-code/output.heta b/latest/cases/00680/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0b5236714 --- /dev/null +++ b/latest/cases/00680/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.79; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00680/l3v2/index.heta b/latest/cases/00680/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00680/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00680/l3v2/json/output.json b/latest/cases/00680/l3v2/json/output.json new file mode 100644 index 000000000..5ae2041f7 --- /dev/null +++ b/latest/cases/00680/l3v2/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.79" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.375 / C", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + } +] \ No newline at end of file diff --git a/latest/cases/00680/model-sbml-l2v5.xml b/latest/cases/00680/model-sbml-l2v5.xml new file mode 100644 index 000000000..4bb5571b0 --- /dev/null +++ b/latest/cases/00680/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00680/model-sbml-l3v2.xml b/latest/cases/00680/model-sbml-l3v2.xml new file mode 100644 index 000000000..942de62e9 --- /dev/null +++ b/latest/cases/00680/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00680/output.heta b/latest/cases/00680/output.heta new file mode 100644 index 000000000..345042865 --- /dev/null +++ b/latest/cases/00680/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 0.79$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.79; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00680/synopsis.txt b/latest/cases/00680/synopsis.txt new file mode 100644 index 000000000..896328521 --- /dev/null +++ b/latest/cases/00680/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 0.79$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00681/l2v5/heta-code/output.heta b/latest/cases/00681/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6eff058e3 --- /dev/null +++ b/latest/cases/00681/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 7.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 3.75 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00681/l2v5/index.heta b/latest/cases/00681/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00681/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00681/l2v5/json/output.json b/latest/cases/00681/l2v5/json/output.json new file mode 100644 index 000000000..5c7655121 --- /dev/null +++ b/latest/cases/00681/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "7.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "3.75 / C", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00681/l3v2/heta-code/output.heta b/latest/cases/00681/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f19c92715 --- /dev/null +++ b/latest/cases/00681/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 7.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00681/l3v2/index.heta b/latest/cases/00681/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00681/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00681/l3v2/json/output.json b/latest/cases/00681/l3v2/json/output.json new file mode 100644 index 000000000..b8c78c142 --- /dev/null +++ b/latest/cases/00681/l3v2/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "7.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "3.75 / C", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + } +] \ No newline at end of file diff --git a/latest/cases/00681/model-sbml-l2v5.xml b/latest/cases/00681/model-sbml-l2v5.xml new file mode 100644 index 000000000..e26d5021a --- /dev/null +++ b/latest/cases/00681/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00681/model-sbml-l3v2.xml b/latest/cases/00681/model-sbml-l3v2.xml new file mode 100644 index 000000000..492d65128 --- /dev/null +++ b/latest/cases/00681/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00681/output.heta b/latest/cases/00681/output.heta new file mode 100644 index 000000000..0e58f785c --- /dev/null +++ b/latest/cases/00681/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 7.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75 / C; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00681/synopsis.txt b/latest/cases/00681/synopsis.txt new file mode 100644 index 000000000..ba58f8406 --- /dev/null +++ b/latest/cases/00681/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00682/l2v5/build.log b/latest/cases/00682/l2v5/build.log new file mode 100644 index 000000000..0dc69c4ad --- /dev/null +++ b/latest/cases/00682/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00682/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00682/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00682/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00682/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00682/l2v5/index.heta b/latest/cases/00682/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00682/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00682/l3v2/build.log b/latest/cases/00682/l3v2/build.log new file mode 100644 index 000000000..4fedc76e5 --- /dev/null +++ b/latest/cases/00682/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00682/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00682/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00682/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00682/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00682/l3v2/index.heta b/latest/cases/00682/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00682/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00682/model-sbml-l2v5.xml b/latest/cases/00682/model-sbml-l2v5.xml new file mode 100644 index 000000000..26ee24c22 --- /dev/null +++ b/latest/cases/00682/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00682/model-sbml-l3v2.xml b/latest/cases/00682/model-sbml-l3v2.xml new file mode 100644 index 000000000..aaf0094bf --- /dev/null +++ b/latest/cases/00682/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00682/synopsis.txt b/latest/cases/00682/synopsis.txt new file mode 100644 index 000000000..538b65ee9 --- /dev/null +++ b/latest/cases/00682/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00683/l2v5/build.log b/latest/cases/00683/l2v5/build.log new file mode 100644 index 000000000..eb97be914 --- /dev/null +++ b/latest/cases/00683/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00683/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00683/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00683/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00683/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00683/l2v5/index.heta b/latest/cases/00683/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00683/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00683/l3v2/build.log b/latest/cases/00683/l3v2/build.log new file mode 100644 index 000000000..65341bbb2 --- /dev/null +++ b/latest/cases/00683/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00683/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00683/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00683/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00683/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00683/l3v2/index.heta b/latest/cases/00683/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00683/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00683/model-sbml-l2v5.xml b/latest/cases/00683/model-sbml-l2v5.xml new file mode 100644 index 000000000..1c1c1420b --- /dev/null +++ b/latest/cases/00683/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1.5 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00683/model-sbml-l3v2.xml b/latest/cases/00683/model-sbml-l3v2.xml new file mode 100644 index 000000000..523899a5d --- /dev/null +++ b/latest/cases/00683/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1.5 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00683/synopsis.txt b/latest/cases/00683/synopsis.txt new file mode 100644 index 000000000..21947225e --- /dev/null +++ b/latest/cases/00683/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1.5$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 0.63$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00684/l2v5/build.log b/latest/cases/00684/l2v5/build.log new file mode 100644 index 000000000..6f6766936 --- /dev/null +++ b/latest/cases/00684/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00684/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00684/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00684/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00684/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00684/l2v5/index.heta b/latest/cases/00684/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00684/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00684/l3v2/build.log b/latest/cases/00684/l3v2/build.log new file mode 100644 index 000000000..c05566a05 --- /dev/null +++ b/latest/cases/00684/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00684/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00684/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00684/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00684/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00684/l3v2/index.heta b/latest/cases/00684/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00684/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00684/model-sbml-l2v5.xml b/latest/cases/00684/model-sbml-l2v5.xml new file mode 100644 index 000000000..11a956414 --- /dev/null +++ b/latest/cases/00684/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00684/model-sbml-l3v2.xml b/latest/cases/00684/model-sbml-l3v2.xml new file mode 100644 index 000000000..07b71cd88 --- /dev/null +++ b/latest/cases/00684/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00684/synopsis.txt b/latest/cases/00684/synopsis.txt new file mode 100644 index 000000000..9041110f5 --- /dev/null +++ b/latest/cases/00684/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Amount, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $0.5$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1.4$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00685/l2v5/heta-code/output.heta b/latest/cases/00685/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c0060ae9c --- /dev/null +++ b/latest/cases/00685/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 1.5; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00685/l2v5/index.heta b/latest/cases/00685/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00685/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00685/l2v5/json/output.json b/latest/cases/00685/l2v5/json/output.json new file mode 100644 index 000000000..bca80af77 --- /dev/null +++ b/latest/cases/00685/l2v5/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00685/l3v2/heta-code/output.heta b/latest/cases/00685/l3v2/heta-code/output.heta new file mode 100644 index 000000000..57ee0a902 --- /dev/null +++ b/latest/cases/00685/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 1.5; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00685/l3v2/index.heta b/latest/cases/00685/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00685/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00685/l3v2/json/output.json b/latest/cases/00685/l3v2/json/output.json new file mode 100644 index 000000000..0d2acc8d9 --- /dev/null +++ b/latest/cases/00685/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00685/model-sbml-l2v5.xml b/latest/cases/00685/model-sbml-l2v5.xml new file mode 100644 index 000000000..83cca4d9e --- /dev/null +++ b/latest/cases/00685/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00685/model-sbml-l3v2.xml b/latest/cases/00685/model-sbml-l3v2.xml new file mode 100644 index 000000000..50cf93681 --- /dev/null +++ b/latest/cases/00685/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00685/output.heta b/latest/cases/00685/output.heta new file mode 100644 index 000000000..e7164262e --- /dev/null +++ b/latest/cases/00685/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with a + functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S3 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 1.5; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00685/synopsis.txt b/latest/cases/00685/synopsis.txt new file mode 100644 index 000000000..d8dc8c9b9 --- /dev/null +++ b/latest/cases/00685/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with a + functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S3 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + + diff --git a/latest/cases/00686/l2v5/heta-code/output.heta b/latest/cases/00686/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bd825ffaa --- /dev/null +++ b/latest/cases/00686/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 2.25; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00686/l2v5/index.heta b/latest/cases/00686/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00686/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00686/l2v5/json/output.json b/latest/cases/00686/l2v5/json/output.json new file mode 100644 index 000000000..8e0fd867b --- /dev/null +++ b/latest/cases/00686/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00686/l3v2/heta-code/output.heta b/latest/cases/00686/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6e6ee1baa --- /dev/null +++ b/latest/cases/00686/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00686/l3v2/index.heta b/latest/cases/00686/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00686/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00686/l3v2/json/output.json b/latest/cases/00686/l3v2/json/output.json new file mode 100644 index 000000000..267000d06 --- /dev/null +++ b/latest/cases/00686/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00686/model-sbml-l2v5.xml b/latest/cases/00686/model-sbml-l2v5.xml new file mode 100644 index 000000000..849abc479 --- /dev/null +++ b/latest/cases/00686/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00686/model-sbml-l3v2.xml b/latest/cases/00686/model-sbml-l3v2.xml new file mode 100644 index 000000000..f2d8d8ecd --- /dev/null +++ b/latest/cases/00686/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00686/output.heta b/latest/cases/00686/output.heta new file mode 100644 index 000000000..980a94920 --- /dev/null +++ b/latest/cases/00686/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S4 |$ 2.25$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 2.5$ |litre |] + + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00686/synopsis.txt b/latest/cases/00686/synopsis.txt new file mode 100644 index 000000000..2c7b76920 --- /dev/null +++ b/latest/cases/00686/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S4 |$ 2.25$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 2.5$ |litre |] + + diff --git a/latest/cases/00687/l2v5/build.log b/latest/cases/00687/l2v5/build.log new file mode 100644 index 000000000..06aa6de19 --- /dev/null +++ b/latest/cases/00687/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00687/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00687/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00687/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00687/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00687/l2v5/index.heta b/latest/cases/00687/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00687/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00687/l3v2/build.log b/latest/cases/00687/l3v2/build.log new file mode 100644 index 000000000..45c5233c0 --- /dev/null +++ b/latest/cases/00687/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00687/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00687/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00687/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00687/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00687/l3v2/index.heta b/latest/cases/00687/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00687/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00687/model-sbml-l2v5.xml b/latest/cases/00687/model-sbml-l2v5.xml new file mode 100644 index 000000000..120b012d9 --- /dev/null +++ b/latest/cases/00687/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00687/model-sbml-l3v2.xml b/latest/cases/00687/model-sbml-l3v2.xml new file mode 100644 index 000000000..bba042ab3 --- /dev/null +++ b/latest/cases/00687/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00687/synopsis.txt b/latest/cases/00687/synopsis.txt new file mode 100644 index 000000000..7cbe05e2f --- /dev/null +++ b/latest/cases/00687/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $0.1$ |] + +The assignment rule assigns a value to parameter k1 which is consistent with the value +attributed to the parameter by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of X0 |$1$ |mole litre^-1^ | +|Initial concentration of X1 |$0$ |mole litre^-1^ | +|Initial concentration of T |$0$ |mole litre^-1^ | +|Initial concentration of S1 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$2.5$ |litre |] + + diff --git a/latest/cases/00688/l2v5/heta-code/output.heta b/latest/cases/00688/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e0b0db385 --- /dev/null +++ b/latest/cases/00688/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00688/l2v5/index.heta b/latest/cases/00688/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00688/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00688/l2v5/json/output.json b/latest/cases/00688/l2v5/json/output.json new file mode 100644 index 000000000..b7f6a36ab --- /dev/null +++ b/latest/cases/00688/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00688/l3v2/heta-code/output.heta b/latest/cases/00688/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e9f2de9b0 --- /dev/null +++ b/latest/cases/00688/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00688/l3v2/index.heta b/latest/cases/00688/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00688/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00688/l3v2/json/output.json b/latest/cases/00688/l3v2/json/output.json new file mode 100644 index 000000000..c66738c50 --- /dev/null +++ b/latest/cases/00688/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00688/model-sbml-l2v5.xml b/latest/cases/00688/model-sbml-l2v5.xml new file mode 100644 index 000000000..f1cd0dd1d --- /dev/null +++ b/latest/cases/00688/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00688/model-sbml-l3v2.xml b/latest/cases/00688/model-sbml-l3v2.xml new file mode 100644 index 000000000..860c995a5 --- /dev/null +++ b/latest/cases/00688/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00688/output.heta b/latest/cases/00688/output.heta new file mode 100644 index 000000000..fc0b161ef --- /dev/null +++ b/latest/cases/00688/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$undeclared$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0.15$ |mole litre^-1^ | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00688/synopsis.txt b/latest/cases/00688/synopsis.txt new file mode 100644 index 000000000..e5dd37e3c --- /dev/null +++ b/latest/cases/00688/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$undeclared$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0.15$ |mole litre^-1^ | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + diff --git a/latest/cases/00689/l2v5/heta-code/output.heta b/latest/cases/00689/l2v5/heta-code/output.heta new file mode 100644 index 000000000..57975be1a --- /dev/null +++ b/latest/cases/00689/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00689/l2v5/index.heta b/latest/cases/00689/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00689/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00689/l2v5/json/output.json b/latest/cases/00689/l2v5/json/output.json new file mode 100644 index 000000000..a3bc86e3d --- /dev/null +++ b/latest/cases/00689/l2v5/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00689/l3v2/heta-code/output.heta b/latest/cases/00689/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9af9407eb --- /dev/null +++ b/latest/cases/00689/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00689/l3v2/index.heta b/latest/cases/00689/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00689/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00689/l3v2/json/output.json b/latest/cases/00689/l3v2/json/output.json new file mode 100644 index 000000000..32b361d1b --- /dev/null +++ b/latest/cases/00689/l3v2/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + } +] \ No newline at end of file diff --git a/latest/cases/00689/model-sbml-l2v5.xml b/latest/cases/00689/model-sbml-l2v5.xml new file mode 100644 index 000000000..2643b658c --- /dev/null +++ b/latest/cases/00689/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00689/model-sbml-l3v2.xml b/latest/cases/00689/model-sbml-l3v2.xml new file mode 100644 index 000000000..fc5a63c62 --- /dev/null +++ b/latest/cases/00689/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00689/output.heta b/latest/cases/00689/output.heta new file mode 100644 index 000000000..dbc785366 --- /dev/null +++ b/latest/cases/00689/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00689/synopsis.txt b/latest/cases/00689/synopsis.txt new file mode 100644 index 000000000..eee2a7425 --- /dev/null +++ b/latest/cases/00689/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + diff --git a/latest/cases/00690/l2v5/build.log b/latest/cases/00690/l2v5/build.log new file mode 100644 index 000000000..86a38ec93 --- /dev/null +++ b/latest/cases/00690/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00690/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00690/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00690/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00690/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00690/l2v5/index.heta b/latest/cases/00690/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00690/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00690/l3v2/build.log b/latest/cases/00690/l3v2/build.log new file mode 100644 index 000000000..621e90ac3 --- /dev/null +++ b/latest/cases/00690/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00690/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00690/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00690/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00690/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00690/l3v2/index.heta b/latest/cases/00690/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00690/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00690/model-sbml-l2v5.xml b/latest/cases/00690/model-sbml-l2v5.xml new file mode 100644 index 000000000..e25a997f5 --- /dev/null +++ b/latest/cases/00690/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00690/model-sbml-l3v2.xml b/latest/cases/00690/model-sbml-l3v2.xml new file mode 100644 index 000000000..087702eec --- /dev/null +++ b/latest/cases/00690/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00690/synopsis.txt b/latest/cases/00690/synopsis.txt new file mode 100644 index 000000000..08d9404a3 --- /dev/null +++ b/latest/cases/00690/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + diff --git a/latest/cases/00691/l2v5/heta-code/output.heta b/latest/cases/00691/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c84883de0 --- /dev/null +++ b/latest/cases/00691/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 1.5; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00691/l2v5/index.heta b/latest/cases/00691/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00691/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00691/l2v5/json/output.json b/latest/cases/00691/l2v5/json/output.json new file mode 100644 index 000000000..429aaaac5 --- /dev/null +++ b/latest/cases/00691/l2v5/json/output.json @@ -0,0 +1,115 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00691/l3v2/heta-code/output.heta b/latest/cases/00691/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d2a3c449d --- /dev/null +++ b/latest/cases/00691/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 1.5; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00691/l3v2/index.heta b/latest/cases/00691/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00691/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00691/l3v2/json/output.json b/latest/cases/00691/l3v2/json/output.json new file mode 100644 index 000000000..19dc1866e --- /dev/null +++ b/latest/cases/00691/l3v2/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00691/model-sbml-l2v5.xml b/latest/cases/00691/model-sbml-l2v5.xml new file mode 100644 index 000000000..7ead6799a --- /dev/null +++ b/latest/cases/00691/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00691/model-sbml-l3v2.xml b/latest/cases/00691/model-sbml-l3v2.xml new file mode 100644 index 000000000..df71acd70 --- /dev/null +++ b/latest/cases/00691/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00691/output.heta b/latest/cases/00691/output.heta new file mode 100644 index 000000000..f8260d196 --- /dev/null +++ b/latest/cases/00691/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S1 +is labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S3 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 1.5; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00691/synopsis.txt b/latest/cases/00691/synopsis.txt new file mode 100644 index 000000000..20cab92de --- /dev/null +++ b/latest/cases/00691/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S1 +is labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S3 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00692/l2v5/heta-code/output.heta b/latest/cases/00692/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c454deed0 --- /dev/null +++ b/latest/cases/00692/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 1.5; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00692/l2v5/index.heta b/latest/cases/00692/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00692/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00692/l2v5/json/output.json b/latest/cases/00692/l2v5/json/output.json new file mode 100644 index 000000000..9708dcc3a --- /dev/null +++ b/latest/cases/00692/l2v5/json/output.json @@ -0,0 +1,115 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00692/l3v2/heta-code/output.heta b/latest/cases/00692/l3v2/heta-code/output.heta new file mode 100644 index 000000000..17e80dd77 --- /dev/null +++ b/latest/cases/00692/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 1.5; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00692/l3v2/index.heta b/latest/cases/00692/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00692/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00692/l3v2/json/output.json b/latest/cases/00692/l3v2/json/output.json new file mode 100644 index 000000000..a1a276ff6 --- /dev/null +++ b/latest/cases/00692/l3v2/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "multiply(k1, S2)" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00692/model-sbml-l2v5.xml b/latest/cases/00692/model-sbml-l2v5.xml new file mode 100644 index 000000000..0685deabc --- /dev/null +++ b/latest/cases/00692/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00692/model-sbml-l3v2.xml b/latest/cases/00692/model-sbml-l3v2.xml new file mode 100644 index 000000000..54d8aa1e8 --- /dev/null +++ b/latest/cases/00692/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00692/output.heta b/latest/cases/00692/output.heta new file mode 100644 index 000000000..ba1d33662 --- /dev/null +++ b/latest/cases/00692/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S3 +is labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S3 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, }; +S3 := multiply(k1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 1.5; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00692/synopsis.txt b/latest/cases/00692/synopsis.txt new file mode 100644 index 000000000..b7396631b --- /dev/null +++ b/latest/cases/00692/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. Species S3 +is labeled as an SBML boundary species. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $multiply(k1, S1)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S3 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0.5$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00693/l2v5/heta-code/output.heta b/latest/cases/00693/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b2b0758e4 --- /dev/null +++ b/latest/cases/00693/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00693/l2v5/index.heta b/latest/cases/00693/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00693/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00693/l2v5/json/output.json b/latest/cases/00693/l2v5/json/output.json new file mode 100644 index 000000000..1c7593752 --- /dev/null +++ b/latest/cases/00693/l2v5/json/output.json @@ -0,0 +1,160 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00693/l3v2/heta-code/output.heta b/latest/cases/00693/l3v2/heta-code/output.heta new file mode 100644 index 000000000..51608a206 --- /dev/null +++ b/latest/cases/00693/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00693/l3v2/index.heta b/latest/cases/00693/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00693/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00693/l3v2/json/output.json b/latest/cases/00693/l3v2/json/output.json new file mode 100644 index 000000000..451b475ba --- /dev/null +++ b/latest/cases/00693/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25 / C", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00693/model-sbml-l2v5.xml b/latest/cases/00693/model-sbml-l2v5.xml new file mode 100644 index 000000000..7bfda2803 --- /dev/null +++ b/latest/cases/00693/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00693/model-sbml-l3v2.xml b/latest/cases/00693/model-sbml-l3v2.xml new file mode 100644 index 000000000..e8f8f1b5e --- /dev/null +++ b/latest/cases/00693/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00693/output.heta b/latest/cases/00693/output.heta new file mode 100644 index 000000000..6656de878 --- /dev/null +++ b/latest/cases/00693/output.heta @@ -0,0 +1,71 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00693/synopsis.txt b/latest/cases/00693/synopsis.txt new file mode 100644 index 000000000..1de264464 --- /dev/null +++ b/latest/cases/00693/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00694/l2v5/heta-code/output.heta b/latest/cases/00694/l2v5/heta-code/output.heta new file mode 100644 index 000000000..21a1c8257 --- /dev/null +++ b/latest/cases/00694/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00694/l2v5/index.heta b/latest/cases/00694/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00694/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00694/l2v5/json/output.json b/latest/cases/00694/l2v5/json/output.json new file mode 100644 index 000000000..6d793f983 --- /dev/null +++ b/latest/cases/00694/l2v5/json/output.json @@ -0,0 +1,160 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "2.25 / C", + "ode_": "k3 * S1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00694/l3v2/heta-code/output.heta b/latest/cases/00694/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3da434b99 --- /dev/null +++ b/latest/cases/00694/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00694/l3v2/index.heta b/latest/cases/00694/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00694/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00694/l3v2/json/output.json b/latest/cases/00694/l3v2/json/output.json new file mode 100644 index 000000000..aa35cd62b --- /dev/null +++ b/latest/cases/00694/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "2.25 / C", + "ode_": "k3 * S1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00694/model-sbml-l2v5.xml b/latest/cases/00694/model-sbml-l2v5.xml new file mode 100644 index 000000000..a14eaeee1 --- /dev/null +++ b/latest/cases/00694/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00694/model-sbml-l3v2.xml b/latest/cases/00694/model-sbml-l3v2.xml new file mode 100644 index 000000000..1743e23b6 --- /dev/null +++ b/latest/cases/00694/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00694/output.heta b/latest/cases/00694/output.heta new file mode 100644 index 000000000..3c7536681 --- /dev/null +++ b/latest/cases/00694/output.heta @@ -0,0 +1,71 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S4 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2.25 / C; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00694/synopsis.txt b/latest/cases/00694/synopsis.txt new file mode 100644 index 000000000..65301e31e --- /dev/null +++ b/latest/cases/00694/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using both an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S4 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is +inconsistent with the value calculated by the assignmentRule. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ 2.25$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00695/l2v5/build.log b/latest/cases/00695/l2v5/build.log new file mode 100644 index 000000000..2765567b7 --- /dev/null +++ b/latest/cases/00695/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00695/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00695/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00695/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00695/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00695/l2v5/index.heta b/latest/cases/00695/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00695/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00695/l3v2/build.log b/latest/cases/00695/l3v2/build.log new file mode 100644 index 000000000..a3ce948a8 --- /dev/null +++ b/latest/cases/00695/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00695/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00695/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00695/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00695/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00695/l3v2/index.heta b/latest/cases/00695/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00695/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00695/model-sbml-l2v5.xml b/latest/cases/00695/model-sbml-l2v5.xml new file mode 100644 index 000000000..6e3bd417f --- /dev/null +++ b/latest/cases/00695/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00695/model-sbml-l3v2.xml b/latest/cases/00695/model-sbml-l3v2.xml new file mode 100644 index 000000000..390ad2fba --- /dev/null +++ b/latest/cases/00695/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00695/synopsis.txt b/latest/cases/00695/synopsis.txt new file mode 100644 index 000000000..ee0b4a7f0 --- /dev/null +++ b/latest/cases/00695/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $0.1$ |] + +The assignment rule assigns a value to parameter k1 which is consistent with the value +attributed to the parameter by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00696/l2v5/build.log b/latest/cases/00696/l2v5/build.log new file mode 100644 index 000000000..1ea6b4d96 --- /dev/null +++ b/latest/cases/00696/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00696/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00696/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00696/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00696/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00696/l2v5/index.heta b/latest/cases/00696/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00696/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00696/l3v2/build.log b/latest/cases/00696/l3v2/build.log new file mode 100644 index 000000000..e5dfbba7c --- /dev/null +++ b/latest/cases/00696/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00696/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00696/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00696/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00696/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00696/l3v2/index.heta b/latest/cases/00696/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00696/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00696/model-sbml-l2v5.xml b/latest/cases/00696/model-sbml-l2v5.xml new file mode 100644 index 000000000..e4e196924 --- /dev/null +++ b/latest/cases/00696/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00696/model-sbml-l3v2.xml b/latest/cases/00696/model-sbml-l3v2.xml new file mode 100644 index 000000000..7c2c92cdb --- /dev/null +++ b/latest/cases/00696/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00696/synopsis.txt b/latest/cases/00696/synopsis.txt new file mode 100644 index 000000000..f3cbf0146 --- /dev/null +++ b/latest/cases/00696/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. +Species X0 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k1 | $0.1$ |] + +The assignment rule assigns a value to parameter k1 which is consistent with the value +attributed to the parameter by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00697/l2v5/heta-code/output.heta b/latest/cases/00697/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cc14189bc --- /dev/null +++ b/latest/cases/00697/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00697/l2v5/index.heta b/latest/cases/00697/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00697/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00697/l2v5/json/output.json b/latest/cases/00697/l2v5/json/output.json new file mode 100644 index 000000000..a4a7fc4d1 --- /dev/null +++ b/latest/cases/00697/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00697/l3v2/heta-code/output.heta b/latest/cases/00697/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0ddaf6ad7 --- /dev/null +++ b/latest/cases/00697/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00697/l3v2/index.heta b/latest/cases/00697/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00697/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00697/l3v2/json/output.json b/latest/cases/00697/l3v2/json/output.json new file mode 100644 index 000000000..8201a2430 --- /dev/null +++ b/latest/cases/00697/l3v2/json/output.json @@ -0,0 +1,64 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00697/model-sbml-l2v5.xml b/latest/cases/00697/model-sbml-l2v5.xml new file mode 100644 index 000000000..7255c5550 --- /dev/null +++ b/latest/cases/00697/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00697/model-sbml-l3v2.xml b/latest/cases/00697/model-sbml-l3v2.xml new file mode 100644 index 000000000..51cb9e12d --- /dev/null +++ b/latest/cases/00697/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00697/output.heta b/latest/cases/00697/output.heta new file mode 100644 index 000000000..cb3f74a93 --- /dev/null +++ b/latest/cases/00697/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Species S1 +is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00697/synopsis.txt b/latest/cases/00697/synopsis.txt new file mode 100644 index 000000000..946e65db9 --- /dev/null +++ b/latest/cases/00697/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Species S1 +is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00698/l2v5/heta-code/output.heta b/latest/cases/00698/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2350cdca7 --- /dev/null +++ b/latest/cases/00698/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00698/l2v5/index.heta b/latest/cases/00698/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00698/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00698/l2v5/json/output.json b/latest/cases/00698/l2v5/json/output.json new file mode 100644 index 000000000..daada063f --- /dev/null +++ b/latest/cases/00698/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00698/l3v2/heta-code/output.heta b/latest/cases/00698/l3v2/heta-code/output.heta new file mode 100644 index 000000000..33e6c43d9 --- /dev/null +++ b/latest/cases/00698/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00698/l3v2/index.heta b/latest/cases/00698/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00698/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00698/l3v2/json/output.json b/latest/cases/00698/l3v2/json/output.json new file mode 100644 index 000000000..ca6ced351 --- /dev/null +++ b/latest/cases/00698/l3v2/json/output.json @@ -0,0 +1,64 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00698/model-sbml-l2v5.xml b/latest/cases/00698/model-sbml-l2v5.xml new file mode 100644 index 000000000..6efc0fabc --- /dev/null +++ b/latest/cases/00698/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00698/model-sbml-l3v2.xml b/latest/cases/00698/model-sbml-l3v2.xml new file mode 100644 index 000000000..47203570d --- /dev/null +++ b/latest/cases/00698/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00698/output.heta b/latest/cases/00698/output.heta new file mode 100644 index 000000000..76aa997e6 --- /dev/null +++ b/latest/cases/00698/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Species S2 +is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00698/synopsis.txt b/latest/cases/00698/synopsis.txt new file mode 100644 index 000000000..7b58c524e --- /dev/null +++ b/latest/cases/00698/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Species S2 +is labeled as an SBML boundary species. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is undeclared and so must be calculated +by the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00699/l2v5/heta-code/output.heta b/latest/cases/00699/l2v5/heta-code/output.heta new file mode 100644 index 000000000..df34650ca --- /dev/null +++ b/latest/cases/00699/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00699/l2v5/index.heta b/latest/cases/00699/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00699/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00699/l2v5/json/output.json b/latest/cases/00699/l2v5/json/output.json new file mode 100644 index 000000000..160074a67 --- /dev/null +++ b/latest/cases/00699/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00699/l3v2/heta-code/output.heta b/latest/cases/00699/l3v2/heta-code/output.heta new file mode 100644 index 000000000..138246a9b --- /dev/null +++ b/latest/cases/00699/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00699/l3v2/index.heta b/latest/cases/00699/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00699/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00699/l3v2/json/output.json b/latest/cases/00699/l3v2/json/output.json new file mode 100644 index 000000000..59a7ddc9d --- /dev/null +++ b/latest/cases/00699/l3v2/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + } +] \ No newline at end of file diff --git a/latest/cases/00699/model-sbml-l2v5.xml b/latest/cases/00699/model-sbml-l2v5.xml new file mode 100644 index 000000000..410bd640d --- /dev/null +++ b/latest/cases/00699/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00699/model-sbml-l3v2.xml b/latest/cases/00699/model-sbml-l3v2.xml new file mode 100644 index 000000000..5d8bccd40 --- /dev/null +++ b/latest/cases/00699/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00699/output.heta b/latest/cases/00699/output.heta new file mode 100644 index 000000000..a7c7a6f44 --- /dev/null +++ b/latest/cases/00699/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Species S1 is labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00699/synopsis.txt b/latest/cases/00699/synopsis.txt new file mode 100644 index 000000000..85b69afe6 --- /dev/null +++ b/latest/cases/00699/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Species S1 is labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00700/l2v5/heta-code/output.heta b/latest/cases/00700/l2v5/heta-code/output.heta new file mode 100644 index 000000000..135a1895a --- /dev/null +++ b/latest/cases/00700/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00700/l2v5/index.heta b/latest/cases/00700/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00700/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00700/l2v5/json/output.json b/latest/cases/00700/l2v5/json/output.json new file mode 100644 index 000000000..68cd7f6d6 --- /dev/null +++ b/latest/cases/00700/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00700/l3v2/heta-code/output.heta b/latest/cases/00700/l3v2/heta-code/output.heta new file mode 100644 index 000000000..33e4071a7 --- /dev/null +++ b/latest/cases/00700/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00700/l3v2/index.heta b/latest/cases/00700/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00700/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00700/l3v2/json/output.json b/latest/cases/00700/l3v2/json/output.json new file mode 100644 index 000000000..519060ab5 --- /dev/null +++ b/latest/cases/00700/l3v2/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + } +] \ No newline at end of file diff --git a/latest/cases/00700/model-sbml-l2v5.xml b/latest/cases/00700/model-sbml-l2v5.xml new file mode 100644 index 000000000..f5d0a7ce6 --- /dev/null +++ b/latest/cases/00700/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00700/model-sbml-l3v2.xml b/latest/cases/00700/model-sbml-l3v2.xml new file mode 100644 index 000000000..654fd9d69 --- /dev/null +++ b/latest/cases/00700/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00700/output.heta b/latest/cases/00700/output.heta new file mode 100644 index 000000000..eacdaaf29 --- /dev/null +++ b/latest/cases/00700/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Species S3 is labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00700/synopsis.txt b/latest/cases/00700/synopsis.txt new file mode 100644 index 000000000..037ab68ba --- /dev/null +++ b/latest/cases/00700/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Species S3 is labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00701/l2v5/build.log b/latest/cases/00701/l2v5/build.log new file mode 100644 index 000000000..3e568f0ad --- /dev/null +++ b/latest/cases/00701/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00701/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00701/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00701/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00701/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00701/l2v5/index.heta b/latest/cases/00701/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00701/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00701/l3v2/build.log b/latest/cases/00701/l3v2/build.log new file mode 100644 index 000000000..b918ec87b --- /dev/null +++ b/latest/cases/00701/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00701/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00701/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00701/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00701/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00701/l3v2/index.heta b/latest/cases/00701/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00701/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00701/model-sbml-l2v5.xml b/latest/cases/00701/model-sbml-l2v5.xml new file mode 100644 index 000000000..c8e18674b --- /dev/null +++ b/latest/cases/00701/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00701/model-sbml-l3v2.xml b/latest/cases/00701/model-sbml-l3v2.xml new file mode 100644 index 000000000..96d3fe595 --- /dev/null +++ b/latest/cases/00701/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00701/synopsis.txt b/latest/cases/00701/synopsis.txt new file mode 100644 index 000000000..ba66964be --- /dev/null +++ b/latest/cases/00701/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Species S1 is labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00702/l2v5/build.log b/latest/cases/00702/l2v5/build.log new file mode 100644 index 000000000..0f068b1a2 --- /dev/null +++ b/latest/cases/00702/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00702/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00702/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00702/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00702/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00702/l2v5/index.heta b/latest/cases/00702/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00702/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00702/l3v2/build.log b/latest/cases/00702/l3v2/build.log new file mode 100644 index 000000000..2c8f6867e --- /dev/null +++ b/latest/cases/00702/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00702/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00702/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00702/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00702/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00702/l3v2/index.heta b/latest/cases/00702/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00702/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00702/model-sbml-l2v5.xml b/latest/cases/00702/model-sbml-l2v5.xml new file mode 100644 index 000000000..7b2381348 --- /dev/null +++ b/latest/cases/00702/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00702/model-sbml-l3v2.xml b/latest/cases/00702/model-sbml-l3v2.xml new file mode 100644 index 000000000..4a56b8e3f --- /dev/null +++ b/latest/cases/00702/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00702/synopsis.txt b/latest/cases/00702/synopsis.txt new file mode 100644 index 000000000..553cbda2c --- /dev/null +++ b/latest/cases/00702/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Amount, BoundaryCondition, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. +Species S3 is labeled as an SBML boundary species. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00703/l2v5/heta-code/output.heta b/latest/cases/00703/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bf49e1b4c --- /dev/null +++ b/latest/cases/00703/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5e-4 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := multiply(k, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k @Record 'k' { } .= 0.75; + +k__reaction1_local @Const { } = 7500; +k__reaction2_local @Const { } = 0.0025; + diff --git a/latest/cases/00703/l2v5/index.heta b/latest/cases/00703/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00703/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00703/l2v5/json/output.json b/latest/cases/00703/l2v5/json/output.json new file mode 100644 index 000000000..67a9f894c --- /dev/null +++ b/latest/cases/00703/l2v5/json/output.json @@ -0,0 +1,153 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "multiply(k, S2)" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 7500 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.0025 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00703/l3v2/heta-code/output.heta b/latest/cases/00703/l3v2/heta-code/output.heta new file mode 100644 index 000000000..06fe9cf22 --- /dev/null +++ b/latest/cases/00703/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := multiply(k, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 7500; +k__reaction2_local @Const { } = 0.0025; +k @Const 'k' { } = 0.75; + diff --git a/latest/cases/00703/l3v2/index.heta b/latest/cases/00703/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00703/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00703/l3v2/json/output.json b/latest/cases/00703/l3v2/json/output.json new file mode 100644 index 000000000..bab6acf5f --- /dev/null +++ b/latest/cases/00703/l3v2/json/output.json @@ -0,0 +1,127 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "multiply(k, S2)" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 7500 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.0025 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 0.75 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00703/model-sbml-l2v5.xml b/latest/cases/00703/model-sbml-l2v5.xml new file mode 100644 index 000000000..5fb536af7 --- /dev/null +++ b/latest/cases/00703/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k + S2 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00703/model-sbml-l3v2.xml b/latest/cases/00703/model-sbml-l3v2.xml new file mode 100644 index 000000000..078b6e25b --- /dev/null +++ b/latest/cases/00703/model-sbml-l3v2.xml @@ -0,0 +1,111 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k + S2 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00703/output.heta b/latest/cases/00703/output.heta new file mode 100644 index 000000000..73074403d --- /dev/null +++ b/latest/cases/00703/output.heta @@ -0,0 +1,76 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction S1 + S2 -> S3 defines one local parameter k which has a +scope local to the defining reaction. Reaction S3 -> S1 + S2 defines another +(different) local parameter k. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(k, S2)$ |] + +The model contains one FunctionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S4 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.5 \x 10^-4$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k |$ 0.75$ |dimensionless | +|Value of local parameter k (R1) |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of local parameter k (R2) |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := multiply(k, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; + +k__reaction1_local @Const { } = 7500; +k__reaction2_local @Const { } = 0.0025; +k @Const 'k' { } = 0.75; + diff --git a/latest/cases/00703/synopsis.txt b/latest/cases/00703/synopsis.txt new file mode 100644 index 000000000..806e6fad8 --- /dev/null +++ b/latest/cases/00703/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Reaction S1 + S2 -> S3 defines one local parameter k which has a +scope local to the defining reaction. Reaction S3 -> S1 + S2 defines another +(different) local parameter k. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(k, S2)$ |] + +The model contains one FunctionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S4 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.5 \x 10^-4$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k |$ 0.75$ |dimensionless | +|Value of local parameter k (R1) |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of local parameter k (R2) |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00704/l2v5/heta-code/output.heta b/latest/cases/00704/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9d16f1f9b --- /dev/null +++ b/latest/cases/00704/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := k * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k @Record 'k' { } .= 1.5; + +k__reaction1_local @Const { } = 0.015; +k__reaction2_local @Const { } = 0.5; + diff --git a/latest/cases/00704/l2v5/index.heta b/latest/cases/00704/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00704/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00704/l2v5/json/output.json b/latest/cases/00704/l2v5/json/output.json new file mode 100644 index 000000000..114edb4ea --- /dev/null +++ b/latest/cases/00704/l2v5/json/output.json @@ -0,0 +1,168 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k * S1" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.015 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.5 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00704/l3v2/heta-code/output.heta b/latest/cases/00704/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a8030d4db --- /dev/null +++ b/latest/cases/00704/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k__reaction1_local @Const { } = 0.015; +k__reaction2_local @Const { } = 0.5; +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k @Const 'k' { } = 1.5; + diff --git a/latest/cases/00704/l3v2/index.heta b/latest/cases/00704/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00704/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00704/l3v2/json/output.json b/latest/cases/00704/l3v2/json/output.json new file mode 100644 index 000000000..e358d1329 --- /dev/null +++ b/latest/cases/00704/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k * S1" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.015 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.5 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00704/model-sbml-l2v5.xml b/latest/cases/00704/model-sbml-l2v5.xml new file mode 100644 index 000000000..95de211cf --- /dev/null +++ b/latest/cases/00704/model-sbml-l2v5.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + k + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00704/model-sbml-l3v2.xml b/latest/cases/00704/model-sbml-l3v2.xml new file mode 100644 index 000000000..80fc7f27b --- /dev/null +++ b/latest/cases/00704/model-sbml-l3v2.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00704/output.heta b/latest/cases/00704/output.heta new file mode 100644 index 000000000..b1de8c848 --- /dev/null +++ b/latest/cases/00704/output.heta @@ -0,0 +1,77 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k * S1 * C$ | +| S3 -> S1 | $k * S3 * C$ |] + +Reaction S1 -> S3 defines one local parameter k which has a +scope local to the defining reaction. Reaction S3 -> S1 defines another +(different) local parameter k. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k |$ 1.5$ |dimensionless | +|Value of local parameter k (R1) |$ 0.015$ |second^-1^ | +|Value of local parameter k (R2) |$ 0.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k__reaction1_local @Const { } = 0.015; +k__reaction2_local @Const { } = 0.5; +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k @Const 'k' { } = 1.5; + diff --git a/latest/cases/00704/synopsis.txt b/latest/cases/00704/synopsis.txt new file mode 100644 index 000000000..9a6041cd9 --- /dev/null +++ b/latest/cases/00704/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k * S1 * C$ | +| S3 -> S1 | $k * S3 * C$ |] + +Reaction S1 -> S3 defines one local parameter k which has a +scope local to the defining reaction. Reaction S3 -> S1 defines another +(different) local parameter k. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k |$ 1.5$ |dimensionless | +|Value of local parameter k (R1) |$ 0.015$ |second^-1^ | +|Value of local parameter k (R2) |$ 0.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00705/l2v5/build.log b/latest/cases/00705/l2v5/build.log new file mode 100644 index 000000000..3dfa94bf9 --- /dev/null +++ b/latest/cases/00705/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00705/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00705/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00705/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00705/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00705/l2v5/index.heta b/latest/cases/00705/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00705/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00705/l3v2/build.log b/latest/cases/00705/l3v2/build.log new file mode 100644 index 000000000..952fa40b1 --- /dev/null +++ b/latest/cases/00705/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00705/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00705/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00705/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00705/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00705/l3v2/index.heta b/latest/cases/00705/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00705/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00705/model-sbml-l2v5.xml b/latest/cases/00705/model-sbml-l2v5.xml new file mode 100644 index 000000000..d26805941 --- /dev/null +++ b/latest/cases/00705/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k + X0 + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00705/model-sbml-l3v2.xml b/latest/cases/00705/model-sbml-l3v2.xml new file mode 100644 index 000000000..cfc1bf2e6 --- /dev/null +++ b/latest/cases/00705/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k + X0 + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00705/synopsis.txt b/latest/cases/00705/synopsis.txt new file mode 100644 index 000000000..7e7bf05d8 --- /dev/null +++ b/latest/cases/00705/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k * X0$ | +| T -> X1 | $C * k * S1$ |] + +Reaction T -> X1 defines one local parameter k which has a +scope local to the defining reaction and is different from the global parameter k +used in reaction X0 -> T. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ | + | assignmentRule | k | $0.1$ |] + +The assignment rule assigns a value to parameter k which has no value +attributed to it by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k |$undeclared$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Value of local parameter k |$0.375$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00706/l2v5/heta-code/output.heta b/latest/cases/00706/l2v5/heta-code/output.heta new file mode 100644 index 000000000..11fe11d56 --- /dev/null +++ b/latest/cases/00706/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k @Record 'k' { }; +k := 0.75; + +k__reaction1_local @Const { } = 0.75; + diff --git a/latest/cases/00706/l2v5/index.heta b/latest/cases/00706/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00706/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00706/l2v5/json/output.json b/latest/cases/00706/l2v5/json/output.json new file mode 100644 index 000000000..e01359cd2 --- /dev/null +++ b/latest/cases/00706/l2v5/json/output.json @@ -0,0 +1,92 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00706/l3v2/heta-code/output.heta b/latest/cases/00706/l3v2/heta-code/output.heta new file mode 100644 index 000000000..08a960880 --- /dev/null +++ b/latest/cases/00706/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k @Record 'k' { }; +k := 0.75; + +k__reaction1_local @Const { } = 0.75; + diff --git a/latest/cases/00706/l3v2/index.heta b/latest/cases/00706/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00706/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00706/l3v2/json/output.json b/latest/cases/00706/l3v2/json/output.json new file mode 100644 index 000000000..24ef7b02a --- /dev/null +++ b/latest/cases/00706/l3v2/json/output.json @@ -0,0 +1,68 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 0.75 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00706/model-sbml-l2v5.xml b/latest/cases/00706/model-sbml-l2v5.xml new file mode 100644 index 000000000..e57b7a9ce --- /dev/null +++ b/latest/cases/00706/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00706/model-sbml-l3v2.xml b/latest/cases/00706/model-sbml-l3v2.xml new file mode 100644 index 000000000..f1bb54189 --- /dev/null +++ b/latest/cases/00706/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + diff --git a/latest/cases/00706/output.heta b/latest/cases/00706/output.heta new file mode 100644 index 000000000..37cd0abe4 --- /dev/null +++ b/latest/cases/00706/output.heta @@ -0,0 +1,71 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction S1 -> S2 defines one local parameter k which has a +scope local to the defining reaction and is different from the global parameter k +used in the initialAssignment. + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k | $0.75$ |] + +In this case there is no initial value declared for parameter k. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$10$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k |$ undeclared$ |second^-1^ | +|Value of local parameter k |$ 0.75$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k @Record 'k' { }; +k := 0.75; + +k__reaction1_local @Const { } = 0.75; + diff --git a/latest/cases/00706/synopsis.txt b/latest/cases/00706/synopsis.txt new file mode 100644 index 000000000..dbaf350d5 --- /dev/null +++ b/latest/cases/00706/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction S1 -> S2 defines one local parameter k which has a +scope local to the defining reaction and is different from the global parameter k +used in the initialAssignment. + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k | $0.75$ |] + +In this case there is no initial value declared for parameter k. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$10$ |mole | +|Initial amount of S2 |$ 0.15$ |mole | +|Value of parameter k |$ undeclared$ |second^-1^ | +|Value of local parameter k |$ 0.75$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00707/l2v5/heta-code/output.heta b/latest/cases/00707/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6870532c9 --- /dev/null +++ b/latest/cases/00707/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.375 / C; +S3 := k * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k @Record 'k' { } .= 0.75; + +k__reaction1_local @Const { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00707/l2v5/index.heta b/latest/cases/00707/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00707/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00707/l2v5/json/output.json b/latest/cases/00707/l2v5/json/output.json new file mode 100644 index 000000000..b55728bd6 --- /dev/null +++ b/latest/cases/00707/l2v5/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.375 / C", + "ode_": "k * S2" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00707/l3v2/heta-code/output.heta b/latest/cases/00707/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4463138e7 --- /dev/null +++ b/latest/cases/00707/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C; +S3 := k * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 5; +k @Const 'k' { } = 0.75; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00707/l3v2/index.heta b/latest/cases/00707/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00707/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00707/l3v2/json/output.json b/latest/cases/00707/l3v2/json/output.json new file mode 100644 index 000000000..0a80edac6 --- /dev/null +++ b/latest/cases/00707/l3v2/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.375 / C", + "ode_": "k * S2" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 5 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 0.75 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + } +] \ No newline at end of file diff --git a/latest/cases/00707/model-sbml-l2v5.xml b/latest/cases/00707/model-sbml-l2v5.xml new file mode 100644 index 000000000..094526611 --- /dev/null +++ b/latest/cases/00707/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + k + S2 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00707/model-sbml-l3v2.xml b/latest/cases/00707/model-sbml-l3v2.xml new file mode 100644 index 000000000..c8b325b6d --- /dev/null +++ b/latest/cases/00707/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k + S2 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00707/output.heta b/latest/cases/00707/output.heta new file mode 100644 index 000000000..3e2505ad8 --- /dev/null +++ b/latest/cases/00707/output.heta @@ -0,0 +1,73 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction S1 -> S2 defines one local parameter k which has a +scope local to the defining reaction and is different from the global parameter k +used in the assignmentRule. + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k |$ 0.75$ |dimensionless | +|Value of local parameter k |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C; +S3 := k * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k__reaction1_local * S1; + +k__reaction1_local @Const { } = 5; +k @Const 'k' { } = 0.75; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00707/synopsis.txt b/latest/cases/00707/synopsis.txt new file mode 100644 index 000000000..fed109161 --- /dev/null +++ b/latest/cases/00707/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k * S1$ |] + +Reaction S1 -> S2 defines one local parameter k which has a +scope local to the defining reaction and is different from the global parameter k +used in the assignmentRule. + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0.375$ |mole | +|Value of parameter k |$ 0.75$ |dimensionless | +|Value of local parameter k |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00708/l2v5/build.log b/latest/cases/00708/l2v5/build.log new file mode 100644 index 000000000..ef0f35605 --- /dev/null +++ b/latest/cases/00708/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00708/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00708/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00708/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00708/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00708/l2v5/index.heta b/latest/cases/00708/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00708/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00708/l3v2/build.log b/latest/cases/00708/l3v2/build.log new file mode 100644 index 000000000..1081c5505 --- /dev/null +++ b/latest/cases/00708/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00708/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00708/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00708/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00708/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00708/l3v2/index.heta b/latest/cases/00708/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00708/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00708/model-sbml-l2v5.xml b/latest/cases/00708/model-sbml-l2v5.xml new file mode 100644 index 000000000..ee56538be --- /dev/null +++ b/latest/cases/00708/model-sbml-l2v5.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + k + S2 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00708/model-sbml-l3v2.xml b/latest/cases/00708/model-sbml-l3v2.xml new file mode 100644 index 000000000..a948aa86e --- /dev/null +++ b/latest/cases/00708/model-sbml-l3v2.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k + S2 + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00708/synopsis.txt b/latest/cases/00708/synopsis.txt new file mode 100644 index 000000000..599b31b96 --- /dev/null +++ b/latest/cases/00708/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +Reaction S1 -> S2 defines one local parameter k which has a +scope local to the defining reaction and is different from the global parameter k +used in the assignmentRule. + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $0.5$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 3.75$ |mole | +|Value of parameter k |$ 0.75$ |dimensionless | +|Value of local parameter k |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00709/l2v5/heta-code/output.heta b/latest/cases/00709/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6396a0128 --- /dev/null +++ b/latest/cases/00709/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00709/l2v5/index.heta b/latest/cases/00709/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00709/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00709/l2v5/json/output.json b/latest/cases/00709/l2v5/json/output.json new file mode 100644 index 000000000..5dca30664 --- /dev/null +++ b/latest/cases/00709/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00709/l3v2/heta-code/output.heta b/latest/cases/00709/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2ea196032 --- /dev/null +++ b/latest/cases/00709/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00709/l3v2/index.heta b/latest/cases/00709/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00709/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00709/l3v2/json/output.json b/latest/cases/00709/l3v2/json/output.json new file mode 100644 index 000000000..ea3ee3bd7 --- /dev/null +++ b/latest/cases/00709/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00709/model-sbml-l2v5.xml b/latest/cases/00709/model-sbml-l2v5.xml new file mode 100644 index 000000000..0cfe83819 --- /dev/null +++ b/latest/cases/00709/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00709/model-sbml-l3v2.xml b/latest/cases/00709/model-sbml-l3v2.xml new file mode 100644 index 000000000..7ec3ef4af --- /dev/null +++ b/latest/cases/00709/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00709/output.heta b/latest/cases/00709/output.heta new file mode 100644 index 000000000..4817fd625 --- /dev/null +++ b/latest/cases/00709/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S4 |$ 4$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 0.5$ |litre |] + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00709/synopsis.txt b/latest/cases/00709/synopsis.txt new file mode 100644 index 000000000..65bccea1d --- /dev/null +++ b/latest/cases/00709/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S4 |$ 4$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 0.5$ |litre |] + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00710/l2v5/heta-code/output.heta b/latest/cases/00710/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1e300e470 --- /dev/null +++ b/latest/cases/00710/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.75; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00710/l2v5/index.heta b/latest/cases/00710/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00710/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00710/l2v5/json/output.json b/latest/cases/00710/l2v5/json/output.json new file mode 100644 index 000000000..054891e6a --- /dev/null +++ b/latest/cases/00710/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.75" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00710/l3v2/heta-code/output.heta b/latest/cases/00710/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2c0909b1b --- /dev/null +++ b/latest/cases/00710/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.75; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00710/l3v2/index.heta b/latest/cases/00710/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00710/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00710/l3v2/json/output.json b/latest/cases/00710/l3v2/json/output.json new file mode 100644 index 000000000..0b63be669 --- /dev/null +++ b/latest/cases/00710/l3v2/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.75" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00710/model-sbml-l2v5.xml b/latest/cases/00710/model-sbml-l2v5.xml new file mode 100644 index 000000000..7a355e52f --- /dev/null +++ b/latest/cases/00710/model-sbml-l2v5.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00710/model-sbml-l3v2.xml b/latest/cases/00710/model-sbml-l3v2.xml new file mode 100644 index 000000000..96741375a --- /dev/null +++ b/latest/cases/00710/model-sbml-l3v2.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00710/output.heta b/latest/cases/00710/output.heta new file mode 100644 index 000000000..f015010e6 --- /dev/null +++ b/latest/cases/00710/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1.75$ |litre |] + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.75; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00710/synopsis.txt b/latest/cases/00710/synopsis.txt new file mode 100644 index 000000000..942519e03 --- /dev/null +++ b/latest/cases/00710/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1.75$ |litre |] + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00711/l2v5/heta-code/output.heta b/latest/cases/00711/l2v5/heta-code/output.heta new file mode 100644 index 000000000..666a0dea8 --- /dev/null +++ b/latest/cases/00711/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.93; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5e-4; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5e-4; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 1e-4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 0.0025; + diff --git a/latest/cases/00711/l2v5/index.heta b/latest/cases/00711/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00711/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00711/l2v5/json/output.json b/latest/cases/00711/l2v5/json/output.json new file mode 100644 index 000000000..d133038b5 --- /dev/null +++ b/latest/cases/00711/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.93" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0025" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1e-4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00711/l3v2/heta-code/output.heta b/latest/cases/00711/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a15e0b335 --- /dev/null +++ b/latest/cases/00711/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.93; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 1e-4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0.0025; + diff --git a/latest/cases/00711/l3v2/index.heta b/latest/cases/00711/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00711/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00711/l3v2/json/output.json b/latest/cases/00711/l3v2/json/output.json new file mode 100644 index 000000000..a92b4e172 --- /dev/null +++ b/latest/cases/00711/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.93" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1e-4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00711/model-sbml-l2v5.xml b/latest/cases/00711/model-sbml-l2v5.xml new file mode 100644 index 000000000..7521a4dff --- /dev/null +++ b/latest/cases/00711/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 0.0001 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00711/model-sbml-l3v2.xml b/latest/cases/00711/model-sbml-l3v2.xml new file mode 100644 index 000000000..034c276cd --- /dev/null +++ b/latest/cases/00711/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0001 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00711/output.heta b/latest/cases/00711/output.heta new file mode 100644 index 000000000..d7f92fcb8 --- /dev/null +++ b/latest/cases/00711/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S4 |$ 1 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.93; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 1e-4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0.0025; + diff --git a/latest/cases/00711/synopsis.txt b/latest/cases/00711/synopsis.txt new file mode 100644 index 000000000..841bddae4 --- /dev/null +++ b/latest/cases/00711/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-4$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$1.5 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S4 |$ 1 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + diff --git a/latest/cases/00712/l2v5/heta-code/output.heta b/latest/cases/00712/l2v5/heta-code/output.heta new file mode 100644 index 000000000..71e241fb3 --- /dev/null +++ b/latest/cases/00712/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.15 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := add(k2, k3); + +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.2; +k3 @Record 'k3' { } .= 0.3; + diff --git a/latest/cases/00712/l2v5/index.heta b/latest/cases/00712/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00712/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00712/l2v5/json/output.json b/latest/cases/00712/l2v5/json/output.json new file mode 100644 index 000000000..dc0305d97 --- /dev/null +++ b/latest/cases/00712/l2v5/json/output.json @@ -0,0 +1,128 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.3" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00712/l3v2/heta-code/output.heta b/latest/cases/00712/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a63893444 --- /dev/null +++ b/latest/cases/00712/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.15 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := add(k2, k3); + +k1 @Record 'k1' { } .= 1; + +k2 @Const 'k2' { } = 0.2; +k3 @Const 'k3' { } = 0.3; + diff --git a/latest/cases/00712/l3v2/index.heta b/latest/cases/00712/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00712/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00712/l3v2/json/output.json b/latest/cases/00712/l3v2/json/output.json new file mode 100644 index 000000000..d06cdc017 --- /dev/null +++ b/latest/cases/00712/l3v2/json/output.json @@ -0,0 +1,100 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.2 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.3 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00712/model-sbml-l2v5.xml b/latest/cases/00712/model-sbml-l2v5.xml new file mode 100644 index 000000000..16c560884 --- /dev/null +++ b/latest/cases/00712/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + add + k2 + k3 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00712/model-sbml-l3v2.xml b/latest/cases/00712/model-sbml-l3v2.xml new file mode 100644 index 000000000..8074272fa --- /dev/null +++ b/latest/cases/00712/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + add + k2 + k3 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00712/output.heta b/latest/cases/00712/output.heta new file mode 100644 index 000000000..13d3a266c --- /dev/null +++ b/latest/cases/00712/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2; two constant parameters called k2 and k3 and one varying +parameter called k1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0.2$ |second^-1^ | +|Value of parameter k3 |$ 0.3$ |lsecond^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.15 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := add(k2, k3); + +k1 @Record 'k1' { } .= 1; + +k2 @Const 'k2' { } = 0.2; +k3 @Const 'k3' { } = 0.3; + diff --git a/latest/cases/00712/synopsis.txt b/latest/cases/00712/synopsis.txt new file mode 100644 index 000000000..dd522c491 --- /dev/null +++ b/latest/cases/00712/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2; two constant parameters called k2 and k3 and one varying +parameter called k1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0.2$ |second^-1^ | +|Value of parameter k3 |$ 0.3$ |lsecond^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00713/l2v5/heta-code/output.heta b/latest/cases/00713/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3fd4708dc --- /dev/null +++ b/latest/cases/00713/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.15; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-6 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-6 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2e-6 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5e-7 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2, k3); + +k1 @Record 'k1' { } .= 1e+6; +k2 @Record 'k2' { } .= 3e+5; +k3 @Record 'k3' { } .= 7e+5; +p1 @Record 'p1' { } .= 1; + diff --git a/latest/cases/00713/l2v5/index.heta b/latest/cases/00713/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00713/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00713/l2v5/json/output.json b/latest/cases/00713/l2v5/json/output.json new file mode 100644 index 000000000..3e0a983d1 --- /dev/null +++ b/latest/cases/00713/l2v5/json/output.json @@ -0,0 +1,191 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.15" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5e-7 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "3e+5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "7e+5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00713/l3v2/heta-code/output.heta b/latest/cases/00713/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e9ad4c28d --- /dev/null +++ b/latest/cases/00713/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.15; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-6 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-6 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-7 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2, k3); + +k1 @Record 'k1' { } .= 1e+6; + +k2 @Const 'k2' { } = 300000; +k3 @Const 'k3' { } = 700000; +p1 @Const 'p1' { } = 1; + diff --git a/latest/cases/00713/l3v2/index.heta b/latest/cases/00713/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00713/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00713/l3v2/json/output.json b/latest/cases/00713/l3v2/json/output.json new file mode 100644 index 000000000..8d97a47f3 --- /dev/null +++ b/latest/cases/00713/l3v2/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.15" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5e-7 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1e+6" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 300000 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 700000 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00713/model-sbml-l2v5.xml b/latest/cases/00713/model-sbml-l2v5.xml new file mode 100644 index 000000000..ea1455507 --- /dev/null +++ b/latest/cases/00713/model-sbml-l2v5.xml @@ -0,0 +1,98 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + k2 + k3 + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00713/model-sbml-l3v2.xml b/latest/cases/00713/model-sbml-l3v2.xml new file mode 100644 index 000000000..44c67d770 --- /dev/null +++ b/latest/cases/00713/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + k2 + k3 + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00713/output.heta b/latest/cases/00713/output.heta new file mode 100644 index 000000000..7122ceba2 --- /dev/null +++ b/latest/cases/00713/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4; three constant parameters called k2, k3 and +p1 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3) * p1$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k3 |$ 0.7 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 0.15$ |litre |] +The species values are given as amounts of substance to make it easier to + +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.15; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-6 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-6 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-7 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2, k3); + +k1 @Record 'k1' { } .= 1e+6; + +k2 @Const 'k2' { } = 300000; +k3 @Const 'k3' { } = 700000; +p1 @Const 'p1' { } = 1; + diff --git a/latest/cases/00713/synopsis.txt b/latest/cases/00713/synopsis.txt new file mode 100644 index 000000000..4de6ce060 --- /dev/null +++ b/latest/cases/00713/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4; three constant parameters called k2, k3 and +p1 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3) * p1$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k3 |$ 0.7 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 0.15$ |litre |] +The species values are given as amounts of substance to make it easier to + +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00714/l2v5/heta-code/output.heta b/latest/cases/00714/l2v5/heta-code/output.heta new file mode 100644 index 000000000..94402730d --- /dev/null +++ b/latest/cases/00714/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.25; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2 * p2, k3); + +k1 @Record 'k1' { } .= 1.7; +k2 @Record 'k2' { } .= 0.3; +k3 @Record 'k3' { } .= -0.1; +p1 @Record 'p1' { } .= 1; +p2 @Record 'p2' { } .= 1; + diff --git a/latest/cases/00714/l2v5/index.heta b/latest/cases/00714/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00714/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00714/l2v5/json/output.json b/latest/cases/00714/l2v5/json/output.json new file mode 100644 index 000000000..a77c4d47a --- /dev/null +++ b/latest/cases/00714/l2v5/json/output.json @@ -0,0 +1,181 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.25" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "-0.1" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2 * p2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00714/l3v2/heta-code/output.heta b/latest/cases/00714/l3v2/heta-code/output.heta new file mode 100644 index 000000000..41305827c --- /dev/null +++ b/latest/cases/00714/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.25; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2 * p2, k3); + +k1 @Record 'k1' { } .= 1.7; + +k2 @Const 'k2' { } = 0.3; +k3 @Const 'k3' { } = -0.1; +p1 @Const 'p1' { } = 1; +p2 @Const 'p2' { } = 1; + diff --git a/latest/cases/00714/l3v2/index.heta b/latest/cases/00714/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00714/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00714/l3v2/json/output.json b/latest/cases/00714/l3v2/json/output.json new file mode 100644 index 000000000..184cb0fe2 --- /dev/null +++ b/latest/cases/00714/l3v2/json/output.json @@ -0,0 +1,149 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.25" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": -0.1 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 1 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2 * p2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00714/model-sbml-l2v5.xml b/latest/cases/00714/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef3adbcf8 --- /dev/null +++ b/latest/cases/00714/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + + + k2 + p2 + + k3 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00714/model-sbml-l3v2.xml b/latest/cases/00714/model-sbml-l3v2.xml new file mode 100644 index 000000000..857bf7acf --- /dev/null +++ b/latest/cases/00714/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + + + k2 + p2 + + k3 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00714/output.heta b/latest/cases/00714/output.heta new file mode 100644 index 000000000..79ffbfe14 --- /dev/null +++ b/latest/cases/00714/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3; four constant parameters called k2, k3, p1 and +p2 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $p1* add(p2 * k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter k3 |$ -0.1$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Value of parameter p2 |$ 1$ |litre mole^-1^ | +|Volume of compartment C |$ 1.25$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.25; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2 * p2, k3); + +k1 @Record 'k1' { } .= 1.7; + +k2 @Const 'k2' { } = 0.3; +k3 @Const 'k3' { } = -0.1; +p1 @Const 'p1' { } = 1; +p2 @Const 'p2' { } = 1; + diff --git a/latest/cases/00714/synopsis.txt b/latest/cases/00714/synopsis.txt new file mode 100644 index 000000000..ec050ef88 --- /dev/null +++ b/latest/cases/00714/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3; four constant parameters called k2, k3, p1 and +p2 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $p1* add(p2 * k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.0$ |mole | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter k3 |$ -0.1$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Value of parameter p2 |$ 1$ |litre mole^-1^ | +|Volume of compartment C |$ 1.25$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00715/l2v5/heta-code/output.heta b/latest/cases/00715/l2v5/heta-code/output.heta new file mode 100644 index 000000000..91fc96780 --- /dev/null +++ b/latest/cases/00715/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.76; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00715/l2v5/index.heta b/latest/cases/00715/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00715/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00715/l2v5/json/output.json b/latest/cases/00715/l2v5/json/output.json new file mode 100644 index 000000000..9b6af81d9 --- /dev/null +++ b/latest/cases/00715/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.76" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00715/l3v2/heta-code/output.heta b/latest/cases/00715/l3v2/heta-code/output.heta new file mode 100644 index 000000000..355b3c662 --- /dev/null +++ b/latest/cases/00715/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.76; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00715/l3v2/index.heta b/latest/cases/00715/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00715/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00715/l3v2/json/output.json b/latest/cases/00715/l3v2/json/output.json new file mode 100644 index 000000000..eb257707b --- /dev/null +++ b/latest/cases/00715/l3v2/json/output.json @@ -0,0 +1,128 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.76" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00715/model-sbml-l2v5.xml b/latest/cases/00715/model-sbml-l2v5.xml new file mode 100644 index 000000000..22eab01f5 --- /dev/null +++ b/latest/cases/00715/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00715/model-sbml-l3v2.xml b/latest/cases/00715/model-sbml-l3v2.xml new file mode 100644 index 000000000..d87ee567d --- /dev/null +++ b/latest/cases/00715/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00715/output.heta b/latest/cases/00715/output.heta new file mode 100644 index 000000000..7d056e87c --- /dev/null +++ b/latest/cases/00715/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S4 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 0.76$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.76; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00715/synopsis.txt b/latest/cases/00715/synopsis.txt new file mode 100644 index 000000000..5b5ac1d42 --- /dev/null +++ b/latest/cases/00715/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S4 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 0.76$ |litre |] + diff --git a/latest/cases/00716/l2v5/heta-code/output.heta b/latest/cases/00716/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4b211a53a --- /dev/null +++ b/latest/cases/00716/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.4; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00716/l2v5/index.heta b/latest/cases/00716/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00716/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00716/l2v5/json/output.json b/latest/cases/00716/l2v5/json/output.json new file mode 100644 index 000000000..17935bdc0 --- /dev/null +++ b/latest/cases/00716/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.4" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00716/l3v2/heta-code/output.heta b/latest/cases/00716/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a0854bd90 --- /dev/null +++ b/latest/cases/00716/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.4; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00716/l3v2/index.heta b/latest/cases/00716/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00716/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00716/l3v2/json/output.json b/latest/cases/00716/l3v2/json/output.json new file mode 100644 index 000000000..35484e666 --- /dev/null +++ b/latest/cases/00716/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.4" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5", + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00716/model-sbml-l2v5.xml b/latest/cases/00716/model-sbml-l2v5.xml new file mode 100644 index 000000000..dd3e0a1d8 --- /dev/null +++ b/latest/cases/00716/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00716/model-sbml-l3v2.xml b/latest/cases/00716/model-sbml-l3v2.xml new file mode 100644 index 000000000..069707845 --- /dev/null +++ b/latest/cases/00716/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00716/output.heta b/latest/cases/00716/output.heta new file mode 100644 index 000000000..517719fa1 --- /dev/null +++ b/latest/cases/00716/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S4 |$ 5$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1.4$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.4; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00716/synopsis.txt b/latest/cases/00716/synopsis.txt new file mode 100644 index 000000000..819f9fe4c --- /dev/null +++ b/latest/cases/00716/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value declared for species S4 is inconsistent +with the value calculated by the assignmentRule. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1 \x 10^-5$ |mole litre^-1^ | +|Initial concentration of S4 |$ 5$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1.4$ |litre |] + diff --git a/latest/cases/00717/l2v5/heta-code/output.heta b/latest/cases/00717/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7f971a3ba --- /dev/null +++ b/latest/cases/00717/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00717/l2v5/index.heta b/latest/cases/00717/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00717/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00717/l2v5/json/output.json b/latest/cases/00717/l2v5/json/output.json new file mode 100644 index 000000000..e66a840c0 --- /dev/null +++ b/latest/cases/00717/l2v5/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00717/l3v2/heta-code/output.heta b/latest/cases/00717/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dbb5812c9 --- /dev/null +++ b/latest/cases/00717/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00717/l3v2/index.heta b/latest/cases/00717/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00717/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00717/l3v2/json/output.json b/latest/cases/00717/l3v2/json/output.json new file mode 100644 index 000000000..a5df8a382 --- /dev/null +++ b/latest/cases/00717/l3v2/json/output.json @@ -0,0 +1,98 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00717/model-sbml-l2v5.xml b/latest/cases/00717/model-sbml-l2v5.xml new file mode 100644 index 000000000..79ab70a12 --- /dev/null +++ b/latest/cases/00717/model-sbml-l2v5.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00717/model-sbml-l3v2.xml b/latest/cases/00717/model-sbml-l3v2.xml new file mode 100644 index 000000000..483f0b9cc --- /dev/null +++ b/latest/cases/00717/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00717/output.heta b/latest/cases/00717/output.heta new file mode 100644 index 000000000..3cfac2cbe --- /dev/null +++ b/latest/cases/00717/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k1. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.15; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00717/synopsis.txt b/latest/cases/00717/synopsis.txt new file mode 100644 index 000000000..022b83d2f --- /dev/null +++ b/latest/cases/00717/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, ConstantSpecies +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k1. Species S4 is +labeled as constant and therefore cannot be changed by rules or reactions. +The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Initial amount of S4 |$ 1.0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00718/l2v5/heta-code/output.heta b/latest/cases/00718/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1642a60bc --- /dev/null +++ b/latest/cases/00718/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.0015 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.0015 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: 2*S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 1000); + +k1 @Record 'k1' { } .= 750; +k2 @Record 'k2' { } .= 0.0025; + diff --git a/latest/cases/00718/l2v5/index.heta b/latest/cases/00718/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00718/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00718/l2v5/json/output.json b/latest/cases/00718/l2v5/json/output.json new file mode 100644 index 000000000..9cf82e727 --- /dev/null +++ b/latest/cases/00718/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "750" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0025" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 1000)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00718/l3v2/heta-code/output.heta b/latest/cases/00718/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8b0acf2af --- /dev/null +++ b/latest/cases/00718/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.0015 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: 2*S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 1000); + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 0.0025; + diff --git a/latest/cases/00718/l3v2/index.heta b/latest/cases/00718/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00718/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00718/l3v2/json/output.json b/latest/cases/00718/l3v2/json/output.json new file mode 100644 index 000000000..cdd5d786c --- /dev/null +++ b/latest/cases/00718/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1 / 1000)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00718/model-sbml-l2v5.xml b/latest/cases/00718/model-sbml-l2v5.xml new file mode 100644 index 000000000..d744d4e6b --- /dev/null +++ b/latest/cases/00718/model-sbml-l2v5.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + 1 1000 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00718/model-sbml-l3v2.xml b/latest/cases/00718/model-sbml-l3v2.xml new file mode 100644 index 000000000..0e64051f4 --- /dev/null +++ b/latest/cases/00718/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 1000 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00718/output.heta b/latest/cases/00718/output.heta new file mode 100644 index 000000000..78647ed77 --- /dev/null +++ b/latest/cases/00718/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| 2S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 1 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.0015 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.001 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: 2*S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1 / 1000); + +k1 @Const 'k1' { } = 750; +k2 @Const 'k2' { } = 0.0025; + diff --git a/latest/cases/00718/synopsis.txt b/latest/cases/00718/synopsis.txt new file mode 100644 index 000000000..ad2649d35 --- /dev/null +++ b/latest/cases/00718/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| 2S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 1 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00719/l2v5/heta-code/output.heta b/latest/cases/00719/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ee7c1597b --- /dev/null +++ b/latest/cases/00719/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00719/l2v5/index.heta b/latest/cases/00719/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00719/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00719/l2v5/json/output.json b/latest/cases/00719/l2v5/json/output.json new file mode 100644 index 000000000..b4b1c2a1e --- /dev/null +++ b/latest/cases/00719/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00719/l3v2/heta-code/output.heta b/latest/cases/00719/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2ee80f222 --- /dev/null +++ b/latest/cases/00719/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00719/l3v2/index.heta b/latest/cases/00719/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00719/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00719/l3v2/json/output.json b/latest/cases/00719/l3v2/json/output.json new file mode 100644 index 000000000..113f3010c --- /dev/null +++ b/latest/cases/00719/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00719/model-sbml-l2v5.xml b/latest/cases/00719/model-sbml-l2v5.xml new file mode 100644 index 000000000..90fb066a0 --- /dev/null +++ b/latest/cases/00719/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00719/model-sbml-l3v2.xml b/latest/cases/00719/model-sbml-l3v2.xml new file mode 100644 index 000000000..9f6189a6c --- /dev/null +++ b/latest/cases/00719/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00719/output.heta b/latest/cases/00719/output.heta new file mode 100644 index 000000000..4072c101b --- /dev/null +++ b/latest/cases/00719/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00719/synopsis.txt b/latest/cases/00719/synopsis.txt new file mode 100644 index 000000000..32dba8688 --- /dev/null +++ b/latest/cases/00719/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00720/l2v5/heta-code/output.heta b/latest/cases/00720/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d104a16b4 --- /dev/null +++ b/latest/cases/00720/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5e-6 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-6 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5e-6 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1e-7 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := multiply(k2, (1 / 2.5e+5)); + +k1 @Record 'k1' { } .= 7.5e+5; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00720/l2v5/index.heta b/latest/cases/00720/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00720/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00720/l2v5/json/output.json b/latest/cases/00720/l2v5/json/output.json new file mode 100644 index 000000000..b8e52d225 --- /dev/null +++ b/latest/cases/00720/l2v5/json/output.json @@ -0,0 +1,167 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-7 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(k2, (1 / 2.5e+5))" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00720/l3v2/heta-code/output.heta b/latest/cases/00720/l3v2/heta-code/output.heta new file mode 100644 index 000000000..946ec3b05 --- /dev/null +++ b/latest/cases/00720/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-6 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-7 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := multiply(k2, (1 / 2.5e+5)); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00720/l3v2/index.heta b/latest/cases/00720/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00720/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00720/l3v2/json/output.json b/latest/cases/00720/l3v2/json/output.json new file mode 100644 index 000000000..42becba7d --- /dev/null +++ b/latest/cases/00720/l3v2/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-7 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(k2, (1 / 2.5e+5))" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00720/model-sbml-l2v5.xml b/latest/cases/00720/model-sbml-l2v5.xml new file mode 100644 index 000000000..078d54ee9 --- /dev/null +++ b/latest/cases/00720/model-sbml-l2v5.xml @@ -0,0 +1,89 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + multiply + k2 + 1 250000 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00720/model-sbml-l3v2.xml b/latest/cases/00720/model-sbml-l3v2.xml new file mode 100644 index 000000000..94955d77f --- /dev/null +++ b/latest/cases/00720/model-sbml-l3v2.xml @@ -0,0 +1,106 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k2 + 1 250000 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00720/output.heta b/latest/cases/00720/output.heta new file mode 100644 index 000000000..b1e07a48d --- /dev/null +++ b/latest/cases/00720/output.heta @@ -0,0 +1,68 @@ +/* +category: Test +synopsis: Two reactions and a rate rule that applies a functionDefinition + with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $multiply(k2, 4 \x 10^-6$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-7$ |mole | +|Value of parameter k1 |$ 0.75 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-6 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-7 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := multiply(k2, (1 / 2.5e+5)); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00720/synopsis.txt b/latest/cases/00720/synopsis.txt new file mode 100644 index 000000000..fcc34266c --- /dev/null +++ b/latest/cases/00720/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Two reactions and a rate rule that applies a functionDefinition + with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $multiply(k2, 4 \x 10^-6$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-7$ |mole | +|Value of parameter k1 |$ 0.75 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00721/l2v5/heta-code/output.heta b/latest/cases/00721/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1db3c6b33 --- /dev/null +++ b/latest/cases/00721/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/00721/l2v5/index.heta b/latest/cases/00721/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00721/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00721/l2v5/json/output.json b/latest/cases/00721/l2v5/json/output.json new file mode 100644 index 000000000..34c157f32 --- /dev/null +++ b/latest/cases/00721/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00721/l3v2/heta-code/output.heta b/latest/cases/00721/l3v2/heta-code/output.heta new file mode 100644 index 000000000..65c08e718 --- /dev/null +++ b/latest/cases/00721/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00721/l3v2/index.heta b/latest/cases/00721/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00721/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00721/l3v2/json/output.json b/latest/cases/00721/l3v2/json/output.json new file mode 100644 index 000000000..3b43d27cc --- /dev/null +++ b/latest/cases/00721/l3v2/json/output.json @@ -0,0 +1,128 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00721/model-sbml-l2v5.xml b/latest/cases/00721/model-sbml-l2v5.xml new file mode 100644 index 000000000..0af510c19 --- /dev/null +++ b/latest/cases/00721/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00721/model-sbml-l3v2.xml b/latest/cases/00721/model-sbml-l3v2.xml new file mode 100644 index 000000000..d50286e65 --- /dev/null +++ b/latest/cases/00721/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00721/output.heta b/latest/cases/00721/output.heta new file mode 100644 index 000000000..ebc2a5b1d --- /dev/null +++ b/latest/cases/00721/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: 2*S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2 * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00721/synopsis.txt b/latest/cases/00721/synopsis.txt new file mode 100644 index 000000000..10babc21a --- /dev/null +++ b/latest/cases/00721/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| 2S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00722/l2v5/heta-code/output.heta b/latest/cases/00722/l2v5/heta-code/output.heta new file mode 100644 index 000000000..94d4e8e84 --- /dev/null +++ b/latest/cases/00722/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.5; +p1 @Record 'p1' { } .= 0.75; + diff --git a/latest/cases/00722/l2v5/index.heta b/latest/cases/00722/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00722/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00722/l2v5/json/output.json b/latest/cases/00722/l2v5/json/output.json new file mode 100644 index 000000000..849259c1f --- /dev/null +++ b/latest/cases/00722/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00722/l3v2/heta-code/output.heta b/latest/cases/00722/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1599b796c --- /dev/null +++ b/latest/cases/00722/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.5; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00722/l3v2/index.heta b/latest/cases/00722/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00722/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00722/l3v2/json/output.json b/latest/cases/00722/l3v2/json/output.json new file mode 100644 index 000000000..ced0196dd --- /dev/null +++ b/latest/cases/00722/l3v2/json/output.json @@ -0,0 +1,125 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.75 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00722/model-sbml-l2v5.xml b/latest/cases/00722/model-sbml-l2v5.xml new file mode 100644 index 000000000..d6d7f675d --- /dev/null +++ b/latest/cases/00722/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00722/model-sbml-l3v2.xml b/latest/cases/00722/model-sbml-l3v2.xml new file mode 100644 index 000000000..49c16d995 --- /dev/null +++ b/latest/cases/00722/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00722/output.heta b/latest/cases/00722/output.heta new file mode 100644 index 000000000..3b2889809 --- /dev/null +++ b/latest/cases/00722/output.heta @@ -0,0 +1,71 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter p |$ 0.75$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.5; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00722/synopsis.txt b/latest/cases/00722/synopsis.txt new file mode 100644 index 000000000..3728082a6 --- /dev/null +++ b/latest/cases/00722/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter p |$ 0.75$ |mole litre^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00723/l2v5/heta-code/output.heta b/latest/cases/00723/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5118d02c6 --- /dev/null +++ b/latest/cases/00723/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00723/l2v5/index.heta b/latest/cases/00723/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00723/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00723/l2v5/json/output.json b/latest/cases/00723/l2v5/json/output.json new file mode 100644 index 000000000..9ae38dc65 --- /dev/null +++ b/latest/cases/00723/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00723/l3v2/heta-code/output.heta b/latest/cases/00723/l3v2/heta-code/output.heta new file mode 100644 index 000000000..37a345ae4 --- /dev/null +++ b/latest/cases/00723/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00723/l3v2/index.heta b/latest/cases/00723/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00723/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00723/l3v2/json/output.json b/latest/cases/00723/l3v2/json/output.json new file mode 100644 index 000000000..d2a46ea46 --- /dev/null +++ b/latest/cases/00723/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + } +] \ No newline at end of file diff --git a/latest/cases/00723/model-sbml-l2v5.xml b/latest/cases/00723/model-sbml-l2v5.xml new file mode 100644 index 000000000..a3fa94db2 --- /dev/null +++ b/latest/cases/00723/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00723/model-sbml-l3v2.xml b/latest/cases/00723/model-sbml-l3v2.xml new file mode 100644 index 000000000..b572079a6 --- /dev/null +++ b/latest/cases/00723/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00723/output.heta b/latest/cases/00723/output.heta new file mode 100644 index 000000000..0685b9957 --- /dev/null +++ b/latest/cases/00723/output.heta @@ -0,0 +1,69 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00723/synopsis.txt b/latest/cases/00723/synopsis.txt new file mode 100644 index 000000000..310cc40e2 --- /dev/null +++ b/latest/cases/00723/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00724/l2v5/build.log b/latest/cases/00724/l2v5/build.log new file mode 100644 index 000000000..49c68909d --- /dev/null +++ b/latest/cases/00724/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00724/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00724/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00724/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00724/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00724/l2v5/index.heta b/latest/cases/00724/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00724/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00724/l3v2/build.log b/latest/cases/00724/l3v2/build.log new file mode 100644 index 000000000..348d59c5f --- /dev/null +++ b/latest/cases/00724/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00724/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00724/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00724/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00724/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00724/l3v2/index.heta b/latest/cases/00724/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00724/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00724/model-sbml-l2v5.xml b/latest/cases/00724/model-sbml-l2v5.xml new file mode 100644 index 000000000..e62fd9cf8 --- /dev/null +++ b/latest/cases/00724/model-sbml-l2v5.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 2.5 + + + + + + 2 + + + + + + + diff --git a/latest/cases/00724/model-sbml-l3v2.xml b/latest/cases/00724/model-sbml-l3v2.xml new file mode 100644 index 000000000..184fb8758 --- /dev/null +++ b/latest/cases/00724/model-sbml-l3v2.xml @@ -0,0 +1,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 2.5 + + + + + + 2 + + + + + + + diff --git a/latest/cases/00724/synopsis.txt b/latest/cases/00724/synopsis.txt new file mode 100644 index 000000000..bcfacb7f5 --- /dev/null +++ b/latest/cases/00724/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventWithDelay +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + 2S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $2.5$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.5$ |mole | +|Initial amount of S4 |$ 1$ |mole | +|Value of parameter k1 |$0.$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.00025$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00725/l2v5/build.log b/latest/cases/00725/l2v5/build.log new file mode 100644 index 000000000..c75271aa6 --- /dev/null +++ b/latest/cases/00725/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00725/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00725/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00725/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00725/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00725/l2v5/index.heta b/latest/cases/00725/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00725/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00725/l3v2/index.heta b/latest/cases/00725/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00725/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00725/model-sbml-l2v5.xml b/latest/cases/00725/model-sbml-l2v5.xml new file mode 100644 index 000000000..c1c6ae2ff --- /dev/null +++ b/latest/cases/00725/model-sbml-l2v5.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + 1 100 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00725/synopsis.txt b/latest/cases/00725/synopsis.txt new file mode 100644 index 000000000..d789eaff9 --- /dev/null +++ b/latest/cases/00725/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| (4 * p1) S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.5 \x 10^-2$ |mole | +|Initial amount of S4 |$ 1 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00726/l2v5/build.log b/latest/cases/00726/l2v5/build.log new file mode 100644 index 000000000..1b8383f07 --- /dev/null +++ b/latest/cases/00726/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00726/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00726/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00726/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00726/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00726/l2v5/index.heta b/latest/cases/00726/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00726/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00726/l3v2/index.heta b/latest/cases/00726/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00726/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00726/model-sbml-l2v5.xml b/latest/cases/00726/model-sbml-l2v5.xml new file mode 100644 index 000000000..936f4df77 --- /dev/null +++ b/latest/cases/00726/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00726/synopsis.txt b/latest/cases/00726/synopsis.txt new file mode 100644 index 000000000..7521eac46 --- /dev/null +++ b/latest/cases/00726/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00727/l2v5/build.log b/latest/cases/00727/l2v5/build.log new file mode 100644 index 000000000..d2355d364 --- /dev/null +++ b/latest/cases/00727/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00727/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00727/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00727/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00727/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00727/l2v5/index.heta b/latest/cases/00727/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00727/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00727/l3v2/index.heta b/latest/cases/00727/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00727/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00727/model-sbml-l2v5.xml b/latest/cases/00727/model-sbml-l2v5.xml new file mode 100644 index 000000000..d92b900bd --- /dev/null +++ b/latest/cases/00727/model-sbml-l2v5.xml @@ -0,0 +1,100 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + multiply + k2 + 1 250000 + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00727/synopsis.txt b/latest/cases/00727/synopsis.txt new file mode 100644 index 000000000..95e12c430 --- /dev/null +++ b/latest/cases/00727/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Two reactions and a rate rule that applies a functionDefinition + with four species in a compartment. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $multiply(k2, 4 \x 10^-6$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-7$ |mole | +|Value of parameter k1 |$ 0.75 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00728/l2v5/build.log b/latest/cases/00728/l2v5/build.log new file mode 100644 index 000000000..7d558981f --- /dev/null +++ b/latest/cases/00728/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00728/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00728/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00728/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00728/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00728/l2v5/index.heta b/latest/cases/00728/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00728/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00728/l3v2/index.heta b/latest/cases/00728/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00728/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00728/model-sbml-l2v5.xml b/latest/cases/00728/model-sbml-l2v5.xml new file mode 100644 index 000000000..eecee1223 --- /dev/null +++ b/latest/cases/00728/model-sbml-l2v5.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00728/synopsis.txt b/latest/cases/00728/synopsis.txt new file mode 100644 index 000000000..efd6dbda8 --- /dev/null +++ b/latest/cases/00728/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| (4 * p1)S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00729/l2v5/build.log b/latest/cases/00729/l2v5/build.log new file mode 100644 index 000000000..818af3a2b --- /dev/null +++ b/latest/cases/00729/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00729/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00729/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00729/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00729/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00729/l2v5/index.heta b/latest/cases/00729/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00729/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00729/l3v2/index.heta b/latest/cases/00729/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00729/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00729/model-sbml-l2v5.xml b/latest/cases/00729/model-sbml-l2v5.xml new file mode 100644 index 000000000..3085d3eb4 --- /dev/null +++ b/latest/cases/00729/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + 4 + p2 + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00729/synopsis.txt b/latest/cases/00729/synopsis.txt new file mode 100644 index 000000000..490759ee4 --- /dev/null +++ b/latest/cases/00729/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and four parameters called k1, k2, p1 and p2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p2)S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter p1 |$ 0.75$ |mole litre^-1^ | +|Value of parameter p2 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00730/l2v5/build.log b/latest/cases/00730/l2v5/build.log new file mode 100644 index 000000000..0875f5f3b --- /dev/null +++ b/latest/cases/00730/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00730/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00730/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00730/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00730/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00730/l2v5/index.heta b/latest/cases/00730/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00730/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00730/l3v2/index.heta b/latest/cases/00730/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00730/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00730/model-sbml-l2v5.xml b/latest/cases/00730/model-sbml-l2v5.xml new file mode 100644 index 000000000..8924ab026 --- /dev/null +++ b/latest/cases/00730/model-sbml-l2v5.xml @@ -0,0 +1,89 @@ + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00730/synopsis.txt b/latest/cases/00730/synopsis.txt new file mode 100644 index 000000000..fd112398c --- /dev/null +++ b/latest/cases/00730/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00731/l2v5/build.log b/latest/cases/00731/l2v5/build.log new file mode 100644 index 000000000..2a455e811 --- /dev/null +++ b/latest/cases/00731/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00731/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00731/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00731/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00731/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00731/l2v5/index.heta b/latest/cases/00731/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00731/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00731/l3v2/index.heta b/latest/cases/00731/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00731/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00731/model-sbml-l2v5.xml b/latest/cases/00731/model-sbml-l2v5.xml new file mode 100644 index 000000000..3461930f7 --- /dev/null +++ b/latest/cases/00731/model-sbml-l2v5.xml @@ -0,0 +1,102 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 2.5 + + + + + + 2 + + + + + + + diff --git a/latest/cases/00731/synopsis.txt b/latest/cases/00731/synopsis.txt new file mode 100644 index 000000000..45e224be6 --- /dev/null +++ b/latest/cases/00731/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, RateRule, EventWithDelay +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + (4 * p1)S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $2.5$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.5$ |mole | +|Initial amount of S4 |$ 1$ |mole | +|Value of parameter k1 |$0.$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.00025$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00732/l2v5/heta-code/output.heta b/latest/cases/00732/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bbc6e7bca --- /dev/null +++ b/latest/cases/00732/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +k1__reaction1_local @Const { } = 0.9; + diff --git a/latest/cases/00732/l2v5/index.heta b/latest/cases/00732/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00732/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00732/l2v5/json/output.json b/latest/cases/00732/l2v5/json/output.json new file mode 100644 index 000000000..0e76c6222 --- /dev/null +++ b/latest/cases/00732/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k1__reaction1_local", + "num": 0.9 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00732/l3v2/heta-code/output.heta b/latest/cases/00732/l3v2/heta-code/output.heta new file mode 100644 index 000000000..586f0e719 --- /dev/null +++ b/latest/cases/00732/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1__reaction1_local @Const { } = 0.9; +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00732/l3v2/index.heta b/latest/cases/00732/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00732/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00732/l3v2/json/output.json b/latest/cases/00732/l3v2/json/output.json new file mode 100644 index 000000000..f753ee79e --- /dev/null +++ b/latest/cases/00732/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k1__reaction1_local", + "num": 0.9 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00732/model-sbml-l2v5.xml b/latest/cases/00732/model-sbml-l2v5.xml new file mode 100644 index 000000000..20c6a190a --- /dev/null +++ b/latest/cases/00732/model-sbml-l2v5.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + diff --git a/latest/cases/00732/model-sbml-l3v2.xml b/latest/cases/00732/model-sbml-l3v2.xml new file mode 100644 index 000000000..5fea72f6a --- /dev/null +++ b/latest/cases/00732/model-sbml-l3v2.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + diff --git a/latest/cases/00732/output.heta b/latest/cases/00732/output.heta new file mode 100644 index 000000000..f42814e0c --- /dev/null +++ b/latest/cases/00732/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +Reaction S1 -> S2 defines one local parameter k1 which has a +scope local to the defining reaction and is different from the global parameter k1 +used in the RateRule. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of local parameter k1 |$0.9$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1__reaction1_local @Const { } = 0.9; +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00732/synopsis.txt b/latest/cases/00732/synopsis.txt new file mode 100644 index 000000000..9521f0f6b --- /dev/null +++ b/latest/cases/00732/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +Reaction S1 -> S2 defines one local parameter k1 which has a +scope local to the defining reaction and is different from the global parameter k1 +used in the RateRule. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of local parameter k1 |$0.9$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00733/l2v5/heta-code/output.heta b/latest/cases/00733/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b93a65238 --- /dev/null +++ b/latest/cases/00733/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5e-6 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-6 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5e-6 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1e-7 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := multiply(k, (1 / 2.5e+5)); + +k @Record 'k' { } .= 0.25; + +k__reaction1_local @Const { } = 750000; +k__reaction2_local @Const { } = 0.3; + diff --git a/latest/cases/00733/l2v5/index.heta b/latest/cases/00733/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00733/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00733/l2v5/json/output.json b/latest/cases/00733/l2v5/json/output.json new file mode 100644 index 000000000..d87564c26 --- /dev/null +++ b/latest/cases/00733/l2v5/json/output.json @@ -0,0 +1,169 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-7 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 750000 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.3 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(k, (1 / 2.5e+5))" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00733/l3v2/heta-code/output.heta b/latest/cases/00733/l3v2/heta-code/output.heta new file mode 100644 index 000000000..148afd323 --- /dev/null +++ b/latest/cases/00733/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-6 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-7 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := multiply(k, (1 / 2.5e+5)); + +k__reaction1_local @Const { } = 750000; +k__reaction2_local @Const { } = 0.3; +k @Const 'k' { } = 0.25; + diff --git a/latest/cases/00733/l3v2/index.heta b/latest/cases/00733/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00733/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00733/l3v2/json/output.json b/latest/cases/00733/l3v2/json/output.json new file mode 100644 index 000000000..e818e3e10 --- /dev/null +++ b/latest/cases/00733/l3v2/json/output.json @@ -0,0 +1,143 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-7 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k__reaction1_local", + "num": 750000 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k__reaction1_local * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k__reaction2_local", + "num": 0.3 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 0.25 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(k, (1 / 2.5e+5))" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00733/model-sbml-l2v5.xml b/latest/cases/00733/model-sbml-l2v5.xml new file mode 100644 index 000000000..ddfc31795 --- /dev/null +++ b/latest/cases/00733/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + multiply + k + 1 250000 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00733/model-sbml-l3v2.xml b/latest/cases/00733/model-sbml-l3v2.xml new file mode 100644 index 000000000..209857d79 --- /dev/null +++ b/latest/cases/00733/model-sbml-l3v2.xml @@ -0,0 +1,111 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k + 1 250000 + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + + + + + + + + + + + + + + C + k + S3 + + + + + + + + + + diff --git a/latest/cases/00733/output.heta b/latest/cases/00733/output.heta new file mode 100644 index 000000000..283747bbe --- /dev/null +++ b/latest/cases/00733/output.heta @@ -0,0 +1,74 @@ +/* +category: Test +synopsis: Two reactions and a rate rule that applies a functionDefinition + with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Each reaction defines one local parameter k which has a +scope local to the defining reaction and is different from the global parameter k +used in the RateRule. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $multiply(k2, 4 \x 10^-6$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-7$ |mole | +|Value of parameter k |$ 0.25$ |second^-1^ | +|Value of local parameter k (R1) |$ 0.75 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of local parameter k (R2) |$ 0.3$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-6 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-6 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-7 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k__reaction1_local * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k__reaction2_local * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := multiply(k, (1 / 2.5e+5)); + +k__reaction1_local @Const { } = 750000; +k__reaction2_local @Const { } = 0.3; +k @Const 'k' { } = 0.25; + diff --git a/latest/cases/00733/synopsis.txt b/latest/cases/00733/synopsis.txt new file mode 100644 index 000000000..db59a30b7 --- /dev/null +++ b/latest/cases/00733/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Two reactions and a rate rule that applies a functionDefinition + with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k * S3 * C$ |] + +Each reaction defines one local parameter k which has a +scope local to the defining reaction and is different from the global parameter k +used in the RateRule. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $multiply(k2, 4 \x 10^-6$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-7$ |mole | +|Value of parameter k |$ 0.25$ |second^-1^ | +|Value of local parameter k (R1) |$ 0.75 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of local parameter k (R2) |$ 0.3$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00734/l2v5/heta-code/output.heta b/latest/cases/00734/l2v5/heta-code/output.heta new file mode 100644 index 000000000..268c44746 --- /dev/null +++ b/latest/cases/00734/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2__reaction2_local * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1 @Record 'k1' { } .= 0.015; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1.5; + +k1__reaction1_local @Const { } = 0.01; +k2__reaction2_local @Const { } = 0.4; + diff --git a/latest/cases/00734/l2v5/index.heta b/latest/cases/00734/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00734/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00734/l2v5/json/output.json b/latest/cases/00734/l2v5/json/output.json new file mode 100644 index 000000000..d27af6187 --- /dev/null +++ b/latest/cases/00734/l2v5/json/output.json @@ -0,0 +1,168 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k1__reaction1_local", + "num": 0.01 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1__reaction1_local * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k2__reaction2_local", + "num": 0.4 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00734/l3v2/heta-code/output.heta b/latest/cases/00734/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f77addb46 --- /dev/null +++ b/latest/cases/00734/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2__reaction2_local * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1__reaction1_local @Const { } = 0.01; +k2__reaction2_local @Const { } = 0.4; +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00734/l3v2/index.heta b/latest/cases/00734/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00734/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00734/l3v2/json/output.json b/latest/cases/00734/l3v2/json/output.json new file mode 100644 index 000000000..e82114934 --- /dev/null +++ b/latest/cases/00734/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "k3 * S1" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k1__reaction1_local", + "num": 0.01 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1__reaction1_local * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k2__reaction2_local", + "num": 0.4 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2__reaction2_local * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.015 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + }, + { + "class": "Process", + "id": "S2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k2 * S3 + (-1) * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00734/model-sbml-l2v5.xml b/latest/cases/00734/model-sbml-l2v5.xml new file mode 100644 index 000000000..91f99187d --- /dev/null +++ b/latest/cases/00734/model-sbml-l2v5.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + diff --git a/latest/cases/00734/model-sbml-l3v2.xml b/latest/cases/00734/model-sbml-l3v2.xml new file mode 100644 index 000000000..9e7915e80 --- /dev/null +++ b/latest/cases/00734/model-sbml-l3v2.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + diff --git a/latest/cases/00734/output.heta b/latest/cases/00734/output.heta new file mode 100644 index 000000000..41bede62b --- /dev/null +++ b/latest/cases/00734/output.heta @@ -0,0 +1,77 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +Reaction S1 -> S3 defines one local parameter k1 and reaction S3 -> S2 defines one +local parameter k2. These parameters have a scope local to the defining reaction +and are different from the global parameters k1 and k2 used in the rules. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of local parameter k1 |$ 0.01$ |second^-1^ | +|Value of local parameter k2 |$ 0.4$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := k3 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, }; +reaction2 := C * k2__reaction2_local * S3; +S2_proc @Process { actors: = S2, aux: {{"metaid":"rule2"}}, }; +S2_proc := k2 * S3 + (-1) * k1 * S1; + +k1__reaction1_local @Const { } = 0.01; +k2__reaction2_local @Const { } = 0.4; +k1 @Const 'k1' { } = 0.015; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/00734/synopsis.txt b/latest/cases/00734/synopsis.txt new file mode 100644 index 000000000..1f03a9c4b --- /dev/null +++ b/latest/cases/00734/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and three parameters called k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +Reaction S1 -> S3 defines one local parameter k1 and reaction S3 -> S2 defines one +local parameter k2. These parameters have a scope local to the defining reaction +and are different from the global parameters k1 and k2 used in the rules. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of local parameter k1 |$ 0.01$ |second^-1^ | +|Value of local parameter k2 |$ 0.4$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00735/l2v5/heta-code/output.heta b/latest/cases/00735/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1805886e8 --- /dev/null +++ b/latest/cases/00735/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.5; + +k1__reaction1_local @Const { } = 0.8; + diff --git a/latest/cases/00735/l2v5/index.heta b/latest/cases/00735/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00735/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00735/l2v5/json/output.json b/latest/cases/00735/l2v5/json/output.json new file mode 100644 index 000000000..157e0588b --- /dev/null +++ b/latest/cases/00735/l2v5/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k1__reaction1_local", + "num": 0.8 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00735/l3v2/heta-code/output.heta b/latest/cases/00735/l3v2/heta-code/output.heta new file mode 100644 index 000000000..448df8a77 --- /dev/null +++ b/latest/cases/00735/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1__reaction1_local @Const { } = 0.8; +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00735/l3v2/index.heta b/latest/cases/00735/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00735/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00735/l3v2/json/output.json b/latest/cases/00735/l3v2/json/output.json new file mode 100644 index 000000000..a236d63d1 --- /dev/null +++ b/latest/cases/00735/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k1__reaction1_local", + "num": 0.8 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * S4" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * k2 * S4" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00735/model-sbml-l2v5.xml b/latest/cases/00735/model-sbml-l2v5.xml new file mode 100644 index 000000000..f9b63a3dc --- /dev/null +++ b/latest/cases/00735/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + k1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + diff --git a/latest/cases/00735/model-sbml-l3v2.xml b/latest/cases/00735/model-sbml-l3v2.xml new file mode 100644 index 000000000..f873536b4 --- /dev/null +++ b/latest/cases/00735/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + k1 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + diff --git a/latest/cases/00735/output.heta b/latest/cases/00735/output.heta new file mode 100644 index 000000000..c8d6ec7ec --- /dev/null +++ b/latest/cases/00735/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +Reaction S1 -> S2 defines one local parameter k1 which has a +scope local to the defining reaction and is different from the global parameter k1 +used in the InitialAssignment. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |mole litre^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of local parameter k1 |$ 0.8$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k2 * S4; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-1) * k2 * S4; + +k1__reaction1_local @Const { } = 0.8; +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00735/synopsis.txt b/latest/cases/00735/synopsis.txt new file mode 100644 index 000000000..c189f4d75 --- /dev/null +++ b/latest/cases/00735/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment +testTags: Amount, LocalParameters, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +Reaction S1 -> S2 defines one local parameter k1 which has a +scope local to the defining reaction and is different from the global parameter k1 +used in the InitialAssignment. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |mole litre^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of local parameter k1 |$ 0.8$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00736/l2v5/heta-code/output.heta b/latest/cases/00736/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f7809370d --- /dev/null +++ b/latest/cases/00736/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +k1__reaction1_local @Const { } = 0.8; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00736/l2v5/index.heta b/latest/cases/00736/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00736/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00736/l2v5/json/output.json b/latest/cases/00736/l2v5/json/output.json new file mode 100644 index 000000000..96fa5a403 --- /dev/null +++ b/latest/cases/00736/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k1__reaction1_local", + "num": 0.8 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00736/l3v2/heta-code/output.heta b/latest/cases/00736/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e66f48ca3 --- /dev/null +++ b/latest/cases/00736/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1__reaction1_local @Const { } = 0.8; +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00736/l3v2/index.heta b/latest/cases/00736/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00736/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00736/l3v2/json/output.json b/latest/cases/00736/l3v2/json/output.json new file mode 100644 index 000000000..42ccfdcd8 --- /dev/null +++ b/latest/cases/00736/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k1__reaction1_local", + "num": 0.8 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1__reaction1_local * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + } +] \ No newline at end of file diff --git a/latest/cases/00736/model-sbml-l2v5.xml b/latest/cases/00736/model-sbml-l2v5.xml new file mode 100644 index 000000000..5c67d7c19 --- /dev/null +++ b/latest/cases/00736/model-sbml-l2v5.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00736/model-sbml-l3v2.xml b/latest/cases/00736/model-sbml-l3v2.xml new file mode 100644 index 000000000..2b0cf3767 --- /dev/null +++ b/latest/cases/00736/model-sbml-l3v2.xml @@ -0,0 +1,98 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00736/output.heta b/latest/cases/00736/output.heta new file mode 100644 index 000000000..9ebf16a1d --- /dev/null +++ b/latest/cases/00736/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $k1 * S1 * C$ |] + +Reaction S1 -> S2 defines one local parameter k1 which has a +scope local to the defining reaction and is different from the global parameter k1 +used in the rateRule. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of local parameter k1 |$ 0.8$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1__reaction1_local * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1__reaction1_local @Const { } = 0.8; +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00736/synopsis.txt b/latest/cases/00736/synopsis.txt new file mode 100644 index 000000000..a0098049a --- /dev/null +++ b/latest/cases/00736/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $k1 * S1 * C$ |] + +Reaction S1 -> S2 defines one local parameter k1 which has a +scope local to the defining reaction and is different from the global parameter k1 +used in the rateRule. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of local parameter k1 |$ 0.8$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00737/l2v5/build.log b/latest/cases/00737/l2v5/build.log new file mode 100644 index 000000000..1672ef92e --- /dev/null +++ b/latest/cases/00737/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00737/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00737/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00737/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00737/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00737/l2v5/index.heta b/latest/cases/00737/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00737/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00737/l3v2/build.log b/latest/cases/00737/l3v2/build.log new file mode 100644 index 000000000..dcad86403 --- /dev/null +++ b/latest/cases/00737/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00737/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00737/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00737/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00737/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00737/l3v2/index.heta b/latest/cases/00737/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00737/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00737/model-sbml-l2v5.xml b/latest/cases/00737/model-sbml-l2v5.xml new file mode 100644 index 000000000..4b23885ef --- /dev/null +++ b/latest/cases/00737/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 1 + + + + + + 2 + + + + + + + diff --git a/latest/cases/00737/model-sbml-l3v2.xml b/latest/cases/00737/model-sbml-l3v2.xml new file mode 100644 index 000000000..b57953d31 --- /dev/null +++ b/latest/cases/00737/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 1 + + + + + + 2 + + + + + + + diff --git a/latest/cases/00737/synopsis.txt b/latest/cases/00737/synopsis.txt new file mode 100644 index 000000000..3a8342004 --- /dev/null +++ b/latest/cases/00737/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule, EventWithDelay +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $k1 * S1 * C$ |] + +Reaction S1 -> S2 defines one local parameter k1 which has a +scope local to the defining reaction and is different from the global parameter k1 +used in the rateRule. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of local parameter k1 |$ 0.8$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00738/l2v5/heta-code/output.heta b/latest/cases/00738/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c629a1801 --- /dev/null +++ b/latest/cases/00738/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.86; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.015; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := multiply(p1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 0.025; +p1 @Record 'p1' { } .= 0.75; + diff --git a/latest/cases/00738/l2v5/index.heta b/latest/cases/00738/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00738/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00738/l2v5/json/output.json b/latest/cases/00738/l2v5/json/output.json new file mode 100644 index 000000000..9fce38352 --- /dev/null +++ b/latest/cases/00738/l2v5/json/output.json @@ -0,0 +1,159 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.86" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "multiply(p1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.025" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00738/l3v2/heta-code/output.heta b/latest/cases/00738/l3v2/heta-code/output.heta new file mode 100644 index 000000000..63790e757 --- /dev/null +++ b/latest/cases/00738/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.86; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.015; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := multiply(p1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 0.025; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00738/l3v2/index.heta b/latest/cases/00738/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00738/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00738/l3v2/json/output.json b/latest/cases/00738/l3v2/json/output.json new file mode 100644 index 000000000..13adf8921 --- /dev/null +++ b/latest/cases/00738/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.86" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "multiply(p1, S2)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.025 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.75 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00738/model-sbml-l2v5.xml b/latest/cases/00738/model-sbml-l2v5.xml new file mode 100644 index 000000000..4e94fa39b --- /dev/null +++ b/latest/cases/00738/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + S2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00738/model-sbml-l3v2.xml b/latest/cases/00738/model-sbml-l3v2.xml new file mode 100644 index 000000000..30a800426 --- /dev/null +++ b/latest/cases/00738/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + p1 + S2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00738/output.heta b/latest/cases/00738/output.heta new file mode 100644 index 000000000..e11348a71 --- /dev/null +++ b/latest/cases/00738/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(p1, S2)$ |] + +The model contains one FunctionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S4 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.5 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S4 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Value of parameter p1 |$ 0.75$ |dimensionless | +|Volume of compartment C |$ 0.86$ |litre |] + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.86; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.015; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := multiply(p1, S2); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 0.025; +p1 @Const 'p1' { } = 0.75; + diff --git a/latest/cases/00738/synopsis.txt b/latest/cases/00738/synopsis.txt new file mode 100644 index 000000000..2a9c8e651 --- /dev/null +++ b/latest/cases/00738/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule with a functionDefinition to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $multiply(p1, S2)$ |] + +The model contains one FunctionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +Note that in this case the initial value of the species S4 is not explicitly +declared and must be calculated by the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.5 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S4 |$ undeclared$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Value of parameter p1 |$ 0.75$ |dimensionless | +|Volume of compartment C |$ 0.86$ |litre |] + diff --git a/latest/cases/00739/l2v5/heta-code/output.heta b/latest/cases/00739/l2v5/heta-code/output.heta new file mode 100644 index 000000000..11dfe3928 --- /dev/null +++ b/latest/cases/00739/l2v5/heta-code/output.heta @@ -0,0 +1,30 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; +func1 #defineFunction { arguments: [x, y], math: x * pow(y + 1, (-1)), }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0; +S4 := func1(S3, p1); +S5 @Species 'S5' { units: substance/volume, compartment: C, } .= 0; +S5 := multiply(S4, p1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S2, modifiers: [S5], reversible: false, }; +reaction2 := C * k2 * S5; + +k1 @Record 'k1' { } .= 0.1; +k2 @Record 'k2' { } .= 0.15; +p1 @Record 'p1' { } .= 2.5; + diff --git a/latest/cases/00739/l2v5/index.heta b/latest/cases/00739/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00739/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00739/l2v5/json/output.json b/latest/cases/00739/l2v5/json/output.json new file mode 100644 index 000000000..4243bab24 --- /dev/null +++ b/latest/cases/00739/l2v5/json/output.json @@ -0,0 +1,177 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0", + "ode_": "func1(S3, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "substance/volume", + "assignments": { + "start_": "0", + "ode_": "multiply(S4, p1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S5" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "2.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + }, + { + "id": "func1", + "arguments": [ + "x", + "y" + ], + "math": "x * pow(y + 1, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00739/l3v2/heta-code/output.heta b/latest/cases/00739/l3v2/heta-code/output.heta new file mode 100644 index 000000000..029f97b57 --- /dev/null +++ b/latest/cases/00739/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; +func1 #defineFunction { arguments: [x, y], math: x * pow(y + 1, (-1)), }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; +S4 := func1(S3, p1); +S5 @Species 'S5' { units: mole/litre, compartment: C, } .= 0; +S5 := multiply(S4, p1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S2, modifiers: [S5], reversible: false, }; +reaction2 := C * k2 * S5; + +k1 @Const 'k1' { } = 0.1; +k2 @Const 'k2' { } = 0.15; +p1 @Const 'p1' { } = 2.5; + diff --git a/latest/cases/00739/l3v2/index.heta b/latest/cases/00739/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00739/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00739/l3v2/json/output.json b/latest/cases/00739/l3v2/json/output.json new file mode 100644 index 000000000..420cce3cb --- /dev/null +++ b/latest/cases/00739/l3v2/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0", + "ode_": "func1(S3, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S5", + "title": "S5", + "units": "mole/litre", + "assignments": { + "start_": "0", + "ode_": "multiply(S4, p1)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S5" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "S5" + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.15 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 2.5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + }, + { + "id": "func1", + "arguments": [ + "x", + "y" + ], + "math": "x * pow(y + 1, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00739/model-sbml-l2v5.xml b/latest/cases/00739/model-sbml-l2v5.xml new file mode 100644 index 000000000..af59b225c --- /dev/null +++ b/latest/cases/00739/model-sbml-l2v5.xml @@ -0,0 +1,125 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + + + y + 1 + + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + func1 + S3 + p1 + + + + + + + multiply + S4 + p1 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + + + + C + k2 + S5 + + + + + + + diff --git a/latest/cases/00739/model-sbml-l3v2.xml b/latest/cases/00739/model-sbml-l3v2.xml new file mode 100644 index 000000000..995bd611b --- /dev/null +++ b/latest/cases/00739/model-sbml-l3v2.xml @@ -0,0 +1,142 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + + + y + 1 + + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + func1 + S3 + p1 + + + + + + + multiply + S4 + p1 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + + + + C + k2 + S5 + + + + + + + diff --git a/latest/cases/00739/output.heta b/latest/cases/00739/output.heta new file mode 100644 index 000000000..48e3226e8 --- /dev/null +++ b/latest/cases/00739/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Two reactions with five species in one +compartment using an assignmentRules with functionDefinitions to vary two species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are five +species called S1, S2, S3, S4 and S5 and three parameters called k1, k2 and +p1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S2 | $k2 * S5 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $func1(S3, p1)$ | + | Assignment | S5 | $multiply(S4, p1)$ |] + +The model contains two functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | func1 | x, y | $x / (1 + y)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Initial concentration of S4 |$ 0$ |mole litre^-1^ | +|Initial concentration of S5 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.1$ |second^-1^ | +|Value of parameter k2 |$ 0.15$ |second^-1^ | +|Value of parameter p1 |$ 2.5$ |dimensionless | +|Volume of compartment C |$ 2.5$ |litre |] + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; +func1 #defineFunction { arguments: [x, y], math: x * pow(y + 1, (-1)), }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; +S4 := func1(S3, p1); +S5 @Species 'S5' { units: mole/litre, compartment: C, } .= 0; +S5 := multiply(S4, p1); + +reaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S3 = S2, modifiers: [S5], reversible: false, }; +reaction2 := C * k2 * S5; + +k1 @Const 'k1' { } = 0.1; +k2 @Const 'k2' { } = 0.15; +p1 @Const 'p1' { } = 2.5; + diff --git a/latest/cases/00739/synopsis.txt b/latest/cases/00739/synopsis.txt new file mode 100644 index 000000000..5d44be8ac --- /dev/null +++ b/latest/cases/00739/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reactions with five species in one +compartment using an assignmentRules with functionDefinitions to vary two species. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are five +species called S1, S2, S3, S4 and S5 and three parameters called k1, k2 and +p1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S2 | $k2 * S5 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $func1(S3, p1)$ | + | Assignment | S5 | $multiply(S4, p1)$ |] + +The model contains two functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | func1 | x, y | $x / (1 + y)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0$ |mole litre^-1^ | +|Initial concentration of S4 |$ 0$ |mole litre^-1^ | +|Initial concentration of S5 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.1$ |second^-1^ | +|Value of parameter k2 |$ 0.15$ |second^-1^ | +|Value of parameter p1 |$ 2.5$ |dimensionless | +|Volume of compartment C |$ 2.5$ |litre |] + diff --git a/latest/cases/00740/l2v5/heta-code/output.heta b/latest/cases/00740/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7891b268a --- /dev/null +++ b/latest/cases/00740/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := add(k2, k3); + +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.2; +k3 @Record 'k3' { } .= 0.3; + diff --git a/latest/cases/00740/l2v5/index.heta b/latest/cases/00740/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00740/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00740/l2v5/json/output.json b/latest/cases/00740/l2v5/json/output.json new file mode 100644 index 000000000..3b438d194 --- /dev/null +++ b/latest/cases/00740/l2v5/json/output.json @@ -0,0 +1,128 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.3" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00740/l3v2/heta-code/output.heta b/latest/cases/00740/l3v2/heta-code/output.heta new file mode 100644 index 000000000..20a2d4703 --- /dev/null +++ b/latest/cases/00740/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := add(k2, k3); + +k1 @Record 'k1' { } .= 1; + +k2 @Const 'k2' { } = 0.2; +k3 @Const 'k3' { } = 0.3; + diff --git a/latest/cases/00740/l3v2/index.heta b/latest/cases/00740/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00740/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00740/l3v2/json/output.json b/latest/cases/00740/l3v2/json/output.json new file mode 100644 index 000000000..2d7a193ee --- /dev/null +++ b/latest/cases/00740/l3v2/json/output.json @@ -0,0 +1,100 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.2 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.3 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00740/model-sbml-l2v5.xml b/latest/cases/00740/model-sbml-l2v5.xml new file mode 100644 index 000000000..c4e9e0553 --- /dev/null +++ b/latest/cases/00740/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + add + k2 + k3 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00740/model-sbml-l3v2.xml b/latest/cases/00740/model-sbml-l3v2.xml new file mode 100644 index 000000000..0ab9ae33e --- /dev/null +++ b/latest/cases/00740/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + add + k2 + k3 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00740/output.heta b/latest/cases/00740/output.heta new file mode 100644 index 000000000..820101927 --- /dev/null +++ b/latest/cases/00740/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Concentration, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2; two constant parameters called k2 and k3 and one varying +parameter called k1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0.2$ |second^-1^ | +|Value of parameter k3 |$ 0.3$ |lsecond^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := add(k2, k3); + +k1 @Record 'k1' { } .= 1; + +k2 @Const 'k2' { } = 0.2; +k3 @Const 'k3' { } = 0.3; + diff --git a/latest/cases/00740/synopsis.txt b/latest/cases/00740/synopsis.txt new file mode 100644 index 000000000..38ea02ddf --- /dev/null +++ b/latest/cases/00740/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Concentration, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2; two constant parameters called k2 and k3 and one varying +parameter called k1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0.2$ |second^-1^ | +|Value of parameter k3 |$ 0.3$ |lsecond^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + diff --git a/latest/cases/00741/l2v5/heta-code/output.heta b/latest/cases/00741/l2v5/heta-code/output.heta new file mode 100644 index 000000000..dd4a03d87 --- /dev/null +++ b/latest/cases/00741/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.15; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-6; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-6; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2e-6; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2, k3); + +k1 @Record 'k1' { } .= 1e+6; +k2 @Record 'k2' { } .= 3e+5; +k3 @Record 'k3' { } .= 7e+5; +p1 @Record 'p1' { } .= 1; + diff --git a/latest/cases/00741/l2v5/index.heta b/latest/cases/00741/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00741/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00741/l2v5/json/output.json b/latest/cases/00741/l2v5/json/output.json new file mode 100644 index 000000000..17dc51471 --- /dev/null +++ b/latest/cases/00741/l2v5/json/output.json @@ -0,0 +1,191 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.15" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5e-7" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "3e+5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "7e+5" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00741/l3v2/heta-code/output.heta b/latest/cases/00741/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1995af7b7 --- /dev/null +++ b/latest/cases/00741/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.15; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-6; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-6; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-6; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2, k3); + +k1 @Record 'k1' { } .= 1e+6; + +k2 @Const 'k2' { } = 300000; +k3 @Const 'k3' { } = 700000; +p1 @Const 'p1' { } = 1; + diff --git a/latest/cases/00741/l3v2/index.heta b/latest/cases/00741/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00741/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00741/l3v2/json/output.json b/latest/cases/00741/l3v2/json/output.json new file mode 100644 index 000000000..6f8d6134e --- /dev/null +++ b/latest/cases/00741/l3v2/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.15" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-6" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5e-7" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1e+6" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 300000 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 700000 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00741/model-sbml-l2v5.xml b/latest/cases/00741/model-sbml-l2v5.xml new file mode 100644 index 000000000..17b9b3c19 --- /dev/null +++ b/latest/cases/00741/model-sbml-l2v5.xml @@ -0,0 +1,98 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + k2 + k3 + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00741/model-sbml-l3v2.xml b/latest/cases/00741/model-sbml-l3v2.xml new file mode 100644 index 000000000..a4cc1262d --- /dev/null +++ b/latest/cases/00741/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + k2 + k3 + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/00741/output.heta b/latest/cases/00741/output.heta new file mode 100644 index 000000000..5958e40fb --- /dev/null +++ b/latest/cases/00741/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Concentration, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4; three constant parameters called k2, k3 and +p1 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3) * p1$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2.0 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S4 |$ 0.5 \x 10^-6$ |mole litre^-1^ | +|Value of parameter k1 |$ 1 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k3 |$ 0.7 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 0.15$ |litre |] + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.15; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-6; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-6; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-6; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2, k3); + +k1 @Record 'k1' { } .= 1e+6; + +k2 @Const 'k2' { } = 300000; +k3 @Const 'k3' { } = 700000; +p1 @Const 'p1' { } = 1; + diff --git a/latest/cases/00741/synopsis.txt b/latest/cases/00741/synopsis.txt new file mode 100644 index 000000000..0857f5bd7 --- /dev/null +++ b/latest/cases/00741/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Concentration, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4; three constant parameters called k2, k3 and +p1 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $add(k2, k3) * p1$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S2 |$ 1.5 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S3 |$ 2.0 \x 10^-6$ |mole litre^-1^ | +|Initial concentration of S4 |$ 0.5 \x 10^-6$ |mole litre^-1^ | +|Value of parameter k1 |$ 1 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k3 |$ 0.7 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Volume of compartment C |$ 0.15$ |litre |] + diff --git a/latest/cases/00742/l2v5/heta-code/output.heta b/latest/cases/00742/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c6ea47a8c --- /dev/null +++ b/latest/cases/00742/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.25; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2 * p2, k3); + +k1 @Record 'k1' { } .= 1.7; +k2 @Record 'k2' { } .= 0.3; +k3 @Record 'k3' { } .= -0.1; +p1 @Record 'p1' { } .= 1; +p2 @Record 'p2' { } .= 1; + diff --git a/latest/cases/00742/l2v5/index.heta b/latest/cases/00742/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00742/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00742/l2v5/json/output.json b/latest/cases/00742/l2v5/json/output.json new file mode 100644 index 000000000..64483c0bb --- /dev/null +++ b/latest/cases/00742/l2v5/json/output.json @@ -0,0 +1,181 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.25" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "-0.1" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2 * p2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00742/l3v2/heta-code/output.heta b/latest/cases/00742/l3v2/heta-code/output.heta new file mode 100644 index 000000000..08a340419 --- /dev/null +++ b/latest/cases/00742/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.25; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2 * p2, k3); + +k1 @Record 'k1' { } .= 1.7; + +k2 @Const 'k2' { } = 0.3; +k3 @Const 'k3' { } = -0.1; +p1 @Const 'p1' { } = 1; +p2 @Const 'p2' { } = 1; + diff --git a/latest/cases/00742/l3v2/index.heta b/latest/cases/00742/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00742/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00742/l3v2/json/output.json b/latest/cases/00742/l3v2/json/output.json new file mode 100644 index 000000000..635f217da --- /dev/null +++ b/latest/cases/00742/l3v2/json/output.json @@ -0,0 +1,149 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.25" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": -0.1 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 1 + }, + { + "class": "Const", + "id": "p2", + "title": "p2", + "num": 1 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "p1 * add(k2 * p2, k3)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00742/model-sbml-l2v5.xml b/latest/cases/00742/model-sbml-l2v5.xml new file mode 100644 index 000000000..7ddad08c6 --- /dev/null +++ b/latest/cases/00742/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + + + k2 + p2 + + k3 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00742/model-sbml-l3v2.xml b/latest/cases/00742/model-sbml-l3v2.xml new file mode 100644 index 000000000..972382d91 --- /dev/null +++ b/latest/cases/00742/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + + add + + + k2 + p2 + + k3 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00742/output.heta b/latest/cases/00742/output.heta new file mode 100644 index 000000000..40199eb59 --- /dev/null +++ b/latest/cases/00742/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Concentration, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3; four constant parameters called k2, k3, p1 and +p2 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $p1* add(p2 * k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1.0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter k3 |$ -0.1$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Value of parameter p2 |$ 1$ |litre mole^-1^ | +|Volume of compartment C |$ 1.25$ |litre |] + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.25; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := p1 * add(k2 * p2, k3); + +k1 @Record 'k1' { } .= 1.7; + +k2 @Const 'k2' { } = 0.3; +k3 @Const 'k3' { } = -0.1; +p1 @Const 'p1' { } = 1; +p2 @Const 'p2' { } = 1; + diff --git a/latest/cases/00742/synopsis.txt b/latest/cases/00742/synopsis.txt new file mode 100644 index 000000000..e7da16b3d --- /dev/null +++ b/latest/cases/00742/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Rate rule using a functionDefinition used to determine value of parameter + which is used in a reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: Concentration, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3; four constant parameters called k2, k3, p1 and +p2 and one varying parameter called k1. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule that determines the value of parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $p1* add(p2 * k2, k3)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$ 2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 1.0$ |mole litre^-1^ | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter k3 |$ -0.1$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 1$ |second^-1^ | +|Value of parameter p2 |$ 1$ |litre mole^-1^ | +|Volume of compartment C |$ 1.25$ |litre |] + diff --git a/latest/cases/00743/l2v5/heta-code/output.heta b/latest/cases/00743/l2v5/heta-code/output.heta new file mode 100644 index 000000000..493331b9b --- /dev/null +++ b/latest/cases/00743/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00743/l2v5/index.heta b/latest/cases/00743/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00743/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00743/l2v5/json/output.json b/latest/cases/00743/l2v5/json/output.json new file mode 100644 index 000000000..5e1ed266d --- /dev/null +++ b/latest/cases/00743/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00743/l3v2/heta-code/output.heta b/latest/cases/00743/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c832823ee --- /dev/null +++ b/latest/cases/00743/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00743/l3v2/index.heta b/latest/cases/00743/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00743/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00743/l3v2/json/output.json b/latest/cases/00743/l3v2/json/output.json new file mode 100644 index 000000000..773644b94 --- /dev/null +++ b/latest/cases/00743/l3v2/json/output.json @@ -0,0 +1,111 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00743/model-sbml-l2v5.xml b/latest/cases/00743/model-sbml-l2v5.xml new file mode 100644 index 000000000..f0dd65d23 --- /dev/null +++ b/latest/cases/00743/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00743/model-sbml-l3v2.xml b/latest/cases/00743/model-sbml-l3v2.xml new file mode 100644 index 000000000..21e86b6e1 --- /dev/null +++ b/latest/cases/00743/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00743/output.heta b/latest/cases/00743/output.heta new file mode 100644 index 000000000..64d2cc43d --- /dev/null +++ b/latest/cases/00743/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00743/synopsis.txt b/latest/cases/00743/synopsis.txt new file mode 100644 index 000000000..53d06f0ab --- /dev/null +++ b/latest/cases/00743/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + diff --git a/latest/cases/00744/l2v5/heta-code/output.heta b/latest/cases/00744/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4d4f623e1 --- /dev/null +++ b/latest/cases/00744/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.43; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S1 [event2]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00744/l2v5/index.heta b/latest/cases/00744/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00744/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00744/l2v5/json/output.json b/latest/cases/00744/l2v5/json/output.json new file mode 100644 index 000000000..2b1ef9e68 --- /dev/null +++ b/latest/cases/00744/l2v5/json/output.json @@ -0,0 +1,146 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.43" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00744/l3v2/heta-code/output.heta b/latest/cases/00744/l3v2/heta-code/output.heta new file mode 100644 index 000000000..26967a472 --- /dev/null +++ b/latest/cases/00744/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.43; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00744/l3v2/index.heta b/latest/cases/00744/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00744/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00744/l3v2/json/output.json b/latest/cases/00744/l3v2/json/output.json new file mode 100644 index 000000000..f84e8a1b4 --- /dev/null +++ b/latest/cases/00744/l3v2/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.43" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1", + "event2": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + } +] \ No newline at end of file diff --git a/latest/cases/00744/model-sbml-l2v5.xml b/latest/cases/00744/model-sbml-l2v5.xml new file mode 100644 index 000000000..1ddc165e2 --- /dev/null +++ b/latest/cases/00744/model-sbml-l2v5.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00744/model-sbml-l3v2.xml b/latest/cases/00744/model-sbml-l3v2.xml new file mode 100644 index 000000000..bb2697c11 --- /dev/null +++ b/latest/cases/00744/model-sbml-l3v2.xml @@ -0,0 +1,113 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00744/output.heta b/latest/cases/00744/output.heta new file mode 100644 index 000000000..b6161de88 --- /dev/null +++ b/latest/cases/00744/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1.43$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.43; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S1 [event2]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00744/synopsis.txt b/latest/cases/00744/synopsis.txt new file mode 100644 index 000000000..8ffbaaaa7 --- /dev/null +++ b/latest/cases/00744/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1.43$ |litre |] + diff --git a/latest/cases/00745/l2v5/heta-code/output.heta b/latest/cases/00745/l2v5/heta-code/output.heta new file mode 100644 index 000000000..22ef407c9 --- /dev/null +++ b/latest/cases/00745/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.9; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S1 [event1]= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.65, }; + diff --git a/latest/cases/00745/l2v5/index.heta b/latest/cases/00745/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00745/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00745/l2v5/json/output.json b/latest/cases/00745/l2v5/json/output.json new file mode 100644 index 000000000..a45791ad3 --- /dev/null +++ b/latest/cases/00745/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.9" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.65" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00745/l3v2/heta-code/output.heta b/latest/cases/00745/l3v2/heta-code/output.heta new file mode 100644 index 000000000..565c2c7ac --- /dev/null +++ b/latest/cases/00745/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.65, }; + diff --git a/latest/cases/00745/l3v2/index.heta b/latest/cases/00745/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00745/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00745/l3v2/json/output.json b/latest/cases/00745/l3v2/json/output.json new file mode 100644 index 000000000..6f93849c1 --- /dev/null +++ b/latest/cases/00745/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.9" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.65" + } +] \ No newline at end of file diff --git a/latest/cases/00745/model-sbml-l2v5.xml b/latest/cases/00745/model-sbml-l2v5.xml new file mode 100644 index 000000000..a306877fd --- /dev/null +++ b/latest/cases/00745/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00745/model-sbml-l3v2.xml b/latest/cases/00745/model-sbml-l3v2.xml new file mode 100644 index 000000000..cf9eac391 --- /dev/null +++ b/latest/cases/00745/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00745/output.heta b/latest/cases/00745/output.heta new file mode 100644 index 000000000..662f980a9 --- /dev/null +++ b/latest/cases/00745/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.9$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S1 [event1]= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.65, }; + diff --git a/latest/cases/00745/synopsis.txt b/latest/cases/00745/synopsis.txt new file mode 100644 index 000000000..0b941ee2a --- /dev/null +++ b/latest/cases/00745/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.9$ |litre |] + diff --git a/latest/cases/00746/l2v5/heta-code/output.heta b/latest/cases/00746/l2v5/heta-code/output.heta new file mode 100644 index 000000000..58cc41c78 --- /dev/null +++ b/latest/cases/00746/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.24; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1; +S1 [event1]= 0.2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.12; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.2; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 2.5; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00746/l2v5/index.heta b/latest/cases/00746/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00746/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00746/l2v5/json/output.json b/latest/cases/00746/l2v5/json/output.json new file mode 100644 index 000000000..4fc80f136 --- /dev/null +++ b/latest/cases/00746/l2v5/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.24" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1", + "event1": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.12" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00746/l3v2/heta-code/output.heta b/latest/cases/00746/l3v2/heta-code/output.heta new file mode 100644 index 000000000..46e62457f --- /dev/null +++ b/latest/cases/00746/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.24; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S1 [event1]= 0.2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00746/l3v2/index.heta b/latest/cases/00746/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00746/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00746/l3v2/json/output.json b/latest/cases/00746/l3v2/json/output.json new file mode 100644 index 000000000..29aff19f9 --- /dev/null +++ b/latest/cases/00746/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.24" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1", + "event1": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.12" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + } +] \ No newline at end of file diff --git a/latest/cases/00746/model-sbml-l2v5.xml b/latest/cases/00746/model-sbml-l2v5.xml new file mode 100644 index 000000000..151c475c2 --- /dev/null +++ b/latest/cases/00746/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/00746/model-sbml-l3v2.xml b/latest/cases/00746/model-sbml-l3v2.xml new file mode 100644 index 000000000..5ef0a4e39 --- /dev/null +++ b/latest/cases/00746/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/00746/output.heta b/latest/cases/00746/output.heta new file mode 100644 index 000000000..209e2ce94 --- /dev/null +++ b/latest/cases/00746/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.24$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.24; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S1 [event1]= 0.2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 2.5; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00746/synopsis.txt b/latest/cases/00746/synopsis.txt new file mode 100644 index 000000000..fc6d27cd6 --- /dev/null +++ b/latest/cases/00746/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.24$ |litre |] + diff --git a/latest/cases/00747/l2v5/heta-code/output.heta b/latest/cases/00747/l2v5/heta-code/output.heta new file mode 100644 index 000000000..91dcbca55 --- /dev/null +++ b/latest/cases/00747/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4; +S1 [event1]= (1 / 5000); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.2e-4; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1e-4; +S4 [event2]= (1 / 10000); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 2500; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (9 / 40000), }; + diff --git a/latest/cases/00747/l2v5/index.heta b/latest/cases/00747/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00747/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00747/l2v5/json/output.json b/latest/cases/00747/l2v5/json/output.json new file mode 100644 index 000000000..25f638823 --- /dev/null +++ b/latest/cases/00747/l2v5/json/output.json @@ -0,0 +1,164 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4", + "event1": "(1 / 5000)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-4", + "event2": "(1 / 10000)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2500" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > (9 / 40000)" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00747/l3v2/heta-code/output.heta b/latest/cases/00747/l3v2/heta-code/output.heta new file mode 100644 index 000000000..718beb455 --- /dev/null +++ b/latest/cases/00747/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4; +S1 [event1]= (1 / 5000); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.2e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4; +S4 [event2]= (1 / 10000); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (9 / 40000), }; + diff --git a/latest/cases/00747/l3v2/index.heta b/latest/cases/00747/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00747/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00747/l3v2/json/output.json b/latest/cases/00747/l3v2/json/output.json new file mode 100644 index 000000000..f8cb1564c --- /dev/null +++ b/latest/cases/00747/l3v2/json/output.json @@ -0,0 +1,136 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4", + "event1": "(1 / 5000)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-4", + "event2": "(1 / 10000)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2500 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > (9 / 40000)" + } +] \ No newline at end of file diff --git a/latest/cases/00747/model-sbml-l2v5.xml b/latest/cases/00747/model-sbml-l2v5.xml new file mode 100644 index 000000000..c291ae8c8 --- /dev/null +++ b/latest/cases/00747/model-sbml-l2v5.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5000 + + + + + + + + + + S3 + 9 40000 + + + + + + + 1 10000 + + + + + + + diff --git a/latest/cases/00747/model-sbml-l3v2.xml b/latest/cases/00747/model-sbml-l3v2.xml new file mode 100644 index 000000000..198a81522 --- /dev/null +++ b/latest/cases/00747/model-sbml-l3v2.xml @@ -0,0 +1,117 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5000 + + + + + + + + + + S3 + 9 40000 + + + + + + + 1 10000 + + + + + + + diff --git a/latest/cases/00747/output.heta b/latest/cases/00747/output.heta new file mode 100644 index 000000000..ecfd0a93f --- /dev/null +++ b/latest/cases/00747/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-4$ |] + | Event2 | $S3 > 2.25 \x 10^-4$ | $-$ | $S4 -> 1 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4; +S1 [event1]= (1 / 5000); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.2e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4; +S4 [event2]= (1 / 10000); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 2500; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; +event2 @DSwitcher 'event2' { trigger: S3 > (9 / 40000), }; + diff --git a/latest/cases/00747/synopsis.txt b/latest/cases/00747/synopsis.txt new file mode 100644 index 000000000..3c65fe4b8 --- /dev/null +++ b/latest/cases/00747/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-4$ |] + | Event2 | $S3 > 2.25 \x 10^-4$ | $-$ | $S4 -> 1 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + diff --git a/latest/cases/00748/l2v5/heta-code/output.heta b/latest/cases/00748/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ce8b4adf5 --- /dev/null +++ b/latest/cases/00748/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.25; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01; +S1 [event1]= (1 / 50); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.012; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.02; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.01; +S4 [event1]= (1 / 200); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 25; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00748/l2v5/index.heta b/latest/cases/00748/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00748/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00748/l2v5/json/output.json b/latest/cases/00748/l2v5/json/output.json new file mode 100644 index 000000000..43ec3b88e --- /dev/null +++ b/latest/cases/00748/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.25" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01", + "event1": "(1 / 50)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.012" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.01", + "event1": "(1 / 200)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00748/l3v2/heta-code/output.heta b/latest/cases/00748/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d2b1bf964 --- /dev/null +++ b/latest/cases/00748/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.25; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S1 [event1]= (1 / 50); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.01; +S4 [event1]= (1 / 200); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00748/l3v2/index.heta b/latest/cases/00748/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00748/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00748/l3v2/json/output.json b/latest/cases/00748/l3v2/json/output.json new file mode 100644 index 000000000..364981c05 --- /dev/null +++ b/latest/cases/00748/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.25" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01", + "event1": "(1 / 50)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.012" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.01", + "event1": "(1 / 200)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S4 > S2" + } +] \ No newline at end of file diff --git a/latest/cases/00748/model-sbml-l2v5.xml b/latest/cases/00748/model-sbml-l2v5.xml new file mode 100644 index 000000000..4fe6d0e50 --- /dev/null +++ b/latest/cases/00748/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 50 + + + + + 1 200 + + + + + + + diff --git a/latest/cases/00748/model-sbml-l3v2.xml b/latest/cases/00748/model-sbml-l3v2.xml new file mode 100644 index 000000000..e1939e7a2 --- /dev/null +++ b/latest/cases/00748/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 50 + + + + + 1 200 + + + + + + + diff --git a/latest/cases/00748/output.heta b/latest/cases/00748/output.heta new file mode 100644 index 000000000..c00743ae0 --- /dev/null +++ b/latest/cases/00748/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-2$ | + | | | | $S4 -> 0.5 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.25$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.25; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S1 [event1]= (1 / 50); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.01; +S4 [event1]= (1 / 200); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + +event1 @DSwitcher 'event1' { trigger: S4 > S2, }; + diff --git a/latest/cases/00748/synopsis.txt b/latest/cases/00748/synopsis.txt new file mode 100644 index 000000000..0448aa298 --- /dev/null +++ b/latest/cases/00748/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns a value to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-2$ | + | | | | $S4 -> 0.5 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.25$ |litre |] + diff --git a/latest/cases/00749/l2v5/heta-code/output.heta b/latest/cases/00749/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e3eaf0509 --- /dev/null +++ b/latest/cases/00749/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.79; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.375; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00749/l2v5/index.heta b/latest/cases/00749/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00749/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00749/l2v5/json/output.json b/latest/cases/00749/l2v5/json/output.json new file mode 100644 index 000000000..af1f794b2 --- /dev/null +++ b/latest/cases/00749/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.79" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.375", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00749/l3v2/heta-code/output.heta b/latest/cases/00749/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ed9be8f1e --- /dev/null +++ b/latest/cases/00749/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.79; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00749/l3v2/index.heta b/latest/cases/00749/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00749/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00749/l3v2/json/output.json b/latest/cases/00749/l3v2/json/output.json new file mode 100644 index 000000000..668be8fb9 --- /dev/null +++ b/latest/cases/00749/l3v2/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.79" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.375", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.25" + } +] \ No newline at end of file diff --git a/latest/cases/00749/model-sbml-l2v5.xml b/latest/cases/00749/model-sbml-l2v5.xml new file mode 100644 index 000000000..c4b3dc990 --- /dev/null +++ b/latest/cases/00749/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00749/model-sbml-l3v2.xml b/latest/cases/00749/model-sbml-l3v2.xml new file mode 100644 index 000000000..59556ff75 --- /dev/null +++ b/latest/cases/00749/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00749/output.heta b/latest/cases/00749/output.heta new file mode 100644 index 000000000..7e2ee9ce7 --- /dev/null +++ b/latest/cases/00749/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0.375$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 0.79$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.79; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.25, }; + diff --git a/latest/cases/00749/synopsis.txt b/latest/cases/00749/synopsis.txt new file mode 100644 index 000000000..720734719 --- /dev/null +++ b/latest/cases/00749/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0.375$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 0.79$ |litre |] + diff --git a/latest/cases/00750/l2v5/heta-code/output.heta b/latest/cases/00750/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d2d295ac5 --- /dev/null +++ b/latest/cases/00750/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 7.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5; +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 3.75; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00750/l2v5/index.heta b/latest/cases/00750/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00750/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00750/l2v5/json/output.json b/latest/cases/00750/l2v5/json/output.json new file mode 100644 index 000000000..7054ac260 --- /dev/null +++ b/latest/cases/00750/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "7.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "3.75", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00750/l3v2/heta-code/output.heta b/latest/cases/00750/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b4fea3755 --- /dev/null +++ b/latest/cases/00750/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 7.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00750/l3v2/index.heta b/latest/cases/00750/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00750/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00750/l3v2/json/output.json b/latest/cases/00750/l3v2/json/output.json new file mode 100644 index 000000000..ad840aad2 --- /dev/null +++ b/latest/cases/00750/l3v2/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "7.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "3.75", + "ode_": "k1 * S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.1" + } +] \ No newline at end of file diff --git a/latest/cases/00750/model-sbml-l2v5.xml b/latest/cases/00750/model-sbml-l2v5.xml new file mode 100644 index 000000000..e98a08cf3 --- /dev/null +++ b/latest/cases/00750/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00750/model-sbml-l3v2.xml b/latest/cases/00750/model-sbml-l3v2.xml new file mode 100644 index 000000000..0d09b3e3e --- /dev/null +++ b/latest/cases/00750/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00750/output.heta b/latest/cases/00750/output.heta new file mode 100644 index 000000000..762622cdc --- /dev/null +++ b/latest/cases/00750/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 3.75$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 7.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.1, }; + diff --git a/latest/cases/00750/synopsis.txt b/latest/cases/00750/synopsis.txt new file mode 100644 index 000000000..23e2a1cca --- /dev/null +++ b/latest/cases/00750/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 3.75$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 2.5$ |litre |] + diff --git a/latest/cases/00751/l2v5/heta-code/output.heta b/latest/cases/00751/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f7672bbf4 --- /dev/null +++ b/latest/cases/00751/l2v5/heta-code/output.heta @@ -0,0 +1,32 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 [event1]= add(k3, k4); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := k2 * add(S1, S3); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.8; +k4 @Record 'k4' { } .= 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00751/l2v5/index.heta b/latest/cases/00751/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00751/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00751/l2v5/json/output.json b/latest/cases/00751/l2v5/json/output.json new file mode 100644 index 000000000..57a572bf9 --- /dev/null +++ b/latest/cases/00751/l2v5/json/output.json @@ -0,0 +1,190 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.8" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * add(S1, S3)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00751/l3v2/heta-code/output.heta b/latest/cases/00751/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8364b54ba --- /dev/null +++ b/latest/cases/00751/l3v2/heta-code/output.heta @@ -0,0 +1,27 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event1]= add(k3, k4); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := k2 * add(S1, S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00751/l3v2/index.heta b/latest/cases/00751/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00751/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00751/l3v2/json/output.json b/latest/cases/00751/l3v2/json/output.json new file mode 100644 index 000000000..0e6b59c59 --- /dev/null +++ b/latest/cases/00751/l3v2/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.8 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.2 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * add(S1, S3)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00751/model-sbml-l2v5.xml b/latest/cases/00751/model-sbml-l2v5.xml new file mode 100644 index 000000000..56b8a93bd --- /dev/null +++ b/latest/cases/00751/model-sbml-l2v5.xml @@ -0,0 +1,119 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + add + S1 + S3 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00751/model-sbml-l3v2.xml b/latest/cases/00751/model-sbml-l3v2.xml new file mode 100644 index 000000000..6493ba0c3 --- /dev/null +++ b/latest/cases/00751/model-sbml-l3v2.xml @@ -0,0 +1,136 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + add + S1 + S3 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00751/output.heta b/latest/cases/00751/output.heta new file mode 100644 index 000000000..de5c9e6b3 --- /dev/null +++ b/latest/cases/00751/output.heta @@ -0,0 +1,80 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule that determines the rate at which species S4 +is changing: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $k2 * add(S1, S3)$ |] + +The model contains one event that assigns a value to species S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +Both the rateRule and the eventAssignment uses the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event1]= add(k3, k4); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := k2 * add(S1, S3); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00751/synopsis.txt b/latest/cases/00751/synopsis.txt new file mode 100644 index 000000000..89ddf3467 --- /dev/null +++ b/latest/cases/00751/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule that determines the rate at which species S4 +is changing: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $k2 * add(S1, S3)$ |] + +The model contains one event that assigns a value to species S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +Both the rateRule and the eventAssignment uses the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00752/l2v5/heta-code/output.heta b/latest/cases/00752/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6e03ae5e1 --- /dev/null +++ b/latest/cases/00752/l2v5/heta-code/output.heta @@ -0,0 +1,35 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; +divide #defineFunction { arguments: [x, y], math: x * pow(y, (-1)), }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 [event2]= divide(k3, k4); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := k2 * add(S1, S2); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.5; +k4 @Record 'k4' { } .= 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00752/l2v5/index.heta b/latest/cases/00752/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00752/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00752/l2v5/json/output.json b/latest/cases/00752/l2v5/json/output.json new file mode 100644 index 000000000..b8a39271d --- /dev/null +++ b/latest/cases/00752/l2v5/json/output.json @@ -0,0 +1,206 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C", + "event2": "divide(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * add(S1, S2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.2" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + }, + { + "id": "divide", + "arguments": [ + "x", + "y" + ], + "math": "x * pow(y, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00752/l3v2/heta-code/output.heta b/latest/cases/00752/l3v2/heta-code/output.heta new file mode 100644 index 000000000..06e4efbab --- /dev/null +++ b/latest/cases/00752/l3v2/heta-code/output.heta @@ -0,0 +1,30 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; +divide #defineFunction { arguments: [x, y], math: x * pow(y, (-1)), }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event2]= divide(k3, k4); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := k2 * add(S1, S2); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.5; +k4 @Const 'k4' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00752/l3v2/index.heta b/latest/cases/00752/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00752/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00752/l3v2/json/output.json b/latest/cases/00752/l3v2/json/output.json new file mode 100644 index 000000000..347ada621 --- /dev/null +++ b/latest/cases/00752/l3v2/json/output.json @@ -0,0 +1,174 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C", + "event2": "divide(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.5 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.5 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k2 * add(S1, S2)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.2" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + }, + { + "id": "divide", + "arguments": [ + "x", + "y" + ], + "math": "x * pow(y, (-1))", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00752/model-sbml-l2v5.xml b/latest/cases/00752/model-sbml-l2v5.xml new file mode 100644 index 000000000..fb442eee3 --- /dev/null +++ b/latest/cases/00752/model-sbml-l2v5.xml @@ -0,0 +1,162 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + add + S1 + S2 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + add + k3 + k4 + + + + + + + + + + + S3 + 1.2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00752/model-sbml-l3v2.xml b/latest/cases/00752/model-sbml-l3v2.xml new file mode 100644 index 000000000..1abbd31de --- /dev/null +++ b/latest/cases/00752/model-sbml-l3v2.xml @@ -0,0 +1,179 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + add + S1 + S2 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + add + k3 + k4 + + + + + + + + + + + S3 + 1.2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00752/output.heta b/latest/cases/00752/output.heta new file mode 100644 index 000000000..8c12fdfe7 --- /dev/null +++ b/latest/cases/00752/output.heta @@ -0,0 +1,85 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule that determines the rate at which species S4 +is changing: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $k2 * add(S1, S2)$ |] + +The model contains two events that assign values to species S2 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = add(k3, k4)$ | + | Event2 | $S3 > 1.2$ | $-$ | $S4 = 1 * divide(k3, k4)$ |] + +The rateRule and both eventAssignments use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; +divide #defineFunction { arguments: [x, y], math: x * pow(y, (-1)), }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event2]= divide(k3, k4); + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := k2 * add(S1, S2); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.5; +k4 @Const 'k4' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.2, }; + diff --git a/latest/cases/00752/synopsis.txt b/latest/cases/00752/synopsis.txt new file mode 100644 index 000000000..d33afb936 --- /dev/null +++ b/latest/cases/00752/synopsis.txt @@ -0,0 +1,53 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule that determines the rate at which species S4 +is changing: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $k2 * add(S1, S2)$ |] + +The model contains two events that assign values to species S2 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = add(k3, k4)$ | + | Event2 | $S3 > 1.2$ | $-$ | $S4 = 1 * divide(k3, k4)$ |] + +The rateRule and both eventAssignments use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00753/l2v5/build.log b/latest/cases/00753/l2v5/build.log new file mode 100644 index 000000000..9a3e20f11 --- /dev/null +++ b/latest/cases/00753/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00753/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00753/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00753/model-sbml-l2v5.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 97 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00753/l2v5/index.heta b/latest/cases/00753/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00753/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00753/l3v2/build.log b/latest/cases/00753/l3v2/build.log new file mode 100644 index 000000000..059c9f5ed --- /dev/null +++ b/latest/cases/00753/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00753/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00753/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00753/model-sbml-l3v2.xml"... +[error] Function math "lessthan" should be a numeric expression. +[error] DSwitcher trigger "event1" should be a boolean expression. +[info] Setting references in elements, total length 92 +[error] No required "trigger" property for "event1" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00753/l3v2/index.heta b/latest/cases/00753/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00753/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00753/model-sbml-l2v5.xml b/latest/cases/00753/model-sbml-l2v5.xml new file mode 100644 index 000000000..9849e6675 --- /dev/null +++ b/latest/cases/00753/model-sbml-l2v5.xml @@ -0,0 +1,141 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + add + S1 + S2 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.6 + + + + + + + 1 + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00753/model-sbml-l3v2.xml b/latest/cases/00753/model-sbml-l3v2.xml new file mode 100644 index 000000000..cdb90ea72 --- /dev/null +++ b/latest/cases/00753/model-sbml-l3v2.xml @@ -0,0 +1,158 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + add + S1 + S2 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.6 + + + + + + + 1 + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00753/synopsis.txt b/latest/cases/00753/synopsis.txt new file mode 100644 index 000000000..ebedf13dd --- /dev/null +++ b/latest/cases/00753/synopsis.txt @@ -0,0 +1,53 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule that determines the rate at which species S4 +is changing: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $k2 * add(S1, S2)$ |] + +The model contains one event that assign values to species S2 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.6)$ | $-$ | $S2 = 1$ | + | | | | $S4 = add(k3, k4)$ |] + +Both the event trigger and assignment and the rateRule use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ | +| lessthan | x, y | $x < y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00754/l2v5/heta-code/output.heta b/latest/cases/00754/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1550ad339 --- /dev/null +++ b/latest/cases/00754/l2v5/heta-code/output.heta @@ -0,0 +1,30 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= add(p1, p1); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.8; +k4 @Record 'k4' { } .= 0.2; +p1 @Record 'p1' { } .= 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00754/l2v5/index.heta b/latest/cases/00754/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00754/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00754/l2v5/json/output.json b/latest/cases/00754/l2v5/json/output.json new file mode 100644 index 000000000..60ad72f3b --- /dev/null +++ b/latest/cases/00754/l2v5/json/output.json @@ -0,0 +1,172 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "add(p1, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.8" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00754/l3v2/heta-code/output.heta b/latest/cases/00754/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0fa5bcf71 --- /dev/null +++ b/latest/cases/00754/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= add(p1, p1); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00754/l3v2/index.heta b/latest/cases/00754/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00754/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00754/l3v2/json/output.json b/latest/cases/00754/l3v2/json/output.json new file mode 100644 index 000000000..449568d69 --- /dev/null +++ b/latest/cases/00754/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "add(p1, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.8 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.2 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00754/model-sbml-l2v5.xml b/latest/cases/00754/model-sbml-l2v5.xml new file mode 100644 index 000000000..20655eee5 --- /dev/null +++ b/latest/cases/00754/model-sbml-l2v5.xml @@ -0,0 +1,115 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + add + p1 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00754/model-sbml-l3v2.xml b/latest/cases/00754/model-sbml-l3v2.xml new file mode 100644 index 000000000..d0984c935 --- /dev/null +++ b/latest/cases/00754/model-sbml-l3v2.xml @@ -0,0 +1,132 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + add + p1 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00754/output.heta b/latest/cases/00754/output.heta new file mode 100644 index 000000000..3d955dff7 --- /dev/null +++ b/latest/cases/00754/output.heta @@ -0,0 +1,81 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and five parameters called k1, k2, k3, k4 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $add(p1, p1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +Both the eventAssignment and the initialAssignment use the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= add(p1, p1); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00754/synopsis.txt b/latest/cases/00754/synopsis.txt new file mode 100644 index 000000000..2ebeb126e --- /dev/null +++ b/latest/cases/00754/synopsis.txt @@ -0,0 +1,54 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and five parameters called k1, k2, k3, k4 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $add(p1, p1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +Both the eventAssignment and the initialAssignment use the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00755/l2v5/heta-code/output.heta b/latest/cases/00755/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1550ad339 --- /dev/null +++ b/latest/cases/00755/l2v5/heta-code/output.heta @@ -0,0 +1,30 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= add(p1, p1); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.8; +k4 @Record 'k4' { } .= 0.2; +p1 @Record 'p1' { } .= 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00755/l2v5/index.heta b/latest/cases/00755/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00755/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00755/l2v5/json/output.json b/latest/cases/00755/l2v5/json/output.json new file mode 100644 index 000000000..60ad72f3b --- /dev/null +++ b/latest/cases/00755/l2v5/json/output.json @@ -0,0 +1,172 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "add(p1, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.8" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00755/l3v2/heta-code/output.heta b/latest/cases/00755/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0fa5bcf71 --- /dev/null +++ b/latest/cases/00755/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= add(p1, p1); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00755/l3v2/index.heta b/latest/cases/00755/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00755/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00755/l3v2/json/output.json b/latest/cases/00755/l3v2/json/output.json new file mode 100644 index 000000000..449568d69 --- /dev/null +++ b/latest/cases/00755/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "add(p1, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.8 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.2 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00755/model-sbml-l2v5.xml b/latest/cases/00755/model-sbml-l2v5.xml new file mode 100644 index 000000000..49b6d7edc --- /dev/null +++ b/latest/cases/00755/model-sbml-l2v5.xml @@ -0,0 +1,115 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + add + p1 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00755/model-sbml-l3v2.xml b/latest/cases/00755/model-sbml-l3v2.xml new file mode 100644 index 000000000..803384cdd --- /dev/null +++ b/latest/cases/00755/model-sbml-l3v2.xml @@ -0,0 +1,132 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + add + p1 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00755/output.heta b/latest/cases/00755/output.heta new file mode 100644 index 000000000..d18ced408 --- /dev/null +++ b/latest/cases/00755/output.heta @@ -0,0 +1,81 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and five parameters called k1, k2, k3, k4 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $add(p1, p1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +Both the eventAssignment and the initialAssignment use the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$5.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= add(p1, p1); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00755/synopsis.txt b/latest/cases/00755/synopsis.txt new file mode 100644 index 000000000..a77008b24 --- /dev/null +++ b/latest/cases/00755/synopsis.txt @@ -0,0 +1,54 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and five parameters called k1, k2, k3, k4 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $add(p1, p1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +Both the eventAssignment and the initialAssignment use the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$5.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00756/l2v5/heta-code/output.heta b/latest/cases/00756/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1550ad339 --- /dev/null +++ b/latest/cases/00756/l2v5/heta-code/output.heta @@ -0,0 +1,30 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= add(p1, p1); +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 0.8; +k4 @Record 'k4' { } .= 0.2; +p1 @Record 'p1' { } .= 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00756/l2v5/index.heta b/latest/cases/00756/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00756/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00756/l2v5/json/output.json b/latest/cases/00756/l2v5/json/output.json new file mode 100644 index 000000000..60ad72f3b --- /dev/null +++ b/latest/cases/00756/l2v5/json/output.json @@ -0,0 +1,172 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "add(p1, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.8" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00756/l3v2/heta-code/output.heta b/latest/cases/00756/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0fa5bcf71 --- /dev/null +++ b/latest/cases/00756/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= add(p1, p1); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00756/l3v2/index.heta b/latest/cases/00756/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00756/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00756/l3v2/json/output.json b/latest/cases/00756/l3v2/json/output.json new file mode 100644 index 000000000..449568d69 --- /dev/null +++ b/latest/cases/00756/l3v2/json/output.json @@ -0,0 +1,138 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "add(p1, p1)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "add(k3, k4)" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.8 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.2 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "add", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00756/model-sbml-l2v5.xml b/latest/cases/00756/model-sbml-l2v5.xml new file mode 100644 index 000000000..15d5703b7 --- /dev/null +++ b/latest/cases/00756/model-sbml-l2v5.xml @@ -0,0 +1,115 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + add + p1 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00756/model-sbml-l3v2.xml b/latest/cases/00756/model-sbml-l3v2.xml new file mode 100644 index 000000000..6617c716c --- /dev/null +++ b/latest/cases/00756/model-sbml-l3v2.xml @@ -0,0 +1,132 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + add + p1 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + add + k3 + k4 + + + + + + + + diff --git a/latest/cases/00756/output.heta b/latest/cases/00756/output.heta new file mode 100644 index 000000000..f6b7e906c --- /dev/null +++ b/latest/cases/00756/output.heta @@ -0,0 +1,81 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and five parameters called k1, k2, k3, k4 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $add(p1, p1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value has not been declared for species S1 +and must be calculated using the InitialAssignment. + +Both the eventAssignment and the initialAssignment use the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +add #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= add(p1, p1); +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= add(k3, k4); +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 0.8; +k4 @Const 'k4' { } = 0.2; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00756/synopsis.txt b/latest/cases/00756/synopsis.txt new file mode 100644 index 000000000..59222e86f --- /dev/null +++ b/latest/cases/00756/synopsis.txt @@ -0,0 +1,54 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and five parameters called k1, k2, k3, k4 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $add(p1, p1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value has not been declared for species S1 +and must be calculated using the InitialAssignment. + +Both the eventAssignment and the initialAssignment use the functionDefinition defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.8$ |mole litre^-1^ | +|Value of parameter k4 |$0.2$ |mole litre^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00757/l2v5/build.log b/latest/cases/00757/l2v5/build.log new file mode 100644 index 000000000..3b6d3728c --- /dev/null +++ b/latest/cases/00757/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00757/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00757/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00757/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00757/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00757/l2v5/index.heta b/latest/cases/00757/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00757/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00757/l3v2/build.log b/latest/cases/00757/l3v2/build.log new file mode 100644 index 000000000..9d508585f --- /dev/null +++ b/latest/cases/00757/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00757/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00757/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00757/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00757/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00757/l3v2/index.heta b/latest/cases/00757/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00757/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00757/model-sbml-l2v5.xml b/latest/cases/00757/model-sbml-l2v5.xml new file mode 100644 index 000000000..85bc067bd --- /dev/null +++ b/latest/cases/00757/model-sbml-l2v5.xml @@ -0,0 +1,147 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.77 + + + + + + + 1.2 + + + + + + + + + + S3 + 1.2 + + + + + + 1.3 + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00757/model-sbml-l3v2.xml b/latest/cases/00757/model-sbml-l3v2.xml new file mode 100644 index 000000000..382a92a86 --- /dev/null +++ b/latest/cases/00757/model-sbml-l3v2.xml @@ -0,0 +1,164 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.77 + + + + + + + 1.2 + + + + + + + + + + S3 + 1.2 + + + + + + 1.3 + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00757/synopsis.txt b/latest/cases/00757/synopsis.txt new file mode 100644 index 000000000..362a1e9bf --- /dev/null +++ b/latest/cases/00757/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, EventWithDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.77)$ | $-$ | $S2 = 1.2$ | + | Event2 | $S3 > 1.2$ | $1.3$ | $S1 = 1 * divide(k3, k4)$ |] + +Both events use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | lessthan | x, y | $x < y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00758/l2v5/build.log b/latest/cases/00758/l2v5/build.log new file mode 100644 index 000000000..d622164f6 --- /dev/null +++ b/latest/cases/00758/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00758/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00758/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00758/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00758/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00758/l2v5/index.heta b/latest/cases/00758/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00758/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00758/l3v2/build.log b/latest/cases/00758/l3v2/build.log new file mode 100644 index 000000000..c4f035f88 --- /dev/null +++ b/latest/cases/00758/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00758/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00758/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00758/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00758/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00758/l3v2/index.heta b/latest/cases/00758/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00758/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00758/model-sbml-l2v5.xml b/latest/cases/00758/model-sbml-l2v5.xml new file mode 100644 index 000000000..e9c1ef652 --- /dev/null +++ b/latest/cases/00758/model-sbml-l2v5.xml @@ -0,0 +1,151 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.77 + + + + + + + 1.2 + + + + + + + + + + S3 + 1.2 + + + + + + + divide + 0.325 + k2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00758/model-sbml-l3v2.xml b/latest/cases/00758/model-sbml-l3v2.xml new file mode 100644 index 000000000..08949ec5a --- /dev/null +++ b/latest/cases/00758/model-sbml-l3v2.xml @@ -0,0 +1,168 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + lessthan + S1 + 0.77 + + + + + + + 1.2 + + + + + + + + + + S3 + 1.2 + + + + + + + divide + 0.325 + k2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00758/synopsis.txt b/latest/cases/00758/synopsis.txt new file mode 100644 index 000000000..b5cd78ac9 --- /dev/null +++ b/latest/cases/00758/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, EventWithDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $lessthan(S1, 0.77)$ | $-$ | $S2 = 1.2$ | + | Event2 | $S3 > 1.2$ | $divide(0.325, k2)$ | $S1 = 1 * divide(k3, k4)$ |] + +Both events use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | lessthan | x, y | $x < y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00759/l2v5/build.log b/latest/cases/00759/l2v5/build.log new file mode 100644 index 000000000..f14add293 --- /dev/null +++ b/latest/cases/00759/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00759/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00759/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00759/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00759/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00759/l2v5/index.heta b/latest/cases/00759/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00759/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00759/l3v2/build.log b/latest/cases/00759/l3v2/build.log new file mode 100644 index 000000000..06ee7e078 --- /dev/null +++ b/latest/cases/00759/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00759/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00759/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00759/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00759/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00759/l3v2/index.heta b/latest/cases/00759/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00759/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00759/model-sbml-l2v5.xml b/latest/cases/00759/model-sbml-l2v5.xml new file mode 100644 index 000000000..2748370ee --- /dev/null +++ b/latest/cases/00759/model-sbml-l2v5.xml @@ -0,0 +1,155 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + add + k3 + k4 + + + + + + + + + + + S3 + 1.2 + + + + + + + divide + 1 + k2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00759/model-sbml-l3v2.xml b/latest/cases/00759/model-sbml-l3v2.xml new file mode 100644 index 000000000..d20bfcdf5 --- /dev/null +++ b/latest/cases/00759/model-sbml-l3v2.xml @@ -0,0 +1,172 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + y + -1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + add + k3 + k4 + + + + + + + + + + + S3 + 1.2 + + + + + + + divide + 1 + k2 + + + + + + + + divide + k3 + k4 + + + + + + + + diff --git a/latest/cases/00759/synopsis.txt b/latest/cases/00759/synopsis.txt new file mode 100644 index 000000000..f2277124e --- /dev/null +++ b/latest/cases/00759/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assigns value to a species using a function. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, EventWithDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = add(k3, k4)$ | + | Event2 | $S3 > 1.2$ | $divide(1, k2)$ | $S1 = 1 * divide(k3, k4)$ |] + +Both eventAssignments use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | add | x, y | $x + y$ | + | divide | x, y | $x / y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$0.5$ |mole litre^-1^ | +|Value of parameter k4 |$0.5$ |mole litre^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00760/l2v5/build.log b/latest/cases/00760/l2v5/build.log new file mode 100644 index 000000000..92ce95e34 --- /dev/null +++ b/latest/cases/00760/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00760/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00760/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00760/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00760/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00760/l2v5/index.heta b/latest/cases/00760/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00760/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00760/l3v2/build.log b/latest/cases/00760/l3v2/build.log new file mode 100644 index 000000000..7bb89fbed --- /dev/null +++ b/latest/cases/00760/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00760/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00760/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00760/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00760/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00760/l3v2/index.heta b/latest/cases/00760/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00760/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00760/model-sbml-l2v5.xml b/latest/cases/00760/model-sbml-l2v5.xml new file mode 100644 index 000000000..97b3b7c2c --- /dev/null +++ b/latest/cases/00760/model-sbml-l2v5.xml @@ -0,0 +1,132 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + + add + X0 + X1 + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + greaterthan + X1 + 2 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00760/model-sbml-l3v2.xml b/latest/cases/00760/model-sbml-l3v2.xml new file mode 100644 index 000000000..a923a0d95 --- /dev/null +++ b/latest/cases/00760/model-sbml-l3v2.xml @@ -0,0 +1,149 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + S1 + + T + + add + X0 + X1 + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + greaterthan + X1 + 2 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00760/synopsis.txt b/latest/cases/00760/synopsis.txt new file mode 100644 index 000000000..b589cd23f --- /dev/null +++ b/latest/cases/00760/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventNoDelay, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $add(X0, X1) + T - S1$ |] + +The model contains one event that assigns value to species X1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $greaterthan(X1, 2)$ | $-$ | $X1 = 1$ |] + +Both the rule and the event use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | greaterthan | x, y | $x > y$ | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1.25$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Initial amount of S1 |$3.75$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00761/l2v5/build.log b/latest/cases/00761/l2v5/build.log new file mode 100644 index 000000000..0a2441855 --- /dev/null +++ b/latest/cases/00761/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00761/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00761/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00761/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00761/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00761/l2v5/index.heta b/latest/cases/00761/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00761/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00761/l3v2/build.log b/latest/cases/00761/l3v2/build.log new file mode 100644 index 000000000..44bb39429 --- /dev/null +++ b/latest/cases/00761/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00761/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00761/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00761/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00761/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00761/l3v2/index.heta b/latest/cases/00761/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00761/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00761/model-sbml-l2v5.xml b/latest/cases/00761/model-sbml-l2v5.xml new file mode 100644 index 000000000..3342fa9cf --- /dev/null +++ b/latest/cases/00761/model-sbml-l2v5.xml @@ -0,0 +1,139 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + + add + 1 + k3 + + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + greaterthan + X1 + 0.5 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00761/model-sbml-l3v2.xml b/latest/cases/00761/model-sbml-l3v2.xml new file mode 100644 index 000000000..228b43df6 --- /dev/null +++ b/latest/cases/00761/model-sbml-l3v2.xml @@ -0,0 +1,156 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + + add + 1 + k3 + + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + greaterthan + X1 + 0.5 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00761/synopsis.txt b/latest/cases/00761/synopsis.txt new file mode 100644 index 000000000..5cfce2ab6 --- /dev/null +++ b/latest/cases/00761/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventNoDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $add(1, k3) * S1 - T$ |] + +The model contains one event that assigns value to species X1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $greaterthan(X1, 0.5)$ | $-$ | $X1 = 1$ |] + +Both the rule and the event use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | greaterthan | x, y | $x > y$ | + | add | x, y | $x + y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00762/l2v5/build.log b/latest/cases/00762/l2v5/build.log new file mode 100644 index 000000000..a41bae790 --- /dev/null +++ b/latest/cases/00762/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00762/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00762/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00762/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00762/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00762/l2v5/index.heta b/latest/cases/00762/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00762/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00762/l3v2/build.log b/latest/cases/00762/l3v2/build.log new file mode 100644 index 000000000..c9f626aff --- /dev/null +++ b/latest/cases/00762/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00762/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00762/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00762/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00762/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00762/l3v2/index.heta b/latest/cases/00762/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00762/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00762/model-sbml-l2v5.xml b/latest/cases/00762/model-sbml-l2v5.xml new file mode 100644 index 000000000..ebdda4613 --- /dev/null +++ b/latest/cases/00762/model-sbml-l2v5.xml @@ -0,0 +1,154 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + subtract + k2 + 0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + greaterthan + S4 + S3 + + + + + + + + + 2 + S4 + + + + + + + + diff --git a/latest/cases/00762/model-sbml-l3v2.xml b/latest/cases/00762/model-sbml-l3v2.xml new file mode 100644 index 000000000..7c92cd15e --- /dev/null +++ b/latest/cases/00762/model-sbml-l3v2.xml @@ -0,0 +1,171 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subtract + k2 + 0.9 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + + + + + greaterthan + S4 + S3 + + + + + + + + + 2 + S4 + + + + + + + + diff --git a/latest/cases/00762/synopsis.txt b/latest/cases/00762/synopsis.txt new file mode 100644 index 000000000..08f297739 --- /dev/null +++ b/latest/cases/00762/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Three reactions with four species in one compartment, +with an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventNoDelay, FunctionDefinition +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ | +| S3 -> S1 + S4 | $k3 * S3 * C$ |] + +The model contains one rule which must be used to determine the value of +parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $subtract(k2, 0.9)$ |] + +The model contains one event that assigns value to species S4 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $greaterthan(S4, S3)$ | $-$ | $S4 = 2 * S4$ |] + +Both the rule and the event use functionDefinitions defined as: +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | greaterthan | x, y | $x > y$ | + | subtract | x, y | $x - y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter k3 |$0.7$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00763/l2v5/build.log b/latest/cases/00763/l2v5/build.log new file mode 100644 index 000000000..698c4a366 --- /dev/null +++ b/latest/cases/00763/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00763/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00763/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00763/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00763/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00763/l2v5/index.heta b/latest/cases/00763/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00763/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00763/l3v2/build.log b/latest/cases/00763/l3v2/build.log new file mode 100644 index 000000000..b8af06147 --- /dev/null +++ b/latest/cases/00763/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00763/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00763/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00763/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00763/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00763/l3v2/index.heta b/latest/cases/00763/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00763/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00763/model-sbml-l2v5.xml b/latest/cases/00763/model-sbml-l2v5.xml new file mode 100644 index 000000000..ca2e40519 --- /dev/null +++ b/latest/cases/00763/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 5.7 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00763/model-sbml-l3v2.xml b/latest/cases/00763/model-sbml-l3v2.xml new file mode 100644 index 000000000..c5971e60a --- /dev/null +++ b/latest/cases/00763/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 5.7 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00763/synopsis.txt b/latest/cases/00763/synopsis.txt new file mode 100644 index 000000000..a84afe96c --- /dev/null +++ b/latest/cases/00763/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $5.7$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + diff --git a/latest/cases/00764/l2v5/build.log b/latest/cases/00764/l2v5/build.log new file mode 100644 index 000000000..5b380ab19 --- /dev/null +++ b/latest/cases/00764/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00764/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00764/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00764/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00764/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00764/l2v5/index.heta b/latest/cases/00764/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00764/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00764/l3v2/build.log b/latest/cases/00764/l3v2/build.log new file mode 100644 index 000000000..6babbc463 --- /dev/null +++ b/latest/cases/00764/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00764/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00764/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00764/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00764/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00764/l3v2/index.heta b/latest/cases/00764/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00764/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00764/model-sbml-l2v5.xml b/latest/cases/00764/model-sbml-l2v5.xml new file mode 100644 index 000000000..8a0ba1483 --- /dev/null +++ b/latest/cases/00764/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.75 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 1.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00764/model-sbml-l3v2.xml b/latest/cases/00764/model-sbml-l3v2.xml new file mode 100644 index 000000000..4d1b6ca33 --- /dev/null +++ b/latest/cases/00764/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.75 + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 1.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00764/synopsis.txt b/latest/cases/00764/synopsis.txt new file mode 100644 index 000000000..e74e98b62 --- /dev/null +++ b/latest/cases/00764/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Concentration, NonUnityCompartment, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $0.75$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $1.5$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1.43$ |litre |] + diff --git a/latest/cases/00765/l2v5/build.log b/latest/cases/00765/l2v5/build.log new file mode 100644 index 000000000..77bde0379 --- /dev/null +++ b/latest/cases/00765/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00765/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00765/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00765/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00765/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00765/l2v5/index.heta b/latest/cases/00765/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00765/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00765/l3v2/build.log b/latest/cases/00765/l3v2/build.log new file mode 100644 index 000000000..8ef0e1099 --- /dev/null +++ b/latest/cases/00765/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00765/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00765/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00765/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00765/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00765/l3v2/index.heta b/latest/cases/00765/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00765/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00765/model-sbml-l2v5.xml b/latest/cases/00765/model-sbml-l2v5.xml new file mode 100644 index 000000000..6d3572b6b --- /dev/null +++ b/latest/cases/00765/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + 1 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00765/model-sbml-l3v2.xml b/latest/cases/00765/model-sbml-l3v2.xml new file mode 100644 index 000000000..2ee00df41 --- /dev/null +++ b/latest/cases/00765/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.65 + + + + + + 1 + + + + + + 1.5 + + + + + 1 + + + + + + + diff --git a/latest/cases/00765/synopsis.txt b/latest/cases/00765/synopsis.txt new file mode 100644 index 000000000..c0aacd808 --- /dev/null +++ b/latest/cases/00765/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.65$ | $1$ | $S2 = 1.5$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$0.9$ |litre |] + diff --git a/latest/cases/00766/l2v5/build.log b/latest/cases/00766/l2v5/build.log new file mode 100644 index 000000000..733cdf9e8 --- /dev/null +++ b/latest/cases/00766/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00766/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00766/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00766/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00766/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00766/l2v5/index.heta b/latest/cases/00766/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00766/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00766/l3v2/build.log b/latest/cases/00766/l3v2/build.log new file mode 100644 index 000000000..463f9959a --- /dev/null +++ b/latest/cases/00766/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00766/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00766/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00766/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00766/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00766/l3v2/index.heta b/latest/cases/00766/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00766/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00766/model-sbml-l2v5.xml b/latest/cases/00766/model-sbml-l2v5.xml new file mode 100644 index 000000000..5b0f139a9 --- /dev/null +++ b/latest/cases/00766/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1.2 + + + + + + 1 500 + + + + + + + diff --git a/latest/cases/00766/model-sbml-l3v2.xml b/latest/cases/00766/model-sbml-l3v2.xml new file mode 100644 index 000000000..8d02e57b9 --- /dev/null +++ b/latest/cases/00766/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 1.2 + + + + + + 1 500 + + + + + + + diff --git a/latest/cases/00766/synopsis.txt b/latest/cases/00766/synopsis.txt new file mode 100644 index 000000000..42e8ed75c --- /dev/null +++ b/latest/cases/00766/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns value to species S1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $1.2$ | $S1 -> 2 \x 10^-3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^3$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.24$ |litre |] + diff --git a/latest/cases/00767/l2v5/build.log b/latest/cases/00767/l2v5/build.log new file mode 100644 index 000000000..965161af9 --- /dev/null +++ b/latest/cases/00767/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00767/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00767/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00767/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00767/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00767/l2v5/index.heta b/latest/cases/00767/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00767/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00767/l3v2/build.log b/latest/cases/00767/l3v2/build.log new file mode 100644 index 000000000..b725b3c99 --- /dev/null +++ b/latest/cases/00767/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00767/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00767/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00767/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00767/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00767/l3v2/index.heta b/latest/cases/00767/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00767/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00767/model-sbml-l2v5.xml b/latest/cases/00767/model-sbml-l2v5.xml new file mode 100644 index 000000000..edc937c24 --- /dev/null +++ b/latest/cases/00767/model-sbml-l2v5.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 5 + + + + + + + + + + S3 + 0.225 + + + + + + 1 + + + + + + 1 10 + + + + + + + diff --git a/latest/cases/00767/model-sbml-l3v2.xml b/latest/cases/00767/model-sbml-l3v2.xml new file mode 100644 index 000000000..b9cdbf77b --- /dev/null +++ b/latest/cases/00767/model-sbml-l3v2.xml @@ -0,0 +1,127 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 5 + + + + + + + + + + S3 + 0.225 + + + + + + 1 + + + + + + 1 10 + + + + + + + diff --git a/latest/cases/00767/synopsis.txt b/latest/cases/00767/synopsis.txt new file mode 100644 index 000000000..8aa8128f2 --- /dev/null +++ b/latest/cases/00767/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign value to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $0.5$ | $S1 -> 2 \x 10^-1$ |] + | Event2 | $S3 > 2.25 \x 10^-1$ | $1$ | $S4 -> 1 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.1$ |litre |] + diff --git a/latest/cases/00768/l2v5/build.log b/latest/cases/00768/l2v5/build.log new file mode 100644 index 000000000..e6612ab70 --- /dev/null +++ b/latest/cases/00768/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00768/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00768/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00768/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00768/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00768/l2v5/index.heta b/latest/cases/00768/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00768/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00768/l3v2/build.log b/latest/cases/00768/l3v2/build.log new file mode 100644 index 000000000..dc4ac85b8 --- /dev/null +++ b/latest/cases/00768/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00768/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00768/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00768/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00768/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00768/l3v2/index.heta b/latest/cases/00768/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00768/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00768/model-sbml-l2v5.xml b/latest/cases/00768/model-sbml-l2v5.xml new file mode 100644 index 000000000..f7d009d6f --- /dev/null +++ b/latest/cases/00768/model-sbml-l2v5.xml @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 2.5 + + + + + + 1 5000 + + + + + 1 20000 + + + + + + + diff --git a/latest/cases/00768/model-sbml-l3v2.xml b/latest/cases/00768/model-sbml-l3v2.xml new file mode 100644 index 000000000..6f86a0fc0 --- /dev/null +++ b/latest/cases/00768/model-sbml-l3v2.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 2.5 + + + + + + 1 5000 + + + + + 1 20000 + + + + + + + diff --git a/latest/cases/00768/synopsis.txt b/latest/cases/00768/synopsis.txt new file mode 100644 index 000000000..45dc319e8 --- /dev/null +++ b/latest/cases/00768/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and an event that assigns value to two species, subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $2.5$ | $S1 -> 2 \x 10^-4$ |] + | | | | $S4 -> 0.5 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S4 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.25$ |litre |] + diff --git a/latest/cases/00769/l2v5/build.log b/latest/cases/00769/l2v5/build.log new file mode 100644 index 000000000..7704c1b84 --- /dev/null +++ b/latest/cases/00769/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00769/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00769/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00769/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00769/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00769/l2v5/index.heta b/latest/cases/00769/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00769/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00769/l3v2/build.log b/latest/cases/00769/l3v2/build.log new file mode 100644 index 000000000..1061e151d --- /dev/null +++ b/latest/cases/00769/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00769/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00769/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00769/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00769/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00769/l3v2/index.heta b/latest/cases/00769/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00769/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00769/model-sbml-l2v5.xml b/latest/cases/00769/model-sbml-l2v5.xml new file mode 100644 index 000000000..022d931e8 --- /dev/null +++ b/latest/cases/00769/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1.5 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00769/model-sbml-l3v2.xml b/latest/cases/00769/model-sbml-l3v2.xml new file mode 100644 index 000000000..7b30ae917 --- /dev/null +++ b/latest/cases/00769/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1.5 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00769/synopsis.txt b/latest/cases/00769/synopsis.txt new file mode 100644 index 000000000..9305a97fa --- /dev/null +++ b/latest/cases/00769/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is consistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1.5$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$ 0.375$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 0.63$ |litre |] + diff --git a/latest/cases/00770/l2v5/build.log b/latest/cases/00770/l2v5/build.log new file mode 100644 index 000000000..d3afa1167 --- /dev/null +++ b/latest/cases/00770/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00770/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00770/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00770/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00770/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00770/l2v5/index.heta b/latest/cases/00770/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00770/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00770/l3v2/build.log b/latest/cases/00770/l3v2/build.log new file mode 100644 index 000000000..5fc3f5e07 --- /dev/null +++ b/latest/cases/00770/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00770/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00770/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00770/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00770/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00770/l3v2/index.heta b/latest/cases/00770/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00770/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00770/model-sbml-l2v5.xml b/latest/cases/00770/model-sbml-l2v5.xml new file mode 100644 index 000000000..1c93a33b5 --- /dev/null +++ b/latest/cases/00770/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00770/model-sbml-l3v2.xml b/latest/cases/00770/model-sbml-l3v2.xml new file mode 100644 index 000000000..027336f1f --- /dev/null +++ b/latest/cases/00770/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.1 + + + + + + 0.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00770/synopsis.txt b/latest/cases/00770/synopsis.txt new file mode 100644 index 000000000..efac25249 --- /dev/null +++ b/latest/cases/00770/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case the initial value declared for species S3 is inconsistent with +the value calculated by the assignmentRule. Note that since this +assignmentRule must always remain true, it should be considered during +simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.1$ | $0.5$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$ 1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0$ |mole litre^-1^ | +|Initial concentration of S3 |$ 3.75$ |mole litre^-1^ | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1.4$ |litre |] + diff --git a/latest/cases/00771/l2v5/build.log b/latest/cases/00771/l2v5/build.log new file mode 100644 index 000000000..505ea64e6 --- /dev/null +++ b/latest/cases/00771/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00771/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00771/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00771/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00771/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00771/l2v5/index.heta b/latest/cases/00771/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00771/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00771/l3v2/build.log b/latest/cases/00771/l3v2/build.log new file mode 100644 index 000000000..e7808df8a --- /dev/null +++ b/latest/cases/00771/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00771/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00771/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00771/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00771/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00771/l3v2/index.heta b/latest/cases/00771/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00771/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00771/model-sbml-l2v5.xml b/latest/cases/00771/model-sbml-l2v5.xml new file mode 100644 index 000000000..fe5a73011 --- /dev/null +++ b/latest/cases/00771/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00771/model-sbml-l3v2.xml b/latest/cases/00771/model-sbml-l3v2.xml new file mode 100644 index 000000000..1381e310f --- /dev/null +++ b/latest/cases/00771/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00771/synopsis.txt b/latest/cases/00771/synopsis.txt new file mode 100644 index 000000000..9a4bddc0e --- /dev/null +++ b/latest/cases/00771/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.5$ | $S2 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S2 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$undeclared$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00772/l2v5/build.log b/latest/cases/00772/l2v5/build.log new file mode 100644 index 000000000..76e784ab5 --- /dev/null +++ b/latest/cases/00772/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00772/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00772/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00772/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00772/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00772/l2v5/index.heta b/latest/cases/00772/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00772/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00772/l3v2/build.log b/latest/cases/00772/l3v2/build.log new file mode 100644 index 000000000..3dfb88da2 --- /dev/null +++ b/latest/cases/00772/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00772/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00772/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00772/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00772/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00772/l3v2/index.heta b/latest/cases/00772/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00772/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00772/model-sbml-l2v5.xml b/latest/cases/00772/model-sbml-l2v5.xml new file mode 100644 index 000000000..3ab106636 --- /dev/null +++ b/latest/cases/00772/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00772/model-sbml-l3v2.xml b/latest/cases/00772/model-sbml-l3v2.xml new file mode 100644 index 000000000..df89bdccf --- /dev/null +++ b/latest/cases/00772/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00772/synopsis.txt b/latest/cases/00772/synopsis.txt new file mode 100644 index 000000000..e3680dc78 --- /dev/null +++ b/latest/cases/00772/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.5$ | $S2 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S2 is inconsistent +with the value be calculated using the InitialAssignment; the calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$4.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00773/l2v5/build.log b/latest/cases/00773/l2v5/build.log new file mode 100644 index 000000000..8d2899254 --- /dev/null +++ b/latest/cases/00773/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00773/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00773/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00773/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00773/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00773/l2v5/index.heta b/latest/cases/00773/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00773/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00773/l3v2/build.log b/latest/cases/00773/l3v2/build.log new file mode 100644 index 000000000..ae3d576f8 --- /dev/null +++ b/latest/cases/00773/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00773/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00773/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00773/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00773/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00773/l3v2/index.heta b/latest/cases/00773/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00773/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00773/model-sbml-l2v5.xml b/latest/cases/00773/model-sbml-l2v5.xml new file mode 100644 index 000000000..1e577e31f --- /dev/null +++ b/latest/cases/00773/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00773/model-sbml-l3v2.xml b/latest/cases/00773/model-sbml-l3v2.xml new file mode 100644 index 000000000..78c8908cb --- /dev/null +++ b/latest/cases/00773/model-sbml-l3v2.xml @@ -0,0 +1,116 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.5 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00773/synopsis.txt b/latest/cases/00773/synopsis.txt new file mode 100644 index 000000000..076f92abd --- /dev/null +++ b/latest/cases/00773/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.5$ | $S2 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S2 is consistent +with the value calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00774/l2v5/build.log b/latest/cases/00774/l2v5/build.log new file mode 100644 index 000000000..1c54d4a05 --- /dev/null +++ b/latest/cases/00774/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00774/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00774/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00774/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00774/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00774/l2v5/index.heta b/latest/cases/00774/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00774/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00774/l3v2/build.log b/latest/cases/00774/l3v2/build.log new file mode 100644 index 000000000..8213160a0 --- /dev/null +++ b/latest/cases/00774/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00774/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00774/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00774/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00774/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00774/l3v2/index.heta b/latest/cases/00774/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00774/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00774/model-sbml-l2v5.xml b/latest/cases/00774/model-sbml-l2v5.xml new file mode 100644 index 000000000..1089ccb9f --- /dev/null +++ b/latest/cases/00774/model-sbml-l2v5.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 0.25 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00774/model-sbml-l3v2.xml b/latest/cases/00774/model-sbml-l3v2.xml new file mode 100644 index 000000000..dd15ea88d --- /dev/null +++ b/latest/cases/00774/model-sbml-l3v2.xml @@ -0,0 +1,118 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + 0.25 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00774/synopsis.txt b/latest/cases/00774/synopsis.txt new file mode 100644 index 000000000..bbaa8e8fa --- /dev/null +++ b/latest/cases/00774/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events, one of which is subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $0.25$ | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00775/l2v5/build.log b/latest/cases/00775/l2v5/build.log new file mode 100644 index 000000000..1129cc635 --- /dev/null +++ b/latest/cases/00775/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00775/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00775/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00775/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00775/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00775/l2v5/index.heta b/latest/cases/00775/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00775/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00775/l3v2/build.log b/latest/cases/00775/l3v2/build.log new file mode 100644 index 000000000..0603f149f --- /dev/null +++ b/latest/cases/00775/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00775/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00775/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00775/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00775/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00775/l3v2/index.heta b/latest/cases/00775/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00775/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00775/model-sbml-l2v5.xml b/latest/cases/00775/model-sbml-l2v5.xml new file mode 100644 index 000000000..9e5651fad --- /dev/null +++ b/latest/cases/00775/model-sbml-l2v5.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 50 + + + + + + + + + + S3 + 9 400 + + + + + + 0.75 + + + + + + 1 100 + + + + + + + diff --git a/latest/cases/00775/model-sbml-l3v2.xml b/latest/cases/00775/model-sbml-l3v2.xml new file mode 100644 index 000000000..db4169a3f --- /dev/null +++ b/latest/cases/00775/model-sbml-l3v2.xml @@ -0,0 +1,122 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 50 + + + + + + + + + + S3 + 9 400 + + + + + + 0.75 + + + + + + 1 100 + + + + + + + diff --git a/latest/cases/00775/synopsis.txt b/latest/cases/00775/synopsis.txt new file mode 100644 index 000000000..ddfdff391 --- /dev/null +++ b/latest/cases/00775/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events, one of which is subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $0.5$ | $S1 -> 2 \x 10^-2$ |] + | Event2 | $S3 > 2.25 \x 10^-2$ | $0.75$ | $S4 -> 1 \x 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00776/l2v5/build.log b/latest/cases/00776/l2v5/build.log new file mode 100644 index 000000000..172d47ee1 --- /dev/null +++ b/latest/cases/00776/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00776/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00776/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00776/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00776/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00776/l2v5/index.heta b/latest/cases/00776/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00776/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00776/l3v2/build.log b/latest/cases/00776/l3v2/build.log new file mode 100644 index 000000000..20a3a59c7 --- /dev/null +++ b/latest/cases/00776/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00776/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00776/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00776/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00776/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00776/l3v2/index.heta b/latest/cases/00776/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00776/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00776/model-sbml-l2v5.xml b/latest/cases/00776/model-sbml-l2v5.xml new file mode 100644 index 000000000..55bb24fa8 --- /dev/null +++ b/latest/cases/00776/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.5 + + + + + 1 + + + + + + + + + + S3 + 1.75 + + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00776/model-sbml-l3v2.xml b/latest/cases/00776/model-sbml-l3v2.xml new file mode 100644 index 000000000..4454ab698 --- /dev/null +++ b/latest/cases/00776/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2 + + + + + + 1.5 + + + + + 1 + + + + + + + + + + S3 + 1.75 + + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00776/synopsis.txt b/latest/cases/00776/synopsis.txt new file mode 100644 index 000000000..61c9e336c --- /dev/null +++ b/latest/cases/00776/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and two events, one of which is subject to delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay, EventNoDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S1, S2 and S3: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2$ | $S2 = 1.5$ | + | | | | $S1 = 1$ | + | Event2 | $S3 < 1.75$ | $-$ | $S3 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00777/l2v5/build.log b/latest/cases/00777/l2v5/build.log new file mode 100644 index 000000000..108c00270 --- /dev/null +++ b/latest/cases/00777/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00777/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00777/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00777/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00777/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00777/l2v5/index.heta b/latest/cases/00777/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00777/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00777/l3v2/build.log b/latest/cases/00777/l3v2/build.log new file mode 100644 index 000000000..429471831 --- /dev/null +++ b/latest/cases/00777/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00777/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00777/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00777/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00777/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00777/l3v2/index.heta b/latest/cases/00777/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00777/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00777/model-sbml-l2v5.xml b/latest/cases/00777/model-sbml-l2v5.xml new file mode 100644 index 000000000..dbf250564 --- /dev/null +++ b/latest/cases/00777/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + k2 + -2.5 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00777/model-sbml-l3v2.xml b/latest/cases/00777/model-sbml-l3v2.xml new file mode 100644 index 000000000..ba4de2af8 --- /dev/null +++ b/latest/cases/00777/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + k2 + -2.5 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + + + + + + S1 + 0.25 + + + + + + 1 + + + + + + 0.75 + + + + + + + diff --git a/latest/cases/00777/synopsis.txt b/latest/cases/00777/synopsis.txt new file mode 100644 index 000000000..0ce173ed8 --- /dev/null +++ b/latest/cases/00777/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventWithDelay, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains two rules which assign value to species S3 and parameter k2: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ | + | Algebraic | n/a | $k2 - 2.5$ |] + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.25$ | $1$ | $S2 = 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00778/l2v5/build.log b/latest/cases/00778/l2v5/build.log new file mode 100644 index 000000000..800849fba --- /dev/null +++ b/latest/cases/00778/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00778/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00778/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00778/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00778/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00778/l2v5/index.heta b/latest/cases/00778/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00778/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00778/l3v2/build.log b/latest/cases/00778/l3v2/build.log new file mode 100644 index 000000000..ed4b77ed3 --- /dev/null +++ b/latest/cases/00778/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00778/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00778/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00778/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00778/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00778/l3v2/index.heta b/latest/cases/00778/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00778/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00778/model-sbml-l2v5.xml b/latest/cases/00778/model-sbml-l2v5.xml new file mode 100644 index 000000000..abf9e9de7 --- /dev/null +++ b/latest/cases/00778/model-sbml-l2v5.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + X1 + -0.25 + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + 4.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00778/model-sbml-l3v2.xml b/latest/cases/00778/model-sbml-l3v2.xml new file mode 100644 index 000000000..ccfe64f0d --- /dev/null +++ b/latest/cases/00778/model-sbml-l3v2.xml @@ -0,0 +1,126 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + X1 + -0.25 + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + 4.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00778/synopsis.txt b/latest/cases/00778/synopsis.txt new file mode 100644 index 000000000..fe30e65bc --- /dev/null +++ b/latest/cases/00778/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventWithDelay, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $X0 + X1 + T - S1$ |] + +The model contains one event that assigns value to species X1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $X1 > 2$ | $4.3$ | $X1 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | X0 | $X1 - 0.25$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species X0 is consistent +with the value calculated using the InitialAssignment. +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1.25$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Initial amount of S1 |$3.75$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00779/l2v5/build.log b/latest/cases/00779/l2v5/build.log new file mode 100644 index 000000000..fc455a963 --- /dev/null +++ b/latest/cases/00779/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00779/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00779/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00779/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00779/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00779/l2v5/index.heta b/latest/cases/00779/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00779/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00779/l3v2/build.log b/latest/cases/00779/l3v2/build.log new file mode 100644 index 000000000..d69df6acf --- /dev/null +++ b/latest/cases/00779/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00779/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00779/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00779/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00779/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00779/l3v2/index.heta b/latest/cases/00779/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00779/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00779/model-sbml-l2v5.xml b/latest/cases/00779/model-sbml-l2v5.xml new file mode 100644 index 000000000..cbe7abcb4 --- /dev/null +++ b/latest/cases/00779/model-sbml-l2v5.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + X1 + -0.25 + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + 4.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00779/model-sbml-l3v2.xml b/latest/cases/00779/model-sbml-l3v2.xml new file mode 100644 index 000000000..eb5913874 --- /dev/null +++ b/latest/cases/00779/model-sbml-l3v2.xml @@ -0,0 +1,126 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + X1 + -0.25 + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + 4.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00779/synopsis.txt b/latest/cases/00779/synopsis.txt new file mode 100644 index 000000000..306f04703 --- /dev/null +++ b/latest/cases/00779/synopsis.txt @@ -0,0 +1,53 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventWithDelay, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $X0 + X1 + T - S1$ |] + +The model contains one event that assigns value to species X1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $X1 > 2$ | $4.3$ | $X1 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | X0 | $X1 - 0.25$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species X0 is inconsistent +with the value calculated using the InitialAssignment. The calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$3$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Initial amount of S1 |$3.75$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00780/l2v5/build.log b/latest/cases/00780/l2v5/build.log new file mode 100644 index 000000000..30bdd0deb --- /dev/null +++ b/latest/cases/00780/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00780/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00780/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00780/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00780/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00780/l2v5/index.heta b/latest/cases/00780/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00780/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00780/l3v2/build.log b/latest/cases/00780/l3v2/build.log new file mode 100644 index 000000000..3f0523d93 --- /dev/null +++ b/latest/cases/00780/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00780/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00780/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00780/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00780/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00780/l3v2/index.heta b/latest/cases/00780/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00780/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00780/model-sbml-l2v5.xml b/latest/cases/00780/model-sbml-l2v5.xml new file mode 100644 index 000000000..70371b1e2 --- /dev/null +++ b/latest/cases/00780/model-sbml-l2v5.xml @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + X1 + -0.25 + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + 4.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00780/model-sbml-l3v2.xml b/latest/cases/00780/model-sbml-l3v2.xml new file mode 100644 index 000000000..3cacea1e9 --- /dev/null +++ b/latest/cases/00780/model-sbml-l3v2.xml @@ -0,0 +1,126 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + X1 + -0.25 + + + + + + + + + + + + -1 + S1 + + T + X0 + X1 + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + C + k2 + T + + + + + + + + + + + + X1 + 2 + + + + + + 4.3 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00780/synopsis.txt b/latest/cases/00780/synopsis.txt new file mode 100644 index 000000000..dc1773d90 --- /dev/null +++ b/latest/cases/00780/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule, EventWithDelay, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * T$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $X0 + X1 + T - S1$ |] + +The model contains one event that assigns value to species X1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $X1 > 2$ | $4.3$ | $X1 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | X0 | $X1 - 0.25$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species X0 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$undeclared$ |mole | +|Initial amount of X1 |$1.5$ |mole | +|Initial amount of T |$1$ |mole | +|Initial amount of S1 |$3.75$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00781/l2v5/heta-code/output.heta b/latest/cases/00781/l2v5/heta-code/output.heta new file mode 100644 index 000000000..aaf2228e6 --- /dev/null +++ b/latest/cases/00781/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= k2 * pow(9, (-1)); + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00781/l2v5/index.heta b/latest/cases/00781/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00781/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00781/l2v5/json/output.json b/latest/cases/00781/l2v5/json/output.json new file mode 100644 index 000000000..efca9b627 --- /dev/null +++ b/latest/cases/00781/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 * pow(9, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00781/l3v2/heta-code/output.heta b/latest/cases/00781/l3v2/heta-code/output.heta new file mode 100644 index 000000000..12cff9238 --- /dev/null +++ b/latest/cases/00781/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(9, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00781/l3v2/index.heta b/latest/cases/00781/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00781/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00781/l3v2/json/output.json b/latest/cases/00781/l3v2/json/output.json new file mode 100644 index 000000000..a1e038770 --- /dev/null +++ b/latest/cases/00781/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 * pow(9, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00781/model-sbml-l2v5.xml b/latest/cases/00781/model-sbml-l2v5.xml new file mode 100644 index 000000000..db8f5f9bf --- /dev/null +++ b/latest/cases/00781/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + k2 + + + 9 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00781/model-sbml-l3v2.xml b/latest/cases/00781/model-sbml-l3v2.xml new file mode 100644 index 000000000..6b3bda38f --- /dev/null +++ b/latest/cases/00781/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + 9 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00781/output.heta b/latest/cases/00781/output.heta new file mode 100644 index 000000000..7f4463ca1 --- /dev/null +++ b/latest/cases/00781/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 9$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5.4$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(9, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00781/synopsis.txt b/latest/cases/00781/synopsis.txt new file mode 100644 index 000000000..6f63c74be --- /dev/null +++ b/latest/cases/00781/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 9$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5.4$ |litre |] + diff --git a/latest/cases/00782/l2v5/heta-code/output.heta b/latest/cases/00782/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9cadf9e3d --- /dev/null +++ b/latest/cases/00782/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= k2 * pow(10, (-1)); + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00782/l2v5/index.heta b/latest/cases/00782/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00782/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00782/l2v5/json/output.json b/latest/cases/00782/l2v5/json/output.json new file mode 100644 index 000000000..00cf77206 --- /dev/null +++ b/latest/cases/00782/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 * pow(10, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00782/l3v2/heta-code/output.heta b/latest/cases/00782/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0621ad397 --- /dev/null +++ b/latest/cases/00782/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(10, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00782/l3v2/index.heta b/latest/cases/00782/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00782/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00782/l3v2/json/output.json b/latest/cases/00782/l3v2/json/output.json new file mode 100644 index 000000000..20c967a09 --- /dev/null +++ b/latest/cases/00782/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 * pow(10, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00782/model-sbml-l2v5.xml b/latest/cases/00782/model-sbml-l2v5.xml new file mode 100644 index 000000000..14cb7ea47 --- /dev/null +++ b/latest/cases/00782/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + k2 + + + 10 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00782/model-sbml-l3v2.xml b/latest/cases/00782/model-sbml-l3v2.xml new file mode 100644 index 000000000..67b5bb822 --- /dev/null +++ b/latest/cases/00782/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + 10 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00782/output.heta b/latest/cases/00782/output.heta new file mode 100644 index 000000000..077b4f52e --- /dev/null +++ b/latest/cases/00782/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 10$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(10, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00782/synopsis.txt b/latest/cases/00782/synopsis.txt new file mode 100644 index 000000000..0fa154032 --- /dev/null +++ b/latest/cases/00782/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 10$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5$ |litre |] + diff --git a/latest/cases/00783/l2v5/heta-code/output.heta b/latest/cases/00783/l2v5/heta-code/output.heta new file mode 100644 index 000000000..aaf2228e6 --- /dev/null +++ b/latest/cases/00783/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= k2 * pow(9, (-1)); + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00783/l2v5/index.heta b/latest/cases/00783/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00783/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00783/l2v5/json/output.json b/latest/cases/00783/l2v5/json/output.json new file mode 100644 index 000000000..efca9b627 --- /dev/null +++ b/latest/cases/00783/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 * pow(9, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00783/l3v2/heta-code/output.heta b/latest/cases/00783/l3v2/heta-code/output.heta new file mode 100644 index 000000000..12cff9238 --- /dev/null +++ b/latest/cases/00783/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(9, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00783/l3v2/index.heta b/latest/cases/00783/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00783/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00783/l3v2/json/output.json b/latest/cases/00783/l3v2/json/output.json new file mode 100644 index 000000000..a1e038770 --- /dev/null +++ b/latest/cases/00783/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 * pow(9, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00783/model-sbml-l2v5.xml b/latest/cases/00783/model-sbml-l2v5.xml new file mode 100644 index 000000000..3703ea78f --- /dev/null +++ b/latest/cases/00783/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + k2 + + + 9 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00783/model-sbml-l3v2.xml b/latest/cases/00783/model-sbml-l3v2.xml new file mode 100644 index 000000000..d33eb4ac6 --- /dev/null +++ b/latest/cases/00783/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + 9 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00783/output.heta b/latest/cases/00783/output.heta new file mode 100644 index 000000000..8d774b70f --- /dev/null +++ b/latest/cases/00783/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 9$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(9, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00783/synopsis.txt b/latest/cases/00783/synopsis.txt new file mode 100644 index 000000000..a40dc0af8 --- /dev/null +++ b/latest/cases/00783/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / 9$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + diff --git a/latest/cases/00784/l2v5/heta-code/output.heta b/latest/cases/00784/l2v5/heta-code/output.heta new file mode 100644 index 000000000..688925aad --- /dev/null +++ b/latest/cases/00784/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.25; + diff --git a/latest/cases/00784/l2v5/index.heta b/latest/cases/00784/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00784/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00784/l2v5/json/output.json b/latest/cases/00784/l2v5/json/output.json new file mode 100644 index 000000000..3637f74c0 --- /dev/null +++ b/latest/cases/00784/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00784/l3v2/heta-code/output.heta b/latest/cases/00784/l3v2/heta-code/output.heta new file mode 100644 index 000000000..218317371 --- /dev/null +++ b/latest/cases/00784/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00784/l3v2/index.heta b/latest/cases/00784/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00784/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00784/l3v2/json/output.json b/latest/cases/00784/l3v2/json/output.json new file mode 100644 index 000000000..df30a7c3c --- /dev/null +++ b/latest/cases/00784/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00784/model-sbml-l2v5.xml b/latest/cases/00784/model-sbml-l2v5.xml new file mode 100644 index 000000000..99d7a2e79 --- /dev/null +++ b/latest/cases/00784/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00784/model-sbml-l3v2.xml b/latest/cases/00784/model-sbml-l3v2.xml new file mode 100644 index 000000000..d75b3d5a6 --- /dev/null +++ b/latest/cases/00784/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00784/output.heta b/latest/cases/00784/output.heta new file mode 100644 index 000000000..4d2a6d252 --- /dev/null +++ b/latest/cases/00784/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$0.5$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00784/synopsis.txt b/latest/cases/00784/synopsis.txt new file mode 100644 index 000000000..675eefa70 --- /dev/null +++ b/latest/cases/00784/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$0.5$ |litre |] + diff --git a/latest/cases/00785/l2v5/heta-code/output.heta b/latest/cases/00785/l2v5/heta-code/output.heta new file mode 100644 index 000000000..667c467bb --- /dev/null +++ b/latest/cases/00785/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.25; + diff --git a/latest/cases/00785/l2v5/index.heta b/latest/cases/00785/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00785/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00785/l2v5/json/output.json b/latest/cases/00785/l2v5/json/output.json new file mode 100644 index 000000000..82110a19c --- /dev/null +++ b/latest/cases/00785/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00785/l3v2/heta-code/output.heta b/latest/cases/00785/l3v2/heta-code/output.heta new file mode 100644 index 000000000..560f7df0b --- /dev/null +++ b/latest/cases/00785/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00785/l3v2/index.heta b/latest/cases/00785/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00785/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00785/l3v2/json/output.json b/latest/cases/00785/l3v2/json/output.json new file mode 100644 index 000000000..199c73878 --- /dev/null +++ b/latest/cases/00785/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00785/model-sbml-l2v5.xml b/latest/cases/00785/model-sbml-l2v5.xml new file mode 100644 index 000000000..17884a4fa --- /dev/null +++ b/latest/cases/00785/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00785/model-sbml-l3v2.xml b/latest/cases/00785/model-sbml-l3v2.xml new file mode 100644 index 000000000..5492491ff --- /dev/null +++ b/latest/cases/00785/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00785/output.heta b/latest/cases/00785/output.heta new file mode 100644 index 000000000..609c58f9c --- /dev/null +++ b/latest/cases/00785/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$3.5$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00785/synopsis.txt b/latest/cases/00785/synopsis.txt new file mode 100644 index 000000000..c59eb103c --- /dev/null +++ b/latest/cases/00785/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$3.5$ |litre |] + diff --git a/latest/cases/00786/l2v5/heta-code/output.heta b/latest/cases/00786/l2v5/heta-code/output.heta new file mode 100644 index 000000000..db92eb957 --- /dev/null +++ b/latest/cases/00786/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= 2 * p1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.25; + diff --git a/latest/cases/00786/l2v5/index.heta b/latest/cases/00786/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00786/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00786/l2v5/json/output.json b/latest/cases/00786/l2v5/json/output.json new file mode 100644 index 000000000..59a70cd50 --- /dev/null +++ b/latest/cases/00786/l2v5/json/output.json @@ -0,0 +1,139 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00786/l3v2/heta-code/output.heta b/latest/cases/00786/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6b7a94c27 --- /dev/null +++ b/latest/cases/00786/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00786/l3v2/index.heta b/latest/cases/00786/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00786/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00786/l3v2/json/output.json b/latest/cases/00786/l3v2/json/output.json new file mode 100644 index 000000000..8f51f5b56 --- /dev/null +++ b/latest/cases/00786/l3v2/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.25 + } +] \ No newline at end of file diff --git a/latest/cases/00786/model-sbml-l2v5.xml b/latest/cases/00786/model-sbml-l2v5.xml new file mode 100644 index 000000000..3f53d85e9 --- /dev/null +++ b/latest/cases/00786/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00786/model-sbml-l3v2.xml b/latest/cases/00786/model-sbml-l3v2.xml new file mode 100644 index 000000000..f7d29fc38 --- /dev/null +++ b/latest/cases/00786/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00786/output.heta b/latest/cases/00786/output.heta new file mode 100644 index 000000000..5a0f1ce26 --- /dev/null +++ b/latest/cases/00786/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= 2 * p1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.25; + diff --git a/latest/cases/00786/synopsis.txt b/latest/cases/00786/synopsis.txt new file mode 100644 index 000000000..7af5b4bbc --- /dev/null +++ b/latest/cases/00786/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + diff --git a/latest/cases/00787/l2v5/heta-code/output.heta b/latest/cases/00787/l2v5/heta-code/output.heta new file mode 100644 index 000000000..298313c2a --- /dev/null +++ b/latest/cases/00787/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.47; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00787/l2v5/index.heta b/latest/cases/00787/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00787/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00787/l2v5/json/output.json b/latest/cases/00787/l2v5/json/output.json new file mode 100644 index 000000000..e37458cc5 --- /dev/null +++ b/latest/cases/00787/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.47" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00787/l3v2/heta-code/output.heta b/latest/cases/00787/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d2b9bd101 --- /dev/null +++ b/latest/cases/00787/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.47; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00787/l3v2/index.heta b/latest/cases/00787/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00787/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00787/l3v2/json/output.json b/latest/cases/00787/l3v2/json/output.json new file mode 100644 index 000000000..577e3126f --- /dev/null +++ b/latest/cases/00787/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.47" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00787/model-sbml-l2v5.xml b/latest/cases/00787/model-sbml-l2v5.xml new file mode 100644 index 000000000..ba66cecd6 --- /dev/null +++ b/latest/cases/00787/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00787/model-sbml-l3v2.xml b/latest/cases/00787/model-sbml-l3v2.xml new file mode 100644 index 000000000..7c46fc71e --- /dev/null +++ b/latest/cases/00787/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00787/output.heta b/latest/cases/00787/output.heta new file mode 100644 index 000000000..e9b4eff1e --- /dev/null +++ b/latest/cases/00787/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$10$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0.15$ |mole litre^-1^ | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 0.47$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.47; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00787/synopsis.txt b/latest/cases/00787/synopsis.txt new file mode 100644 index 000000000..43b393432 --- /dev/null +++ b/latest/cases/00787/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is inconsisent with the value declared by the model definition. +The value calculated by the initialAssignment should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$10$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0.15$ |mole litre^-1^ | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 0.47$ |litre |] + diff --git a/latest/cases/00788/l2v5/heta-code/output.heta b/latest/cases/00788/l2v5/heta-code/output.heta new file mode 100644 index 000000000..07361c461 --- /dev/null +++ b/latest/cases/00788/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 6.6; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00788/l2v5/index.heta b/latest/cases/00788/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00788/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00788/l2v5/json/output.json b/latest/cases/00788/l2v5/json/output.json new file mode 100644 index 000000000..efaab28ef --- /dev/null +++ b/latest/cases/00788/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "6.6" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00788/l3v2/heta-code/output.heta b/latest/cases/00788/l3v2/heta-code/output.heta new file mode 100644 index 000000000..932b8bcbf --- /dev/null +++ b/latest/cases/00788/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 6.6; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00788/l3v2/index.heta b/latest/cases/00788/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00788/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00788/l3v2/json/output.json b/latest/cases/00788/l3v2/json/output.json new file mode 100644 index 000000000..b79d05e10 --- /dev/null +++ b/latest/cases/00788/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "6.6" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.133333333333333 * k1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.15" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "0.75" + } + } +] \ No newline at end of file diff --git a/latest/cases/00788/model-sbml-l2v5.xml b/latest/cases/00788/model-sbml-l2v5.xml new file mode 100644 index 000000000..49caa982a --- /dev/null +++ b/latest/cases/00788/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00788/model-sbml-l3v2.xml b/latest/cases/00788/model-sbml-l3v2.xml new file mode 100644 index 000000000..03e0ce0c3 --- /dev/null +++ b/latest/cases/00788/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.133333333333333 + k1 + + + + + + + + 0.75 + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00788/output.heta b/latest/cases/00788/output.heta new file mode 100644 index 000000000..f0bd6266d --- /dev/null +++ b/latest/cases/00788/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is consisent with the value declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$0.1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0.15$ |mole litre^-1^ | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 6.6$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 6.6; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { }; +k1 := 0.75; + diff --git a/latest/cases/00788/synopsis.txt b/latest/cases/00788/synopsis.txt new file mode 100644 index 000000000..500268d4b --- /dev/null +++ b/latest/cases/00788/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic reaction with two species in one +compartment using an assignmentRule to assign value to a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment +testTags: Concentration, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one rule which assigns value to parameter k1: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | k1 | $0.75$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 / 7.5$ |] + +Note: InitialAssignments override any declared initial values. The initial +value of species S1 is consisent with the value declared by the model definition. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$0.1$ |mole litre^-1^ | +|Initial concentration of S2 |$ 0.15$ |mole litre^-1^ | +|Value of parameter k1 |$ undeclared$ |second^-1^ | +|Volume of compartment C |$ 6.6$ |litre |] + diff --git a/latest/cases/00789/l2v5/heta-code/output.heta b/latest/cases/00789/l2v5/heta-code/output.heta new file mode 100644 index 000000000..79c143d44 --- /dev/null +++ b/latest/cases/00789/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= S1 * pow(p1, (-1)); +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00789/l2v5/index.heta b/latest/cases/00789/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00789/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00789/l2v5/json/output.json b/latest/cases/00789/l2v5/json/output.json new file mode 100644 index 000000000..930d5bb3e --- /dev/null +++ b/latest/cases/00789/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "S1 * pow(p1, (-1))", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00789/l3v2/heta-code/output.heta b/latest/cases/00789/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3a3ceac64 --- /dev/null +++ b/latest/cases/00789/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= S1 * pow(p1, (-1)); +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00789/l3v2/index.heta b/latest/cases/00789/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00789/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00789/l3v2/json/output.json b/latest/cases/00789/l3v2/json/output.json new file mode 100644 index 000000000..d7b00d4dc --- /dev/null +++ b/latest/cases/00789/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "S1 * pow(p1, (-1))", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00789/model-sbml-l2v5.xml b/latest/cases/00789/model-sbml-l2v5.xml new file mode 100644 index 000000000..9657b8529 --- /dev/null +++ b/latest/cases/00789/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00789/model-sbml-l3v2.xml b/latest/cases/00789/model-sbml-l3v2.xml new file mode 100644 index 000000000..8a73ace98 --- /dev/null +++ b/latest/cases/00789/model-sbml-l3v2.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00789/output.heta b/latest/cases/00789/output.heta new file mode 100644 index 000000000..363a55386 --- /dev/null +++ b/latest/cases/00789/output.heta @@ -0,0 +1,72 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event and one initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S2 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$undeclared$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= S1 * pow(p1, (-1)); +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00789/synopsis.txt b/latest/cases/00789/synopsis.txt new file mode 100644 index 000000000..feed24a21 --- /dev/null +++ b/latest/cases/00789/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event and one initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S2 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$undeclared$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00790/l2v5/heta-code/output.heta b/latest/cases/00790/l2v5/heta-code/output.heta new file mode 100644 index 000000000..79c143d44 --- /dev/null +++ b/latest/cases/00790/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= S1 * pow(p1, (-1)); +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00790/l2v5/index.heta b/latest/cases/00790/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00790/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00790/l2v5/json/output.json b/latest/cases/00790/l2v5/json/output.json new file mode 100644 index 000000000..930d5bb3e --- /dev/null +++ b/latest/cases/00790/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "S1 * pow(p1, (-1))", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00790/l3v2/heta-code/output.heta b/latest/cases/00790/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3a3ceac64 --- /dev/null +++ b/latest/cases/00790/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= S1 * pow(p1, (-1)); +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00790/l3v2/index.heta b/latest/cases/00790/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00790/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00790/l3v2/json/output.json b/latest/cases/00790/l3v2/json/output.json new file mode 100644 index 000000000..d7b00d4dc --- /dev/null +++ b/latest/cases/00790/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "S1 * pow(p1, (-1))", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00790/model-sbml-l2v5.xml b/latest/cases/00790/model-sbml-l2v5.xml new file mode 100644 index 000000000..2697b0dcf --- /dev/null +++ b/latest/cases/00790/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00790/model-sbml-l3v2.xml b/latest/cases/00790/model-sbml-l3v2.xml new file mode 100644 index 000000000..f75db2818 --- /dev/null +++ b/latest/cases/00790/model-sbml-l3v2.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00790/output.heta b/latest/cases/00790/output.heta new file mode 100644 index 000000000..25b0c51c5 --- /dev/null +++ b/latest/cases/00790/output.heta @@ -0,0 +1,73 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event and one initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S2 is inconsistent +with the value be calculated using the InitialAssignment; the calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$4.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= S1 * pow(p1, (-1)); +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00790/synopsis.txt b/latest/cases/00790/synopsis.txt new file mode 100644 index 000000000..159f57b1e --- /dev/null +++ b/latest/cases/00790/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event and one initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S2 is inconsistent +with the value be calculated using the InitialAssignment; the calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$4.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00791/l2v5/heta-code/output.heta b/latest/cases/00791/l2v5/heta-code/output.heta new file mode 100644 index 000000000..79c143d44 --- /dev/null +++ b/latest/cases/00791/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= S1 * pow(p1, (-1)); +S2 [event1]= 1; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00791/l2v5/index.heta b/latest/cases/00791/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00791/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00791/l2v5/json/output.json b/latest/cases/00791/l2v5/json/output.json new file mode 100644 index 000000000..930d5bb3e --- /dev/null +++ b/latest/cases/00791/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "S1 * pow(p1, (-1))", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00791/l3v2/heta-code/output.heta b/latest/cases/00791/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3a3ceac64 --- /dev/null +++ b/latest/cases/00791/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= S1 * pow(p1, (-1)); +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00791/l3v2/index.heta b/latest/cases/00791/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00791/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00791/l3v2/json/output.json b/latest/cases/00791/l3v2/json/output.json new file mode 100644 index 000000000..d7b00d4dc --- /dev/null +++ b/latest/cases/00791/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "S1 * pow(p1, (-1))", + "event1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00791/model-sbml-l2v5.xml b/latest/cases/00791/model-sbml-l2v5.xml new file mode 100644 index 000000000..b7c103136 --- /dev/null +++ b/latest/cases/00791/model-sbml-l2v5.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00791/model-sbml-l3v2.xml b/latest/cases/00791/model-sbml-l3v2.xml new file mode 100644 index 000000000..b60ed01c3 --- /dev/null +++ b/latest/cases/00791/model-sbml-l3v2.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S1 + + + p1 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00791/output.heta b/latest/cases/00791/output.heta new file mode 100644 index 000000000..e4d3f61c2 --- /dev/null +++ b/latest/cases/00791/output.heta @@ -0,0 +1,72 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event and one initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S2 is consistent +with the value calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= S1 * pow(p1, (-1)); +S2 [event1]= 1; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.5; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00791/synopsis.txt b/latest/cases/00791/synopsis.txt new file mode 100644 index 000000000..ab156f3ac --- /dev/null +++ b/latest/cases/00791/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event and one initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S2 is consistent +with the value calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00792/l2v5/heta-code/output.heta b/latest/cases/00792/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c0648de76 --- /dev/null +++ b/latest/cases/00792/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= k2 * pow(100, (-1)); +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00792/l2v5/index.heta b/latest/cases/00792/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00792/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00792/l2v5/json/output.json b/latest/cases/00792/l2v5/json/output.json new file mode 100644 index 000000000..9c06a48c7 --- /dev/null +++ b/latest/cases/00792/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "k2 * pow(100, (-1))" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00792/l3v2/heta-code/output.heta b/latest/cases/00792/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9afd60461 --- /dev/null +++ b/latest/cases/00792/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= k2 * pow(100, (-1)); + +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00792/l3v2/index.heta b/latest/cases/00792/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00792/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00792/l3v2/json/output.json b/latest/cases/00792/l3v2/json/output.json new file mode 100644 index 000000000..0016a728e --- /dev/null +++ b/latest/cases/00792/l3v2/json/output.json @@ -0,0 +1,69 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "k2 * pow(100, (-1))" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00792/model-sbml-l2v5.xml b/latest/cases/00792/model-sbml-l2v5.xml new file mode 100644 index 000000000..8d68239dd --- /dev/null +++ b/latest/cases/00792/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + k2 + + + 100 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00792/model-sbml-l3v2.xml b/latest/cases/00792/model-sbml-l3v2.xml new file mode 100644 index 000000000..34cdd2dfe --- /dev/null +++ b/latest/cases/00792/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + 100 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00792/output.heta b/latest/cases/00792/output.heta new file mode 100644 index 000000000..3dad71ac5 --- /dev/null +++ b/latest/cases/00792/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k1 has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= k2 * pow(100, (-1)); + +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00792/synopsis.txt b/latest/cases/00792/synopsis.txt new file mode 100644 index 000000000..21b032796 --- /dev/null +++ b/latest/cases/00792/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k1 has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$undeclared$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00793/l2v5/heta-code/output.heta b/latest/cases/00793/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c0648de76 --- /dev/null +++ b/latest/cases/00793/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= k2 * pow(100, (-1)); +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00793/l2v5/index.heta b/latest/cases/00793/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00793/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00793/l2v5/json/output.json b/latest/cases/00793/l2v5/json/output.json new file mode 100644 index 000000000..9c06a48c7 --- /dev/null +++ b/latest/cases/00793/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "k2 * pow(100, (-1))" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00793/l3v2/heta-code/output.heta b/latest/cases/00793/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9afd60461 --- /dev/null +++ b/latest/cases/00793/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= k2 * pow(100, (-1)); + +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00793/l3v2/index.heta b/latest/cases/00793/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00793/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00793/l3v2/json/output.json b/latest/cases/00793/l3v2/json/output.json new file mode 100644 index 000000000..0016a728e --- /dev/null +++ b/latest/cases/00793/l3v2/json/output.json @@ -0,0 +1,69 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "k2 * pow(100, (-1))" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00793/model-sbml-l2v5.xml b/latest/cases/00793/model-sbml-l2v5.xml new file mode 100644 index 000000000..3fb96752c --- /dev/null +++ b/latest/cases/00793/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + k2 + + + 100 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00793/model-sbml-l3v2.xml b/latest/cases/00793/model-sbml-l3v2.xml new file mode 100644 index 000000000..f8ebcc0cc --- /dev/null +++ b/latest/cases/00793/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + 100 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00793/output.heta b/latest/cases/00793/output.heta new file mode 100644 index 000000000..acfb1c690 --- /dev/null +++ b/latest/cases/00793/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for parameter k1 is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$100$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= k2 * pow(100, (-1)); + +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00793/synopsis.txt b/latest/cases/00793/synopsis.txt new file mode 100644 index 000000000..5050494a6 --- /dev/null +++ b/latest/cases/00793/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 / 100$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for parameter k1 is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$100$ |second^-1^ | +|Value of parameter k2 |$50$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00794/l2v5/heta-code/output.heta b/latest/cases/00794/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c03282972 --- /dev/null +++ b/latest/cases/00794/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= k2 * pow(50, (-1)); + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00794/l2v5/index.heta b/latest/cases/00794/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00794/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00794/l2v5/json/output.json b/latest/cases/00794/l2v5/json/output.json new file mode 100644 index 000000000..d0729f506 --- /dev/null +++ b/latest/cases/00794/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 * pow(50, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00794/l3v2/heta-code/output.heta b/latest/cases/00794/l3v2/heta-code/output.heta new file mode 100644 index 000000000..36266c1cf --- /dev/null +++ b/latest/cases/00794/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(50, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00794/l3v2/index.heta b/latest/cases/00794/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00794/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00794/l3v2/json/output.json b/latest/cases/00794/l3v2/json/output.json new file mode 100644 index 000000000..d5fc3a6f4 --- /dev/null +++ b/latest/cases/00794/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 * pow(50, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00794/model-sbml-l2v5.xml b/latest/cases/00794/model-sbml-l2v5.xml new file mode 100644 index 000000000..75aef4fd4 --- /dev/null +++ b/latest/cases/00794/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + k2 + + + 50 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00794/model-sbml-l3v2.xml b/latest/cases/00794/model-sbml-l3v2.xml new file mode 100644 index 000000000..eaa81210c --- /dev/null +++ b/latest/cases/00794/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + 50 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00794/output.heta b/latest/cases/00794/output.heta new file mode 100644 index 000000000..bb172eae9 --- /dev/null +++ b/latest/cases/00794/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2*(50^-1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5.4$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(50, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00794/synopsis.txt b/latest/cases/00794/synopsis.txt new file mode 100644 index 000000000..800d82840 --- /dev/null +++ b/latest/cases/00794/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2*(50^-1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$5.4$ |litre |] + diff --git a/latest/cases/00795/l2v5/heta-code/output.heta b/latest/cases/00795/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c03282972 --- /dev/null +++ b/latest/cases/00795/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= k2 * pow(50, (-1)); + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00795/l2v5/index.heta b/latest/cases/00795/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00795/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00795/l2v5/json/output.json b/latest/cases/00795/l2v5/json/output.json new file mode 100644 index 000000000..d0729f506 --- /dev/null +++ b/latest/cases/00795/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 * pow(50, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00795/l3v2/heta-code/output.heta b/latest/cases/00795/l3v2/heta-code/output.heta new file mode 100644 index 000000000..36266c1cf --- /dev/null +++ b/latest/cases/00795/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(50, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00795/l3v2/index.heta b/latest/cases/00795/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00795/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00795/l3v2/json/output.json b/latest/cases/00795/l3v2/json/output.json new file mode 100644 index 000000000..d5fc3a6f4 --- /dev/null +++ b/latest/cases/00795/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 * pow(50, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00795/model-sbml-l2v5.xml b/latest/cases/00795/model-sbml-l2v5.xml new file mode 100644 index 000000000..d985b2bc3 --- /dev/null +++ b/latest/cases/00795/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + k2 + + + 50 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00795/model-sbml-l3v2.xml b/latest/cases/00795/model-sbml-l3v2.xml new file mode 100644 index 000000000..03e223294 --- /dev/null +++ b/latest/cases/00795/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + 50 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00795/output.heta b/latest/cases/00795/output.heta new file mode 100644 index 000000000..3e7945674 --- /dev/null +++ b/latest/cases/00795/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / (50^-1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(50, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00795/synopsis.txt b/latest/cases/00795/synopsis.txt new file mode 100644 index 000000000..96c19cef4 --- /dev/null +++ b/latest/cases/00795/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2 / (50^-1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for compartment C is +consistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00796/l2v5/heta-code/output.heta b/latest/cases/00796/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c03282972 --- /dev/null +++ b/latest/cases/00796/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, } .= k2 * pow(50, (-1)); + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 0.5; +k2 @Record 'k2' { } .= 50; + diff --git a/latest/cases/00796/l2v5/index.heta b/latest/cases/00796/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00796/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00796/l2v5/json/output.json b/latest/cases/00796/l2v5/json/output.json new file mode 100644 index 000000000..d0729f506 --- /dev/null +++ b/latest/cases/00796/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "k2 * pow(50, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00796/l3v2/heta-code/output.heta b/latest/cases/00796/l3v2/heta-code/output.heta new file mode 100644 index 000000000..36266c1cf --- /dev/null +++ b/latest/cases/00796/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(50, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00796/l3v2/index.heta b/latest/cases/00796/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00796/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00796/l3v2/json/output.json b/latest/cases/00796/l3v2/json/output.json new file mode 100644 index 000000000..d5fc3a6f4 --- /dev/null +++ b/latest/cases/00796/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "k2 * pow(50, (-1))" + } + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + } +] \ No newline at end of file diff --git a/latest/cases/00796/model-sbml-l2v5.xml b/latest/cases/00796/model-sbml-l2v5.xml new file mode 100644 index 000000000..f2cdb9f1f --- /dev/null +++ b/latest/cases/00796/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + k2 + + + 50 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00796/model-sbml-l3v2.xml b/latest/cases/00796/model-sbml-l3v2.xml new file mode 100644 index 000000000..99ced3c89 --- /dev/null +++ b/latest/cases/00796/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + 50 + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00796/output.heta b/latest/cases/00796/output.heta new file mode 100644 index 000000000..d6f5c02c6 --- /dev/null +++ b/latest/cases/00796/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2*(50^-1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, } .= k2 * pow(50, (-1)); + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 50; + diff --git a/latest/cases/00796/synopsis.txt b/latest/cases/00796/synopsis.txt new file mode 100644 index 000000000..f4dc9a6e1 --- /dev/null +++ b/latest/cases/00796/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of the compartment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called k1 and k2. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k1 * S1$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | C | $k2*(50^-1)$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment C has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1$ |mole litre^-1^ | +|Initial concentration of S2 |$1.5$ |mole litre^-1^ | +|Value of parameter k1 |$0.5$ |second^-1^ | +|Value of parameter k2 |$50$ |litre | +|Volume of compartment C |$undeclared$ |litre |] + diff --git a/latest/cases/00797/l2v5/heta-code/output.heta b/latest/cases/00797/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f39cb27e7 --- /dev/null +++ b/latest/cases/00797/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 0.00125; + diff --git a/latest/cases/00797/l2v5/index.heta b/latest/cases/00797/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00797/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00797/l2v5/json/output.json b/latest/cases/00797/l2v5/json/output.json new file mode 100644 index 000000000..9a85eb45e --- /dev/null +++ b/latest/cases/00797/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.00125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00797/l3v2/heta-code/output.heta b/latest/cases/00797/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f02c79c84 --- /dev/null +++ b/latest/cases/00797/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00797/l3v2/index.heta b/latest/cases/00797/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00797/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00797/l3v2/json/output.json b/latest/cases/00797/l3v2/json/output.json new file mode 100644 index 000000000..7c510fe20 --- /dev/null +++ b/latest/cases/00797/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.02" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.01" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.00125 + } +] \ No newline at end of file diff --git a/latest/cases/00797/model-sbml-l2v5.xml b/latest/cases/00797/model-sbml-l2v5.xml new file mode 100644 index 000000000..c19370ad6 --- /dev/null +++ b/latest/cases/00797/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00797/model-sbml-l3v2.xml b/latest/cases/00797/model-sbml-l3v2.xml new file mode 100644 index 000000000..0e1e67145 --- /dev/null +++ b/latest/cases/00797/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00797/output.heta b/latest/cases/00797/output.heta new file mode 100644 index 000000000..8da0cb222 --- /dev/null +++ b/latest/cases/00797/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.00125; + diff --git a/latest/cases/00797/synopsis.txt b/latest/cases/00797/synopsis.txt new file mode 100644 index 000000000..2fc659a30 --- /dev/null +++ b/latest/cases/00797/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-2$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-2$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00798/l2v5/heta-code/output.heta b/latest/cases/00798/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5b0a75584 --- /dev/null +++ b/latest/cases/00798/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 1.25e-5; + diff --git a/latest/cases/00798/l2v5/index.heta b/latest/cases/00798/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00798/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00798/l2v5/json/output.json b/latest/cases/00798/l2v5/json/output.json new file mode 100644 index 000000000..1b785b636 --- /dev/null +++ b/latest/cases/00798/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00798/l3v2/heta-code/output.heta b/latest/cases/00798/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6437e7fb9 --- /dev/null +++ b/latest/cases/00798/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00798/l3v2/index.heta b/latest/cases/00798/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00798/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00798/l3v2/json/output.json b/latest/cases/00798/l3v2/json/output.json new file mode 100644 index 000000000..54e97284f --- /dev/null +++ b/latest/cases/00798/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1e-4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.0000125 + } +] \ No newline at end of file diff --git a/latest/cases/00798/model-sbml-l2v5.xml b/latest/cases/00798/model-sbml-l2v5.xml new file mode 100644 index 000000000..71285a279 --- /dev/null +++ b/latest/cases/00798/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00798/model-sbml-l3v2.xml b/latest/cases/00798/model-sbml-l3v2.xml new file mode 100644 index 000000000..383555bae --- /dev/null +++ b/latest/cases/00798/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00798/output.heta b/latest/cases/00798/output.heta new file mode 100644 index 000000000..d35c214c5 --- /dev/null +++ b/latest/cases/00798/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$0.25 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.0000125; + diff --git a/latest/cases/00798/synopsis.txt b/latest/cases/00798/synopsis.txt new file mode 100644 index 000000000..cfd3fa8f2 --- /dev/null +++ b/latest/cases/00798/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$0.25 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-4$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-4$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00799/l2v5/heta-code/output.heta b/latest/cases/00799/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a5ec7df03 --- /dev/null +++ b/latest/cases/00799/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +p1 @Record 'p1' { } .= 1.25e-4; + diff --git a/latest/cases/00799/l2v5/index.heta b/latest/cases/00799/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00799/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00799/l2v5/json/output.json b/latest/cases/00799/l2v5/json/output.json new file mode 100644 index 000000000..92ce5c387 --- /dev/null +++ b/latest/cases/00799/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "1.25e-4" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00799/l3v2/heta-code/output.heta b/latest/cases/00799/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3378d94bb --- /dev/null +++ b/latest/cases/00799/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.000125; + diff --git a/latest/cases/00799/l3v2/index.heta b/latest/cases/00799/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00799/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00799/l3v2/json/output.json b/latest/cases/00799/l3v2/json/output.json new file mode 100644 index 000000000..0398411a8 --- /dev/null +++ b/latest/cases/00799/l3v2/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.002" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.001" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.000125 + } +] \ No newline at end of file diff --git a/latest/cases/00799/model-sbml-l2v5.xml b/latest/cases/00799/model-sbml-l2v5.xml new file mode 100644 index 000000000..25657954a --- /dev/null +++ b/latest/cases/00799/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00799/model-sbml-l3v2.xml b/latest/cases/00799/model-sbml-l3v2.xml new file mode 100644 index 000000000..0810576de --- /dev/null +++ b/latest/cases/00799/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00799/output.heta b/latest/cases/00799/output.heta new file mode 100644 index 000000000..13b7b33a5 --- /dev/null +++ b/latest/cases/00799/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$undeclared$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-4$ |mole | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +p1 @Const 'p1' { } = 0.000125; + diff --git a/latest/cases/00799/synopsis.txt b/latest/cases/00799/synopsis.txt new file mode 100644 index 000000000..732da4059 --- /dev/null +++ b/latest/cases/00799/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + + The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$undeclared$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-3$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-4$ |mole | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00800/l2v5/heta-code/output.heta b/latest/cases/00800/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8982cfedc --- /dev/null +++ b/latest/cases/00800/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2 * p1; +p1 @Record 'p1' { } .= 0.125; + diff --git a/latest/cases/00800/l2v5/index.heta b/latest/cases/00800/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00800/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00800/l2v5/json/output.json b/latest/cases/00800/l2v5/json/output.json new file mode 100644 index 000000000..ad608b856 --- /dev/null +++ b/latest/cases/00800/l2v5/json/output.json @@ -0,0 +1,140 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.125" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00800/l3v2/heta-code/output.heta b/latest/cases/00800/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2686599d7 --- /dev/null +++ b/latest/cases/00800/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k2 @Record 'k2' { } .= 2 * p1; + +k1 @Const 'k1' { } = 0.75; +p1 @Const 'p1' { } = 0.125; + diff --git a/latest/cases/00800/l3v2/index.heta b/latest/cases/00800/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00800/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00800/l3v2/json/output.json b/latest/cases/00800/l3v2/json/output.json new file mode 100644 index 000000000..489116ce4 --- /dev/null +++ b/latest/cases/00800/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2 * p1" + } + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.125 + } +] \ No newline at end of file diff --git a/latest/cases/00800/model-sbml-l2v5.xml b/latest/cases/00800/model-sbml-l2v5.xml new file mode 100644 index 000000000..d184d00b4 --- /dev/null +++ b/latest/cases/00800/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00800/model-sbml-l3v2.xml b/latest/cases/00800/model-sbml-l3v2.xml new file mode 100644 index 000000000..5f98bc0a3 --- /dev/null +++ b/latest/cases/00800/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00800/output.heta b/latest/cases/00800/output.heta new file mode 100644 index 000000000..4b7e2d5df --- /dev/null +++ b/latest/cases/00800/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k2 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k2 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter p1 |$0.125$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k2 @Record 'k2' { } .= 2 * p1; + +k1 @Const 'k1' { } = 0.75; +p1 @Const 'p1' { } = 0.125; + diff --git a/latest/cases/00800/synopsis.txt b/latest/cases/00800/synopsis.txt new file mode 100644 index 000000000..2cbc922ca --- /dev/null +++ b/latest/cases/00800/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one parameter. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Concentration, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called k1, k2 and p1. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k2 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the parameter k2 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S3 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$undeclared$ |second^-1^ | +|Value of parameter p1 |$0.125$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + diff --git a/latest/cases/00801/l2v5/heta-code/output.heta b/latest/cases/00801/l2v5/heta-code/output.heta new file mode 100644 index 000000000..52284daab --- /dev/null +++ b/latest/cases/00801/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k; + +k @Record 'k' { } .= 0.075; + diff --git a/latest/cases/00801/l2v5/index.heta b/latest/cases/00801/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00801/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00801/l2v5/json/output.json b/latest/cases/00801/l2v5/json/output.json new file mode 100644 index 000000000..e39693446 --- /dev/null +++ b/latest/cases/00801/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00801/l3v2/heta-code/output.heta b/latest/cases/00801/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0b690e9f5 --- /dev/null +++ b/latest/cases/00801/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k; + +k @Const 'k' { } = 0.075; + diff --git a/latest/cases/00801/l3v2/index.heta b/latest/cases/00801/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00801/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00801/l3v2/json/output.json b/latest/cases/00801/l3v2/json/output.json new file mode 100644 index 000000000..47ee76514 --- /dev/null +++ b/latest/cases/00801/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/00801/model-sbml-l2v5.xml b/latest/cases/00801/model-sbml-l2v5.xml new file mode 100644 index 000000000..1cbdfe3b0 --- /dev/null +++ b/latest/cases/00801/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + + + + + + + diff --git a/latest/cases/00801/model-sbml-l3v2.xml b/latest/cases/00801/model-sbml-l3v2.xml new file mode 100644 index 000000000..a1326f82c --- /dev/null +++ b/latest/cases/00801/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + + + + + + + diff --git a/latest/cases/00801/output.heta b/latest/cases/00801/output.heta new file mode 100644 index 000000000..5ae030e0b --- /dev/null +++ b/latest/cases/00801/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Zeroth order mass action kinetics. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines zero order mass action kinetics (as referenced by +SBO:0000047): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$0.075$ |mole litre^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k; + +k @Const 'k' { } = 0.075; + diff --git a/latest/cases/00801/synopsis.txt b/latest/cases/00801/synopsis.txt new file mode 100644 index 000000000..e5ae65dd4 --- /dev/null +++ b/latest/cases/00801/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Zeroth order mass action kinetics. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines zero order mass action kinetics (as referenced by +SBO:0000047): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$0.075$ |mole litre^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00802/l2v5/heta-code/output.heta b/latest/cases/00802/l2v5/heta-code/output.heta new file mode 100644 index 000000000..495054d45 --- /dev/null +++ b/latest/cases/00802/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * S1; + +k @Record 'k' { } .= 2.5; + diff --git a/latest/cases/00802/l2v5/index.heta b/latest/cases/00802/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00802/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00802/l2v5/json/output.json b/latest/cases/00802/l2v5/json/output.json new file mode 100644 index 000000000..fc4a6336e --- /dev/null +++ b/latest/cases/00802/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "2.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00802/l3v2/heta-code/output.heta b/latest/cases/00802/l3v2/heta-code/output.heta new file mode 100644 index 000000000..85a74a8c3 --- /dev/null +++ b/latest/cases/00802/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * S1; + +k @Const 'k' { } = 2.5; + diff --git a/latest/cases/00802/l3v2/index.heta b/latest/cases/00802/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00802/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00802/l3v2/json/output.json b/latest/cases/00802/l3v2/json/output.json new file mode 100644 index 000000000..a603e21b5 --- /dev/null +++ b/latest/cases/00802/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 2.5 + } +] \ No newline at end of file diff --git a/latest/cases/00802/model-sbml-l2v5.xml b/latest/cases/00802/model-sbml-l2v5.xml new file mode 100644 index 000000000..3c048bf06 --- /dev/null +++ b/latest/cases/00802/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + diff --git a/latest/cases/00802/model-sbml-l3v2.xml b/latest/cases/00802/model-sbml-l3v2.xml new file mode 100644 index 000000000..2552ccda6 --- /dev/null +++ b/latest/cases/00802/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + + + + + + + diff --git a/latest/cases/00802/output.heta b/latest/cases/00802/output.heta new file mode 100644 index 000000000..2739f19de --- /dev/null +++ b/latest/cases/00802/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: First order mass action kinetics. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines first order mass action kinetics (as referenced by +SBO:0000049): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$2.5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * S1; + +k @Const 'k' { } = 2.5; + diff --git a/latest/cases/00802/synopsis.txt b/latest/cases/00802/synopsis.txt new file mode 100644 index 000000000..56c6ce3d6 --- /dev/null +++ b/latest/cases/00802/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: First order mass action kinetics. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines first order mass action kinetics (as referenced by +SBO:0000049): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$2.5$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00803/l2v5/heta-code/output.heta b/latest/cases/00803/l2v5/heta-code/output.heta new file mode 100644 index 000000000..96da38614 --- /dev/null +++ b/latest/cases/00803/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * S1 * pow(k, (-1)); + +k @Record 'k' { } .= 1.5; + diff --git a/latest/cases/00803/l2v5/index.heta b/latest/cases/00803/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00803/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00803/l2v5/json/output.json b/latest/cases/00803/l2v5/json/output.json new file mode 100644 index 000000000..e6bceae4f --- /dev/null +++ b/latest/cases/00803/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * S1 * pow(k, (-1))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00803/l3v2/heta-code/output.heta b/latest/cases/00803/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7a0ada60f --- /dev/null +++ b/latest/cases/00803/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * S1 * pow(k, (-1)); + +k @Const 'k' { } = 1.5; + diff --git a/latest/cases/00803/l3v2/index.heta b/latest/cases/00803/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00803/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00803/l3v2/json/output.json b/latest/cases/00803/l3v2/json/output.json new file mode 100644 index 000000000..561324039 --- /dev/null +++ b/latest/cases/00803/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * S1 * pow(k, (-1))" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00803/model-sbml-l2v5.xml b/latest/cases/00803/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef248ffbe --- /dev/null +++ b/latest/cases/00803/model-sbml-l2v5.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + S1 + + + k + -1 + + + + + + + + diff --git a/latest/cases/00803/model-sbml-l3v2.xml b/latest/cases/00803/model-sbml-l3v2.xml new file mode 100644 index 000000000..d69189498 --- /dev/null +++ b/latest/cases/00803/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + S1 + + + k + -1 + + + + + + + + diff --git a/latest/cases/00803/output.heta b/latest/cases/00803/output.heta new file mode 100644 index 000000000..10c68ac1c --- /dev/null +++ b/latest/cases/00803/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: First order mass action kinetics with monoexponential decay. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines first order mass action kinetics with monoexponential +decay (as referenced by SBO:0000333): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $(S1 * C) / k$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$1.5$ |second| +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * S1 * pow(k, (-1)); + +k @Const 'k' { } = 1.5; + diff --git a/latest/cases/00803/synopsis.txt b/latest/cases/00803/synopsis.txt new file mode 100644 index 000000000..bef514498 --- /dev/null +++ b/latest/cases/00803/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: First order mass action kinetics with monoexponential decay. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines first order mass action kinetics with monoexponential +decay (as referenced by SBO:0000333): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $(S1 * C) / k$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$1.5$ |second| +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00804/l2v5/heta-code/output.heta b/latest/cases/00804/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1a7f642ab --- /dev/null +++ b/latest/cases/00804/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * pow(S1, 2); + +k @Record 'k' { } .= 1.5; + diff --git a/latest/cases/00804/l2v5/index.heta b/latest/cases/00804/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00804/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00804/l2v5/json/output.json b/latest/cases/00804/l2v5/json/output.json new file mode 100644 index 000000000..b653fae80 --- /dev/null +++ b/latest/cases/00804/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * pow(S1, 2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00804/l3v2/heta-code/output.heta b/latest/cases/00804/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1fc230a8b --- /dev/null +++ b/latest/cases/00804/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * pow(S1, 2); + +k @Const 'k' { } = 1.5; + diff --git a/latest/cases/00804/l3v2/index.heta b/latest/cases/00804/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00804/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00804/l3v2/json/output.json b/latest/cases/00804/l3v2/json/output.json new file mode 100644 index 000000000..9ea3faf68 --- /dev/null +++ b/latest/cases/00804/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * pow(S1, 2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/00804/model-sbml-l2v5.xml b/latest/cases/00804/model-sbml-l2v5.xml new file mode 100644 index 000000000..a55851b59 --- /dev/null +++ b/latest/cases/00804/model-sbml-l2v5.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + + + S1 + 2 + + + + + + + + diff --git a/latest/cases/00804/model-sbml-l3v2.xml b/latest/cases/00804/model-sbml-l3v2.xml new file mode 100644 index 000000000..2c7732c8f --- /dev/null +++ b/latest/cases/00804/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + + + S1 + 2 + + + + + + + + diff --git a/latest/cases/00804/output.heta b/latest/cases/00804/output.heta new file mode 100644 index 000000000..8243077d5 --- /dev/null +++ b/latest/cases/00804/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Second order mass action kinetics with one reactant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines second order mass action kinetics with one reactant +(as referenced by SBO:0000052): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$1.5$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * pow(S1, 2); + +k @Const 'k' { } = 1.5; + diff --git a/latest/cases/00804/synopsis.txt b/latest/cases/00804/synopsis.txt new file mode 100644 index 000000000..c12a7744c --- /dev/null +++ b/latest/cases/00804/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Second order mass action kinetics with one reactant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines second order mass action kinetics with one reactant +(as referenced by SBO:0000052): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$1.5$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00805/l2v5/heta-code/output.heta b/latest/cases/00805/l2v5/heta-code/output.heta new file mode 100644 index 000000000..51fbde9fb --- /dev/null +++ b/latest/cases/00805/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k * S1 * S2; + +k @Record 'k' { } .= 1.1; + diff --git a/latest/cases/00805/l2v5/index.heta b/latest/cases/00805/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00805/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00805/l2v5/json/output.json b/latest/cases/00805/l2v5/json/output.json new file mode 100644 index 000000000..a456b6d04 --- /dev/null +++ b/latest/cases/00805/l2v5/json/output.json @@ -0,0 +1,101 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "1.1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00805/l3v2/heta-code/output.heta b/latest/cases/00805/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e018e722b --- /dev/null +++ b/latest/cases/00805/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k * S1 * S2; + +k @Const 'k' { } = 1.1; + diff --git a/latest/cases/00805/l3v2/index.heta b/latest/cases/00805/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00805/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00805/l3v2/json/output.json b/latest/cases/00805/l3v2/json/output.json new file mode 100644 index 000000000..cca897d92 --- /dev/null +++ b/latest/cases/00805/l3v2/json/output.json @@ -0,0 +1,75 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 1.1 + } +] \ No newline at end of file diff --git a/latest/cases/00805/model-sbml-l2v5.xml b/latest/cases/00805/model-sbml-l2v5.xml new file mode 100644 index 000000000..47cad368c --- /dev/null +++ b/latest/cases/00805/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + diff --git a/latest/cases/00805/model-sbml-l3v2.xml b/latest/cases/00805/model-sbml-l3v2.xml new file mode 100644 index 000000000..8d408206a --- /dev/null +++ b/latest/cases/00805/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + + + + + + + diff --git a/latest/cases/00805/output.heta b/latest/cases/00805/output.heta new file mode 100644 index 000000000..c90e9baae --- /dev/null +++ b/latest/cases/00805/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Second order mass action kinetics with two reactants. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameter called k. The model contains one reaction that has +a kinetic law that defines second order mass action kinetics with two reactants +(as referenced by SBO:0000054): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter k |$1.1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k * S1 * S2; + +k @Const 'k' { } = 1.1; + diff --git a/latest/cases/00805/synopsis.txt b/latest/cases/00805/synopsis.txt new file mode 100644 index 000000000..142eaa7a3 --- /dev/null +++ b/latest/cases/00805/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Second order mass action kinetics with two reactants. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameter called k. The model contains one reaction that has +a kinetic law that defines second order mass action kinetics with two reactants +(as referenced by SBO:0000054): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S2 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter k |$1.1$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00806/l2v5/heta-code/output.heta b/latest/cases/00806/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6421765d8 --- /dev/null +++ b/latest/cases/00806/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * pow(S1, 3); + +k @Record 'k' { } .= 0.65; + diff --git a/latest/cases/00806/l2v5/index.heta b/latest/cases/00806/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00806/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00806/l2v5/json/output.json b/latest/cases/00806/l2v5/json/output.json new file mode 100644 index 000000000..13a26d5ef --- /dev/null +++ b/latest/cases/00806/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * pow(S1, 3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "0.65" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00806/l3v2/heta-code/output.heta b/latest/cases/00806/l3v2/heta-code/output.heta new file mode 100644 index 000000000..15316f0be --- /dev/null +++ b/latest/cases/00806/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * pow(S1, 3); + +k @Const 'k' { } = 0.65; + diff --git a/latest/cases/00806/l3v2/index.heta b/latest/cases/00806/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00806/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00806/l3v2/json/output.json b/latest/cases/00806/l3v2/json/output.json new file mode 100644 index 000000000..4fb2374b3 --- /dev/null +++ b/latest/cases/00806/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * pow(S1, 3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 0.65 + } +] \ No newline at end of file diff --git a/latest/cases/00806/model-sbml-l2v5.xml b/latest/cases/00806/model-sbml-l2v5.xml new file mode 100644 index 000000000..1a3ee1a31 --- /dev/null +++ b/latest/cases/00806/model-sbml-l2v5.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + + + S1 + 3 + + + + + + + + diff --git a/latest/cases/00806/model-sbml-l3v2.xml b/latest/cases/00806/model-sbml-l3v2.xml new file mode 100644 index 000000000..05653c878 --- /dev/null +++ b/latest/cases/00806/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + + + S1 + 3 + + + + + + + + diff --git a/latest/cases/00806/output.heta b/latest/cases/00806/output.heta new file mode 100644 index 000000000..47ae47750 --- /dev/null +++ b/latest/cases/00806/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Third order mass action kinetics with one reactant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines third order mass action kinetics with one reactant +(as referenced by SBO:0000057): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * S1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$0.65$ |litre^2^ mole^-2^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k * pow(S1, 3); + +k @Const 'k' { } = 0.65; + diff --git a/latest/cases/00806/synopsis.txt b/latest/cases/00806/synopsis.txt new file mode 100644 index 000000000..1937bb6f6 --- /dev/null +++ b/latest/cases/00806/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Third order mass action kinetics with one reactant. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and one parameter called k. The model contains one reaction that has +a kinetic law that defines third order mass action kinetics with one reactant +(as referenced by SBO:0000057): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k * S1 * S1 * S1 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$0.65$ |litre^2^ mole^-2^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00807/l2v5/heta-code/output.heta b/latest/cases/00807/l2v5/heta-code/output.heta new file mode 100644 index 000000000..562362745 --- /dev/null +++ b/latest/cases/00807/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k * pow(S1, 2) * S2; + +k @Record 'k' { } .= 1.1; + diff --git a/latest/cases/00807/l2v5/index.heta b/latest/cases/00807/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00807/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00807/l2v5/json/output.json b/latest/cases/00807/l2v5/json/output.json new file mode 100644 index 000000000..80b435165 --- /dev/null +++ b/latest/cases/00807/l2v5/json/output.json @@ -0,0 +1,101 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "1.1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00807/l3v2/heta-code/output.heta b/latest/cases/00807/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1f2d0382a --- /dev/null +++ b/latest/cases/00807/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k * pow(S1, 2) * S2; + +k @Const 'k' { } = 1.1; + diff --git a/latest/cases/00807/l3v2/index.heta b/latest/cases/00807/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00807/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00807/l3v2/json/output.json b/latest/cases/00807/l3v2/json/output.json new file mode 100644 index 000000000..092ae986c --- /dev/null +++ b/latest/cases/00807/l3v2/json/output.json @@ -0,0 +1,75 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * pow(S1, 2) * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 1.1 + } +] \ No newline at end of file diff --git a/latest/cases/00807/model-sbml-l2v5.xml b/latest/cases/00807/model-sbml-l2v5.xml new file mode 100644 index 000000000..dfa1f2907 --- /dev/null +++ b/latest/cases/00807/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + + + S1 + 2 + + S2 + + + + + + + diff --git a/latest/cases/00807/model-sbml-l3v2.xml b/latest/cases/00807/model-sbml-l3v2.xml new file mode 100644 index 000000000..de74dedb7 --- /dev/null +++ b/latest/cases/00807/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + + + S1 + 2 + + S2 + + + + + + + diff --git a/latest/cases/00807/output.heta b/latest/cases/00807/output.heta new file mode 100644 index 000000000..8c1b7b1c5 --- /dev/null +++ b/latest/cases/00807/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Third order mass action kinetics with two reactants. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameter called k. The model contains one reaction that has +a kinetic law that defines third order mass action kinetics with two reactants +(as referenced by SBO:0000054): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S1 * S2 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$1.1$ |litre^2^ mole^-2^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k * pow(S1, 2) * S2; + +k @Const 'k' { } = 1.1; + diff --git a/latest/cases/00807/synopsis.txt b/latest/cases/00807/synopsis.txt new file mode 100644 index 000000000..01525fd2d --- /dev/null +++ b/latest/cases/00807/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Third order mass action kinetics with two reactants. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and one parameter called k. The model contains one reaction that has +a kinetic law that defines third order mass action kinetics with two reactants +(as referenced by SBO:0000054): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k * S1 * S1 * S2 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k |$1.1$ |litre^2^ mole^-2^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00808/l2v5/heta-code/output.heta b/latest/cases/00808/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6266fd32f --- /dev/null +++ b/latest/cases/00808/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.75 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 + S3 = S4, reversible: false, }; +reaction1 := C * k * S1 * S2 * S3; + +k @Record 'k' { } .= 0.8; + diff --git a/latest/cases/00808/l2v5/index.heta b/latest/cases/00808/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00808/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00808/l2v5/json/output.json b/latest/cases/00808/l2v5/json/output.json new file mode 100644 index 000000000..37ca1886a --- /dev/null +++ b/latest/cases/00808/l2v5/json/output.json @@ -0,0 +1,115 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.75 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * S1 * S2 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k", + "title": "k", + "assignments": { + "start_": "0.8" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00808/l3v2/heta-code/output.heta b/latest/cases/00808/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c48684fea --- /dev/null +++ b/latest/cases/00808/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.75 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 + S3 = S4, reversible: false, }; +reaction1 := C * k * S1 * S2 * S3; + +k @Const 'k' { } = 0.8; + diff --git a/latest/cases/00808/l3v2/index.heta b/latest/cases/00808/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00808/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00808/l3v2/json/output.json b/latest/cases/00808/l3v2/json/output.json new file mode 100644 index 000000000..e41958ec7 --- /dev/null +++ b/latest/cases/00808/l3v2/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.75 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k * S1 * S2 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k", + "title": "k", + "num": 0.8 + } +] \ No newline at end of file diff --git a/latest/cases/00808/model-sbml-l2v5.xml b/latest/cases/00808/model-sbml-l2v5.xml new file mode 100644 index 000000000..9590eedfe --- /dev/null +++ b/latest/cases/00808/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + S3 + + + + + + + diff --git a/latest/cases/00808/model-sbml-l3v2.xml b/latest/cases/00808/model-sbml-l3v2.xml new file mode 100644 index 000000000..abda45d66 --- /dev/null +++ b/latest/cases/00808/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k + S1 + S2 + S3 + + + + + + + diff --git a/latest/cases/00808/output.heta b/latest/cases/00808/output.heta new file mode 100644 index 000000000..e5ba34d00 --- /dev/null +++ b/latest/cases/00808/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Third order mass action kinetics with three reactants. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and one parameter called k. The model contains one reaction that has +a kinetic law that defines third order mass action kinetics with three reactants +(as referenced by SBO:0000061): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 + S3 -> S4 | $k * S1 * S2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0.75$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k |$0.8$ |litre^2^ mole^-2^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.75 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 + S3 = S4, reversible: false, }; +reaction1 := C * k * S1 * S2 * S3; + +k @Const 'k' { } = 0.8; + diff --git a/latest/cases/00808/synopsis.txt b/latest/cases/00808/synopsis.txt new file mode 100644 index 000000000..539f5f4be --- /dev/null +++ b/latest/cases/00808/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Third order mass action kinetics with three reactants. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and one parameter called k. The model contains one reaction that has +a kinetic law that defines third order mass action kinetics with three reactants +(as referenced by SBO:0000061): + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 + S3 -> S4 | $k * S1 * S2 * S3 * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0.75$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k |$0.8$ |litre^2^ mole^-2^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00809/l2v5/heta-code/output.heta b/latest/cases/00809/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7d22d71f8 --- /dev/null +++ b/latest/cases/00809/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/00809/l2v5/index.heta b/latest/cases/00809/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00809/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00809/l2v5/json/output.json b/latest/cases/00809/l2v5/json/output.json new file mode 100644 index 000000000..fcf3a4e57 --- /dev/null +++ b/latest/cases/00809/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00809/l3v2/heta-code/output.heta b/latest/cases/00809/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1ffaf8157 --- /dev/null +++ b/latest/cases/00809/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00809/l3v2/index.heta b/latest/cases/00809/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00809/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00809/l3v2/json/output.json b/latest/cases/00809/l3v2/json/output.json new file mode 100644 index 000000000..f5fd8888c --- /dev/null +++ b/latest/cases/00809/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/00809/model-sbml-l2v5.xml b/latest/cases/00809/model-sbml-l2v5.xml new file mode 100644 index 000000000..f378a4424 --- /dev/null +++ b/latest/cases/00809/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00809/model-sbml-l3v2.xml b/latest/cases/00809/model-sbml-l3v2.xml new file mode 100644 index 000000000..a85041f23 --- /dev/null +++ b/latest/cases/00809/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00809/output.heta b/latest/cases/00809/output.heta new file mode 100644 index 000000000..4e2d0a3a9 --- /dev/null +++ b/latest/cases/00809/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00809/synopsis.txt b/latest/cases/00809/synopsis.txt new file mode 100644 index 000000000..cda99da05 --- /dev/null +++ b/latest/cases/00809/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00810/l2v5/heta-code/output.heta b/latest/cases/00810/l2v5/heta-code/output.heta new file mode 100644 index 000000000..56485b757 --- /dev/null +++ b/latest/cases/00810/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/00810/l2v5/index.heta b/latest/cases/00810/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00810/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00810/l2v5/json/output.json b/latest/cases/00810/l2v5/json/output.json new file mode 100644 index 000000000..c90a2f4c7 --- /dev/null +++ b/latest/cases/00810/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00810/l3v2/heta-code/output.heta b/latest/cases/00810/l3v2/heta-code/output.heta new file mode 100644 index 000000000..650d8a5ba --- /dev/null +++ b/latest/cases/00810/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00810/l3v2/index.heta b/latest/cases/00810/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00810/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00810/l3v2/json/output.json b/latest/cases/00810/l3v2/json/output.json new file mode 100644 index 000000000..c2762eb72 --- /dev/null +++ b/latest/cases/00810/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/00810/model-sbml-l2v5.xml b/latest/cases/00810/model-sbml-l2v5.xml new file mode 100644 index 000000000..6af67bd16 --- /dev/null +++ b/latest/cases/00810/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00810/model-sbml-l3v2.xml b/latest/cases/00810/model-sbml-l3v2.xml new file mode 100644 index 000000000..bff04b9d4 --- /dev/null +++ b/latest/cases/00810/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00810/output.heta b/latest/cases/00810/output.heta new file mode 100644 index 000000000..04bfda276 --- /dev/null +++ b/latest/cases/00810/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00810/synopsis.txt b/latest/cases/00810/synopsis.txt new file mode 100644 index 000000000..0f59fa816 --- /dev/null +++ b/latest/cases/00810/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00811/l2v5/heta-code/output.heta b/latest/cases/00811/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0d8fcebec --- /dev/null +++ b/latest/cases/00811/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00811/l2v5/index.heta b/latest/cases/00811/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00811/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00811/l2v5/json/output.json b/latest/cases/00811/l2v5/json/output.json new file mode 100644 index 000000000..c048cba2b --- /dev/null +++ b/latest/cases/00811/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00811/l3v2/heta-code/output.heta b/latest/cases/00811/l3v2/heta-code/output.heta new file mode 100644 index 000000000..824ea026d --- /dev/null +++ b/latest/cases/00811/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00811/l3v2/index.heta b/latest/cases/00811/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00811/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00811/l3v2/json/output.json b/latest/cases/00811/l3v2/json/output.json new file mode 100644 index 000000000..496bb9384 --- /dev/null +++ b/latest/cases/00811/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00811/model-sbml-l2v5.xml b/latest/cases/00811/model-sbml-l2v5.xml new file mode 100644 index 000000000..4b71380f1 --- /dev/null +++ b/latest/cases/00811/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00811/model-sbml-l3v2.xml b/latest/cases/00811/model-sbml-l3v2.xml new file mode 100644 index 000000000..b3e837bc4 --- /dev/null +++ b/latest/cases/00811/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00811/output.heta b/latest/cases/00811/output.heta new file mode 100644 index 000000000..c3019822c --- /dev/null +++ b/latest/cases/00811/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00811/synopsis.txt b/latest/cases/00811/synopsis.txt new file mode 100644 index 000000000..0bd2ffae4 --- /dev/null +++ b/latest/cases/00811/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00812/l2v5/heta-code/output.heta b/latest/cases/00812/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b28d2dd87 --- /dev/null +++ b/latest/cases/00812/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/00812/l2v5/index.heta b/latest/cases/00812/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00812/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00812/l2v5/json/output.json b/latest/cases/00812/l2v5/json/output.json new file mode 100644 index 000000000..c2f1ab638 --- /dev/null +++ b/latest/cases/00812/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00812/l3v2/heta-code/output.heta b/latest/cases/00812/l3v2/heta-code/output.heta new file mode 100644 index 000000000..401cc60dd --- /dev/null +++ b/latest/cases/00812/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00812/l3v2/index.heta b/latest/cases/00812/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00812/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00812/l3v2/json/output.json b/latest/cases/00812/l3v2/json/output.json new file mode 100644 index 000000000..b58695de0 --- /dev/null +++ b/latest/cases/00812/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/00812/model-sbml-l2v5.xml b/latest/cases/00812/model-sbml-l2v5.xml new file mode 100644 index 000000000..de813c69b --- /dev/null +++ b/latest/cases/00812/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00812/model-sbml-l3v2.xml b/latest/cases/00812/model-sbml-l3v2.xml new file mode 100644 index 000000000..73f795ca9 --- /dev/null +++ b/latest/cases/00812/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00812/output.heta b/latest/cases/00812/output.heta new file mode 100644 index 000000000..6129e2f1c --- /dev/null +++ b/latest/cases/00812/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$0.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00812/synopsis.txt b/latest/cases/00812/synopsis.txt new file mode 100644 index 000000000..23166b624 --- /dev/null +++ b/latest/cases/00812/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$0.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00813/l2v5/heta-code/output.heta b/latest/cases/00813/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b8aab0da6 --- /dev/null +++ b/latest/cases/00813/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/00813/l2v5/index.heta b/latest/cases/00813/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00813/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00813/l2v5/json/output.json b/latest/cases/00813/l2v5/json/output.json new file mode 100644 index 000000000..0bb2906be --- /dev/null +++ b/latest/cases/00813/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00813/l3v2/heta-code/output.heta b/latest/cases/00813/l3v2/heta-code/output.heta new file mode 100644 index 000000000..aead999a4 --- /dev/null +++ b/latest/cases/00813/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00813/l3v2/index.heta b/latest/cases/00813/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00813/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00813/l3v2/json/output.json b/latest/cases/00813/l3v2/json/output.json new file mode 100644 index 000000000..780a91d6d --- /dev/null +++ b/latest/cases/00813/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/00813/model-sbml-l2v5.xml b/latest/cases/00813/model-sbml-l2v5.xml new file mode 100644 index 000000000..7d0f30c88 --- /dev/null +++ b/latest/cases/00813/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00813/model-sbml-l3v2.xml b/latest/cases/00813/model-sbml-l3v2.xml new file mode 100644 index 000000000..6abb0885f --- /dev/null +++ b/latest/cases/00813/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00813/output.heta b/latest/cases/00813/output.heta new file mode 100644 index 000000000..b30fc8418 --- /dev/null +++ b/latest/cases/00813/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$2.3$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00813/synopsis.txt b/latest/cases/00813/synopsis.txt new file mode 100644 index 000000000..20d6f14f5 --- /dev/null +++ b/latest/cases/00813/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$2.3$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00814/l2v5/heta-code/output.heta b/latest/cases/00814/l2v5/heta-code/output.heta new file mode 100644 index 000000000..384da1c67 --- /dev/null +++ b/latest/cases/00814/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00814/l2v5/index.heta b/latest/cases/00814/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00814/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00814/l2v5/json/output.json b/latest/cases/00814/l2v5/json/output.json new file mode 100644 index 000000000..c44e304b7 --- /dev/null +++ b/latest/cases/00814/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.95" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00814/l3v2/heta-code/output.heta b/latest/cases/00814/l3v2/heta-code/output.heta new file mode 100644 index 000000000..202769587 --- /dev/null +++ b/latest/cases/00814/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00814/l3v2/index.heta b/latest/cases/00814/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00814/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00814/l3v2/json/output.json b/latest/cases/00814/l3v2/json/output.json new file mode 100644 index 000000000..ef2a6a522 --- /dev/null +++ b/latest/cases/00814/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.95" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00814/model-sbml-l2v5.xml b/latest/cases/00814/model-sbml-l2v5.xml new file mode 100644 index 000000000..2fbb1920d --- /dev/null +++ b/latest/cases/00814/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00814/model-sbml-l3v2.xml b/latest/cases/00814/model-sbml-l3v2.xml new file mode 100644 index 000000000..f52d81b37 --- /dev/null +++ b/latest/cases/00814/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00814/output.heta b/latest/cases/00814/output.heta new file mode 100644 index 000000000..f21b97e36 --- /dev/null +++ b/latest/cases/00814/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.95$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00814/synopsis.txt b/latest/cases/00814/synopsis.txt new file mode 100644 index 000000000..7b087e0a1 --- /dev/null +++ b/latest/cases/00814/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.95$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00815/l2v5/heta-code/output.heta b/latest/cases/00815/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7eae620f9 --- /dev/null +++ b/latest/cases/00815/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/00815/l2v5/index.heta b/latest/cases/00815/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00815/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00815/l2v5/json/output.json b/latest/cases/00815/l2v5/json/output.json new file mode 100644 index 000000000..45821cb86 --- /dev/null +++ b/latest/cases/00815/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00815/l3v2/heta-code/output.heta b/latest/cases/00815/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e83243a82 --- /dev/null +++ b/latest/cases/00815/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00815/l3v2/index.heta b/latest/cases/00815/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00815/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00815/l3v2/json/output.json b/latest/cases/00815/l3v2/json/output.json new file mode 100644 index 000000000..22b38dac6 --- /dev/null +++ b/latest/cases/00815/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/00815/model-sbml-l2v5.xml b/latest/cases/00815/model-sbml-l2v5.xml new file mode 100644 index 000000000..69487acba --- /dev/null +++ b/latest/cases/00815/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00815/model-sbml-l3v2.xml b/latest/cases/00815/model-sbml-l3v2.xml new file mode 100644 index 000000000..12b344c44 --- /dev/null +++ b/latest/cases/00815/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00815/output.heta b/latest/cases/00815/output.heta new file mode 100644 index 000000000..5e18b51de --- /dev/null +++ b/latest/cases/00815/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$0.5$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00815/synopsis.txt b/latest/cases/00815/synopsis.txt new file mode 100644 index 000000000..142e9c8f8 --- /dev/null +++ b/latest/cases/00815/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$0.5$ |litre |] + diff --git a/latest/cases/00816/l2v5/heta-code/output.heta b/latest/cases/00816/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d8934e191 --- /dev/null +++ b/latest/cases/00816/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/00816/l2v5/index.heta b/latest/cases/00816/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00816/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00816/l2v5/json/output.json b/latest/cases/00816/l2v5/json/output.json new file mode 100644 index 000000000..befaa9541 --- /dev/null +++ b/latest/cases/00816/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00816/l3v2/heta-code/output.heta b/latest/cases/00816/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4be41c595 --- /dev/null +++ b/latest/cases/00816/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00816/l3v2/index.heta b/latest/cases/00816/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00816/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00816/l3v2/json/output.json b/latest/cases/00816/l3v2/json/output.json new file mode 100644 index 000000000..6ded633c4 --- /dev/null +++ b/latest/cases/00816/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/00816/model-sbml-l2v5.xml b/latest/cases/00816/model-sbml-l2v5.xml new file mode 100644 index 000000000..143731bd1 --- /dev/null +++ b/latest/cases/00816/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00816/model-sbml-l3v2.xml b/latest/cases/00816/model-sbml-l3v2.xml new file mode 100644 index 000000000..f751772dc --- /dev/null +++ b/latest/cases/00816/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00816/output.heta b/latest/cases/00816/output.heta new file mode 100644 index 000000000..ba8b7d5f1 --- /dev/null +++ b/latest/cases/00816/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$2.3$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00816/synopsis.txt b/latest/cases/00816/synopsis.txt new file mode 100644 index 000000000..754cc277e --- /dev/null +++ b/latest/cases/00816/synopsis.txt @@ -0,0 +1,26 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$2.3$ |litre |] + diff --git a/latest/cases/00817/l2v5/heta-code/output.heta b/latest/cases/00817/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0f3bdf25f --- /dev/null +++ b/latest/cases/00817/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00817/l2v5/index.heta b/latest/cases/00817/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00817/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00817/l2v5/json/output.json b/latest/cases/00817/l2v5/json/output.json new file mode 100644 index 000000000..43cf89c0e --- /dev/null +++ b/latest/cases/00817/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.95" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00817/l3v2/heta-code/output.heta b/latest/cases/00817/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a954a990b --- /dev/null +++ b/latest/cases/00817/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00817/l3v2/index.heta b/latest/cases/00817/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00817/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00817/l3v2/json/output.json b/latest/cases/00817/l3v2/json/output.json new file mode 100644 index 000000000..596311921 --- /dev/null +++ b/latest/cases/00817/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.95" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00817/model-sbml-l2v5.xml b/latest/cases/00817/model-sbml-l2v5.xml new file mode 100644 index 000000000..212485cd9 --- /dev/null +++ b/latest/cases/00817/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00817/model-sbml-l3v2.xml b/latest/cases/00817/model-sbml-l3v2.xml new file mode 100644 index 000000000..7e75371db --- /dev/null +++ b/latest/cases/00817/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00817/output.heta b/latest/cases/00817/output.heta new file mode 100644 index 000000000..c13477697 --- /dev/null +++ b/latest/cases/00817/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.95$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00817/synopsis.txt b/latest/cases/00817/synopsis.txt new file mode 100644 index 000000000..e38f44d8a --- /dev/null +++ b/latest/cases/00817/synopsis.txt @@ -0,0 +1,26 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.95$ |litre |] + diff --git a/latest/cases/00818/l2v5/heta-code/output.heta b/latest/cases/00818/l2v5/heta-code/output.heta new file mode 100644 index 000000000..98ce448a7 --- /dev/null +++ b/latest/cases/00818/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/00818/l2v5/index.heta b/latest/cases/00818/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00818/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00818/l2v5/json/output.json b/latest/cases/00818/l2v5/json/output.json new file mode 100644 index 000000000..945999a13 --- /dev/null +++ b/latest/cases/00818/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00818/l3v2/heta-code/output.heta b/latest/cases/00818/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f1b2121a7 --- /dev/null +++ b/latest/cases/00818/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00818/l3v2/index.heta b/latest/cases/00818/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00818/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00818/l3v2/json/output.json b/latest/cases/00818/l3v2/json/output.json new file mode 100644 index 000000000..f0b57e7b5 --- /dev/null +++ b/latest/cases/00818/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/00818/model-sbml-l2v5.xml b/latest/cases/00818/model-sbml-l2v5.xml new file mode 100644 index 000000000..941b2b26a --- /dev/null +++ b/latest/cases/00818/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00818/model-sbml-l3v2.xml b/latest/cases/00818/model-sbml-l3v2.xml new file mode 100644 index 000000000..5191d6794 --- /dev/null +++ b/latest/cases/00818/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00818/output.heta b/latest/cases/00818/output.heta new file mode 100644 index 000000000..cce8fe1ad --- /dev/null +++ b/latest/cases/00818/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. Species S1 is labeled as an +SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00818/synopsis.txt b/latest/cases/00818/synopsis.txt new file mode 100644 index 000000000..f9e01f7cf --- /dev/null +++ b/latest/cases/00818/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. Species S1 is labeled as an +SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00819/l2v5/heta-code/output.heta b/latest/cases/00819/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f3e1a847f --- /dev/null +++ b/latest/cases/00819/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/00819/l2v5/index.heta b/latest/cases/00819/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00819/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00819/l2v5/json/output.json b/latest/cases/00819/l2v5/json/output.json new file mode 100644 index 000000000..da530d921 --- /dev/null +++ b/latest/cases/00819/l2v5/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00819/l3v2/heta-code/output.heta b/latest/cases/00819/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5c72db154 --- /dev/null +++ b/latest/cases/00819/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00819/l3v2/index.heta b/latest/cases/00819/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00819/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00819/l3v2/json/output.json b/latest/cases/00819/l3v2/json/output.json new file mode 100644 index 000000000..cef4a079f --- /dev/null +++ b/latest/cases/00819/l3v2/json/output.json @@ -0,0 +1,81 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/00819/model-sbml-l2v5.xml b/latest/cases/00819/model-sbml-l2v5.xml new file mode 100644 index 000000000..86d714692 --- /dev/null +++ b/latest/cases/00819/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00819/model-sbml-l3v2.xml b/latest/cases/00819/model-sbml-l3v2.xml new file mode 100644 index 000000000..b716b216c --- /dev/null +++ b/latest/cases/00819/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00819/output.heta b/latest/cases/00819/output.heta new file mode 100644 index 000000000..068d8b273 --- /dev/null +++ b/latest/cases/00819/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00819/synopsis.txt b/latest/cases/00819/synopsis.txt new file mode 100644 index 000000000..0d3784037 --- /dev/null +++ b/latest/cases/00819/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00820/l2v5/heta-code/output.heta b/latest/cases/00820/l2v5/heta-code/output.heta new file mode 100644 index 000000000..71b80f9a8 --- /dev/null +++ b/latest/cases/00820/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00820/l2v5/index.heta b/latest/cases/00820/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00820/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00820/l2v5/json/output.json b/latest/cases/00820/l2v5/json/output.json new file mode 100644 index 000000000..bda3a7321 --- /dev/null +++ b/latest/cases/00820/l2v5/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00820/l3v2/heta-code/output.heta b/latest/cases/00820/l3v2/heta-code/output.heta new file mode 100644 index 000000000..309d1f5d8 --- /dev/null +++ b/latest/cases/00820/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00820/l3v2/index.heta b/latest/cases/00820/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00820/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00820/l3v2/json/output.json b/latest/cases/00820/l3v2/json/output.json new file mode 100644 index 000000000..6f9153e13 --- /dev/null +++ b/latest/cases/00820/l3v2/json/output.json @@ -0,0 +1,81 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00820/model-sbml-l2v5.xml b/latest/cases/00820/model-sbml-l2v5.xml new file mode 100644 index 000000000..76403d47b --- /dev/null +++ b/latest/cases/00820/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00820/model-sbml-l3v2.xml b/latest/cases/00820/model-sbml-l3v2.xml new file mode 100644 index 000000000..37957d8eb --- /dev/null +++ b/latest/cases/00820/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00820/output.heta b/latest/cases/00820/output.heta new file mode 100644 index 000000000..72d50dc1e --- /dev/null +++ b/latest/cases/00820/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00820/synopsis.txt b/latest/cases/00820/synopsis.txt new file mode 100644 index 000000000..871bc58e0 --- /dev/null +++ b/latest/cases/00820/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00821/l2v5/heta-code/output.heta b/latest/cases/00821/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8d4d57c96 --- /dev/null +++ b/latest/cases/00821/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/00821/l2v5/index.heta b/latest/cases/00821/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00821/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00821/l2v5/json/output.json b/latest/cases/00821/l2v5/json/output.json new file mode 100644 index 000000000..eeeabf40f --- /dev/null +++ b/latest/cases/00821/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00821/l3v2/heta-code/output.heta b/latest/cases/00821/l3v2/heta-code/output.heta new file mode 100644 index 000000000..acf73df56 --- /dev/null +++ b/latest/cases/00821/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00821/l3v2/index.heta b/latest/cases/00821/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00821/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00821/l3v2/json/output.json b/latest/cases/00821/l3v2/json/output.json new file mode 100644 index 000000000..2c7a04eaf --- /dev/null +++ b/latest/cases/00821/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/00821/model-sbml-l2v5.xml b/latest/cases/00821/model-sbml-l2v5.xml new file mode 100644 index 000000000..243b97391 --- /dev/null +++ b/latest/cases/00821/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00821/model-sbml-l3v2.xml b/latest/cases/00821/model-sbml-l3v2.xml new file mode 100644 index 000000000..223c3fd9e --- /dev/null +++ b/latest/cases/00821/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00821/output.heta b/latest/cases/00821/output.heta new file mode 100644 index 000000000..81f19ec17 --- /dev/null +++ b/latest/cases/00821/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. Species S2 is labeled as an +SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00821/synopsis.txt b/latest/cases/00821/synopsis.txt new file mode 100644 index 000000000..778de2de7 --- /dev/null +++ b/latest/cases/00821/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. Species S2 is labeled as an +SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00822/l2v5/heta-code/output.heta b/latest/cases/00822/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d9536f2dc --- /dev/null +++ b/latest/cases/00822/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 0.4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/00822/l2v5/index.heta b/latest/cases/00822/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00822/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00822/l2v5/json/output.json b/latest/cases/00822/l2v5/json/output.json new file mode 100644 index 000000000..11471c73f --- /dev/null +++ b/latest/cases/00822/l2v5/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.4 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00822/l3v2/heta-code/output.heta b/latest/cases/00822/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cea6284d2 --- /dev/null +++ b/latest/cases/00822/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0.4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00822/l3v2/index.heta b/latest/cases/00822/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00822/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00822/l3v2/json/output.json b/latest/cases/00822/l3v2/json/output.json new file mode 100644 index 000000000..d54e99f1b --- /dev/null +++ b/latest/cases/00822/l3v2/json/output.json @@ -0,0 +1,81 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.4 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/00822/model-sbml-l2v5.xml b/latest/cases/00822/model-sbml-l2v5.xml new file mode 100644 index 000000000..183d4abba --- /dev/null +++ b/latest/cases/00822/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00822/model-sbml-l3v2.xml b/latest/cases/00822/model-sbml-l3v2.xml new file mode 100644 index 000000000..a95ee3d90 --- /dev/null +++ b/latest/cases/00822/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00822/output.heta b/latest/cases/00822/output.heta new file mode 100644 index 000000000..41d7ee681 --- /dev/null +++ b/latest/cases/00822/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S3 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0.4$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0.4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00822/synopsis.txt b/latest/cases/00822/synopsis.txt new file mode 100644 index 000000000..3ea757b36 --- /dev/null +++ b/latest/cases/00822/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S3 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0.4$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00823/l2v5/heta-code/output.heta b/latest/cases/00823/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d40880804 --- /dev/null +++ b/latest/cases/00823/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00823/l2v5/index.heta b/latest/cases/00823/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00823/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00823/l2v5/json/output.json b/latest/cases/00823/l2v5/json/output.json new file mode 100644 index 000000000..d166497fe --- /dev/null +++ b/latest/cases/00823/l2v5/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00823/l3v2/heta-code/output.heta b/latest/cases/00823/l3v2/heta-code/output.heta new file mode 100644 index 000000000..820d9dfd5 --- /dev/null +++ b/latest/cases/00823/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00823/l3v2/index.heta b/latest/cases/00823/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00823/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00823/l3v2/json/output.json b/latest/cases/00823/l3v2/json/output.json new file mode 100644 index 000000000..678abc77e --- /dev/null +++ b/latest/cases/00823/l3v2/json/output.json @@ -0,0 +1,81 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00823/model-sbml-l2v5.xml b/latest/cases/00823/model-sbml-l2v5.xml new file mode 100644 index 000000000..cfef55efe --- /dev/null +++ b/latest/cases/00823/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00823/model-sbml-l3v2.xml b/latest/cases/00823/model-sbml-l3v2.xml new file mode 100644 index 000000000..1a6d18d80 --- /dev/null +++ b/latest/cases/00823/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00823/output.heta b/latest/cases/00823/output.heta new file mode 100644 index 000000000..0c5601343 --- /dev/null +++ b/latest/cases/00823/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S2 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00823/synopsis.txt b/latest/cases/00823/synopsis.txt new file mode 100644 index 000000000..0fbfbf47f --- /dev/null +++ b/latest/cases/00823/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S2 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00824/l2v5/heta-code/output.heta b/latest/cases/00824/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e6425300a --- /dev/null +++ b/latest/cases/00824/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/00824/l2v5/index.heta b/latest/cases/00824/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00824/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00824/l2v5/json/output.json b/latest/cases/00824/l2v5/json/output.json new file mode 100644 index 000000000..c510b45d9 --- /dev/null +++ b/latest/cases/00824/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00824/l3v2/heta-code/output.heta b/latest/cases/00824/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ee567459a --- /dev/null +++ b/latest/cases/00824/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00824/l3v2/index.heta b/latest/cases/00824/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00824/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00824/l3v2/json/output.json b/latest/cases/00824/l3v2/json/output.json new file mode 100644 index 000000000..187feecb8 --- /dev/null +++ b/latest/cases/00824/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/00824/model-sbml-l2v5.xml b/latest/cases/00824/model-sbml-l2v5.xml new file mode 100644 index 000000000..66115635c --- /dev/null +++ b/latest/cases/00824/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00824/model-sbml-l3v2.xml b/latest/cases/00824/model-sbml-l3v2.xml new file mode 100644 index 000000000..c179ed803 --- /dev/null +++ b/latest/cases/00824/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00824/output.heta b/latest/cases/00824/output.heta new file mode 100644 index 000000000..ab579f198 --- /dev/null +++ b/latest/cases/00824/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> 2S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00824/synopsis.txt b/latest/cases/00824/synopsis.txt new file mode 100644 index 000000000..ab22c1404 --- /dev/null +++ b/latest/cases/00824/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> 2S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00825/l2v5/heta-code/output.heta b/latest/cases/00825/l2v5/heta-code/output.heta new file mode 100644 index 000000000..23ea070fb --- /dev/null +++ b/latest/cases/00825/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/00825/l2v5/index.heta b/latest/cases/00825/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00825/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00825/l2v5/json/output.json b/latest/cases/00825/l2v5/json/output.json new file mode 100644 index 000000000..75fd0f2d9 --- /dev/null +++ b/latest/cases/00825/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00825/l3v2/heta-code/output.heta b/latest/cases/00825/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4cc8c156e --- /dev/null +++ b/latest/cases/00825/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00825/l3v2/index.heta b/latest/cases/00825/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00825/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00825/l3v2/json/output.json b/latest/cases/00825/l3v2/json/output.json new file mode 100644 index 000000000..292fa3dfb --- /dev/null +++ b/latest/cases/00825/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/00825/model-sbml-l2v5.xml b/latest/cases/00825/model-sbml-l2v5.xml new file mode 100644 index 000000000..0878fb754 --- /dev/null +++ b/latest/cases/00825/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00825/model-sbml-l3v2.xml b/latest/cases/00825/model-sbml-l3v2.xml new file mode 100644 index 000000000..d54132b53 --- /dev/null +++ b/latest/cases/00825/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00825/output.heta b/latest/cases/00825/output.heta new file mode 100644 index 000000000..7791feb86 --- /dev/null +++ b/latest/cases/00825/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/00825/synopsis.txt b/latest/cases/00825/synopsis.txt new file mode 100644 index 000000000..3c36c88ca --- /dev/null +++ b/latest/cases/00825/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00826/l2v5/heta-code/output.heta b/latest/cases/00826/l2v5/heta-code/output.heta new file mode 100644 index 000000000..eee8bdf7a --- /dev/null +++ b/latest/cases/00826/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + 2*S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00826/l2v5/index.heta b/latest/cases/00826/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00826/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00826/l2v5/json/output.json b/latest/cases/00826/l2v5/json/output.json new file mode 100644 index 000000000..bab975b7e --- /dev/null +++ b/latest/cases/00826/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00826/l3v2/heta-code/output.heta b/latest/cases/00826/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f13d15db5 --- /dev/null +++ b/latest/cases/00826/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + 2*S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00826/l3v2/index.heta b/latest/cases/00826/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00826/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00826/l3v2/json/output.json b/latest/cases/00826/l3v2/json/output.json new file mode 100644 index 000000000..e317ea4e3 --- /dev/null +++ b/latest/cases/00826/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00826/model-sbml-l2v5.xml b/latest/cases/00826/model-sbml-l2v5.xml new file mode 100644 index 000000000..44217d6bd --- /dev/null +++ b/latest/cases/00826/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00826/model-sbml-l3v2.xml b/latest/cases/00826/model-sbml-l3v2.xml new file mode 100644 index 000000000..a5bc34b5f --- /dev/null +++ b/latest/cases/00826/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00826/output.heta b/latest/cases/00826/output.heta new file mode 100644 index 000000000..e5dc61073 --- /dev/null +++ b/latest/cases/00826/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + 2S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + 2*S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00826/synopsis.txt b/latest/cases/00826/synopsis.txt new file mode 100644 index 000000000..87d4623d0 --- /dev/null +++ b/latest/cases/00826/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + 2S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00827/l2v5/build.log b/latest/cases/00827/l2v5/build.log new file mode 100644 index 000000000..ca882c979 --- /dev/null +++ b/latest/cases/00827/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00827/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00827/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00827/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00827/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00827/l2v5/index.heta b/latest/cases/00827/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00827/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00827/l3v2/index.heta b/latest/cases/00827/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00827/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00827/model-sbml-l2v5.xml b/latest/cases/00827/model-sbml-l2v5.xml new file mode 100644 index 000000000..1da15d032 --- /dev/null +++ b/latest/cases/00827/model-sbml-l2v5.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00827/synopsis.txt b/latest/cases/00827/synopsis.txt new file mode 100644 index 000000000..80e52fc6c --- /dev/null +++ b/latest/cases/00827/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are two species called +S1 and S2 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> (4 * p1)S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00828/l2v5/build.log b/latest/cases/00828/l2v5/build.log new file mode 100644 index 000000000..d4f72de1a --- /dev/null +++ b/latest/cases/00828/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00828/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00828/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00828/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00828/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00828/l2v5/index.heta b/latest/cases/00828/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00828/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00828/l3v2/index.heta b/latest/cases/00828/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00828/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00828/model-sbml-l2v5.xml b/latest/cases/00828/model-sbml-l2v5.xml new file mode 100644 index 000000000..f66f12eb9 --- /dev/null +++ b/latest/cases/00828/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00828/synopsis.txt b/latest/cases/00828/synopsis.txt new file mode 100644 index 000000000..ea03cda07 --- /dev/null +++ b/latest/cases/00828/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00829/l2v5/build.log b/latest/cases/00829/l2v5/build.log new file mode 100644 index 000000000..351c8faa2 --- /dev/null +++ b/latest/cases/00829/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00829/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00829/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00829/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00829/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00829/l2v5/index.heta b/latest/cases/00829/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00829/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00829/l3v2/index.heta b/latest/cases/00829/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00829/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00829/model-sbml-l2v5.xml b/latest/cases/00829/model-sbml-l2v5.xml new file mode 100644 index 000000000..b0a2ab8e5 --- /dev/null +++ b/latest/cases/00829/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00829/synopsis.txt b/latest/cases/00829/synopsis.txt new file mode 100644 index 000000000..a312bfc79 --- /dev/null +++ b/latest/cases/00829/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + (4 * p1)S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00830/l2v5/heta-code/output.heta b/latest/cases/00830/l2v5/heta-code/output.heta new file mode 100644 index 000000000..02ab6bacd --- /dev/null +++ b/latest/cases/00830/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (kf * S3 + (-1) * kr * S4); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; + diff --git a/latest/cases/00830/l2v5/index.heta b/latest/cases/00830/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00830/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00830/l2v5/json/output.json b/latest/cases/00830/l2v5/json/output.json new file mode 100644 index 000000000..f6b931927 --- /dev/null +++ b/latest/cases/00830/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "kf__reaction1_local", + "num": 0.8 + }, + { + "class": "Const", + "id": "kr__reaction1_local", + "num": 0.06 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * (kf * S3 + (-1) * kr * S4)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00830/l3v2/heta-code/output.heta b/latest/cases/00830/l3v2/heta-code/output.heta new file mode 100644 index 000000000..91857ffbc --- /dev/null +++ b/latest/cases/00830/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (kf * S3 + (-1) * kr * S4); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00830/l3v2/index.heta b/latest/cases/00830/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00830/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00830/l3v2/json/output.json b/latest/cases/00830/l3v2/json/output.json new file mode 100644 index 000000000..77922183a --- /dev/null +++ b/latest/cases/00830/l3v2/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "kf__reaction1_local", + "num": 0.8 + }, + { + "class": "Const", + "id": "kr__reaction1_local", + "num": 0.06 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * (kf * S3 + (-1) * kr * S4)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/00830/model-sbml-l2v5.xml b/latest/cases/00830/model-sbml-l2v5.xml new file mode 100644 index 000000000..cad7f7404 --- /dev/null +++ b/latest/cases/00830/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S3 + + + + -1 + kr + S4 + + + + + + + + + diff --git a/latest/cases/00830/model-sbml-l3v2.xml b/latest/cases/00830/model-sbml-l3v2.xml new file mode 100644 index 000000000..ee9f45914 --- /dev/null +++ b/latest/cases/00830/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S3 + + + + -1 + kr + S4 + + + + + + + + + diff --git a/latest/cases/00830/output.heta b/latest/cases/00830/output.heta new file mode 100644 index 000000000..f61ea922d --- /dev/null +++ b/latest/cases/00830/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Two reversible reactions with global and local parameters. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |] + +Reaction S1 <-> S2 defines two local parameters kf and kr which have a +scope local to the defining reaction and are different from the global parameters kf +and kr used in the Reaction S3 <-> S4. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Value of local parameter kf |$0.8$ |second^-1^ | +|Value of local parameter kr |$0.06$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (kf * S3 + (-1) * kr * S4); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00830/synopsis.txt b/latest/cases/00830/synopsis.txt new file mode 100644 index 000000000..5c43951eb --- /dev/null +++ b/latest/cases/00830/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Two reversible reactions with global and local parameters. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |] + +Reaction S1 <-> S2 defines two local parameters kf and kr which have a +scope local to the defining reaction and are different from the global parameters kf +and kr used in the Reaction S3 <-> S4. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Value of local parameter kf |$0.8$ |second^-1^ | +|Value of local parameter kr |$0.06$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00831/l2v5/heta-code/output.heta b/latest/cases/00831/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f4e9e2651 --- /dev/null +++ b/latest/cases/00831/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf__reaction2_local @Const { } = 0.9; +kr__reaction2_local @Const { } = 0.075; + diff --git a/latest/cases/00831/l2v5/index.heta b/latest/cases/00831/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00831/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00831/l2v5/json/output.json b/latest/cases/00831/l2v5/json/output.json new file mode 100644 index 000000000..3fbb8a6de --- /dev/null +++ b/latest/cases/00831/l2v5/json/output.json @@ -0,0 +1,136 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "kf__reaction1_local", + "num": 0.8 + }, + { + "class": "Const", + "id": "kr__reaction1_local", + "num": 0.06 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf__reaction2_local", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr__reaction2_local", + "num": 0.075 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00831/l3v2/heta-code/output.heta b/latest/cases/00831/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c8dc31bb0 --- /dev/null +++ b/latest/cases/00831/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf__reaction2_local @Const { } = 0.9; +kr__reaction2_local @Const { } = 0.075; + diff --git a/latest/cases/00831/l3v2/index.heta b/latest/cases/00831/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00831/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00831/l3v2/json/output.json b/latest/cases/00831/l3v2/json/output.json new file mode 100644 index 000000000..2b83d1ccf --- /dev/null +++ b/latest/cases/00831/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "kf__reaction1_local", + "num": 0.8 + }, + { + "class": "Const", + "id": "kr__reaction1_local", + "num": 0.06 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf__reaction2_local", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr__reaction2_local", + "num": 0.075 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00831/model-sbml-l2v5.xml b/latest/cases/00831/model-sbml-l2v5.xml new file mode 100644 index 000000000..13dc9a397 --- /dev/null +++ b/latest/cases/00831/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S3 + + + + -1 + kr + S4 + + + + + + + + + + + + + diff --git a/latest/cases/00831/model-sbml-l3v2.xml b/latest/cases/00831/model-sbml-l3v2.xml new file mode 100644 index 000000000..2074697d2 --- /dev/null +++ b/latest/cases/00831/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S3 + + + + -1 + kr + S4 + + + + + + + + + + + + + diff --git a/latest/cases/00831/output.heta b/latest/cases/00831/output.heta new file mode 100644 index 000000000..ac938efa5 --- /dev/null +++ b/latest/cases/00831/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Two reversible reactions with local parameters. +componentTags: Compartment, Species, Reaction +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |] + +Both reactions define two local parameters kf and kr which have a +scope local to the defining reaction. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of local parameter kf (R1) |$0.8$ |second^-1^ | +|Value of local parameter kr (R1) |$0.06$ |second^-1^ | +|Value of local parameter kf (R1) |$0.9$ |second^-1^ | +|Value of local parameter kr (R2) |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf__reaction2_local @Const { } = 0.9; +kr__reaction2_local @Const { } = 0.075; + diff --git a/latest/cases/00831/synopsis.txt b/latest/cases/00831/synopsis.txt new file mode 100644 index 000000000..df7f9da5f --- /dev/null +++ b/latest/cases/00831/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Two reversible reactions with local parameters. +componentTags: Compartment, Species, Reaction +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |] + +Both reactions define two local parameters kf and kr which have a +scope local to the defining reaction. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of local parameter kf (R1) |$0.8$ |second^-1^ | +|Value of local parameter kr (R1) |$0.06$ |second^-1^ | +|Value of local parameter kf (R1) |$0.9$ |second^-1^ | +|Value of local parameter kr (R2) |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00832/l2v5/heta-code/output.heta b/latest/cases/00832/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c82e99b74 --- /dev/null +++ b/latest/cases/00832/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (multiply(kf, S1) + (-1) * kr * S2); + +kf @Record 'kf' { } .= 0.59; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/00832/l2v5/index.heta b/latest/cases/00832/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00832/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00832/l2v5/json/output.json b/latest/cases/00832/l2v5/json/output.json new file mode 100644 index 000000000..f25f7026e --- /dev/null +++ b/latest/cases/00832/l2v5/json/output.json @@ -0,0 +1,103 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (multiply(kf, S1) + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.59" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00832/l3v2/heta-code/output.heta b/latest/cases/00832/l3v2/heta-code/output.heta new file mode 100644 index 000000000..64194a3e5 --- /dev/null +++ b/latest/cases/00832/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (multiply(kf, S1) + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.59; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00832/l3v2/index.heta b/latest/cases/00832/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00832/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00832/l3v2/json/output.json b/latest/cases/00832/l3v2/json/output.json new file mode 100644 index 000000000..9d242c931 --- /dev/null +++ b/latest/cases/00832/l3v2/json/output.json @@ -0,0 +1,75 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (multiply(kf, S1) + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.59 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00832/model-sbml-l2v5.xml b/latest/cases/00832/model-sbml-l2v5.xml new file mode 100644 index 000000000..97c319c2f --- /dev/null +++ b/latest/cases/00832/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + multiply + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00832/model-sbml-l3v2.xml b/latest/cases/00832/model-sbml-l3v2.xml new file mode 100644 index 000000000..6bb9edbf0 --- /dev/null +++ b/latest/cases/00832/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + multiply + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/00832/output.heta b/latest/cases/00832/output.heta new file mode 100644 index 000000000..72641fac4 --- /dev/null +++ b/latest/cases/00832/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(multiply(kf, S1) - kr * S2) * C$ |] + +The reaction applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.59$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (multiply(kf, S1) + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.59; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/00832/synopsis.txt b/latest/cases/00832/synopsis.txt new file mode 100644 index 000000000..383a1a2e0 --- /dev/null +++ b/latest/cases/00832/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(multiply(kf, S1) - kr * S2) * C$ |] + +The reaction applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.59$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00833/l2v5/heta-code/output.heta b/latest/cases/00833/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d15062580 --- /dev/null +++ b/latest/cases/00833/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.11; + diff --git a/latest/cases/00833/l2v5/index.heta b/latest/cases/00833/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00833/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00833/l2v5/json/output.json b/latest/cases/00833/l2v5/json/output.json new file mode 100644 index 000000000..e27866c83 --- /dev/null +++ b/latest/cases/00833/l2v5/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.11" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00833/l3v2/heta-code/output.heta b/latest/cases/00833/l3v2/heta-code/output.heta new file mode 100644 index 000000000..acbb30c10 --- /dev/null +++ b/latest/cases/00833/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.11; + diff --git a/latest/cases/00833/l3v2/index.heta b/latest/cases/00833/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00833/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00833/l3v2/json/output.json b/latest/cases/00833/l3v2/json/output.json new file mode 100644 index 000000000..f2ef11435 --- /dev/null +++ b/latest/cases/00833/l3v2/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.11 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00833/model-sbml-l2v5.xml b/latest/cases/00833/model-sbml-l2v5.xml new file mode 100644 index 000000000..b38d4bcf6 --- /dev/null +++ b/latest/cases/00833/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + multiply + + multiply + kf + S1 + + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00833/model-sbml-l3v2.xml b/latest/cases/00833/model-sbml-l3v2.xml new file mode 100644 index 000000000..bbb9c74b0 --- /dev/null +++ b/latest/cases/00833/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + multiply + + multiply + kf + S1 + + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00833/output.heta b/latest/cases/00833/output.heta new file mode 100644 index 000000000..00e398059 --- /dev/null +++ b/latest/cases/00833/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(multiply(multiply(kf, S1), S2) - kr * S3) * C$ |] + +The reaction applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.11$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.11; + diff --git a/latest/cases/00833/synopsis.txt b/latest/cases/00833/synopsis.txt new file mode 100644 index 000000000..b73bca2a5 --- /dev/null +++ b/latest/cases/00833/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(multiply(multiply(kf, S1), S2) - kr * S3) * C$ |] + +The reaction applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.11$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00834/l2v5/heta-code/output.heta b/latest/cases/00834/l2v5/heta-code/output.heta new file mode 100644 index 000000000..13851d8e7 --- /dev/null +++ b/latest/cases/00834/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; +minus #defineFunction { arguments: [x, y], math: x + (-1) * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * minus(multiply(kf, S1), kr * S2 * S3); + +kf @Record 'kf' { } .= 1.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00834/l2v5/index.heta b/latest/cases/00834/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00834/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00834/l2v5/json/output.json b/latest/cases/00834/l2v5/json/output.json new file mode 100644 index 000000000..f89d7b7b8 --- /dev/null +++ b/latest/cases/00834/l2v5/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * minus(multiply(kf, S1), kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + }, + { + "id": "minus", + "arguments": [ + "x", + "y" + ], + "math": "x + (-1) * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00834/l3v2/heta-code/output.heta b/latest/cases/00834/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b29309e7e --- /dev/null +++ b/latest/cases/00834/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; +minus #defineFunction { arguments: [x, y], math: x + (-1) * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * minus(multiply(kf, S1), kr * S2 * S3); + +kf @Const 'kf' { } = 1.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00834/l3v2/index.heta b/latest/cases/00834/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00834/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00834/l3v2/json/output.json b/latest/cases/00834/l3v2/json/output.json new file mode 100644 index 000000000..680167a60 --- /dev/null +++ b/latest/cases/00834/l3v2/json/output.json @@ -0,0 +1,98 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * minus(multiply(kf, S1), kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + }, + { + "id": "minus", + "arguments": [ + "x", + "y" + ], + "math": "x + (-1) * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00834/model-sbml-l2v5.xml b/latest/cases/00834/model-sbml-l2v5.xml new file mode 100644 index 000000000..fbeb2f87f --- /dev/null +++ b/latest/cases/00834/model-sbml-l2v5.xml @@ -0,0 +1,90 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + minus + + multiply + kf + S1 + + + + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00834/model-sbml-l3v2.xml b/latest/cases/00834/model-sbml-l3v2.xml new file mode 100644 index 000000000..a9aad51f4 --- /dev/null +++ b/latest/cases/00834/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + minus + + multiply + kf + S1 + + + + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00834/output.heta b/latest/cases/00834/output.heta new file mode 100644 index 000000000..eeb0a0e59 --- /dev/null +++ b/latest/cases/00834/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(minus(multiply(kf, S1), kr * S2 * S3)) * C$ |] + +The reaction applies two functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | minus | x, y | $x - y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; +minus #defineFunction { arguments: [x, y], math: x + (-1) * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * minus(multiply(kf, S1), kr * S2 * S3); + +kf @Const 'kf' { } = 1.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00834/synopsis.txt b/latest/cases/00834/synopsis.txt new file mode 100644 index 000000000..1d6b7f739 --- /dev/null +++ b/latest/cases/00834/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(minus(multiply(kf, S1), kr * S2 * S3)) * C$ |] + +The reaction applies two functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | minus | x, y | $x - y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00835/l2v5/heta-code/output.heta b/latest/cases/00835/l2v5/heta-code/output.heta new file mode 100644 index 000000000..954faecc6 --- /dev/null +++ b/latest/cases/00835/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00835/l2v5/index.heta b/latest/cases/00835/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00835/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00835/l2v5/json/output.json b/latest/cases/00835/l2v5/json/output.json new file mode 100644 index 000000000..0d5bd8615 --- /dev/null +++ b/latest/cases/00835/l2v5/json/output.json @@ -0,0 +1,116 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00835/l3v2/heta-code/output.heta b/latest/cases/00835/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a2e9d51eb --- /dev/null +++ b/latest/cases/00835/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00835/l3v2/index.heta b/latest/cases/00835/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00835/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00835/l3v2/json/output.json b/latest/cases/00835/l3v2/json/output.json new file mode 100644 index 000000000..3796bd065 --- /dev/null +++ b/latest/cases/00835/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00835/model-sbml-l2v5.xml b/latest/cases/00835/model-sbml-l2v5.xml new file mode 100644 index 000000000..cceaa7d92 --- /dev/null +++ b/latest/cases/00835/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00835/model-sbml-l3v2.xml b/latest/cases/00835/model-sbml-l3v2.xml new file mode 100644 index 000000000..f50dfe7a0 --- /dev/null +++ b/latest/cases/00835/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00835/output.heta b/latest/cases/00835/output.heta new file mode 100644 index 000000000..8e05dfeb4 --- /dev/null +++ b/latest/cases/00835/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00835/synopsis.txt b/latest/cases/00835/synopsis.txt new file mode 100644 index 000000000..98c592182 --- /dev/null +++ b/latest/cases/00835/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00836/l2v5/heta-code/output.heta b/latest/cases/00836/l2v5/heta-code/output.heta new file mode 100644 index 000000000..954faecc6 --- /dev/null +++ b/latest/cases/00836/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00836/l2v5/index.heta b/latest/cases/00836/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00836/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00836/l2v5/json/output.json b/latest/cases/00836/l2v5/json/output.json new file mode 100644 index 000000000..0d5bd8615 --- /dev/null +++ b/latest/cases/00836/l2v5/json/output.json @@ -0,0 +1,116 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00836/l3v2/heta-code/output.heta b/latest/cases/00836/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a2e9d51eb --- /dev/null +++ b/latest/cases/00836/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00836/l3v2/index.heta b/latest/cases/00836/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00836/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00836/l3v2/json/output.json b/latest/cases/00836/l3v2/json/output.json new file mode 100644 index 000000000..3796bd065 --- /dev/null +++ b/latest/cases/00836/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00836/model-sbml-l2v5.xml b/latest/cases/00836/model-sbml-l2v5.xml new file mode 100644 index 000000000..c0a7a6866 --- /dev/null +++ b/latest/cases/00836/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00836/model-sbml-l3v2.xml b/latest/cases/00836/model-sbml-l3v2.xml new file mode 100644 index 000000000..1aa12acd1 --- /dev/null +++ b/latest/cases/00836/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00836/output.heta b/latest/cases/00836/output.heta new file mode 100644 index 000000000..461bc3c92 --- /dev/null +++ b/latest/cases/00836/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00836/synopsis.txt b/latest/cases/00836/synopsis.txt new file mode 100644 index 000000000..67864acdc --- /dev/null +++ b/latest/cases/00836/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00837/l2v5/heta-code/output.heta b/latest/cases/00837/l2v5/heta-code/output.heta new file mode 100644 index 000000000..954faecc6 --- /dev/null +++ b/latest/cases/00837/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/00837/l2v5/index.heta b/latest/cases/00837/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00837/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00837/l2v5/json/output.json b/latest/cases/00837/l2v5/json/output.json new file mode 100644 index 000000000..0d5bd8615 --- /dev/null +++ b/latest/cases/00837/l2v5/json/output.json @@ -0,0 +1,116 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00837/l3v2/heta-code/output.heta b/latest/cases/00837/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a2e9d51eb --- /dev/null +++ b/latest/cases/00837/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00837/l3v2/index.heta b/latest/cases/00837/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00837/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00837/l3v2/json/output.json b/latest/cases/00837/l3v2/json/output.json new file mode 100644 index 000000000..3796bd065 --- /dev/null +++ b/latest/cases/00837/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 * S2 + (-1) * kr * S3)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00837/model-sbml-l2v5.xml b/latest/cases/00837/model-sbml-l2v5.xml new file mode 100644 index 000000000..518b633bf --- /dev/null +++ b/latest/cases/00837/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00837/model-sbml-l3v2.xml b/latest/cases/00837/model-sbml-l3v2.xml new file mode 100644 index 000000000..eb31de74b --- /dev/null +++ b/latest/cases/00837/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00837/output.heta b/latest/cases/00837/output.heta new file mode 100644 index 000000000..ab8156806 --- /dev/null +++ b/latest/cases/00837/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, }; +reaction1 := C * (kf * S1 * S2 + (-1) * kr * S3); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/00837/synopsis.txt b/latest/cases/00837/synopsis.txt new file mode 100644 index 000000000..53336326f --- /dev/null +++ b/latest/cases/00837/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00838/l2v5/heta-code/output.heta b/latest/cases/00838/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e3f754fce --- /dev/null +++ b/latest/cases/00838/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { }; +kf := 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00838/l2v5/index.heta b/latest/cases/00838/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00838/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00838/l2v5/json/output.json b/latest/cases/00838/l2v5/json/output.json new file mode 100644 index 000000000..7e99f13d7 --- /dev/null +++ b/latest/cases/00838/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "ode_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00838/l3v2/heta-code/output.heta b/latest/cases/00838/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b6b6b87e0 --- /dev/null +++ b/latest/cases/00838/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { }; +kf := 2.5; + +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00838/l3v2/index.heta b/latest/cases/00838/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00838/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00838/l3v2/json/output.json b/latest/cases/00838/l3v2/json/output.json new file mode 100644 index 000000000..956c1ea70 --- /dev/null +++ b/latest/cases/00838/l3v2/json/output.json @@ -0,0 +1,82 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "ode_": "2.5" + } + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00838/model-sbml-l2v5.xml b/latest/cases/00838/model-sbml-l2v5.xml new file mode 100644 index 000000000..d6bef634f --- /dev/null +++ b/latest/cases/00838/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + 2.5 + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00838/model-sbml-l3v2.xml b/latest/cases/00838/model-sbml-l3v2.xml new file mode 100644 index 000000000..f9eefaf85 --- /dev/null +++ b/latest/cases/00838/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2.5 + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00838/output.heta b/latest/cases/00838/output.heta new file mode 100644 index 000000000..e1271e85a --- /dev/null +++ b/latest/cases/00838/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to parameter kf: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | kf | $2.5$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$undeclared$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { }; +kf := 2.5; + +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00838/synopsis.txt b/latest/cases/00838/synopsis.txt new file mode 100644 index 000000000..8173e09ae --- /dev/null +++ b/latest/cases/00838/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to parameter kf: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | kf | $2.5$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$undeclared$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00839/l2v5/heta-code/output.heta b/latest/cases/00839/l2v5/heta-code/output.heta new file mode 100644 index 000000000..071d7e0fb --- /dev/null +++ b/latest/cases/00839/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, }; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00839/l2v5/index.heta b/latest/cases/00839/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00839/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00839/l2v5/json/output.json b/latest/cases/00839/l2v5/json/output.json new file mode 100644 index 000000000..2a698447a --- /dev/null +++ b/latest/cases/00839/l2v5/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "ode_": "0.5 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00839/l3v2/heta-code/output.heta b/latest/cases/00839/l3v2/heta-code/output.heta new file mode 100644 index 000000000..076d3c95b --- /dev/null +++ b/latest/cases/00839/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00839/l3v2/index.heta b/latest/cases/00839/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00839/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00839/l3v2/json/output.json b/latest/cases/00839/l3v2/json/output.json new file mode 100644 index 000000000..9bbe8a4a4 --- /dev/null +++ b/latest/cases/00839/l3v2/json/output.json @@ -0,0 +1,90 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "0.5 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00839/model-sbml-l2v5.xml b/latest/cases/00839/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef38bfdc4 --- /dev/null +++ b/latest/cases/00839/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + S1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00839/model-sbml-l3v2.xml b/latest/cases/00839/model-sbml-l3v2.xml new file mode 100644 index 000000000..a127aa106 --- /dev/null +++ b/latest/cases/00839/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + S1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00839/output.heta b/latest/cases/00839/output.heta new file mode 100644 index 000000000..a8b411b14 --- /dev/null +++ b/latest/cases/00839/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $0.5 * S1$ |] + +In this case there is no initial value declared for species S4. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$undeclared$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00839/synopsis.txt b/latest/cases/00839/synopsis.txt new file mode 100644 index 000000000..7e6ad7f43 --- /dev/null +++ b/latest/cases/00839/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $0.5 * S1$ |] + +In this case there is no initial value declared for species S4. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$undeclared$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00840/l2v5/heta-code/output.heta b/latest/cases/00840/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3bcbec651 --- /dev/null +++ b/latest/cases/00840/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 5 / C; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00840/l2v5/index.heta b/latest/cases/00840/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00840/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00840/l2v5/json/output.json b/latest/cases/00840/l2v5/json/output.json new file mode 100644 index 000000000..4ac6baea8 --- /dev/null +++ b/latest/cases/00840/l2v5/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "5 / C", + "ode_": "0.5 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00840/l3v2/heta-code/output.heta b/latest/cases/00840/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e3de1aa89 --- /dev/null +++ b/latest/cases/00840/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00840/l3v2/index.heta b/latest/cases/00840/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00840/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00840/l3v2/json/output.json b/latest/cases/00840/l3v2/json/output.json new file mode 100644 index 000000000..20e94dc71 --- /dev/null +++ b/latest/cases/00840/l3v2/json/output.json @@ -0,0 +1,91 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5 / C", + "ode_": "0.5 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00840/model-sbml-l2v5.xml b/latest/cases/00840/model-sbml-l2v5.xml new file mode 100644 index 000000000..7829e6e81 --- /dev/null +++ b/latest/cases/00840/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + S1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00840/model-sbml-l3v2.xml b/latest/cases/00840/model-sbml-l3v2.xml new file mode 100644 index 000000000..712af7e60 --- /dev/null +++ b/latest/cases/00840/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + S1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00840/output.heta b/latest/cases/00840/output.heta new file mode 100644 index 000000000..541d93a35 --- /dev/null +++ b/latest/cases/00840/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $0.5 * S1$ |] + +In this case the initial value declared for species S4 is inconsistent +with the value calculated using the assignmentRule. The calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00840/synopsis.txt b/latest/cases/00840/synopsis.txt new file mode 100644 index 000000000..ad0e4c37b --- /dev/null +++ b/latest/cases/00840/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $0.5 * S1$ |] + +In this case the initial value declared for species S4 is inconsistent +with the value calculated using the assignmentRule. The calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00841/l2v5/heta-code/output.heta b/latest/cases/00841/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a6a6c4ae9 --- /dev/null +++ b/latest/cases/00841/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00841/l2v5/index.heta b/latest/cases/00841/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00841/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00841/l2v5/json/output.json b/latest/cases/00841/l2v5/json/output.json new file mode 100644 index 000000000..0e8cf6a58 --- /dev/null +++ b/latest/cases/00841/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-0.5) * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00841/l3v2/heta-code/output.heta b/latest/cases/00841/l3v2/heta-code/output.heta new file mode 100644 index 000000000..992f0250f --- /dev/null +++ b/latest/cases/00841/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00841/l3v2/index.heta b/latest/cases/00841/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00841/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00841/l3v2/json/output.json b/latest/cases/00841/l3v2/json/output.json new file mode 100644 index 000000000..b5b6edd6b --- /dev/null +++ b/latest/cases/00841/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-0.5) * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00841/model-sbml-l2v5.xml b/latest/cases/00841/model-sbml-l2v5.xml new file mode 100644 index 000000000..c8ea07760 --- /dev/null +++ b/latest/cases/00841/model-sbml-l2v5.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + -0.5 + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00841/model-sbml-l3v2.xml b/latest/cases/00841/model-sbml-l3v2.xml new file mode 100644 index 000000000..680ec6b7c --- /dev/null +++ b/latest/cases/00841/model-sbml-l3v2.xml @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -0.5 + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00841/output.heta b/latest/cases/00841/output.heta new file mode 100644 index 000000000..3c95a009a --- /dev/null +++ b/latest/cases/00841/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $-0.5 * (kf * S1 - kr * S2 * S3)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00841/synopsis.txt b/latest/cases/00841/synopsis.txt new file mode 100644 index 000000000..12b167ab3 --- /dev/null +++ b/latest/cases/00841/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $-0.5 * (kf * S1 - kr * S2 * S3)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00842/l2v5/heta-code/output.heta b/latest/cases/00842/l2v5/heta-code/output.heta new file mode 100644 index 000000000..74dec62a4 --- /dev/null +++ b/latest/cases/00842/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * S1; + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00842/l2v5/index.heta b/latest/cases/00842/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00842/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00842/l2v5/json/output.json b/latest/cases/00842/l2v5/json/output.json new file mode 100644 index 000000000..5e5ac0e6b --- /dev/null +++ b/latest/cases/00842/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-0.5) * S1" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00842/l3v2/heta-code/output.heta b/latest/cases/00842/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c7e436dba --- /dev/null +++ b/latest/cases/00842/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * S1; + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00842/l3v2/index.heta b/latest/cases/00842/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00842/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00842/l3v2/json/output.json b/latest/cases/00842/l3v2/json/output.json new file mode 100644 index 000000000..6cad69d0f --- /dev/null +++ b/latest/cases/00842/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-0.5) * S1" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00842/model-sbml-l2v5.xml b/latest/cases/00842/model-sbml-l2v5.xml new file mode 100644 index 000000000..65c0cb525 --- /dev/null +++ b/latest/cases/00842/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + -0.5 + S1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00842/model-sbml-l3v2.xml b/latest/cases/00842/model-sbml-l3v2.xml new file mode 100644 index 000000000..61243a3c8 --- /dev/null +++ b/latest/cases/00842/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -0.5 + S1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00842/output.heta b/latest/cases/00842/output.heta new file mode 100644 index 000000000..8a31187c5 --- /dev/null +++ b/latest/cases/00842/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $-0.5 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * S1; + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00842/synopsis.txt b/latest/cases/00842/synopsis.txt new file mode 100644 index 000000000..da5ed1346 --- /dev/null +++ b/latest/cases/00842/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $-0.5 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00843/l2v5/heta-code/output.heta b/latest/cases/00843/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b0d84292c --- /dev/null +++ b/latest/cases/00843/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 0.15; + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/00843/l2v5/index.heta b/latest/cases/00843/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00843/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00843/l2v5/json/output.json b/latest/cases/00843/l2v5/json/output.json new file mode 100644 index 000000000..f6a349519 --- /dev/null +++ b/latest/cases/00843/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00843/l3v2/heta-code/output.heta b/latest/cases/00843/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5c82557c1 --- /dev/null +++ b/latest/cases/00843/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 0.15; + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00843/l3v2/index.heta b/latest/cases/00843/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00843/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00843/l3v2/json/output.json b/latest/cases/00843/l3v2/json/output.json new file mode 100644 index 000000000..14bfec7b3 --- /dev/null +++ b/latest/cases/00843/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00843/model-sbml-l2v5.xml b/latest/cases/00843/model-sbml-l2v5.xml new file mode 100644 index 000000000..a4ea238be --- /dev/null +++ b/latest/cases/00843/model-sbml-l2v5.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00843/model-sbml-l3v2.xml b/latest/cases/00843/model-sbml-l3v2.xml new file mode 100644 index 000000000..da9e6e336 --- /dev/null +++ b/latest/cases/00843/model-sbml-l3v2.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/00843/output.heta b/latest/cases/00843/output.heta new file mode 100644 index 000000000..bf344ba4f --- /dev/null +++ b/latest/cases/00843/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $0.15$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2 * S3); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 0.15; + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/00843/synopsis.txt b/latest/cases/00843/synopsis.txt new file mode 100644 index 000000000..1b268d46e --- /dev/null +++ b/latest/cases/00843/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $0.15$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00844/l2v5/build.log b/latest/cases/00844/l2v5/build.log new file mode 100644 index 000000000..811ae854a --- /dev/null +++ b/latest/cases/00844/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00844/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00844/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00844/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00844/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00844/l2v5/index.heta b/latest/cases/00844/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00844/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00844/l3v2/build.log b/latest/cases/00844/l3v2/build.log new file mode 100644 index 000000000..3d1d58c0b --- /dev/null +++ b/latest/cases/00844/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00844/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00844/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00844/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00844/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00844/l3v2/index.heta b/latest/cases/00844/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00844/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00844/model-sbml-l2v5.xml b/latest/cases/00844/model-sbml-l2v5.xml new file mode 100644 index 000000000..09c96cd2e --- /dev/null +++ b/latest/cases/00844/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + kf + -0.75 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00844/model-sbml-l3v2.xml b/latest/cases/00844/model-sbml-l3v2.xml new file mode 100644 index 000000000..bb941bbe8 --- /dev/null +++ b/latest/cases/00844/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + kf + -0.75 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00844/synopsis.txt b/latest/cases/00844/synopsis.txt new file mode 100644 index 000000000..7ccadfde6 --- /dev/null +++ b/latest/cases/00844/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: One reversible reaction with three species in one compartment with +an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called kf and kr. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $kf - 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter kf |$undeclared$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00845/l2v5/heta-code/output.heta b/latest/cases/00845/l2v5/heta-code/output.heta new file mode 100644 index 000000000..400a6554b --- /dev/null +++ b/latest/cases/00845/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00845/l2v5/index.heta b/latest/cases/00845/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00845/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00845/l2v5/json/output.json b/latest/cases/00845/l2v5/json/output.json new file mode 100644 index 000000000..be5760e8a --- /dev/null +++ b/latest/cases/00845/l2v5/json/output.json @@ -0,0 +1,101 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00845/l3v2/heta-code/output.heta b/latest/cases/00845/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f2b2b2770 --- /dev/null +++ b/latest/cases/00845/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00845/l3v2/index.heta b/latest/cases/00845/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00845/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00845/l3v2/json/output.json b/latest/cases/00845/l3v2/json/output.json new file mode 100644 index 000000000..eeb13413f --- /dev/null +++ b/latest/cases/00845/l3v2/json/output.json @@ -0,0 +1,73 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00845/model-sbml-l2v5.xml b/latest/cases/00845/model-sbml-l2v5.xml new file mode 100644 index 000000000..ba854fbc1 --- /dev/null +++ b/latest/cases/00845/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00845/model-sbml-l3v2.xml b/latest/cases/00845/model-sbml-l3v2.xml new file mode 100644 index 000000000..098be57e0 --- /dev/null +++ b/latest/cases/00845/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00845/output.heta b/latest/cases/00845/output.heta new file mode 100644 index 000000000..86e8ae15e --- /dev/null +++ b/latest/cases/00845/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: One reversible reactions with two species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The model contains one event that assigns values to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/00845/synopsis.txt b/latest/cases/00845/synopsis.txt new file mode 100644 index 000000000..ddee2ced8 --- /dev/null +++ b/latest/cases/00845/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: One reversible reactions with two species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The model contains one event that assigns values to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00846/l2v5/heta-code/output.heta b/latest/cases/00846/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f16433eec --- /dev/null +++ b/latest/cases/00846/l2v5/heta-code/output.heta @@ -0,0 +1,30 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 [event1]= S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (k1 * S3 + (-1) * k2 * S4); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.15; +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00846/l2v5/index.heta b/latest/cases/00846/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00846/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00846/l2v5/json/output.json b/latest/cases/00846/l2v5/json/output.json new file mode 100644 index 000000000..2c133ed6b --- /dev/null +++ b/latest/cases/00846/l2v5/json/output.json @@ -0,0 +1,156 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * (k1 * S3 + (-1) * k2 * S4)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00846/l3v2/heta-code/output.heta b/latest/cases/00846/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fd5dd98ac --- /dev/null +++ b/latest/cases/00846/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event1]= S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (k1 * S3 + (-1) * k2 * S4); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.15; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00846/l3v2/index.heta b/latest/cases/00846/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00846/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00846/l3v2/json/output.json b/latest/cases/00846/l3v2/json/output.json new file mode 100644 index 000000000..0d8a47e23 --- /dev/null +++ b/latest/cases/00846/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * (k1 * S3 + (-1) * k2 * S4)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.15 + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + } +] \ No newline at end of file diff --git a/latest/cases/00846/model-sbml-l2v5.xml b/latest/cases/00846/model-sbml-l2v5.xml new file mode 100644 index 000000000..ccb56e69a --- /dev/null +++ b/latest/cases/00846/model-sbml-l2v5.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00846/model-sbml-l3v2.xml b/latest/cases/00846/model-sbml-l3v2.xml new file mode 100644 index 000000000..b423a04b1 --- /dev/null +++ b/latest/cases/00846/model-sbml-l3v2.xml @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00846/output.heta b/latest/cases/00846/output.heta new file mode 100644 index 000000000..b92064ea9 --- /dev/null +++ b/latest/cases/00846/output.heta @@ -0,0 +1,73 @@ +/* +category: Test +synopsis: Two reversible reactions with four species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains one event that assigns values to both species S2 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | | | | $S4 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S4 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event1]= S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (k1 * S3 + (-1) * k2 * S4); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.15; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00846/synopsis.txt b/latest/cases/00846/synopsis.txt new file mode 100644 index 000000000..4a14e31a9 --- /dev/null +++ b/latest/cases/00846/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Two reversible reactions with four species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains one event that assigns values to both species S2 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | | | | $S4 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S4 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00847/l2v5/heta-code/output.heta b/latest/cases/00847/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2284f7d9e --- /dev/null +++ b/latest/cases/00847/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 [event2]= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (k1 * S3 + (-1) * k2 * S4); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.15; +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; +event2 @DSwitcher 'event2' { trigger: S3 < 0.75, }; + diff --git a/latest/cases/00847/l2v5/index.heta b/latest/cases/00847/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00847/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00847/l2v5/json/output.json b/latest/cases/00847/l2v5/json/output.json new file mode 100644 index 000000000..d074f1b7d --- /dev/null +++ b/latest/cases/00847/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C", + "event2": "0.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * (k1 * S3 + (-1) * k2 * S4)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00847/l3v2/heta-code/output.heta b/latest/cases/00847/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5555a130f --- /dev/null +++ b/latest/cases/00847/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event2]= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (k1 * S3 + (-1) * k2 * S4); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.15; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; +event2 @DSwitcher 'event2' { trigger: S3 < 0.75, }; + diff --git a/latest/cases/00847/l3v2/index.heta b/latest/cases/00847/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00847/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00847/l3v2/json/output.json b/latest/cases/00847/l3v2/json/output.json new file mode 100644 index 000000000..ac067c9cf --- /dev/null +++ b/latest/cases/00847/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C", + "event2": "0.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * (kf * S1 + (-1) * kr * S2)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * (k1 * S3 + (-1) * k2 * S4)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.15 + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/00847/model-sbml-l2v5.xml b/latest/cases/00847/model-sbml-l2v5.xml new file mode 100644 index 000000000..80eabadde --- /dev/null +++ b/latest/cases/00847/model-sbml-l2v5.xml @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.5 + + + + + + + + + + S3 + 0.75 + + + + + + + 0.5 + + + + + + + diff --git a/latest/cases/00847/model-sbml-l3v2.xml b/latest/cases/00847/model-sbml-l3v2.xml new file mode 100644 index 000000000..e3c697503 --- /dev/null +++ b/latest/cases/00847/model-sbml-l3v2.xml @@ -0,0 +1,137 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.5 + + + + + + + + + + S3 + 0.75 + + + + + + + 0.5 + + + + + + + diff --git a/latest/cases/00847/output.heta b/latest/cases/00847/output.heta new file mode 100644 index 000000000..51a86abc2 --- /dev/null +++ b/latest/cases/00847/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Two reversible reactions with four species in one compartment + and two events that assigns value to species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains two event that assigns values to species S2 and S4 respectively: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | Event2 | $S3 < 0.75$ | $-$ | $S4 = 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event2]= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, }; +reaction1 := C * (kf * S1 + (-1) * kr * S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S4, }; +reaction2 := C * (k1 * S3 + (-1) * k2 * S4); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.15; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; +event2 @DSwitcher 'event2' { trigger: S3 < 0.75, }; + diff --git a/latest/cases/00847/synopsis.txt b/latest/cases/00847/synopsis.txt new file mode 100644 index 000000000..dc956d773 --- /dev/null +++ b/latest/cases/00847/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reversible reactions with four species in one compartment + and two events that assigns value to species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains two event that assigns values to species S2 and S4 respectively: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | Event2 | $S3 < 0.75$ | $-$ | $S4 = 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00848/l2v5/build.log b/latest/cases/00848/l2v5/build.log new file mode 100644 index 000000000..1c7541141 --- /dev/null +++ b/latest/cases/00848/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00848/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00848/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00848/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00848/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00848/l2v5/index.heta b/latest/cases/00848/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00848/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00848/l3v2/build.log b/latest/cases/00848/l3v2/build.log new file mode 100644 index 000000000..205534809 --- /dev/null +++ b/latest/cases/00848/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00848/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00848/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00848/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00848/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00848/l3v2/index.heta b/latest/cases/00848/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00848/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00848/model-sbml-l2v5.xml b/latest/cases/00848/model-sbml-l2v5.xml new file mode 100644 index 000000000..9e6cec490 --- /dev/null +++ b/latest/cases/00848/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00848/model-sbml-l3v2.xml b/latest/cases/00848/model-sbml-l3v2.xml new file mode 100644 index 000000000..94d52c2a8 --- /dev/null +++ b/latest/cases/00848/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/00848/synopsis.txt b/latest/cases/00848/synopsis.txt new file mode 100644 index 000000000..6aac9e289 --- /dev/null +++ b/latest/cases/00848/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: One reversible reactions with two species in one compartment + and one event that assigns value to a species following a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The model contains one event that assigns values to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1$ | $S2 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00849/l2v5/build.log b/latest/cases/00849/l2v5/build.log new file mode 100644 index 000000000..679e5c472 --- /dev/null +++ b/latest/cases/00849/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00849/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00849/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00849/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00849/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00849/l2v5/index.heta b/latest/cases/00849/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00849/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00849/l3v2/build.log b/latest/cases/00849/l3v2/build.log new file mode 100644 index 000000000..65976374d --- /dev/null +++ b/latest/cases/00849/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00849/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00849/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00849/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00849/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00849/l3v2/index.heta b/latest/cases/00849/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00849/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00849/model-sbml-l2v5.xml b/latest/cases/00849/model-sbml-l2v5.xml new file mode 100644 index 000000000..46e5e807a --- /dev/null +++ b/latest/cases/00849/model-sbml-l2v5.xml @@ -0,0 +1,112 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 1.89 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00849/model-sbml-l3v2.xml b/latest/cases/00849/model-sbml-l3v2.xml new file mode 100644 index 000000000..f9d4a9d03 --- /dev/null +++ b/latest/cases/00849/model-sbml-l3v2.xml @@ -0,0 +1,129 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 1.89 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/00849/synopsis.txt b/latest/cases/00849/synopsis.txt new file mode 100644 index 000000000..51ad07e33 --- /dev/null +++ b/latest/cases/00849/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Two reversible reactions with four species in one compartment + and one event that assigns value to two species subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, ReversibleReaction, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains one event that assigns values to both species S2 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $1.89$ | $S2 = 1.5$ | + | | | | $S4 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S4 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00850/l2v5/build.log b/latest/cases/00850/l2v5/build.log new file mode 100644 index 000000000..f1ba11092 --- /dev/null +++ b/latest/cases/00850/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00850/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00850/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00850/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00850/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00850/l2v5/index.heta b/latest/cases/00850/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00850/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00850/l3v2/build.log b/latest/cases/00850/l3v2/build.log new file mode 100644 index 000000000..1f7bfd846 --- /dev/null +++ b/latest/cases/00850/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00850/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00850/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00850/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00850/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00850/l3v2/index.heta b/latest/cases/00850/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00850/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00850/model-sbml-l2v5.xml b/latest/cases/00850/model-sbml-l2v5.xml new file mode 100644 index 000000000..6d0aca5d0 --- /dev/null +++ b/latest/cases/00850/model-sbml-l2v5.xml @@ -0,0 +1,130 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 2 + + + + + + 1.5 + + + + + + + + + + S3 + 0.75 + + + + + + 2.5 + + + + + + 0.5 + + + + + + + diff --git a/latest/cases/00850/model-sbml-l3v2.xml b/latest/cases/00850/model-sbml-l3v2.xml new file mode 100644 index 000000000..0dd24a085 --- /dev/null +++ b/latest/cases/00850/model-sbml-l3v2.xml @@ -0,0 +1,147 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 2 + + + + + + 1.5 + + + + + + + + + + S3 + 0.75 + + + + + + 2.5 + + + + + + 0.5 + + + + + + + diff --git a/latest/cases/00850/synopsis.txt b/latest/cases/00850/synopsis.txt new file mode 100644 index 000000000..175dd1eec --- /dev/null +++ b/latest/cases/00850/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reversible reactions with four species in one compartment + and two events that assigns value to species subject to delays. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains two event that assigns values to species S2 and S4 respectively: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | Event2 | $S3 < 0.75$ | $-$ | $S4 = 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00851/l2v5/heta-code/output.heta b/latest/cases/00851/l2v5/heta-code/output.heta new file mode 100644 index 000000000..78fbe1744 --- /dev/null +++ b/latest/cases/00851/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00851/l2v5/index.heta b/latest/cases/00851/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00851/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00851/l2v5/json/output.json b/latest/cases/00851/l2v5/json/output.json new file mode 100644 index 000000000..a26cf487c --- /dev/null +++ b/latest/cases/00851/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00851/l3v2/heta-code/output.heta b/latest/cases/00851/l3v2/heta-code/output.heta new file mode 100644 index 000000000..49a546c12 --- /dev/null +++ b/latest/cases/00851/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00851/l3v2/index.heta b/latest/cases/00851/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00851/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00851/l3v2/json/output.json b/latest/cases/00851/l3v2/json/output.json new file mode 100644 index 000000000..f91e053e6 --- /dev/null +++ b/latest/cases/00851/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00851/model-sbml-l2v5.xml b/latest/cases/00851/model-sbml-l2v5.xml new file mode 100644 index 000000000..968c32f86 --- /dev/null +++ b/latest/cases/00851/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00851/model-sbml-l3v2.xml b/latest/cases/00851/model-sbml-l3v2.xml new file mode 100644 index 000000000..7d01faf24 --- /dev/null +++ b/latest/cases/00851/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00851/output.heta b/latest/cases/00851/output.heta new file mode 100644 index 000000000..a258f3ade --- /dev/null +++ b/latest/cases/00851/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00851/synopsis.txt b/latest/cases/00851/synopsis.txt new file mode 100644 index 000000000..f5108b899 --- /dev/null +++ b/latest/cases/00851/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00852/l2v5/heta-code/output.heta b/latest/cases/00852/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9cf8856ea --- /dev/null +++ b/latest/cases/00852/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00852/l2v5/index.heta b/latest/cases/00852/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00852/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00852/l2v5/json/output.json b/latest/cases/00852/l2v5/json/output.json new file mode 100644 index 000000000..612736061 --- /dev/null +++ b/latest/cases/00852/l2v5/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00852/l3v2/heta-code/output.heta b/latest/cases/00852/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9e7399830 --- /dev/null +++ b/latest/cases/00852/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00852/l3v2/index.heta b/latest/cases/00852/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00852/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00852/l3v2/json/output.json b/latest/cases/00852/l3v2/json/output.json new file mode 100644 index 000000000..7c35dc87d --- /dev/null +++ b/latest/cases/00852/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00852/model-sbml-l2v5.xml b/latest/cases/00852/model-sbml-l2v5.xml new file mode 100644 index 000000000..c75ba88ac --- /dev/null +++ b/latest/cases/00852/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00852/model-sbml-l3v2.xml b/latest/cases/00852/model-sbml-l3v2.xml new file mode 100644 index 000000000..e4f1268cb --- /dev/null +++ b/latest/cases/00852/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00852/output.heta b/latest/cases/00852/output.heta new file mode 100644 index 000000000..b709f7473 --- /dev/null +++ b/latest/cases/00852/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00852/synopsis.txt b/latest/cases/00852/synopsis.txt new file mode 100644 index 000000000..39705e735 --- /dev/null +++ b/latest/cases/00852/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00853/l2v5/heta-code/output.heta b/latest/cases/00853/l2v5/heta-code/output.heta new file mode 100644 index 000000000..91c3c7840 --- /dev/null +++ b/latest/cases/00853/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.9; +k3 @Record 'k3' { } .= 0.7; + diff --git a/latest/cases/00853/l2v5/index.heta b/latest/cases/00853/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00853/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00853/l2v5/json/output.json b/latest/cases/00853/l2v5/json/output.json new file mode 100644 index 000000000..e736be37e --- /dev/null +++ b/latest/cases/00853/l2v5/json/output.json @@ -0,0 +1,173 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00853/l3v2/heta-code/output.heta b/latest/cases/00853/l3v2/heta-code/output.heta new file mode 100644 index 000000000..48ba924a4 --- /dev/null +++ b/latest/cases/00853/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00853/l3v2/index.heta b/latest/cases/00853/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00853/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00853/l3v2/json/output.json b/latest/cases/00853/l3v2/json/output.json new file mode 100644 index 000000000..6f2e2056c --- /dev/null +++ b/latest/cases/00853/l3v2/json/output.json @@ -0,0 +1,143 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.9 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00853/model-sbml-l2v5.xml b/latest/cases/00853/model-sbml-l2v5.xml new file mode 100644 index 000000000..5ef767ef6 --- /dev/null +++ b/latest/cases/00853/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00853/model-sbml-l3v2.xml b/latest/cases/00853/model-sbml-l3v2.xml new file mode 100644 index 000000000..457f2016e --- /dev/null +++ b/latest/cases/00853/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00853/output.heta b/latest/cases/00853/output.heta new file mode 100644 index 000000000..e3c8cca25 --- /dev/null +++ b/latest/cases/00853/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00853/synopsis.txt b/latest/cases/00853/synopsis.txt new file mode 100644 index 000000000..52737a19d --- /dev/null +++ b/latest/cases/00853/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00854/l2v5/heta-code/output.heta b/latest/cases/00854/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4c2c455ae --- /dev/null +++ b/latest/cases/00854/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * multiply(k1, S1, t); + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00854/l2v5/index.heta b/latest/cases/00854/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00854/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00854/l2v5/json/output.json b/latest/cases/00854/l2v5/json/output.json new file mode 100644 index 000000000..c84871313 --- /dev/null +++ b/latest/cases/00854/l2v5/json/output.json @@ -0,0 +1,97 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1, t)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00854/l3v2/heta-code/output.heta b/latest/cases/00854/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e8c010d0b --- /dev/null +++ b/latest/cases/00854/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * multiply(k1, S1, t); + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00854/l3v2/index.heta b/latest/cases/00854/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00854/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00854/l3v2/json/output.json b/latest/cases/00854/l3v2/json/output.json new file mode 100644 index 000000000..a21271d4e --- /dev/null +++ b/latest/cases/00854/l3v2/json/output.json @@ -0,0 +1,71 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * multiply(k1, S1, t)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00854/model-sbml-l2v5.xml b/latest/cases/00854/model-sbml-l2v5.xml new file mode 100644 index 000000000..f94b4938f --- /dev/null +++ b/latest/cases/00854/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + t + + + + + + + + diff --git a/latest/cases/00854/model-sbml-l3v2.xml b/latest/cases/00854/model-sbml-l3v2.xml new file mode 100644 index 000000000..bbfe10be5 --- /dev/null +++ b/latest/cases/00854/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + multiply + k1 + S1 + t + + + + + + + + diff --git a/latest/cases/00854/output.heta b/latest/cases/00854/output.heta new file mode 100644 index 000000000..0a6d5ba54 --- /dev/null +++ b/latest/cases/00854/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time passed to a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1, S1, t) * C$ |] +where the symbol 't' denotes the current simulation time. + +The reaction uses one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1 \x 10^-1$ |mole | +|Initial amount of S2 |$0.1 \x 10^-1$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.01 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * multiply(k1, S1, t); + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00854/synopsis.txt b/latest/cases/00854/synopsis.txt new file mode 100644 index 000000000..f6d3fa8eb --- /dev/null +++ b/latest/cases/00854/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time passed to a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1, S1, t) * C$ |] +where the symbol 't' denotes the current simulation time. + +The reaction uses one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1 \x 10^-1$ |mole | +|Initial amount of S2 |$0.1 \x 10^-1$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00855/l2v5/heta-code/output.heta b/latest/cases/00855/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e37f2b18a --- /dev/null +++ b/latest/cases/00855/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * multiply(S1, C, t); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := k2 * multiply(S2, C, t); +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := k3 * multiply(S3, C, t); + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00855/l2v5/index.heta b/latest/cases/00855/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00855/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00855/l2v5/json/output.json b/latest/cases/00855/l2v5/json/output.json new file mode 100644 index 000000000..b2bf876e4 --- /dev/null +++ b/latest/cases/00855/l2v5/json/output.json @@ -0,0 +1,171 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, C, t)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * multiply(S2, C, t)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "k3 * multiply(S3, C, t)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00855/l3v2/heta-code/output.heta b/latest/cases/00855/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e9ede22ca --- /dev/null +++ b/latest/cases/00855/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * multiply(S1, C, t); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := k2 * multiply(S2, C, t); +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := k3 * multiply(S3, C, t); + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00855/l3v2/index.heta b/latest/cases/00855/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00855/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00855/l3v2/json/output.json b/latest/cases/00855/l3v2/json/output.json new file mode 100644 index 000000000..f84988d93 --- /dev/null +++ b/latest/cases/00855/l3v2/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, C, t)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * multiply(S2, C, t)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "k3 * multiply(S3, C, t)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y", + "z" + ], + "math": "x * y * z", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00855/model-sbml-l2v5.xml b/latest/cases/00855/model-sbml-l2v5.xml new file mode 100644 index 000000000..6ff3eafc1 --- /dev/null +++ b/latest/cases/00855/model-sbml-l2v5.xml @@ -0,0 +1,110 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + C + time + + + + + + + + + + + + + + + + + k2 + + multiply + S2 + C + time + + + + + + + + + + + + + + + + + k3 + + multiply + S3 + C + time + + + + + + + + diff --git a/latest/cases/00855/model-sbml-l3v2.xml b/latest/cases/00855/model-sbml-l3v2.xml new file mode 100644 index 000000000..0a2ff99c7 --- /dev/null +++ b/latest/cases/00855/model-sbml-l3v2.xml @@ -0,0 +1,127 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + C + time + + + + + + + + + + + + + + + + + k2 + + multiply + S2 + C + time + + + + + + + + + + + + + + + + + k3 + + multiply + S3 + C + time + + + + + + + + diff --git a/latest/cases/00855/output.heta b/latest/cases/00855/output.heta new file mode 100644 index 000000000..50234b6e7 --- /dev/null +++ b/latest/cases/00855/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time passed to a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * multiply(S1, C, time)$ | +| S2 -> S3 | $k2 * multiply(S2, C, time)$ | +| S3 -> S4 | $k3 * multiply(S3, C, time)$ |] +where the symbol 'time' denotes the current simulation time. + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y, z], math: x * y * z, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * multiply(S1, C, t); +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := k2 * multiply(S2, C, t); +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := k3 * multiply(S3, C, t); + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00855/synopsis.txt b/latest/cases/00855/synopsis.txt new file mode 100644 index 000000000..8deb81d77 --- /dev/null +++ b/latest/cases/00855/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time passed to a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * multiply(S1, C, time)$ | +| S2 -> S3 | $k2 * multiply(S2, C, time)$ | +| S3 -> S4 | $k3 * multiply(S3, C, time)$ |] +where the symbol 'time' denotes the current simulation time. + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y, z | $x * y * z$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00856/l2v5/heta-code/output.heta b/latest/cases/00856/l2v5/heta-code/output.heta new file mode 100644 index 000000000..140b03c5a --- /dev/null +++ b/latest/cases/00856/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := multiply(multiply(k2, S3), multiply(C, t)); +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.9; +k3 @Record 'k3' { } .= 0.7; + diff --git a/latest/cases/00856/l2v5/index.heta b/latest/cases/00856/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00856/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00856/l2v5/json/output.json b/latest/cases/00856/l2v5/json/output.json new file mode 100644 index 000000000..b19ac9bdb --- /dev/null +++ b/latest/cases/00856/l2v5/json/output.json @@ -0,0 +1,182 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "multiply(multiply(k2, S3), multiply(C, t))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00856/l3v2/heta-code/output.heta b/latest/cases/00856/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4e02532de --- /dev/null +++ b/latest/cases/00856/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := multiply(multiply(k2, S3), multiply(C, t)); +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00856/l3v2/index.heta b/latest/cases/00856/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00856/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00856/l3v2/json/output.json b/latest/cases/00856/l3v2/json/output.json new file mode 100644 index 000000000..fb0df39b2 --- /dev/null +++ b/latest/cases/00856/l3v2/json/output.json @@ -0,0 +1,152 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "multiply(multiply(k2, S3), multiply(C, t))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.9 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.7 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00856/model-sbml-l2v5.xml b/latest/cases/00856/model-sbml-l2v5.xml new file mode 100644 index 000000000..feb58f46f --- /dev/null +++ b/latest/cases/00856/model-sbml-l2v5.xml @@ -0,0 +1,107 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + multiply + + multiply + k2 + S3 + + + multiply + C + s + + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00856/model-sbml-l3v2.xml b/latest/cases/00856/model-sbml-l3v2.xml new file mode 100644 index 000000000..cc852a88a --- /dev/null +++ b/latest/cases/00856/model-sbml-l3v2.xml @@ -0,0 +1,124 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + multiply + + multiply + k2 + S3 + + + multiply + C + s + + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00856/output.heta b/latest/cases/00856/output.heta new file mode 100644 index 000000000..10f917edb --- /dev/null +++ b/latest/cases/00856/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time passed to a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $multiply(multiply(k2, S3), multiply(C, s))$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := multiply(multiply(k2, S3), multiply(C, t)); +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00856/synopsis.txt b/latest/cases/00856/synopsis.txt new file mode 100644 index 000000000..c05804102 --- /dev/null +++ b/latest/cases/00856/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time passed to a functionDefinition. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, CSymbolTime +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $multiply(multiply(k2, S3), multiply(C, s))$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00857/l2v5/heta-code/output.heta b/latest/cases/00857/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a72814123 --- /dev/null +++ b/latest/cases/00857/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.57; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00857/l2v5/index.heta b/latest/cases/00857/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00857/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00857/l2v5/json/output.json b/latest/cases/00857/l2v5/json/output.json new file mode 100644 index 000000000..5b32aa433 --- /dev/null +++ b/latest/cases/00857/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.57" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00857/l3v2/heta-code/output.heta b/latest/cases/00857/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8e0dbaef8 --- /dev/null +++ b/latest/cases/00857/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.57; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00857/l3v2/index.heta b/latest/cases/00857/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00857/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00857/l3v2/json/output.json b/latest/cases/00857/l3v2/json/output.json new file mode 100644 index 000000000..dc771513f --- /dev/null +++ b/latest/cases/00857/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.57" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00857/model-sbml-l2v5.xml b/latest/cases/00857/model-sbml-l2v5.xml new file mode 100644 index 000000000..124b5f27e --- /dev/null +++ b/latest/cases/00857/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00857/model-sbml-l3v2.xml b/latest/cases/00857/model-sbml-l3v2.xml new file mode 100644 index 000000000..c9dcf3735 --- /dev/null +++ b/latest/cases/00857/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00857/output.heta b/latest/cases/00857/output.heta new file mode 100644 index 000000000..6b04e9b67 --- /dev/null +++ b/latest/cases/00857/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$0.57$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.57; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00857/synopsis.txt b/latest/cases/00857/synopsis.txt new file mode 100644 index 000000000..2565f9916 --- /dev/null +++ b/latest/cases/00857/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$0.57$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00858/l2v5/heta-code/output.heta b/latest/cases/00858/l2v5/heta-code/output.heta new file mode 100644 index 000000000..297483ff1 --- /dev/null +++ b/latest/cases/00858/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 2.45; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00858/l2v5/index.heta b/latest/cases/00858/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00858/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00858/l2v5/json/output.json b/latest/cases/00858/l2v5/json/output.json new file mode 100644 index 000000000..89d9c826b --- /dev/null +++ b/latest/cases/00858/l2v5/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "2.45" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00858/l3v2/heta-code/output.heta b/latest/cases/00858/l3v2/heta-code/output.heta new file mode 100644 index 000000000..27cabc222 --- /dev/null +++ b/latest/cases/00858/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.45; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00858/l3v2/index.heta b/latest/cases/00858/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00858/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00858/l3v2/json/output.json b/latest/cases/00858/l3v2/json/output.json new file mode 100644 index 000000000..e79f7d1dd --- /dev/null +++ b/latest/cases/00858/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.45" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00858/model-sbml-l2v5.xml b/latest/cases/00858/model-sbml-l2v5.xml new file mode 100644 index 000000000..c06e9553c --- /dev/null +++ b/latest/cases/00858/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00858/model-sbml-l3v2.xml b/latest/cases/00858/model-sbml-l3v2.xml new file mode 100644 index 000000000..9d1aa34d6 --- /dev/null +++ b/latest/cases/00858/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00858/output.heta b/latest/cases/00858/output.heta new file mode 100644 index 000000000..2ee04e43f --- /dev/null +++ b/latest/cases/00858/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$2.45$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.45; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00858/synopsis.txt b/latest/cases/00858/synopsis.txt new file mode 100644 index 000000000..09b7b49df --- /dev/null +++ b/latest/cases/00858/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$2.45$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00859/l2v5/heta-code/output.heta b/latest/cases/00859/l2v5/heta-code/output.heta new file mode 100644 index 000000000..61cac7cf5 --- /dev/null +++ b/latest/cases/00859/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.98; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.9; +k3 @Record 'k3' { } .= 0.7; + diff --git a/latest/cases/00859/l2v5/index.heta b/latest/cases/00859/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00859/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00859/l2v5/json/output.json b/latest/cases/00859/l2v5/json/output.json new file mode 100644 index 000000000..8db84cdf9 --- /dev/null +++ b/latest/cases/00859/l2v5/json/output.json @@ -0,0 +1,173 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.98" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00859/l3v2/heta-code/output.heta b/latest/cases/00859/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b316fe398 --- /dev/null +++ b/latest/cases/00859/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.98; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00859/l3v2/index.heta b/latest/cases/00859/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00859/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00859/l3v2/json/output.json b/latest/cases/00859/l3v2/json/output.json new file mode 100644 index 000000000..634d6d56e --- /dev/null +++ b/latest/cases/00859/l3v2/json/output.json @@ -0,0 +1,143 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.98" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.9 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00859/model-sbml-l2v5.xml b/latest/cases/00859/model-sbml-l2v5.xml new file mode 100644 index 000000000..073502aa2 --- /dev/null +++ b/latest/cases/00859/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00859/model-sbml-l3v2.xml b/latest/cases/00859/model-sbml-l3v2.xml new file mode 100644 index 000000000..e1d511a0c --- /dev/null +++ b/latest/cases/00859/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00859/output.heta b/latest/cases/00859/output.heta new file mode 100644 index 000000000..faf6a4e45 --- /dev/null +++ b/latest/cases/00859/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$0.98$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.98; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00859/synopsis.txt b/latest/cases/00859/synopsis.txt new file mode 100644 index 000000000..59ae79df3 --- /dev/null +++ b/latest/cases/00859/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$0.98$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00860/l2v5/heta-code/output.heta b/latest/cases/00860/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d7395397b --- /dev/null +++ b/latest/cases/00860/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.9; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00860/l2v5/index.heta b/latest/cases/00860/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00860/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00860/l2v5/json/output.json b/latest/cases/00860/l2v5/json/output.json new file mode 100644 index 000000000..72a848ce5 --- /dev/null +++ b/latest/cases/00860/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.9" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00860/l3v2/heta-code/output.heta b/latest/cases/00860/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e4a108ae0 --- /dev/null +++ b/latest/cases/00860/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00860/l3v2/index.heta b/latest/cases/00860/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00860/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00860/l3v2/json/output.json b/latest/cases/00860/l3v2/json/output.json new file mode 100644 index 000000000..09cd01197 --- /dev/null +++ b/latest/cases/00860/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.9" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00860/model-sbml-l2v5.xml b/latest/cases/00860/model-sbml-l2v5.xml new file mode 100644 index 000000000..fd4fa7970 --- /dev/null +++ b/latest/cases/00860/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00860/model-sbml-l3v2.xml b/latest/cases/00860/model-sbml-l3v2.xml new file mode 100644 index 000000000..13683d4bf --- /dev/null +++ b/latest/cases/00860/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00860/output.heta b/latest/cases/00860/output.heta new file mode 100644 index 000000000..840301de7 --- /dev/null +++ b/latest/cases/00860/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$0.9$ |litre |] + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.9; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00860/synopsis.txt b/latest/cases/00860/synopsis.txt new file mode 100644 index 000000000..24f004b63 --- /dev/null +++ b/latest/cases/00860/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.5 \x 10^-3$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$0.9$ |litre |] + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00861/l2v5/heta-code/output.heta b/latest/cases/00861/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f1ef17bfc --- /dev/null +++ b/latest/cases/00861/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1.78; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00861/l2v5/index.heta b/latest/cases/00861/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00861/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00861/l2v5/json/output.json b/latest/cases/00861/l2v5/json/output.json new file mode 100644 index 000000000..bd4127875 --- /dev/null +++ b/latest/cases/00861/l2v5/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1.78" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00861/l3v2/heta-code/output.heta b/latest/cases/00861/l3v2/heta-code/output.heta new file mode 100644 index 000000000..62d8e27a1 --- /dev/null +++ b/latest/cases/00861/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.78; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00861/l3v2/index.heta b/latest/cases/00861/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00861/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00861/l3v2/json/output.json b/latest/cases/00861/l3v2/json/output.json new file mode 100644 index 000000000..12da26f7a --- /dev/null +++ b/latest/cases/00861/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1.78" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00861/model-sbml-l2v5.xml b/latest/cases/00861/model-sbml-l2v5.xml new file mode 100644 index 000000000..a4fd7bb3b --- /dev/null +++ b/latest/cases/00861/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00861/model-sbml-l3v2.xml b/latest/cases/00861/model-sbml-l3v2.xml new file mode 100644 index 000000000..7129d92a0 --- /dev/null +++ b/latest/cases/00861/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00861/output.heta b/latest/cases/00861/output.heta new file mode 100644 index 000000000..ed32db07c --- /dev/null +++ b/latest/cases/00861/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1.78$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1.78; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00861/synopsis.txt b/latest/cases/00861/synopsis.txt new file mode 100644 index 000000000..075332b01 --- /dev/null +++ b/latest/cases/00861/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0 \x 10^-1$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1.78$ |litre |] + diff --git a/latest/cases/00862/l2v5/heta-code/output.heta b/latest/cases/00862/l2v5/heta-code/output.heta new file mode 100644 index 000000000..764adfc4d --- /dev/null +++ b/latest/cases/00862/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 0.002; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.9; +k3 @Record 'k3' { } .= 0.7; + diff --git a/latest/cases/00862/l2v5/index.heta b/latest/cases/00862/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00862/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00862/l2v5/json/output.json b/latest/cases/00862/l2v5/json/output.json new file mode 100644 index 000000000..694786d23 --- /dev/null +++ b/latest/cases/00862/l2v5/json/output.json @@ -0,0 +1,173 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "0.002" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00862/l3v2/heta-code/output.heta b/latest/cases/00862/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d3b46e4e2 --- /dev/null +++ b/latest/cases/00862/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.002; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00862/l3v2/index.heta b/latest/cases/00862/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00862/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00862/l3v2/json/output.json b/latest/cases/00862/l3v2/json/output.json new file mode 100644 index 000000000..55108c305 --- /dev/null +++ b/latest/cases/00862/l3v2/json/output.json @@ -0,0 +1,143 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.002" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.9 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00862/model-sbml-l2v5.xml b/latest/cases/00862/model-sbml-l2v5.xml new file mode 100644 index 000000000..86f50a8f4 --- /dev/null +++ b/latest/cases/00862/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00862/model-sbml-l3v2.xml b/latest/cases/00862/model-sbml-l3v2.xml new file mode 100644 index 000000000..984c7ee00 --- /dev/null +++ b/latest/cases/00862/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00862/output.heta b/latest/cases/00862/output.heta new file mode 100644 index 000000000..0c9d123b8 --- /dev/null +++ b/latest/cases/00862/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$2.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$0.002$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.002; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00862/synopsis.txt b/latest/cases/00862/synopsis.txt new file mode 100644 index 000000000..858257464 --- /dev/null +++ b/latest/cases/00862/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Concentration, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$2.0$ |mole litre^-1^ | +|Initial concentration of S2 |$2.0$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Initial concentration of S4 |$0$ |mole litre^-1^ | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$0.002$ |litre |] + diff --git a/latest/cases/00863/l2v5/heta-code/output.heta b/latest/cases/00863/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7ac100149 --- /dev/null +++ b/latest/cases/00863/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 0.15 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00863/l2v5/index.heta b/latest/cases/00863/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00863/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00863/l2v5/json/output.json b/latest/cases/00863/l2v5/json/output.json new file mode 100644 index 000000000..4213dc37e --- /dev/null +++ b/latest/cases/00863/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00863/l3v2/heta-code/output.heta b/latest/cases/00863/l3v2/heta-code/output.heta new file mode 100644 index 000000000..35a922e7e --- /dev/null +++ b/latest/cases/00863/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.15 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00863/l3v2/index.heta b/latest/cases/00863/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00863/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00863/l3v2/json/output.json b/latest/cases/00863/l3v2/json/output.json new file mode 100644 index 000000000..fd1162267 --- /dev/null +++ b/latest/cases/00863/l3v2/json/output.json @@ -0,0 +1,62 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00863/model-sbml-l2v5.xml b/latest/cases/00863/model-sbml-l2v5.xml new file mode 100644 index 000000000..4d20f16b0 --- /dev/null +++ b/latest/cases/00863/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00863/model-sbml-l3v2.xml b/latest/cases/00863/model-sbml-l3v2.xml new file mode 100644 index 000000000..97235dbed --- /dev/null +++ b/latest/cases/00863/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00863/output.heta b/latest/cases/00863/output.heta new file mode 100644 index 000000000..16a8093b0 --- /dev/null +++ b/latest/cases/00863/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Species S1 +is labeled as an SBML boundary species. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.15 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00863/synopsis.txt b/latest/cases/00863/synopsis.txt new file mode 100644 index 000000000..0bd740bdd --- /dev/null +++ b/latest/cases/00863/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Species S1 +is labeled as an SBML boundary species. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00864/l2v5/heta-code/output.heta b/latest/cases/00864/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ff9343347 --- /dev/null +++ b/latest/cases/00864/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00864/l2v5/index.heta b/latest/cases/00864/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00864/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00864/l2v5/json/output.json b/latest/cases/00864/l2v5/json/output.json new file mode 100644 index 000000000..78618a99d --- /dev/null +++ b/latest/cases/00864/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00864/l3v2/heta-code/output.heta b/latest/cases/00864/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a5096659d --- /dev/null +++ b/latest/cases/00864/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00864/l3v2/index.heta b/latest/cases/00864/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00864/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00864/l3v2/json/output.json b/latest/cases/00864/l3v2/json/output.json new file mode 100644 index 000000000..cfe174adb --- /dev/null +++ b/latest/cases/00864/l3v2/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00864/model-sbml-l2v5.xml b/latest/cases/00864/model-sbml-l2v5.xml new file mode 100644 index 000000000..cfc4d7129 --- /dev/null +++ b/latest/cases/00864/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00864/model-sbml-l3v2.xml b/latest/cases/00864/model-sbml-l3v2.xml new file mode 100644 index 000000000..dde6c1847 --- /dev/null +++ b/latest/cases/00864/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00864/output.heta b/latest/cases/00864/output.heta new file mode 100644 index 000000000..cf603b84d --- /dev/null +++ b/latest/cases/00864/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00864/synopsis.txt b/latest/cases/00864/synopsis.txt new file mode 100644 index 000000000..2c050d57e --- /dev/null +++ b/latest/cases/00864/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00865/l2v5/heta-code/output.heta b/latest/cases/00865/l2v5/heta-code/output.heta new file mode 100644 index 000000000..62dfc5def --- /dev/null +++ b/latest/cases/00865/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.9; +k3 @Record 'k3' { } .= 0.7; + diff --git a/latest/cases/00865/l2v5/index.heta b/latest/cases/00865/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00865/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00865/l2v5/json/output.json b/latest/cases/00865/l2v5/json/output.json new file mode 100644 index 000000000..fa9d82972 --- /dev/null +++ b/latest/cases/00865/l2v5/json/output.json @@ -0,0 +1,174 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00865/l3v2/heta-code/output.heta b/latest/cases/00865/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f075440ee --- /dev/null +++ b/latest/cases/00865/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00865/l3v2/index.heta b/latest/cases/00865/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00865/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00865/l3v2/json/output.json b/latest/cases/00865/l3v2/json/output.json new file mode 100644 index 000000000..a26250537 --- /dev/null +++ b/latest/cases/00865/l3v2/json/output.json @@ -0,0 +1,144 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.9 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00865/model-sbml-l2v5.xml b/latest/cases/00865/model-sbml-l2v5.xml new file mode 100644 index 000000000..4b3566efb --- /dev/null +++ b/latest/cases/00865/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00865/model-sbml-l3v2.xml b/latest/cases/00865/model-sbml-l3v2.xml new file mode 100644 index 000000000..c591f7a49 --- /dev/null +++ b/latest/cases/00865/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00865/output.heta b/latest/cases/00865/output.heta new file mode 100644 index 000000000..f394298e2 --- /dev/null +++ b/latest/cases/00865/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00865/synopsis.txt b/latest/cases/00865/synopsis.txt new file mode 100644 index 000000000..8053eed13 --- /dev/null +++ b/latest/cases/00865/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S1 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00866/l2v5/heta-code/output.heta b/latest/cases/00866/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f4f098ef5 --- /dev/null +++ b/latest/cases/00866/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00866/l2v5/index.heta b/latest/cases/00866/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00866/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00866/l2v5/json/output.json b/latest/cases/00866/l2v5/json/output.json new file mode 100644 index 000000000..e3011bc58 --- /dev/null +++ b/latest/cases/00866/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00866/l3v2/heta-code/output.heta b/latest/cases/00866/l3v2/heta-code/output.heta new file mode 100644 index 000000000..550604c7a --- /dev/null +++ b/latest/cases/00866/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00866/l3v2/index.heta b/latest/cases/00866/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00866/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00866/l3v2/json/output.json b/latest/cases/00866/l3v2/json/output.json new file mode 100644 index 000000000..cb0f8c348 --- /dev/null +++ b/latest/cases/00866/l3v2/json/output.json @@ -0,0 +1,62 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00866/model-sbml-l2v5.xml b/latest/cases/00866/model-sbml-l2v5.xml new file mode 100644 index 000000000..726c25401 --- /dev/null +++ b/latest/cases/00866/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00866/model-sbml-l3v2.xml b/latest/cases/00866/model-sbml-l3v2.xml new file mode 100644 index 000000000..07a0c5802 --- /dev/null +++ b/latest/cases/00866/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00866/output.heta b/latest/cases/00866/output.heta new file mode 100644 index 000000000..504a90df3 --- /dev/null +++ b/latest/cases/00866/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Species S2 +is labeled as an SBML boundary species. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00866/synopsis.txt b/latest/cases/00866/synopsis.txt new file mode 100644 index 000000000..f42f45a96 --- /dev/null +++ b/latest/cases/00866/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. Species S2 +is labeled as an SBML boundary species. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00867/l2v5/heta-code/output.heta b/latest/cases/00867/l2v5/heta-code/output.heta new file mode 100644 index 000000000..174d3671b --- /dev/null +++ b/latest/cases/00867/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: substance/volume, boundary: true, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00867/l2v5/index.heta b/latest/cases/00867/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00867/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00867/l2v5/json/output.json b/latest/cases/00867/l2v5/json/output.json new file mode 100644 index 000000000..d43ff1100 --- /dev/null +++ b/latest/cases/00867/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00867/l3v2/heta-code/output.heta b/latest/cases/00867/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5e6a4a8f3 --- /dev/null +++ b/latest/cases/00867/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00867/l3v2/index.heta b/latest/cases/00867/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00867/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00867/l3v2/json/output.json b/latest/cases/00867/l3v2/json/output.json new file mode 100644 index 000000000..e326778e8 --- /dev/null +++ b/latest/cases/00867/l3v2/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.001 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00867/model-sbml-l2v5.xml b/latest/cases/00867/model-sbml-l2v5.xml new file mode 100644 index 000000000..86204185f --- /dev/null +++ b/latest/cases/00867/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00867/model-sbml-l3v2.xml b/latest/cases/00867/model-sbml-l3v2.xml new file mode 100644 index 000000000..1882c015b --- /dev/null +++ b/latest/cases/00867/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00867/output.heta b/latest/cases/00867/output.heta new file mode 100644 index 000000000..b17fa3d7d --- /dev/null +++ b/latest/cases/00867/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S2 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00867/synopsis.txt b/latest/cases/00867/synopsis.txt new file mode 100644 index 000000000..4f5b80d14 --- /dev/null +++ b/latest/cases/00867/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S2 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00868/l2v5/heta-code/output.heta b/latest/cases/00868/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b3f0e55f9 --- /dev/null +++ b/latest/cases/00868/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.9; +k3 @Record 'k3' { } .= 0.7; + diff --git a/latest/cases/00868/l2v5/index.heta b/latest/cases/00868/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00868/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00868/l2v5/json/output.json b/latest/cases/00868/l2v5/json/output.json new file mode 100644 index 000000000..6df26350c --- /dev/null +++ b/latest/cases/00868/l2v5/json/output.json @@ -0,0 +1,174 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00868/l3v2/heta-code/output.heta b/latest/cases/00868/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e4260103a --- /dev/null +++ b/latest/cases/00868/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00868/l3v2/index.heta b/latest/cases/00868/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00868/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00868/l3v2/json/output.json b/latest/cases/00868/l3v2/json/output.json new file mode 100644 index 000000000..c5521684e --- /dev/null +++ b/latest/cases/00868/l3v2/json/output.json @@ -0,0 +1,144 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.9 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.7 + } +] \ No newline at end of file diff --git a/latest/cases/00868/model-sbml-l2v5.xml b/latest/cases/00868/model-sbml-l2v5.xml new file mode 100644 index 000000000..9f6bbe544 --- /dev/null +++ b/latest/cases/00868/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00868/model-sbml-l3v2.xml b/latest/cases/00868/model-sbml-l3v2.xml new file mode 100644 index 000000000..e6892e229 --- /dev/null +++ b/latest/cases/00868/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k2 + S3 + s + + + + + + + + + + + + + + + + + C + k3 + S3 + s + + + + + + + diff --git a/latest/cases/00868/output.heta b/latest/cases/00868/output.heta new file mode 100644 index 000000000..a554cd21d --- /dev/null +++ b/latest/cases/00868/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S3 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.9; +k3 @Const 'k3' { } = 0.7; + diff --git a/latest/cases/00868/synopsis.txt b/latest/cases/00868/synopsis.txt new file mode 100644 index 000000000..807064aec --- /dev/null +++ b/latest/cases/00868/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S3 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k2 * S3 * C * s$ | +| S3 -> S1 + S4 | $k3 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter k2 |$0.9$ |second^-2^ | +|Value of parameter k3 |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00869/l2v5/heta-code/output.heta b/latest/cases/00869/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2e70a0166 --- /dev/null +++ b/latest/cases/00869/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, boundary: true, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00869/l2v5/index.heta b/latest/cases/00869/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00869/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00869/l2v5/json/output.json b/latest/cases/00869/l2v5/json/output.json new file mode 100644 index 000000000..961f56e78 --- /dev/null +++ b/latest/cases/00869/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00869/l3v2/heta-code/output.heta b/latest/cases/00869/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ab88e6ee8 --- /dev/null +++ b/latest/cases/00869/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00869/l3v2/index.heta b/latest/cases/00869/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00869/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00869/l3v2/json/output.json b/latest/cases/00869/l3v2/json/output.json new file mode 100644 index 000000000..53ac3ebd4 --- /dev/null +++ b/latest/cases/00869/l3v2/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00869/model-sbml-l2v5.xml b/latest/cases/00869/model-sbml-l2v5.xml new file mode 100644 index 000000000..917ff7562 --- /dev/null +++ b/latest/cases/00869/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00869/model-sbml-l3v2.xml b/latest/cases/00869/model-sbml-l3v2.xml new file mode 100644 index 000000000..3f4fdca7c --- /dev/null +++ b/latest/cases/00869/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00869/output.heta b/latest/cases/00869/output.heta new file mode 100644 index 000000000..5a5916d45 --- /dev/null +++ b/latest/cases/00869/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: BoundaryCondition, Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S3 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00869/synopsis.txt b/latest/cases/00869/synopsis.txt new file mode 100644 index 000000000..2d42f0e7e --- /dev/null +++ b/latest/cases/00869/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: BoundaryCondition, Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. +Species S3 is labeled as an SBML boundary species. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00870/l2v5/build.log b/latest/cases/00870/l2v5/build.log new file mode 100644 index 000000000..b56fc8d4d --- /dev/null +++ b/latest/cases/00870/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00870/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00870/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00870/model-sbml-l2v5.xml"... +[error] "fast" reactions "fasterReaction" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00870/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00870/l2v5/index.heta b/latest/cases/00870/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00870/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00870/l3v2/index.heta b/latest/cases/00870/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00870/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00870/model-sbml-l2v5.xml b/latest/cases/00870/model-sbml-l2v5.xml new file mode 100644 index 000000000..3e6d76bc9 --- /dev/null +++ b/latest/cases/00870/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Kf1 + A4 + + + + + + Kr1 + A2 + + + + C + + + + + + + + + + + + + + + + + + + + + Kf + A1 + A2 + + + + + + Kr + A3 + + + + C + + + + + + + diff --git a/latest/cases/00870/synopsis.txt b/latest/cases/00870/synopsis.txt new file mode 100644 index 000000000..66a8b1d66 --- /dev/null +++ b/latest/cases/00870/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Two reversible reactions in one compartment +with one reaction marked as fast. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, FastReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called A1, A2, A3 and A4 and four parameters called Kf1, Kr1, Kf +and Kr. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A4 <-> A2 | $(Kf1 * A4 - Kr1 * A2) * C$ | +| A1 + A2 <-> A3 | $(Kf * A1 * A2 - Kr * A3) * C$ |] +where the first reaction is marked as 'fast' and therefore should be assumed +to be operating on a time scale significantly faster than the second reaction. +Fast reactions are considered to be instantaneous relative to slow +reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of A1 |$2$ |mole | +|Initial amount of A2 |$3$ |mole | +|Initial amount of A3 |$4$ |mole | +|Initial amount of A4 |$1$ |mole | +|Value of parameter Kf1 |$1$ |second^-1^ | +|Value of parameter Kr1 |$2$ |second^-1^ | +|Value of parameter Kf |$1$ |litre mole^-1^ second^-1^ | +|Value of parameter Kr |$2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00871/l2v5/build.log b/latest/cases/00871/l2v5/build.log new file mode 100644 index 000000000..be32273bc --- /dev/null +++ b/latest/cases/00871/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00871/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00871/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00871/model-sbml-l2v5.xml"... +[error] "fast" reactions "reaction1" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00871/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00871/l2v5/index.heta b/latest/cases/00871/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00871/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00871/l3v2/index.heta b/latest/cases/00871/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00871/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00871/model-sbml-l2v5.xml b/latest/cases/00871/model-sbml-l2v5.xml new file mode 100644 index 000000000..d058cdb57 --- /dev/null +++ b/latest/cases/00871/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A4 + C + Kf1 + + + + + + + + + + + + + + + + + A1 + A2 + C + Kf + + + + + + + diff --git a/latest/cases/00871/synopsis.txt b/latest/cases/00871/synopsis.txt new file mode 100644 index 000000000..6de78b9b2 --- /dev/null +++ b/latest/cases/00871/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Two reactions in one compartment +with one reaction marked as fast. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, FastReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called A1, A2, A3 and A4 and four parameters called Kf1, Kr1, Kf +and Kr. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A4 -> A2 | $Kf1 * A4 * C$ | +| A1 + A2 -> A3 | $Kf * A1 * A2 * C$ |] +where the first reaction is marked as 'fast' and therefore should be assumed +to be operating on a time scale significantly faster than the second reaction. +Fast reactions are considered to be instantaneous relative to slow +reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of A1 |$2$ |mole | +|Initial amount of A2 |$3$ |mole | +|Initial amount of A3 |$4$ |mole | +|Initial amount of A4 |$1$ |mole | +|Value of parameter Kf1 |$1$ |second^-1^ | +|Value of parameter Kr1 |$2$ |second^-1^ | +|Value of parameter Kf |$1$ |litre mole^-1^ second^-1^ | +|Value of parameter Kr |$2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00872/l2v5/build.log b/latest/cases/00872/l2v5/build.log new file mode 100644 index 000000000..b44504563 --- /dev/null +++ b/latest/cases/00872/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00872/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00872/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00872/model-sbml-l2v5.xml"... +[error] "fast" reactions "reaction1" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00872/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00872/l2v5/index.heta b/latest/cases/00872/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00872/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00872/l3v2/index.heta b/latest/cases/00872/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00872/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00872/model-sbml-l2v5.xml b/latest/cases/00872/model-sbml-l2v5.xml new file mode 100644 index 000000000..f06dff046 --- /dev/null +++ b/latest/cases/00872/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + A4 + Kf1 + + + + -1 + A2 + Kr1 + + + + + + + + + + + + + + + + + + + C + + + + + A1 + A2 + Kf + + + + -1 + A3 + Kr + + + + + + + + + diff --git a/latest/cases/00872/synopsis.txt b/latest/cases/00872/synopsis.txt new file mode 100644 index 000000000..e75cef158 --- /dev/null +++ b/latest/cases/00872/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reversible reactions in one compartment +with one reaction marked as fast and one species a boundary. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, FastReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called A1, A2, A3 and A4 and four parameters called Kf1, Kr1, Kf +and Kr. Species A1 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A4 <-> A2 | $(Kf1 * A4 - Kr1 * A2) * C$ | +| A1 + A2 <-> A3 | $(Kf * A1 * A2 - Kr * A3) * C$ |] +where the first reaction is marked as 'fast' and therefore should be assumed +to be operating on a time scale significantly faster than the second reaction. +Fast reactions are considered to be instantaneous relative to slow +reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of A1 |$2$ |mole | +|Initial amount of A2 |$3$ |mole | +|Initial amount of A3 |$4$ |mole | +|Initial amount of A4 |$1$ |mole | +|Value of parameter Kf1 |$1$ |second^-1^ | +|Value of parameter Kr1 |$2$ |second^-1^ | +|Value of parameter Kf |$1$ |litre mole^-1^ second^-1^ | +|Value of parameter Kr |$2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00873/l2v5/build.log b/latest/cases/00873/l2v5/build.log new file mode 100644 index 000000000..0d3463af6 --- /dev/null +++ b/latest/cases/00873/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00873/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00873/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00873/model-sbml-l2v5.xml"... +[error] "fast" reactions "reaction1" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00873/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00873/l2v5/index.heta b/latest/cases/00873/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00873/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00873/l3v2/index.heta b/latest/cases/00873/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00873/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00873/model-sbml-l2v5.xml b/latest/cases/00873/model-sbml-l2v5.xml new file mode 100644 index 000000000..c3db07a91 --- /dev/null +++ b/latest/cases/00873/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + A4 + Kf1 + + + + -1 + A2 + Kr1 + + + + + + + + + + + + + + + + + + + C + + + + + A1 + A2 + Kf + + + + -1 + A3 + Kr + + + + + + + + + diff --git a/latest/cases/00873/synopsis.txt b/latest/cases/00873/synopsis.txt new file mode 100644 index 000000000..d795e84fb --- /dev/null +++ b/latest/cases/00873/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reversible reactions in one compartment +with one reaction marked as fast and one species a boundary. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, FastReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called A1, A2, A3 and A4 and four parameters called Kf1, Kr1, Kf +and Kr. Species A2 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A4 <-> A2 | $(Kf1 * A4 - Kr1 * A2) * C$ | +| A1 + A2 <-> A3 | $(Kf * A1 * A2 - Kr * A3) * C$ |] +where the first reaction is marked as 'fast' and therefore should be assumed +to be operating on a time scale significantly faster than the second reaction. +Fast reactions are considered to be instantaneous relative to slow +reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of A1 |$2$ |mole | +|Initial amount of A2 |$3$ |mole | +|Initial amount of A3 |$4$ |mole | +|Initial amount of A4 |$1$ |mole | +|Value of parameter Kf1 |$1$ |second^-1^ | +|Value of parameter Kr1 |$2$ |second^-1^ | +|Value of parameter Kf |$1$ |litre mole^-1^ second^-1^ | +|Value of parameter Kr |$2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00874/l2v5/build.log b/latest/cases/00874/l2v5/build.log new file mode 100644 index 000000000..1bff718a2 --- /dev/null +++ b/latest/cases/00874/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00874/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00874/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00874/model-sbml-l2v5.xml"... +[error] "fast" reactions "reaction1" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00874/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00874/l2v5/index.heta b/latest/cases/00874/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00874/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00874/l3v2/index.heta b/latest/cases/00874/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00874/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00874/model-sbml-l2v5.xml b/latest/cases/00874/model-sbml-l2v5.xml new file mode 100644 index 000000000..c7a4c97e9 --- /dev/null +++ b/latest/cases/00874/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A4 + C + Kf1 + + + + + + + + + + + + + + + + + A1 + A2 + C + Kf + + + + + + + diff --git a/latest/cases/00874/synopsis.txt b/latest/cases/00874/synopsis.txt new file mode 100644 index 000000000..2b3fa6734 --- /dev/null +++ b/latest/cases/00874/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions in one compartment +with one reaction marked as fast and one species as boundary. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, FastReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called A1, A2, A3 and A4 and four parameters called Kf1, Kr1, Kf +and Kr. Species A3 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A4 -> A2 | $Kf1 * A4 * C$ | +| A1 + A2 -> A3 | $Kf * A1 * A2 * C$ |] +where the first reaction is marked as 'fast' and therefore should be assumed +to be operating on a time scale significantly faster than the second reaction. +Fast reactions are considered to be instantaneous relative to slow +reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of A1 |$2$ |mole | +|Initial amount of A2 |$3$ |mole | +|Initial amount of A3 |$4$ |mole | +|Initial amount of A4 |$1$ |mole | +|Value of parameter Kf1 |$1$ |second^-1^ | +|Value of parameter Kr1 |$2$ |second^-1^ | +|Value of parameter Kf |$1$ |litre mole^-1^ second^-1^ | +|Value of parameter Kr |$2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00875/l2v5/build.log b/latest/cases/00875/l2v5/build.log new file mode 100644 index 000000000..09efb1209 --- /dev/null +++ b/latest/cases/00875/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00875/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00875/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00875/model-sbml-l2v5.xml"... +[error] "fast" reactions "reaction1" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00875/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00875/l2v5/index.heta b/latest/cases/00875/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00875/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00875/l3v2/index.heta b/latest/cases/00875/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00875/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00875/model-sbml-l2v5.xml b/latest/cases/00875/model-sbml-l2v5.xml new file mode 100644 index 000000000..8745ecf14 --- /dev/null +++ b/latest/cases/00875/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A4 + C + Kf1 + + + + + + + + + + + + + + + + + A1 + A2 + C + Kf + + + + + + + diff --git a/latest/cases/00875/synopsis.txt b/latest/cases/00875/synopsis.txt new file mode 100644 index 000000000..4d9109372 --- /dev/null +++ b/latest/cases/00875/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions in one compartment +with one reaction marked as fast and one species as boundary. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, FastReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called A1, A2, A3 and A4 and four parameters called Kf1, Kr1, Kf +and Kr. Species A1 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A4 -> A2 | $Kf1 * A4 * C$ | +| A1 + A2 -> A3 | $Kf * A1 * A2 * C$ |] +where the first reaction is marked as 'fast' and therefore should be assumed +to be operating on a time scale significantly faster than the second reaction. +Fast reactions are considered to be instantaneous relative to slow +reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of A1 |$2$ |mole | +|Initial amount of A2 |$3$ |mole | +|Initial amount of A3 |$4$ |mole | +|Initial amount of A4 |$1$ |mole | +|Value of parameter Kf1 |$1$ |second^-1^ | +|Value of parameter Kr1 |$2$ |second^-1^ | +|Value of parameter Kf |$1$ |litre mole^-1^ second^-1^ | +|Value of parameter Kr |$2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00876/l2v5/build.log b/latest/cases/00876/l2v5/build.log new file mode 100644 index 000000000..25f4d3752 --- /dev/null +++ b/latest/cases/00876/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00876/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00876/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00876/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00876/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00876/l2v5/index.heta b/latest/cases/00876/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00876/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00876/l3v2/build.log b/latest/cases/00876/l3v2/build.log new file mode 100644 index 000000000..d623464e4 --- /dev/null +++ b/latest/cases/00876/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00876/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00876/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00876/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00876/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00876/l3v2/index.heta b/latest/cases/00876/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00876/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00876/model-sbml-l2v5.xml b/latest/cases/00876/model-sbml-l2v5.xml new file mode 100644 index 000000000..0a3d0846d --- /dev/null +++ b/latest/cases/00876/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00876/model-sbml-l3v2.xml b/latest/cases/00876/model-sbml-l3v2.xml new file mode 100644 index 000000000..bb7726e28 --- /dev/null +++ b/latest/cases/00876/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/00876/synopsis.txt b/latest/cases/00876/synopsis.txt new file mode 100644 index 000000000..9169162af --- /dev/null +++ b/latest/cases/00876/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: One reversible reaction with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called kf and kr. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00877/l2v5/heta-code/output.heta b/latest/cases/00877/l2v5/heta-code/output.heta new file mode 100644 index 000000000..545bcba3b --- /dev/null +++ b/latest/cases/00877/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.0015 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= p1 * S1 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 1; +p1 @Record 'p1' { } .= -0.5; + diff --git a/latest/cases/00877/l2v5/index.heta b/latest/cases/00877/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00877/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00877/l2v5/json/output.json b/latest/cases/00877/l2v5/json/output.json new file mode 100644 index 000000000..4d075b772 --- /dev/null +++ b/latest/cases/00877/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.0015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "p1 * S1 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "-0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00877/l3v2/heta-code/output.heta b/latest/cases/00877/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f2a81a825 --- /dev/null +++ b/latest/cases/00877/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= p1 * S1 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; +p1 @Const 'p1' { } = -0.5; + diff --git a/latest/cases/00877/l3v2/index.heta b/latest/cases/00877/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00877/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00877/l3v2/json/output.json b/latest/cases/00877/l3v2/json/output.json new file mode 100644 index 000000000..5a1b2c48b --- /dev/null +++ b/latest/cases/00877/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.0015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "p1 * S1 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": -0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00877/model-sbml-l2v5.xml b/latest/cases/00877/model-sbml-l2v5.xml new file mode 100644 index 000000000..366dca1fd --- /dev/null +++ b/latest/cases/00877/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + p1 + S1 + time + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00877/model-sbml-l3v2.xml b/latest/cases/00877/model-sbml-l3v2.xml new file mode 100644 index 000000000..7b0926912 --- /dev/null +++ b/latest/cases/00877/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + S1 + time + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00877/output.heta b/latest/cases/00877/output.heta new file mode 100644 index 000000000..af3810fa9 --- /dev/null +++ b/latest/cases/00877/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within an initialAssignment. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and p1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1 * time$ |] +where the symbol 'time' denotes the current simulation time. + +Note: SBML's InitialAssignment take effect at time t < 0 and continue to have effect +up to and including time t = 0, overriding any initial values. In this model, the +initial value for the species S1 has not been explicitly declared and must be +calculated using the InitialAssignment at time = 0. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$undeclared$ |mole | +|Value of parameter p1 |$-0.5$ |second^-1^ | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= p1 * S1 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; +p1 @Const 'p1' { } = -0.5; + diff --git a/latest/cases/00877/synopsis.txt b/latest/cases/00877/synopsis.txt new file mode 100644 index 000000000..b55e30531 --- /dev/null +++ b/latest/cases/00877/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within an initialAssignment. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and p1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1 * time$ |] +where the symbol 'time' denotes the current simulation time. + +Note: SBML's InitialAssignment take effect at time t < 0 and continue to have effect +up to and including time t = 0, overriding any initial values. In this model, the +initial value for the species S1 has not been explicitly declared and must be +calculated using the InitialAssignment at time = 0. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$undeclared$ |mole | +|Value of parameter p1 |$-0.5$ |second^-1^ | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00878/l2v5/heta-code/output.heta b/latest/cases/00878/l2v5/heta-code/output.heta new file mode 100644 index 000000000..733b65636 --- /dev/null +++ b/latest/cases/00878/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.015 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= p1 * S1 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Record 'k1' { } .= 1; +p1 @Record 'p1' { } .= -0.5; + diff --git a/latest/cases/00878/l2v5/index.heta b/latest/cases/00878/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00878/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00878/l2v5/json/output.json b/latest/cases/00878/l2v5/json/output.json new file mode 100644 index 000000000..eecf80ced --- /dev/null +++ b/latest/cases/00878/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "p1 * S1 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "-0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00878/l3v2/heta-code/output.heta b/latest/cases/00878/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c19051061 --- /dev/null +++ b/latest/cases/00878/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.015 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= p1 * S1 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; +p1 @Const 'p1' { } = -0.5; + diff --git a/latest/cases/00878/l3v2/index.heta b/latest/cases/00878/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00878/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00878/l3v2/json/output.json b/latest/cases/00878/l3v2/json/output.json new file mode 100644 index 000000000..9e35d2aca --- /dev/null +++ b/latest/cases/00878/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.015 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "p1 * S1 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": -0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00878/model-sbml-l2v5.xml b/latest/cases/00878/model-sbml-l2v5.xml new file mode 100644 index 000000000..b5fc0f017 --- /dev/null +++ b/latest/cases/00878/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + p1 + S1 + time + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00878/model-sbml-l3v2.xml b/latest/cases/00878/model-sbml-l3v2.xml new file mode 100644 index 000000000..8033c1ff6 --- /dev/null +++ b/latest/cases/00878/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + S1 + time + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00878/output.heta b/latest/cases/00878/output.heta new file mode 100644 index 000000000..b2860d9b3 --- /dev/null +++ b/latest/cases/00878/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within an initialAssignment. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and p1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1 * time$ |] +where the symbol 'time' denotes the current simulation time. + +Note: SBML's InitialAssignment take effect at time t < 0 and continue to have effect +up to and including time t = 0, overriding any initial values. In this model, the +initial value for the species S1 is inconsistent with the value calculated using +the InitialAssignment at time = 0; the calculated value should be used. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Value of parameter p1 |$-0.5$ |second^-1^ | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.015 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= p1 * S1 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; +p1 @Const 'p1' { } = -0.5; + diff --git a/latest/cases/00878/synopsis.txt b/latest/cases/00878/synopsis.txt new file mode 100644 index 000000000..35de4cd44 --- /dev/null +++ b/latest/cases/00878/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within an initialAssignment. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and p1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S2 | $p1 * S1 * time$ |] +where the symbol 'time' denotes the current simulation time. + +Note: SBML's InitialAssignment take effect at time t < 0 and continue to have effect +up to and including time t = 0, overriding any initial values. In this model, the +initial value for the species S1 is inconsistent with the value calculated using +the InitialAssignment at time = 0; the calculated value should be used. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Value of parameter p1 |$-0.5$ |second^-1^ | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00879/l2v5/heta-code/output.heta b/latest/cases/00879/l2v5/heta-code/output.heta new file mode 100644 index 000000000..50cad3bce --- /dev/null +++ b/latest/cases/00879/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Record 'k1' { } .= k2 * exp(t) + 0.2; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00879/l2v5/index.heta b/latest/cases/00879/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00879/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00879/l2v5/json/output.json b/latest/cases/00879/l2v5/json/output.json new file mode 100644 index 000000000..2e3986710 --- /dev/null +++ b/latest/cases/00879/l2v5/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "k2 * exp(t) + 0.2" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00879/l3v2/build.log b/latest/cases/00879/l3v2/build.log new file mode 100644 index 000000000..7847f4875 --- /dev/null +++ b/latest/cases/00879/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00879/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00879/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00879/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 90 +[error] No required "num" property for "k1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00879/l3v2/index.heta b/latest/cases/00879/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00879/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00879/model-sbml-l2v5.xml b/latest/cases/00879/model-sbml-l2v5.xml new file mode 100644 index 000000000..59b95182c --- /dev/null +++ b/latest/cases/00879/model-sbml-l2v5.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + t + + + 0.2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00879/model-sbml-l3v2.xml b/latest/cases/00879/model-sbml-l3v2.xml new file mode 100644 index 000000000..1d5417879 --- /dev/null +++ b/latest/cases/00879/model-sbml-l3v2.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k2 + + + t + + + 0.2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S2 + + + + + + + + + + + + + + + + C + k3 + S3 + + + + + + + diff --git a/latest/cases/00879/output.heta b/latest/cases/00879/output.heta new file mode 100644 index 000000000..3289029e9 --- /dev/null +++ b/latest/cases/00879/output.heta @@ -0,0 +1,79 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within an initialAssignment. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S4 | $k3 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $0.2 + k2* exp(t)$ |] +where the symbol 't' denotes the current simulation time. + +Note: SBML's InitialAssignment take effect at time t < 0 and continue to have effect +up to and including time t = 0, overriding any initial values. In this model, the +initial value for the parameter k1 has not been explicitly declared and must be +calculated using the InitialAssignment at time = 0. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$undeclared$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3; + +k1 @Record 'k1' { } .= k2 * exp(t) + 0.2; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00879/synopsis.txt b/latest/cases/00879/synopsis.txt new file mode 100644 index 000000000..5b908214a --- /dev/null +++ b/latest/cases/00879/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within an initialAssignment. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, InitialAssignment +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ | +| S2 -> S3 | $k2 * S2 * C$ | +| S3 -> S4 | $k3 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $0.2 + k2* exp(t)$ |] +where the symbol 't' denotes the current simulation time. + +Note: SBML's InitialAssignment take effect at time t < 0 and continue to have effect +up to and including time t = 0, overriding any initial values. In this model, the +initial value for the parameter k1 has not been explicitly declared and must be +calculated using the InitialAssignment at time = 0. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$undeclared$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00880/l2v5/heta-code/output.heta b/latest/cases/00880/l2v5/heta-code/output.heta new file mode 100644 index 000000000..93e075b5f --- /dev/null +++ b/latest/cases/00880/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-15 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, }; +S3 := k1 * S2 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 5; + diff --git a/latest/cases/00880/l2v5/index.heta b/latest/cases/00880/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00880/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00880/l2v5/json/output.json b/latest/cases/00880/l2v5/json/output.json new file mode 100644 index 000000000..1f1622be3 --- /dev/null +++ b/latest/cases/00880/l2v5/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-15 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "ode_": "k1 * S2 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00880/l3v2/heta-code/output.heta b/latest/cases/00880/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7b6beb1b5 --- /dev/null +++ b/latest/cases/00880/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-15 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00880/l3v2/index.heta b/latest/cases/00880/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00880/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00880/l3v2/json/output.json b/latest/cases/00880/l3v2/json/output.json new file mode 100644 index 000000000..735460acd --- /dev/null +++ b/latest/cases/00880/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-15 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "ode_": "k1 * S2 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/00880/model-sbml-l2v5.xml b/latest/cases/00880/model-sbml-l2v5.xml new file mode 100644 index 000000000..8c88a2c5c --- /dev/null +++ b/latest/cases/00880/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + t + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00880/model-sbml-l3v2.xml b/latest/cases/00880/model-sbml-l3v2.xml new file mode 100644 index 000000000..5fb0a8cfa --- /dev/null +++ b/latest/cases/00880/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + t + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00880/output.heta b/latest/cases/00880/output.heta new file mode 100644 index 000000000..dfed8e00b --- /dev/null +++ b/latest/cases/00880/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with csymbol time to vary one species. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2 * t$ |] +where the symbol 't' denotes the current simulation time. + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-15 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, }; +S3 := k1 * S2 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 5; + diff --git a/latest/cases/00880/synopsis.txt b/latest/cases/00880/synopsis.txt new file mode 100644 index 000000000..a6aec8592 --- /dev/null +++ b/latest/cases/00880/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with csymbol time to vary one species. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2 * t$ |] +where the symbol 't' denotes the current simulation time. + +In this case the initial value for species S3 must be calculated by the +assignmentRule. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00881/l2v5/heta-code/output.heta b/latest/cases/00881/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3da7d4610 --- /dev/null +++ b/latest/cases/00881/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5e-15 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; +S3 := k1 * S2 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 2.5; + diff --git a/latest/cases/00881/l2v5/index.heta b/latest/cases/00881/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00881/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00881/l2v5/json/output.json b/latest/cases/00881/l2v5/json/output.json new file mode 100644 index 000000000..40d286359 --- /dev/null +++ b/latest/cases/00881/l2v5/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-15 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "ode_": "k1 * S2 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00881/l3v2/heta-code/output.heta b/latest/cases/00881/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8516d4e2a --- /dev/null +++ b/latest/cases/00881/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-15 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S3 := k1 * S2 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00881/l3v2/index.heta b/latest/cases/00881/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00881/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00881/l3v2/json/output.json b/latest/cases/00881/l3v2/json/output.json new file mode 100644 index 000000000..bae6470d4 --- /dev/null +++ b/latest/cases/00881/l3v2/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-15 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "ode_": "k1 * S2 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 2.5 + } +] \ No newline at end of file diff --git a/latest/cases/00881/model-sbml-l2v5.xml b/latest/cases/00881/model-sbml-l2v5.xml new file mode 100644 index 000000000..09dc541a8 --- /dev/null +++ b/latest/cases/00881/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + t + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00881/model-sbml-l3v2.xml b/latest/cases/00881/model-sbml-l3v2.xml new file mode 100644 index 000000000..f17b32157 --- /dev/null +++ b/latest/cases/00881/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + t + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/00881/output.heta b/latest/cases/00881/output.heta new file mode 100644 index 000000000..eb1d3efd0 --- /dev/null +++ b/latest/cases/00881/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with csymbol time to vary one species. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2 * t$ |] +where the symbol 't' denotes the current simulation time. + +In this case the initial value for species S3 is inconsistent with the +value calculated by the assignmentRule; the calculated value should be +used. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ 1$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-15 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S3 := k1 * S2 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2 * S1; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 2.5; + diff --git a/latest/cases/00881/synopsis.txt b/latest/cases/00881/synopsis.txt new file mode 100644 index 000000000..38db06e73 --- /dev/null +++ b/latest/cases/00881/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule with csymbol time to vary one species. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, AssignmentRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S and two parameters called k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $C * k2 * S1$ |] + +The model contains one rule which assigns value to species S3: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2 * t$ |] +where the symbol 't' denotes the current simulation time. + +In this case the initial value for species S3 is inconsistent with the +value calculated by the assignmentRule; the calculated value should be +used. Note that since this assignmentRule must always remain +true, it should be considered during simulation. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-15$ |mole | +|Initial amount of S3 |$ 1$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 2.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00882/l2v5/heta-code/output.heta b/latest/cases/00882/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f39d0c614 --- /dev/null +++ b/latest/cases/00882/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 0.4; +k2 @Record 'k2' { } .= 0.3; +k3 @Record 'k3' { } .= 0.2; + diff --git a/latest/cases/00882/l2v5/index.heta b/latest/cases/00882/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00882/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00882/l2v5/json/output.json b/latest/cases/00882/l2v5/json/output.json new file mode 100644 index 000000000..6564a47ff --- /dev/null +++ b/latest/cases/00882/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.4" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00882/l3v2/heta-code/output.heta b/latest/cases/00882/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bb7bff5ba --- /dev/null +++ b/latest/cases/00882/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.4; +k2 @Const 'k2' { } = 0.3; +k3 @Const 'k3' { } = 0.2; + diff --git a/latest/cases/00882/l3v2/index.heta b/latest/cases/00882/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00882/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00882/l3v2/json/output.json b/latest/cases/00882/l3v2/json/output.json new file mode 100644 index 000000000..f274adba6 --- /dev/null +++ b/latest/cases/00882/l3v2/json/output.json @@ -0,0 +1,132 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.4 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00882/model-sbml-l2v5.xml b/latest/cases/00882/model-sbml-l2v5.xml new file mode 100644 index 000000000..a635727e4 --- /dev/null +++ b/latest/cases/00882/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00882/model-sbml-l3v2.xml b/latest/cases/00882/model-sbml-l3v2.xml new file mode 100644 index 000000000..8072954b7 --- /dev/null +++ b/latest/cases/00882/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00882/output.heta b/latest/cases/00882/output.heta new file mode 100644 index 000000000..f99c35193 --- /dev/null +++ b/latest/cases/00882/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, ConstantSpecies, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S1 is labeled as constant and a boundaryCondition and therefore +cannot be changed. The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.4$ |second^-2^ | +|Value of parameter k2 |$0.3$ |second^-2^ | +|Value of parameter k3 |$0.2$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.4; +k2 @Const 'k2' { } = 0.3; +k3 @Const 'k3' { } = 0.2; + diff --git a/latest/cases/00882/synopsis.txt b/latest/cases/00882/synopsis.txt new file mode 100644 index 000000000..504ca476f --- /dev/null +++ b/latest/cases/00882/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, ConstantSpecies, BoundaryCondition +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +Species S1 is labeled as constant and a boundaryCondition and therefore +cannot be changed. The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.4$ |second^-2^ | +|Value of parameter k2 |$0.3$ |second^-2^ | +|Value of parameter k3 |$0.2$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00883/l2v5/heta-code/output.heta b/latest/cases/00883/l2v5/heta-code/output.heta new file mode 100644 index 000000000..86144ad98 --- /dev/null +++ b/latest/cases/00883/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= k3 * t; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 1; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00883/l2v5/index.heta b/latest/cases/00883/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00883/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00883/l2v5/json/output.json b/latest/cases/00883/l2v5/json/output.json new file mode 100644 index 000000000..63fc11633 --- /dev/null +++ b/latest/cases/00883/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "k3 * t" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00883/l3v2/heta-code/output.heta b/latest/cases/00883/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5690e758c --- /dev/null +++ b/latest/cases/00883/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= k3 * t; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 1; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00883/l3v2/index.heta b/latest/cases/00883/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00883/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00883/l3v2/json/output.json b/latest/cases/00883/l3v2/json/output.json new file mode 100644 index 000000000..649f44d2a --- /dev/null +++ b/latest/cases/00883/l3v2/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "k3 * t" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + } +] \ No newline at end of file diff --git a/latest/cases/00883/model-sbml-l2v5.xml b/latest/cases/00883/model-sbml-l2v5.xml new file mode 100644 index 000000000..9ddce7555 --- /dev/null +++ b/latest/cases/00883/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + + k3 + t + + + + + + + + diff --git a/latest/cases/00883/model-sbml-l3v2.xml b/latest/cases/00883/model-sbml-l3v2.xml new file mode 100644 index 000000000..02c81d099 --- /dev/null +++ b/latest/cases/00883/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + + + + k3 + t + + + + + + + + diff --git a/latest/cases/00883/output.heta b/latest/cases/00883/output.heta new file mode 100644 index 000000000..0e5e23cb9 --- /dev/null +++ b/latest/cases/00883/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment +and one event that assigns value to a species using csymbol time. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = k3 * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$1$ |mole litre^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= k3 * t; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 1; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/00883/synopsis.txt b/latest/cases/00883/synopsis.txt new file mode 100644 index 000000000..69c3ac9c7 --- /dev/null +++ b/latest/cases/00883/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment +and one event that assigns value to a species using csymbol time. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = k3 * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$1$ |mole litre^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00884/l2v5/heta-code/output.heta b/latest/cases/00884/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e381753d6 --- /dev/null +++ b/latest/cases/00884/l2v5/heta-code/output.heta @@ -0,0 +1,29 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C; +S1 [event2]= 0.25 * t; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S2 [event1]= k3 * t; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; +k3 @Record 'k3' { } .= 4; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00884/l2v5/index.heta b/latest/cases/00884/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00884/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00884/l2v5/json/output.json b/latest/cases/00884/l2v5/json/output.json new file mode 100644 index 000000000..444e83cde --- /dev/null +++ b/latest/cases/00884/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1 / C", + "event2": "0.25 * t" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C", + "event1": "k3 * t" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "4" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00884/l3v2/heta-code/output.heta b/latest/cases/00884/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ce72354a5 --- /dev/null +++ b/latest/cases/00884/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 0.25 * t; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= k3 * t; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 4; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00884/l3v2/index.heta b/latest/cases/00884/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00884/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00884/l3v2/json/output.json b/latest/cases/00884/l3v2/json/output.json new file mode 100644 index 000000000..7ff1a4a2e --- /dev/null +++ b/latest/cases/00884/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C", + "event2": "0.25 * t" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "k3 * t" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 4 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 > 1.4" + } +] \ No newline at end of file diff --git a/latest/cases/00884/model-sbml-l2v5.xml b/latest/cases/00884/model-sbml-l2v5.xml new file mode 100644 index 000000000..a95d276dd --- /dev/null +++ b/latest/cases/00884/model-sbml-l2v5.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + + k3 + s + + + + + + + + + + + S3 + 1.4 + + + + + + + + + 0.25 + s + + + + + + + + diff --git a/latest/cases/00884/model-sbml-l3v2.xml b/latest/cases/00884/model-sbml-l3v2.xml new file mode 100644 index 000000000..042d4658f --- /dev/null +++ b/latest/cases/00884/model-sbml-l3v2.xml @@ -0,0 +1,122 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + + k3 + s + + + + + + + + + + + S3 + 1.4 + + + + + + + + + 0.25 + s + + + + + + + + diff --git a/latest/cases/00884/output.heta b/latest/cases/00884/output.heta new file mode 100644 index 000000000..c2ac96b59 --- /dev/null +++ b/latest/cases/00884/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Basic two reactions with three species in one compartment +and two events that assigns value to a species using csymbol time. +componentTags: Compartment, Species, Reaction, CSymbolTime, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = k3 * s$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 0.25 * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$4$ |mole litre^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S1 [event2]= 0.25 * t; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= k3 * t; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; +k3 @Const 'k3' { } = 4; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; +event2 @DSwitcher 'event2' { trigger: S3 > 1.4, }; + diff --git a/latest/cases/00884/synopsis.txt b/latest/cases/00884/synopsis.txt new file mode 100644 index 000000000..890e6e404 --- /dev/null +++ b/latest/cases/00884/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment +and two events that assigns value to a species using csymbol time. +componentTags: Compartment, Species, Reaction, CSymbolTime, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = k3 * s$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 0.25 * s$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$4$ |mole litre^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00885/l2v5/heta-code/output.heta b/latest/cases/00885/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6f0b28918 --- /dev/null +++ b/latest/cases/00885/l2v5/heta-code/output.heta @@ -0,0 +1,30 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S1 [event1]= k3 * t; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0.012 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0.02 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0.01 / C; +S4 [event1]= k4 * S1 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 25; +k3 @Record 'k3' { } .= 0.02; +k4 @Record 'k4' { } .= 0.02; + +event1 @DSwitcher 'event1' { trigger: S2 > S3, }; + diff --git a/latest/cases/00885/l2v5/index.heta b/latest/cases/00885/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00885/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00885/l2v5/json/output.json b/latest/cases/00885/l2v5/json/output.json new file mode 100644 index 000000000..d15845254 --- /dev/null +++ b/latest/cases/00885/l2v5/json/output.json @@ -0,0 +1,174 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C", + "event1": "k3 * t" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0.012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C", + "event1": "k4 * S1 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "Record", + "id": "k4", + "title": "k4", + "assignments": { + "start_": "0.02" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S2 > S3" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00885/l3v2/heta-code/output.heta b/latest/cases/00885/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b608d829b --- /dev/null +++ b/latest/cases/00885/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S1 [event1]= k3 * t; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.01 / C; +S4 [event1]= k4 * S1 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 25; +k3 @Const 'k3' { } = 0.02; +k4 @Const 'k4' { } = 0.02; + +event1 @DSwitcher 'event1' { trigger: S2 > S3, }; + diff --git a/latest/cases/00885/l3v2/index.heta b/latest/cases/00885/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00885/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00885/l3v2/json/output.json b/latest/cases/00885/l3v2/json/output.json new file mode 100644 index 000000000..e0efa0b1c --- /dev/null +++ b/latest/cases/00885/l3v2/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C", + "event1": "k3 * t" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.012 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.02 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C", + "event1": "k4 * S1 * t" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 0.02 + }, + { + "class": "Const", + "id": "k4", + "title": "k4", + "num": 0.02 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S2 > S3" + } +] \ No newline at end of file diff --git a/latest/cases/00885/model-sbml-l2v5.xml b/latest/cases/00885/model-sbml-l2v5.xml new file mode 100644 index 000000000..e7d4ea833 --- /dev/null +++ b/latest/cases/00885/model-sbml-l2v5.xml @@ -0,0 +1,98 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S3 + + + + + + + + + k3 + time + + + + + + + + k4 + S1 + time + + + + + + + + diff --git a/latest/cases/00885/model-sbml-l3v2.xml b/latest/cases/00885/model-sbml-l3v2.xml new file mode 100644 index 000000000..b459f0d13 --- /dev/null +++ b/latest/cases/00885/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S2 + S3 + + + + + + + + + k3 + time + + + + + + + + k4 + S1 + time + + + + + + + + diff --git a/latest/cases/00885/output.heta b/latest/cases/00885/output.heta new file mode 100644 index 000000000..66ac4ab97 --- /dev/null +++ b/latest/cases/00885/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Basic two reactions with four species in one compartment +and an event that assigns value to two species using csymbol time. +componentTags: Compartment, Species, Reaction, CSymbolTime, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S2 > S3$ | $-$ | $S1 -> k3 * time$ |] + | | | | $S4 -> k4 * S1 * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.075 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k3 |$2 \x 10^-2$ |mole litre^-1^ second^-1^ | +|Value of parameter k4 |$2 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S1 [event1]= k3 * t; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.01 / C; +S4 [event1]= k4 * S1 * t; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3 * S4; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 25; +k3 @Const 'k3' { } = 0.02; +k4 @Const 'k4' { } = 0.02; + +event1 @DSwitcher 'event1' { trigger: S2 > S3, }; + diff --git a/latest/cases/00885/synopsis.txt b/latest/cases/00885/synopsis.txt new file mode 100644 index 000000000..674a656ce --- /dev/null +++ b/latest/cases/00885/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment +and an event that assigns value to two species using csymbol time. +componentTags: Compartment, Species, Reaction, CSymbolTime, Parameter, EventNoDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains one event that assigns values to both species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S2 > S3$ | $-$ | $S1 -> k3 * time$ |] + | | | | $S4 -> k4 * S1 * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.0 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.075 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k3 |$2 \x 10^-2$ |mole litre^-1^ second^-1^ | +|Value of parameter k4 |$2 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00886/l2v5/build.log b/latest/cases/00886/l2v5/build.log new file mode 100644 index 000000000..dc9b4a1de --- /dev/null +++ b/latest/cases/00886/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00886/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00886/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00886/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00886/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00886/l2v5/index.heta b/latest/cases/00886/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00886/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00886/l3v2/build.log b/latest/cases/00886/l3v2/build.log new file mode 100644 index 000000000..80632b790 --- /dev/null +++ b/latest/cases/00886/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00886/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00886/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00886/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00886/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00886/l3v2/index.heta b/latest/cases/00886/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00886/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00886/model-sbml-l2v5.xml b/latest/cases/00886/model-sbml-l2v5.xml new file mode 100644 index 000000000..e55757d83 --- /dev/null +++ b/latest/cases/00886/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + t + + + + + + 1 + + + + + + + diff --git a/latest/cases/00886/model-sbml-l3v2.xml b/latest/cases/00886/model-sbml-l3v2.xml new file mode 100644 index 000000000..b4a4fdcb7 --- /dev/null +++ b/latest/cases/00886/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + t + + + + + + 1 + + + + + + + diff --git a/latest/cases/00886/synopsis.txt b/latest/cases/00886/synopsis.txt new file mode 100644 index 000000000..214fbf213 --- /dev/null +++ b/latest/cases/00886/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment +and one event that assigns value to a species with a delay using csymbol time. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, EventWithDelay +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $t$ | $S2 = 1$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$1$ |mole litre^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00887/l2v5/build.log b/latest/cases/00887/l2v5/build.log new file mode 100644 index 000000000..bf5177c96 --- /dev/null +++ b/latest/cases/00887/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00887/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00887/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00887/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00887/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00887/l2v5/index.heta b/latest/cases/00887/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00887/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00887/l3v2/build.log b/latest/cases/00887/l3v2/build.log new file mode 100644 index 000000000..c45a64756 --- /dev/null +++ b/latest/cases/00887/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00887/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00887/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00887/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00887/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00887/l3v2/index.heta b/latest/cases/00887/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00887/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00887/model-sbml-l2v5.xml b/latest/cases/00887/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef384f770 --- /dev/null +++ b/latest/cases/00887/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + k3 + time + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 0.25 + + + + + + + diff --git a/latest/cases/00887/model-sbml-l3v2.xml b/latest/cases/00887/model-sbml-l3v2.xml new file mode 100644 index 000000000..e59c4e2b6 --- /dev/null +++ b/latest/cases/00887/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + + k3 + time + + + + + + + 1 + + + + + + + + + + S3 + 1.4 + + + + + + + 0.25 + + + + + + + diff --git a/latest/cases/00887/synopsis.txt b/latest/cases/00887/synopsis.txt new file mode 100644 index 000000000..7aa3a1aec --- /dev/null +++ b/latest/cases/00887/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment +and two events that assigns value to a species with a delay using csymbol time. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, EventWithDelay, EventNoDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and three parameters called k1, k2 and k3. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains two events that assign values to species S2 and S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $k3 * time$ | $S2 = 1$ | + | Event2 | $S3 > 1.4$ | $-$ | $S1 = 0.25$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter k3 |$4$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00888/l2v5/heta-code/output.heta b/latest/cases/00888/l2v5/heta-code/output.heta new file mode 100644 index 000000000..014af2d6e --- /dev/null +++ b/latest/cases/00888/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 1.5 * pow(exp(t), (-1)); + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/00888/l2v5/index.heta b/latest/cases/00888/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00888/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00888/l2v5/json/output.json b/latest/cases/00888/l2v5/json/output.json new file mode 100644 index 000000000..5eb06ad02 --- /dev/null +++ b/latest/cases/00888/l2v5/json/output.json @@ -0,0 +1,113 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1.5 * pow(exp(t), (-1))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00888/l3v2/heta-code/output.heta b/latest/cases/00888/l3v2/heta-code/output.heta new file mode 100644 index 000000000..94a4b643b --- /dev/null +++ b/latest/cases/00888/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 1.5 * pow(exp(t), (-1)); + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00888/l3v2/index.heta b/latest/cases/00888/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00888/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00888/l3v2/json/output.json b/latest/cases/00888/l3v2/json/output.json new file mode 100644 index 000000000..1351a4f17 --- /dev/null +++ b/latest/cases/00888/l3v2/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1.5 * pow(exp(t), (-1))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00888/model-sbml-l2v5.xml b/latest/cases/00888/model-sbml-l2v5.xml new file mode 100644 index 000000000..370541807 --- /dev/null +++ b/latest/cases/00888/model-sbml-l2v5.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + 1.5 + + + + + time + + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00888/model-sbml-l3v2.xml b/latest/cases/00888/model-sbml-l3v2.xml new file mode 100644 index 000000000..9df3e583c --- /dev/null +++ b/latest/cases/00888/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1.5 + + + + + time + + -1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00888/output.heta b/latest/cases/00888/output.heta new file mode 100644 index 000000000..b549b82e0 --- /dev/null +++ b/latest/cases/00888/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment +where rate rule uses csymbol time. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15 / exp(time)$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 1.5 * pow(exp(t), (-1)); + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/00888/synopsis.txt b/latest/cases/00888/synopsis.txt new file mode 100644 index 000000000..0bb8123b8 --- /dev/null +++ b/latest/cases/00888/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a compartment +where rate rule uses csymbol time. +componentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and one parameter called k1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $0.15 / exp(time)$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Initial amount of S3 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00889/l2v5/heta-code/output.heta b/latest/cases/00889/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0cf652f3e --- /dev/null +++ b/latest/cases/00889/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5e-4 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := t * pow(1e+5, (-1)); + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 0.0025; + diff --git a/latest/cases/00889/l2v5/index.heta b/latest/cases/00889/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00889/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00889/l2v5/json/output.json b/latest/cases/00889/l2v5/json/output.json new file mode 100644 index 000000000..e9e68106a --- /dev/null +++ b/latest/cases/00889/l2v5/json/output.json @@ -0,0 +1,158 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.0025" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "t * pow(1e+5, (-1))" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00889/l3v2/heta-code/output.heta b/latest/cases/00889/l3v2/heta-code/output.heta new file mode 100644 index 000000000..97a1b163a --- /dev/null +++ b/latest/cases/00889/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := t * pow(1e+5, (-1)); + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0.0025; + diff --git a/latest/cases/00889/l3v2/index.heta b/latest/cases/00889/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00889/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00889/l3v2/json/output.json b/latest/cases/00889/l3v2/json/output.json new file mode 100644 index 000000000..03f877f24 --- /dev/null +++ b/latest/cases/00889/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.0025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "t * pow(1e+5, (-1))" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00889/model-sbml-l2v5.xml b/latest/cases/00889/model-sbml-l2v5.xml new file mode 100644 index 000000000..d21039341 --- /dev/null +++ b/latest/cases/00889/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + t + + + 100000 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00889/model-sbml-l3v2.xml b/latest/cases/00889/model-sbml-l3v2.xml new file mode 100644 index 000000000..abb4c07d8 --- /dev/null +++ b/latest/cases/00889/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + t + + + 100000 + -1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/00889/output.heta b/latest/cases/00889/output.heta new file mode 100644 index 000000000..92d0cf319 --- /dev/null +++ b/latest/cases/00889/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment +where rate rule uses csymbol time. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-5 * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.5 \x 10^-4$ |mole | +|Initial amount of S4 |$ 1 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := t * pow(1e+5, (-1)); + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 0.0025; + diff --git a/latest/cases/00889/synopsis.txt b/latest/cases/00889/synopsis.txt new file mode 100644 index 000000000..f0c2d8b80 --- /dev/null +++ b/latest/cases/00889/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment +where rate rule uses csymbol time. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-5 * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.5 \x 10^-4$ |mole | +|Initial amount of S4 |$ 1 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-2$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00890/l2v5/heta-code/output.heta b/latest/cases/00890/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c8a22844c --- /dev/null +++ b/latest/cases/00890/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1 * abs(1 + (-1) * t); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/00890/l2v5/index.heta b/latest/cases/00890/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00890/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00890/l2v5/json/output.json b/latest/cases/00890/l2v5/json/output.json new file mode 100644 index 000000000..89f5a56dd --- /dev/null +++ b/latest/cases/00890/l2v5/json/output.json @@ -0,0 +1,147 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1 * abs(1 + (-1) * t)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00890/l3v2/heta-code/output.heta b/latest/cases/00890/l3v2/heta-code/output.heta new file mode 100644 index 000000000..933005f9b --- /dev/null +++ b/latest/cases/00890/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1 * abs(1 + (-1) * t); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00890/l3v2/index.heta b/latest/cases/00890/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00890/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00890/l3v2/json/output.json b/latest/cases/00890/l3v2/json/output.json new file mode 100644 index 000000000..30d502219 --- /dev/null +++ b/latest/cases/00890/l3v2/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "4 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * k1 * abs(1 + (-1) * t)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-0.5) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00890/model-sbml-l2v5.xml b/latest/cases/00890/model-sbml-l2v5.xml new file mode 100644 index 000000000..63111e277 --- /dev/null +++ b/latest/cases/00890/model-sbml-l2v5.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + 1 + + + -1 + s + + + + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00890/model-sbml-l3v2.xml b/latest/cases/00890/model-sbml-l3v2.xml new file mode 100644 index 000000000..59a9021a1 --- /dev/null +++ b/latest/cases/00890/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + k1 + + + + + 1 + + + -1 + s + + + + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/00890/output.heta b/latest/cases/00890/output.heta new file mode 100644 index 000000000..dbfef24fd --- /dev/null +++ b/latest/cases/00890/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a compartment +where rate rule uses csymbol time. +componentTags: Compartment, Species, Reaction, CSymbolTime, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 * abs(1 - s)$ | + | Rate | S4 | $-k2 * 0.5$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 0.5 * k1 * abs(1 + (-1) * t); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-0.5) * k2; + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/00890/synopsis.txt b/latest/cases/00890/synopsis.txt new file mode 100644 index 000000000..9b5e55028 --- /dev/null +++ b/latest/cases/00890/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment +where rate rule uses csymbol time. +componentTags: Compartment, Species, Reaction, CSymbolTime, Parameter, RateRule +testTags: Amount +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and k2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5 * abs(1 - s)$ | + | Rate | S4 | $-k2 * 0.5$ |] +where the symbol 's' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00891/l2v5/heta-code/output.heta b/latest/cases/00891/l2v5/heta-code/output.heta new file mode 100644 index 000000000..16176e231 --- /dev/null +++ b/latest/cases/00891/l2v5/heta-code/output.heta @@ -0,0 +1,18 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := (-1) * k1 * k3 * t; +k2_proc @Process { actors: = k2, aux: {{"metaid":"rule2"}}, }; +k2_proc := k1 * k3 * t; + +k1 @Record 'k1' { } .= 1.5e-4; +k2 @Record 'k2' { } .= 0; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00891/l2v5/index.heta b/latest/cases/00891/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00891/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00891/l2v5/json/output.json b/latest/cases/00891/l2v5/json/output.json new file mode 100644 index 000000000..86fe28411 --- /dev/null +++ b/latest/cases/00891/l2v5/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e-4" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * k3 * t" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "k2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * k3 * t" + }, + "actors": [ + { + "target": "k2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00891/l3v2/heta-code/output.heta b/latest/cases/00891/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2a2909739 --- /dev/null +++ b/latest/cases/00891/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := (-1) * k1 * k3 * t; +k2_proc @Process { actors: = k2, aux: {{"metaid":"rule2"}}, }; +k2_proc := k1 * k3 * t; + +k1 @Record 'k1' { } .= 1.5e-4; +k2 @Record 'k2' { } .= 0; + +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00891/l3v2/index.heta b/latest/cases/00891/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00891/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00891/l3v2/json/output.json b/latest/cases/00891/l3v2/json/output.json new file mode 100644 index 000000000..1774822a0 --- /dev/null +++ b/latest/cases/00891/l3v2/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e-4" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + }, + { + "class": "Process", + "id": "k1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * k1 * k3 * t" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "k2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "k1 * k3 * t" + }, + "actors": [ + { + "target": "k2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00891/model-sbml-l2v5.xml b/latest/cases/00891/model-sbml-l2v5.xml new file mode 100644 index 000000000..af41d67c5 --- /dev/null +++ b/latest/cases/00891/model-sbml-l2v5.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + -1 + k1 + k3 + t + + + + + + + + k1 + k3 + t + + + + + + diff --git a/latest/cases/00891/model-sbml-l3v2.xml b/latest/cases/00891/model-sbml-l3v2.xml new file mode 100644 index 000000000..2eb76636f --- /dev/null +++ b/latest/cases/00891/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + -1 + k1 + k3 + t + + + + + + + + k1 + k3 + t + + + + + + diff --git a/latest/cases/00891/output.heta b/latest/cases/00891/output.heta new file mode 100644 index 000000000..59ed7c311 --- /dev/null +++ b/latest/cases/00891/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: Model using parameters and rules only, with csymbol time. +componentTags: Parameter, RateRule, CSymbolTime +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called k1 and k2 and one constant +parameter called k3. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $-k1 * k3 * t$ | + | Rate | k2 | $k1 * k3 * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$1.5 \x 10^-4$ |any | +|Value of parameter k2 |$ 0$ |same as k1 | +|Value of parameter k3 |$ 1$ |second^-2^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +k1_proc @Process { actors: = k1, aux: {{"metaid":"rule1"}}, }; +k1_proc := (-1) * k1 * k3 * t; +k2_proc @Process { actors: = k2, aux: {{"metaid":"rule2"}}, }; +k2_proc := k1 * k3 * t; + +k1 @Record 'k1' { } .= 1.5e-4; +k2 @Record 'k2' { } .= 0; + +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00891/synopsis.txt b/latest/cases/00891/synopsis.txt new file mode 100644 index 000000000..3ad289630 --- /dev/null +++ b/latest/cases/00891/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Model using parameters and rules only, with csymbol time. +componentTags: Parameter, RateRule, CSymbolTime +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called k1 and k2 and one constant +parameter called k3. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | k1 | $-k1 * k3 * t$ | + | Rate | k2 | $k1 * k3 * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$1.5 \x 10^-4$ |any | +|Value of parameter k2 |$ 0$ |same as k1 | +|Value of parameter k3 |$ 1$ |second^-2^ |] + + diff --git a/latest/cases/00892/l2v5/heta-code/output.heta b/latest/cases/00892/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2990afc7a --- /dev/null +++ b/latest/cases/00892/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +P1_proc @Process { actors: = P1, aux: {{"metaid":"rule1"}}, }; +P1_proc := pow(e, (-1) * t) * k2 * P2; +P2_proc @Process { actors: = P2, aux: {{"metaid":"rule2"}}, }; +P2_proc := pow(e, (-1) * t) * k1 * P1; + +P1 @Record 'P1' { } .= 1.5; +P2 @Record 'P2' { } .= 0; +k1 @Record 'k1' { } .= 1; +k2 @Record 'k2' { } .= 0.75; + diff --git a/latest/cases/00892/l2v5/index.heta b/latest/cases/00892/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00892/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00892/l2v5/json/output.json b/latest/cases/00892/l2v5/json/output.json new file mode 100644 index 000000000..a31a75046 --- /dev/null +++ b/latest/cases/00892/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "title": "P1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "P2", + "title": "P2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Process", + "id": "P1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "pow(e, (-1) * t) * k2 * P2" + }, + "actors": [ + { + "target": "P1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "P2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "pow(e, (-1) * t) * k1 * P1" + }, + "actors": [ + { + "target": "P2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00892/l3v2/heta-code/output.heta b/latest/cases/00892/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c48bc68d1 --- /dev/null +++ b/latest/cases/00892/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +P1_proc @Process { actors: = P1, aux: {{"metaid":"rule1"}}, }; +P1_proc := pow(e, (-1) * t) * k2 * P2; +P2_proc @Process { actors: = P2, aux: {{"metaid":"rule2"}}, }; +P2_proc := pow(e, (-1) * t) * k1 * P1; + +P1 @Record 'P1' { } .= 1.5; +P2 @Record 'P2' { } .= 0; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.75; + diff --git a/latest/cases/00892/l3v2/index.heta b/latest/cases/00892/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00892/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00892/l3v2/json/output.json b/latest/cases/00892/l3v2/json/output.json new file mode 100644 index 000000000..85bf04b3a --- /dev/null +++ b/latest/cases/00892/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "P1", + "title": "P1", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "P2", + "title": "P2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.75 + }, + { + "class": "Process", + "id": "P1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "pow(e, (-1) * t) * k2 * P2" + }, + "actors": [ + { + "target": "P1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "P2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "pow(e, (-1) * t) * k1 * P1" + }, + "actors": [ + { + "target": "P2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00892/model-sbml-l2v5.xml b/latest/cases/00892/model-sbml-l2v5.xml new file mode 100644 index 000000000..f1758dafe --- /dev/null +++ b/latest/cases/00892/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + -1 + time + + + k2 + P2 + + + + + + + + + + + + + -1 + time + + + k1 + P1 + + + + + + diff --git a/latest/cases/00892/model-sbml-l3v2.xml b/latest/cases/00892/model-sbml-l3v2.xml new file mode 100644 index 000000000..df60209ce --- /dev/null +++ b/latest/cases/00892/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + time + + + k2 + P2 + + + + + + + + + + + + + -1 + time + + + k1 + P1 + + + + + + diff --git a/latest/cases/00892/output.heta b/latest/cases/00892/output.heta new file mode 100644 index 000000000..38f336843 --- /dev/null +++ b/latest/cases/00892/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Model using parameters and rules only, with csymbol time. +componentTags: Parameter, RateRule, CSymbolTime +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called P1 and P2 and two constant +parameters called k1 and k2. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | P1 | $P2 * k2 / exp(time)$ | + | Rate | P2 | $P1 * k1 / exp(time)$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter P1 |$1.5 \x 10^-15$ |any | +|Value of parameter P2 |$ 0$ |same as P1 | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0.75$ |second^-1^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +P1_proc @Process { actors: = P1, aux: {{"metaid":"rule1"}}, }; +P1_proc := pow(e, (-1) * t) * k2 * P2; +P2_proc @Process { actors: = P2, aux: {{"metaid":"rule2"}}, }; +P2_proc := pow(e, (-1) * t) * k1 * P1; + +P1 @Record 'P1' { } .= 1.5; +P2 @Record 'P2' { } .= 0; + +k1 @Const 'k1' { } = 1; +k2 @Const 'k2' { } = 0.75; + diff --git a/latest/cases/00892/synopsis.txt b/latest/cases/00892/synopsis.txt new file mode 100644 index 000000000..541ef990a --- /dev/null +++ b/latest/cases/00892/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Model using parameters and rules only, with csymbol time. +componentTags: Parameter, RateRule, CSymbolTime +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains two varying parameters called P1 and P2 and two constant +parameters called k1 and k2. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | P1 | $P2 * k2 / exp(time)$ | + | Rate | P2 | $P1 * k1 / exp(time)$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter P1 |$1.5 \x 10^-15$ |any | +|Value of parameter P2 |$ 0$ |same as P1 | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Value of parameter k2 |$ 0.75$ |second^-1^ |] + + diff --git a/latest/cases/00893/l2v5/heta-code/output.heta b/latest/cases/00893/l2v5/heta-code/output.heta new file mode 100644 index 000000000..655de70d1 --- /dev/null +++ b/latest/cases/00893/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +P3_proc @Process { actors: = P3, aux: {{"metaid":"rule1"}}, }; +P3_proc := k1 * t; +P1_proc @Process { actors: = P1, aux: {{"metaid":"rule2"}}, }; +P1_proc := (-1) * P1 * P3; +P2_proc @Process { actors: = P2, aux: {{"metaid":"rule3"}}, }; +P2_proc := P1 * P3; + +P1 @Record 'P1' { } .= 0.0015; +P2 @Record 'P2' { } .= 0; +P3 @Record 'P3' { } .= 0.001; +k1 @Record 'k1' { } .= 0.5; + diff --git a/latest/cases/00893/l2v5/index.heta b/latest/cases/00893/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00893/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00893/l2v5/json/output.json b/latest/cases/00893/l2v5/json/output.json new file mode 100644 index 000000000..ab839bc15 --- /dev/null +++ b/latest/cases/00893/l2v5/json/output.json @@ -0,0 +1,110 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "title": "P1", + "assignments": { + "start_": "0.0015" + } + }, + { + "class": "Record", + "id": "P2", + "title": "P2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "P3", + "title": "P3", + "assignments": { + "start_": "0.001" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "P3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * t" + }, + "actors": [ + { + "target": "P3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "P1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * P1 * P3" + }, + "actors": [ + { + "target": "P1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "P2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "P1 * P3" + }, + "actors": [ + { + "target": "P2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00893/l3v2/heta-code/output.heta b/latest/cases/00893/l3v2/heta-code/output.heta new file mode 100644 index 000000000..725dc364e --- /dev/null +++ b/latest/cases/00893/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +P3_proc @Process { actors: = P3, aux: {{"metaid":"rule1"}}, }; +P3_proc := k1 * t; +P1_proc @Process { actors: = P1, aux: {{"metaid":"rule2"}}, }; +P1_proc := (-1) * P1 * P3; +P2_proc @Process { actors: = P2, aux: {{"metaid":"rule3"}}, }; +P2_proc := P1 * P3; + +P1 @Record 'P1' { } .= 0.0015; +P2 @Record 'P2' { } .= 0; +P3 @Record 'P3' { } .= 0.001; + +k1 @Const 'k1' { } = 0.5; + diff --git a/latest/cases/00893/l3v2/index.heta b/latest/cases/00893/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00893/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00893/l3v2/json/output.json b/latest/cases/00893/l3v2/json/output.json new file mode 100644 index 000000000..a85937aac --- /dev/null +++ b/latest/cases/00893/l3v2/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "P1", + "title": "P1", + "assignments": { + "start_": "0.0015" + } + }, + { + "class": "Record", + "id": "P2", + "title": "P2", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "P3", + "title": "P3", + "assignments": { + "start_": "0.001" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Process", + "id": "P3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * t" + }, + "actors": [ + { + "target": "P3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "P1_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-1) * P1 * P3" + }, + "actors": [ + { + "target": "P1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "P2_proc", + "aux": { + "metaid": "rule3" + }, + "assignments": { + "ode_": "P1 * P3" + }, + "actors": [ + { + "target": "P2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00893/model-sbml-l2v5.xml b/latest/cases/00893/model-sbml-l2v5.xml new file mode 100644 index 000000000..d54109767 --- /dev/null +++ b/latest/cases/00893/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + k1 + s + + + + + + + + -1 + P1 + P3 + + + + + + + + P1 + P3 + + + + + + diff --git a/latest/cases/00893/model-sbml-l3v2.xml b/latest/cases/00893/model-sbml-l3v2.xml new file mode 100644 index 000000000..a2777c01b --- /dev/null +++ b/latest/cases/00893/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + k1 + s + + + + + + + + -1 + P1 + P3 + + + + + + + + P1 + P3 + + + + + + diff --git a/latest/cases/00893/output.heta b/latest/cases/00893/output.heta new file mode 100644 index 000000000..6a21a9417 --- /dev/null +++ b/latest/cases/00893/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Model with parameters and rules only, with csymbol time. +componentTags: Parameter, RateRule, CSymbolTime +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called P1, P2 and P3 and one +constant parameter called k1. + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | P3 | $k1 * s$ | + | Rate | P1 | $-(P3 * P1)$ | + | Rate | P2 | $P3 * P1$ |] +where the symbol 's' denotes the current simulation time. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter P1 |$1.5 \x 10^-3$ |any | +|Value of parameter P2 |$ 0$ |same as P1 | +|Value of parameter P3 |$ 1 \x 10^-3$ |second^-1^ | +|Value of parameter k1 |$ 0.5$ |second^-3^ |] + + +*/ + + + +t @TimeScale { units: second, }; + +P3_proc @Process { actors: = P3, aux: {{"metaid":"rule1"}}, }; +P3_proc := k1 * t; +P1_proc @Process { actors: = P1, aux: {{"metaid":"rule2"}}, }; +P1_proc := (-1) * P1 * P3; +P2_proc @Process { actors: = P2, aux: {{"metaid":"rule3"}}, }; +P2_proc := P1 * P3; + +P1 @Record 'P1' { } .= 0.0015; +P2 @Record 'P2' { } .= 0; +P3 @Record 'P3' { } .= 0.001; + +k1 @Const 'k1' { } = 0.5; + diff --git a/latest/cases/00893/synopsis.txt b/latest/cases/00893/synopsis.txt new file mode 100644 index 000000000..50d5625bd --- /dev/null +++ b/latest/cases/00893/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Model with parameters and rules only, with csymbol time. +componentTags: Parameter, RateRule, CSymbolTime +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains three varying parameters called P1, P2 and P3 and one +constant parameter called k1. + +The model contains three rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | P3 | $k1 * s$ | + | Rate | P1 | $-(P3 * P1)$ | + | Rate | P2 | $P3 * P1$ |] +where the symbol 's' denotes the current simulation time. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter P1 |$1.5 \x 10^-3$ |any | +|Value of parameter P2 |$ 0$ |same as P1 | +|Value of parameter P3 |$ 1 \x 10^-3$ |second^-1^ | +|Value of parameter k1 |$ 0.5$ |second^-3^ |] + + diff --git a/latest/cases/00894/l2v5/heta-code/output.heta b/latest/cases/00894/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8cf8f13bf --- /dev/null +++ b/latest/cases/00894/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.15 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00894/l2v5/index.heta b/latest/cases/00894/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00894/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00894/l2v5/json/output.json b/latest/cases/00894/l2v5/json/output.json new file mode 100644 index 000000000..e0d118871 --- /dev/null +++ b/latest/cases/00894/l2v5/json/output.json @@ -0,0 +1,87 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00894/l3v2/heta-code/output.heta b/latest/cases/00894/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d4f9ccb4c --- /dev/null +++ b/latest/cases/00894/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.15 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00894/l3v2/index.heta b/latest/cases/00894/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00894/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00894/l3v2/json/output.json b/latest/cases/00894/l3v2/json/output.json new file mode 100644 index 000000000..9747b3033 --- /dev/null +++ b/latest/cases/00894/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.15 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00894/model-sbml-l2v5.xml b/latest/cases/00894/model-sbml-l2v5.xml new file mode 100644 index 000000000..e4835d956 --- /dev/null +++ b/latest/cases/00894/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00894/model-sbml-l3v2.xml b/latest/cases/00894/model-sbml-l3v2.xml new file mode 100644 index 000000000..3693a288d --- /dev/null +++ b/latest/cases/00894/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00894/output.heta b/latest/cases/00894/output.heta new file mode 100644 index 000000000..3dcb7d3f0 --- /dev/null +++ b/latest/cases/00894/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.15 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00894/synopsis.txt b/latest/cases/00894/synopsis.txt new file mode 100644 index 000000000..08736c59a --- /dev/null +++ b/latest/cases/00894/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called C. There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> 2S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00895/l2v5/heta-code/output.heta b/latest/cases/00895/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2969f69ab --- /dev/null +++ b/latest/cases/00895/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Record 'k1' { } .= 0.7; +k2 @Record 'k2' { } .= 0.5; +k3 @Record 'k3' { } .= 1; + diff --git a/latest/cases/00895/l2v5/index.heta b/latest/cases/00895/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00895/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00895/l2v5/json/output.json b/latest/cases/00895/l2v5/json/output.json new file mode 100644 index 000000000..4f4c8bdad --- /dev/null +++ b/latest/cases/00895/l2v5/json/output.json @@ -0,0 +1,161 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00895/l3v2/heta-code/output.heta b/latest/cases/00895/l3v2/heta-code/output.heta new file mode 100644 index 000000000..16099c37c --- /dev/null +++ b/latest/cases/00895/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00895/l3v2/index.heta b/latest/cases/00895/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00895/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00895/l3v2/json/output.json b/latest/cases/00895/l3v2/json/output.json new file mode 100644 index 000000000..137377748 --- /dev/null +++ b/latest/cases/00895/l3v2/json/output.json @@ -0,0 +1,131 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0.01 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k3 * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00895/model-sbml-l2v5.xml b/latest/cases/00895/model-sbml-l2v5.xml new file mode 100644 index 000000000..2955a9d9a --- /dev/null +++ b/latest/cases/00895/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00895/model-sbml-l3v2.xml b/latest/cases/00895/model-sbml-l3v2.xml new file mode 100644 index 000000000..0a21dbd6e --- /dev/null +++ b/latest/cases/00895/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00895/output.heta b/latest/cases/00895/output.heta new file mode 100644 index 000000000..f4e28ad09 --- /dev/null +++ b/latest/cases/00895/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| 2S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1 * t; +reaction2 @Reaction 'reaction2' { actors: 2*S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k3 * S3 * t; + +k1 @Const 'k1' { } = 0.7; +k2 @Const 'k2' { } = 0.5; +k3 @Const 'k3' { } = 1; + diff --git a/latest/cases/00895/synopsis.txt b/latest/cases/00895/synopsis.txt new file mode 100644 index 000000000..9b10b4d0e --- /dev/null +++ b/latest/cases/00895/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| 2S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00896/l2v5/heta-code/output.heta b/latest/cases/00896/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cfbc49f88 --- /dev/null +++ b/latest/cases/00896/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k1__reaction2_local * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k1__reaction3_local * S3 * t; + +k1 @Record 'k1' { } .= 1; + +k1__reaction2_local @Const { } = 0.9; +k1__reaction3_local @Const { } = 0.7; + diff --git a/latest/cases/00896/l2v5/index.heta b/latest/cases/00896/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00896/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00896/l2v5/json/output.json b/latest/cases/00896/l2v5/json/output.json new file mode 100644 index 000000000..8068efd00 --- /dev/null +++ b/latest/cases/00896/l2v5/json/output.json @@ -0,0 +1,167 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1__reaction2_local", + "num": 0.9 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k1__reaction2_local * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1__reaction3_local", + "num": 0.7 + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k1__reaction3_local * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00896/l3v2/heta-code/output.heta b/latest/cases/00896/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ada5e77e6 --- /dev/null +++ b/latest/cases/00896/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k1__reaction2_local * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k1__reaction3_local * S3 * t; + +k1__reaction2_local @Const { } = 0.9; +k1__reaction3_local @Const { } = 0.7; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00896/l3v2/index.heta b/latest/cases/00896/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00896/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00896/l3v2/json/output.json b/latest/cases/00896/l3v2/json/output.json new file mode 100644 index 000000000..e4f7dbb66 --- /dev/null +++ b/latest/cases/00896/l3v2/json/output.json @@ -0,0 +1,141 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1__reaction2_local", + "num": 0.9 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k1__reaction2_local * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1__reaction3_local", + "num": 0.7 + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k1__reaction3_local * S3 * t" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/00896/model-sbml-l2v5.xml b/latest/cases/00896/model-sbml-l2v5.xml new file mode 100644 index 000000000..f9208c972 --- /dev/null +++ b/latest/cases/00896/model-sbml-l2v5.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k1 + S3 + s + + + + + + + + + + + + + + + + + + + + C + k1 + S3 + s + + + + + + + + + + diff --git a/latest/cases/00896/model-sbml-l3v2.xml b/latest/cases/00896/model-sbml-l3v2.xml new file mode 100644 index 000000000..a679ed839 --- /dev/null +++ b/latest/cases/00896/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k1 + S3 + s + + + + + + + + + + + + + + + + + + + + C + k1 + S3 + s + + + + + + + + + + diff --git a/latest/cases/00896/output.heta b/latest/cases/00896/output.heta new file mode 100644 index 000000000..2f69b1007 --- /dev/null +++ b/latest/cases/00896/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k1. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k1 * S3 * C * s$ | +| S3 -> S1 + S4 | $k1 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +Both reactions S3 -> S1 + S2 and S3 -> S1 + S4 define a local parameters k1 which has a +scope local to the defining reaction and are different from each other and the global parameter k1 +used in the reaction S1 + S2 -> S3. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of local parameter k1 (R2) |$0.9$ |second^-2^ | +|Value of local parameter k1 (R3) |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := C * k1 * S1 * S2 * t; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := C * k1__reaction2_local * S3 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, }; +reaction3 := C * k1__reaction3_local * S3 * t; + +k1__reaction2_local @Const { } = 0.9; +k1__reaction3_local @Const { } = 0.7; +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00896/synopsis.txt b/latest/cases/00896/synopsis.txt new file mode 100644 index 000000000..3ae403a12 --- /dev/null +++ b/latest/cases/00896/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k1. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k1 * S3 * C * s$ | +| S3 -> S1 + S4 | $k1 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +Both reactions S3 -> S1 + S2 and S3 -> S1 + S4 define a local parameters k1 which has a +scope local to the defining reaction and are different from each other and the global parameter k1 +used in the reaction S1 + S2 -> S3. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of local parameter k1 (R2) |$0.9$ |second^-2^ | +|Value of local parameter k1 (R3) |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00897/l2v5/heta-code/output.heta b/latest/cases/00897/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b85884955 --- /dev/null +++ b/latest/cases/00897/l2v5/heta-code/output.heta @@ -0,0 +1,28 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: volume, boundary: true, } .= 1; + +S1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2__reaction1_local * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k2__reaction3_local * S3 * t; + +k2 @Record 'k2' { } .= 0.5; + +k2__reaction1_local @Const { } = 0.7; +k2__reaction3_local @Const { } = 1; + diff --git a/latest/cases/00897/l2v5/index.heta b/latest/cases/00897/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00897/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00897/l2v5/json/output.json b/latest/cases/00897/l2v5/json/output.json new file mode 100644 index 000000000..95349e6cd --- /dev/null +++ b/latest/cases/00897/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "volume", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance/volume", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance/volume", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k2__reaction1_local", + "num": 0.7 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2__reaction1_local * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k2__reaction3_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k2__reaction3_local * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00897/l3v2/heta-code/output.heta b/latest/cases/00897/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b9373ed9c --- /dev/null +++ b/latest/cases/00897/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2__reaction1_local * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k2__reaction3_local * S3 * t; + +k2__reaction1_local @Const { } = 0.7; +k2__reaction3_local @Const { } = 1; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00897/l3v2/index.heta b/latest/cases/00897/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00897/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00897/l3v2/json/output.json b/latest/cases/00897/l3v2/json/output.json new file mode 100644 index 000000000..e898e3833 --- /dev/null +++ b/latest/cases/00897/l3v2/json/output.json @@ -0,0 +1,129 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k2__reaction1_local", + "num": 0.7 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k2__reaction1_local * S1 * t" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "C * k2 * S2 * t" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k2__reaction3_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "reaction3", + "title": "reaction3", + "assignments": { + "ode_": "C * k2__reaction3_local * S3 * t" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/00897/model-sbml-l2v5.xml b/latest/cases/00897/model-sbml-l2v5.xml new file mode 100644 index 000000000..e8c940548 --- /dev/null +++ b/latest/cases/00897/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k2 + S1 + time + + + + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k2 + S3 + time + + + + + + + + + + diff --git a/latest/cases/00897/model-sbml-l3v2.xml b/latest/cases/00897/model-sbml-l3v2.xml new file mode 100644 index 000000000..e69733d78 --- /dev/null +++ b/latest/cases/00897/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k2 + S1 + time + + + + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k2 + S3 + time + + + + + + + + + + diff --git a/latest/cases/00897/output.heta b/latest/cases/00897/output.heta new file mode 100644 index 000000000..453dc814f --- /dev/null +++ b/latest/cases/00897/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k2. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k2 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k2 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +Both reactions S1 -> S2 and S3 -> S4 define a local parameters k2 which has a +scope local to the defining reaction and are different from each other and the +global parameter k2 used in the reaction S2 -> S3. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of local parameter k2 (R1) |$0.7$ |second^-2^ | +|Value of local parameter k2 (R3) |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k2__reaction1_local * S1 * t; +reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, }; +reaction2 := C * k2 * S2 * t; +reaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, }; +reaction3 := C * k2__reaction3_local * S3 * t; + +k2__reaction1_local @Const { } = 0.7; +k2__reaction3_local @Const { } = 1; +k2 @Const 'k2' { } = 0.5; + diff --git a/latest/cases/00897/synopsis.txt b/latest/cases/00897/synopsis.txt new file mode 100644 index 000000000..ed13938cc --- /dev/null +++ b/latest/cases/00897/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and one parameter called k2. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k2 * S1 * C * time$ | +| S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k2 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +Both reactions S1 -> S2 and S3 -> S4 define a local parameters k2 which has a +scope local to the defining reaction and are different from each other and the +global parameter k2 used in the reaction S2 -> S3. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of local parameter k2 (R1) |$0.7$ |second^-2^ | +|Value of local parameter k2 (R3) |$1$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00898/l2v5/build.log b/latest/cases/00898/l2v5/build.log new file mode 100644 index 000000000..dc9926cbd --- /dev/null +++ b/latest/cases/00898/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00898/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00898/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00898/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00898/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00898/l2v5/index.heta b/latest/cases/00898/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00898/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00898/l3v2/index.heta b/latest/cases/00898/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00898/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00898/model-sbml-l2v5.xml b/latest/cases/00898/model-sbml-l2v5.xml new file mode 100644 index 000000000..383ae3198 --- /dev/null +++ b/latest/cases/00898/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/00898/synopsis.txt b/latest/cases/00898/synopsis.txt new file mode 100644 index 000000000..ff317bc87 --- /dev/null +++ b/latest/cases/00898/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and p1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (2 * p1) S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Value of parameter p1 |$1$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/00899/l2v5/build.log b/latest/cases/00899/l2v5/build.log new file mode 100644 index 000000000..b490df14b --- /dev/null +++ b/latest/cases/00899/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00899/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00899/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00899/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00899/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00899/l2v5/index.heta b/latest/cases/00899/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00899/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00899/l3v2/index.heta b/latest/cases/00899/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00899/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00899/model-sbml-l2v5.xml b/latest/cases/00899/model-sbml-l2v5.xml new file mode 100644 index 000000000..781ece0de --- /dev/null +++ b/latest/cases/00899/model-sbml-l2v5.xml @@ -0,0 +1,89 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/00899/synopsis.txt b/latest/cases/00899/synopsis.txt new file mode 100644 index 000000000..0742c59d9 --- /dev/null +++ b/latest/cases/00899/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and four parameters named k1, k2, k3 and p1. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| (2 * p1)S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Value of parameter p1 |$1$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00900/l2v5/build.log b/latest/cases/00900/l2v5/build.log new file mode 100644 index 000000000..8aaf85f8a --- /dev/null +++ b/latest/cases/00900/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00900/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00900/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00900/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00900/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00900/l2v5/index.heta b/latest/cases/00900/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00900/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00900/l3v2/index.heta b/latest/cases/00900/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00900/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00900/model-sbml-l2v5.xml b/latest/cases/00900/model-sbml-l2v5.xml new file mode 100644 index 000000000..bbda17597 --- /dev/null +++ b/latest/cases/00900/model-sbml-l2v5.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k1 + S3 + s + + + + + + + + + + + + + + + + + + + + C + k1 + S3 + s + + + + + + + + + + diff --git a/latest/cases/00900/synopsis.txt b/latest/cases/00900/synopsis.txt new file mode 100644 index 000000000..8a040892d --- /dev/null +++ b/latest/cases/00900/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: Amount, LocalParameters, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and p1. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| (2 * p1)S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k1 * S3 * C * s$ | +| S3 -> S1 + S4 | $k1 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +Both reactions S3 -> S1 + S2 and S3 -> S1 + S4 define a local parameters k1 which has a +scope local to the defining reaction and are different from each other and the global parameter k1 +used in the reaction S1 + S2 -> S3. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter p1 |$1.0$ |dimensionless | +|Value of local parameter k1 (R2) |$0.9$ |second^-2^ | +|Value of local parameter k1 (R3) |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00901/l2v5/heta-code/output.heta b/latest/cases/00901/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2ab7c7de0 --- /dev/null +++ b/latest/cases/00901/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: volume, } .= 5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := (-1) * c * k1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/00901/l2v5/index.heta b/latest/cases/00901/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00901/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00901/l2v5/json/output.json b/latest/cases/00901/l2v5/json/output.json new file mode 100644 index 000000000..ce6389922 --- /dev/null +++ b/latest/cases/00901/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "volume", + "assignments": { + "start_": "5" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * c * k1" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00901/l3v2/heta-code/output.heta b/latest/cases/00901/l3v2/heta-code/output.heta new file mode 100644 index 000000000..46bcbb175 --- /dev/null +++ b/latest/cases/00901/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := (-1) * c * k1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00901/l3v2/index.heta b/latest/cases/00901/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00901/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00901/l3v2/json/output.json b/latest/cases/00901/l3v2/json/output.json new file mode 100644 index 000000000..85b156b6c --- /dev/null +++ b/latest/cases/00901/l3v2/json/output.json @@ -0,0 +1,37 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "litre", + "assignments": { + "start_": "5" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * c * k1" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00901/model-sbml-l2v5.xml b/latest/cases/00901/model-sbml-l2v5.xml new file mode 100644 index 000000000..068643a28 --- /dev/null +++ b/latest/cases/00901/model-sbml-l2v5.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + -1 + c + k1 + + + + + + diff --git a/latest/cases/00901/model-sbml-l3v2.xml b/latest/cases/00901/model-sbml-l3v2.xml new file mode 100644 index 000000000..34e124c6d --- /dev/null +++ b/latest/cases/00901/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + c + k1 + + + + + + diff --git a/latest/cases/00901/output.heta b/latest/cases/00901/output.heta new file mode 100644 index 000000000..e579ef444 --- /dev/null +++ b/latest/cases/00901/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Parameter, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c and one constant +parameter called k1. (Note that indeed c is a compartment and not +species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $-c * k1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$ 5$ |litre | +|Value of parameter k1 |$ 1$ |second^-1^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := (-1) * c * k1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/00901/synopsis.txt b/latest/cases/00901/synopsis.txt new file mode 100644 index 000000000..91dd01858 --- /dev/null +++ b/latest/cases/00901/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Parameter, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c and one constant +parameter called k1. (Note that indeed c is a compartment and not +species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $-c * k1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$ 5$ |litre | +|Value of parameter k1 |$ 1$ |second^-1^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00902/l2v5/heta-code/output.heta b/latest/cases/00902/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9401c9d3f --- /dev/null +++ b/latest/cases/00902/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: volume, } .= 0.015; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00902/l2v5/index.heta b/latest/cases/00902/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00902/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00902/l2v5/json/output.json b/latest/cases/00902/l2v5/json/output.json new file mode 100644 index 000000000..ad10c20aa --- /dev/null +++ b/latest/cases/00902/l2v5/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "volume", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00902/l3v2/heta-code/output.heta b/latest/cases/00902/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f76a86a75 --- /dev/null +++ b/latest/cases/00902/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 0.015; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00902/l3v2/index.heta b/latest/cases/00902/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00902/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00902/l3v2/json/output.json b/latest/cases/00902/l3v2/json/output.json new file mode 100644 index 000000000..0826b7197 --- /dev/null +++ b/latest/cases/00902/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "litre", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00902/model-sbml-l2v5.xml b/latest/cases/00902/model-sbml-l2v5.xml new file mode 100644 index 000000000..b177128e7 --- /dev/null +++ b/latest/cases/00902/model-sbml-l2v5.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00902/model-sbml-l3v2.xml b/latest/cases/00902/model-sbml-l3v2.xml new file mode 100644 index 000000000..3561b0f68 --- /dev/null +++ b/latest/cases/00902/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00902/output.heta b/latest/cases/00902/output.heta new file mode 100644 index 000000000..5d9dbc93f --- /dev/null +++ b/latest/cases/00902/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c. (Note that +indeed c is a compartment and not species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$1.5 \x 10^-2$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 0.015; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00902/synopsis.txt b/latest/cases/00902/synopsis.txt new file mode 100644 index 000000000..a16b38e79 --- /dev/null +++ b/latest/cases/00902/synopsis.txt @@ -0,0 +1,26 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c. (Note that +indeed c is a compartment and not species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$1.5 \x 10^-2$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00903/l2v5/heta-code/output.heta b/latest/cases/00903/l2v5/heta-code/output.heta new file mode 100644 index 000000000..488fe8fc2 --- /dev/null +++ b/latest/cases/00903/l2v5/heta-code/output.heta @@ -0,0 +1,17 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment 'C1' { units: volume, } .= 1.5; +C2 @Compartment 'C2' { units: volume, } .= 1.5; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.5 * C2 - (0.2 * C1); +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.75 * C1 - (2.1 * C2); + diff --git a/latest/cases/00903/l2v5/index.heta b/latest/cases/00903/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00903/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00903/l2v5/json/output.json b/latest/cases/00903/l2v5/json/output.json new file mode 100644 index 000000000..75e1aaf13 --- /dev/null +++ b/latest/cases/00903/l2v5/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "title": "C1", + "units": "volume", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Compartment", + "id": "C2", + "title": "C2", + "units": "volume", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "C1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * C2 - (0.2 * C1)" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.75 * C1 - (2.1 * C2)" + }, + "actors": [ + { + "target": "C2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00903/l3v2/heta-code/output.heta b/latest/cases/00903/l3v2/heta-code/output.heta new file mode 100644 index 000000000..00dd05e2d --- /dev/null +++ b/latest/cases/00903/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { units: second, }; + +C1 @Compartment 'C1' { units: litre, } .= 1.5; +C2 @Compartment 'C2' { units: litre, } .= 1.5; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.5 * C2 - (0.2 * C1); +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.75 * C1 - (2.1 * C2); + diff --git a/latest/cases/00903/l3v2/index.heta b/latest/cases/00903/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00903/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00903/l3v2/json/output.json b/latest/cases/00903/l3v2/json/output.json new file mode 100644 index 000000000..6c079f126 --- /dev/null +++ b/latest/cases/00903/l3v2/json/output.json @@ -0,0 +1,56 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C1", + "title": "C1", + "units": "litre", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Compartment", + "id": "C2", + "title": "C2", + "units": "litre", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "C1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * C2 - (0.2 * C1)" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.75 * C1 - (2.1 * C2)" + }, + "actors": [ + { + "target": "C2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00903/model-sbml-l2v5.xml b/latest/cases/00903/model-sbml-l2v5.xml new file mode 100644 index 000000000..964ad3888 --- /dev/null +++ b/latest/cases/00903/model-sbml-l2v5.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + 0.5 + C2 + + + + 0.2 + C1 + + + + + + + + + + + 0.75 + C1 + + + + 2.1 + C2 + + + + + + + diff --git a/latest/cases/00903/model-sbml-l3v2.xml b/latest/cases/00903/model-sbml-l3v2.xml new file mode 100644 index 000000000..d2c4b0588 --- /dev/null +++ b/latest/cases/00903/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + C2 + + + + 0.2 + C1 + + + + + + + + + + + 0.75 + C1 + + + + 2.1 + C2 + + + + + + + diff --git a/latest/cases/00903/output.heta b/latest/cases/00903/output.heta new file mode 100644 index 000000000..e205e89a4 --- /dev/null +++ b/latest/cases/00903/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two varying compartments called C1 and C2. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C1 | $C2 * 0.5 - C1 * 0.2$ | + | Rate | C2 | $C1 * 0.75-C2 * 2.1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment C1 |$1.5$ |litre | +|Size of compartment C2 |$1.5$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +C1 @Compartment 'C1' { units: litre, } .= 1.5; +C2 @Compartment 'C2' { units: litre, } .= 1.5; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.5 * C2 - (0.2 * C1); +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.75 * C1 - (2.1 * C2); + diff --git a/latest/cases/00903/synopsis.txt b/latest/cases/00903/synopsis.txt new file mode 100644 index 000000000..d6338f572 --- /dev/null +++ b/latest/cases/00903/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two varying compartments called C1 and C2. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C1 | $C2 * 0.5 - C1 * 0.2$ | + | Rate | C2 | $C1 * 0.75-C2 * 2.1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment C1 |$1.5$ |litre | +|Size of compartment C2 |$1.5$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00904/l2v5/heta-code/output.heta b/latest/cases/00904/l2v5/heta-code/output.heta new file mode 100644 index 000000000..dc15a1853 --- /dev/null +++ b/latest/cases/00904/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: area, } .= 3.2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.25 * c; + diff --git a/latest/cases/00904/l2v5/index.heta b/latest/cases/00904/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00904/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00904/l2v5/json/output.json b/latest/cases/00904/l2v5/json/output.json new file mode 100644 index 000000000..c253fee7e --- /dev/null +++ b/latest/cases/00904/l2v5/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "area", + "assignments": { + "start_": "3.2" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00904/l3v2/heta-code/output.heta b/latest/cases/00904/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bcc62b16b --- /dev/null +++ b/latest/cases/00904/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 3.2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.25 * c; + diff --git a/latest/cases/00904/l3v2/index.heta b/latest/cases/00904/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00904/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00904/l3v2/json/output.json b/latest/cases/00904/l3v2/json/output.json new file mode 100644 index 000000000..80c9b3a01 --- /dev/null +++ b/latest/cases/00904/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre^2", + "assignments": { + "start_": "3.2" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00904/model-sbml-l2v5.xml b/latest/cases/00904/model-sbml-l2v5.xml new file mode 100644 index 000000000..6fe7b36da --- /dev/null +++ b/latest/cases/00904/model-sbml-l2v5.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + 0.25 + c + + + + + + diff --git a/latest/cases/00904/model-sbml-l3v2.xml b/latest/cases/00904/model-sbml-l3v2.xml new file mode 100644 index 000000000..8c09de93b --- /dev/null +++ b/latest/cases/00904/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.25 + c + + + + + + diff --git a/latest/cases/00904/output.heta b/latest/cases/00904/output.heta new file mode 100644 index 000000000..390b7493e --- /dev/null +++ b/latest/cases/00904/output.heta @@ -0,0 +1,36 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.25 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$3.2$ |metre^2 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 3.2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.25 * c; + diff --git a/latest/cases/00904/synopsis.txt b/latest/cases/00904/synopsis.txt new file mode 100644 index 000000000..65b181fea --- /dev/null +++ b/latest/cases/00904/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.25 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$3.2$ |metre^2 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00905/l2v5/heta-code/output.heta b/latest/cases/00905/l2v5/heta-code/output.heta new file mode 100644 index 000000000..acc3d27ab --- /dev/null +++ b/latest/cases/00905/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: length, } .= 1.5e-4; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.1 * c; + diff --git a/latest/cases/00905/l2v5/index.heta b/latest/cases/00905/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00905/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00905/l2v5/json/output.json b/latest/cases/00905/l2v5/json/output.json new file mode 100644 index 000000000..5682c8a7a --- /dev/null +++ b/latest/cases/00905/l2v5/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "length", + "assignments": { + "start_": "1.5e-4" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.1 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00905/l3v2/heta-code/output.heta b/latest/cases/00905/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9e35da8bf --- /dev/null +++ b/latest/cases/00905/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 1.5e-4; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.1 * c; + diff --git a/latest/cases/00905/l3v2/index.heta b/latest/cases/00905/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00905/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00905/l3v2/json/output.json b/latest/cases/00905/l3v2/json/output.json new file mode 100644 index 000000000..d03b22082 --- /dev/null +++ b/latest/cases/00905/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre", + "assignments": { + "start_": "1.5e-4" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.1 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00905/model-sbml-l2v5.xml b/latest/cases/00905/model-sbml-l2v5.xml new file mode 100644 index 000000000..9bb1cea71 --- /dev/null +++ b/latest/cases/00905/model-sbml-l2v5.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + 0.1 + c + + + + + + diff --git a/latest/cases/00905/model-sbml-l3v2.xml b/latest/cases/00905/model-sbml-l3v2.xml new file mode 100644 index 000000000..46d78bfad --- /dev/null +++ b/latest/cases/00905/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + c + + + + + + diff --git a/latest/cases/00905/output.heta b/latest/cases/00905/output.heta new file mode 100644 index 000000000..b781a32dd --- /dev/null +++ b/latest/cases/00905/output.heta @@ -0,0 +1,36 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.1 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$1.5 \x 10^-4$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 1.5e-4; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.1 * c; + diff --git a/latest/cases/00905/synopsis.txt b/latest/cases/00905/synopsis.txt new file mode 100644 index 000000000..83dff9388 --- /dev/null +++ b/latest/cases/00905/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.1 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$1.5 \x 10^-4$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00906/l2v5/heta-code/output.heta b/latest/cases/00906/l2v5/heta-code/output.heta new file mode 100644 index 000000000..866438df7 --- /dev/null +++ b/latest/cases/00906/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: area, } .= 0.002; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := (-1) * c * k1; + +k1 @Record 'k1' { } .= 1.1; + diff --git a/latest/cases/00906/l2v5/index.heta b/latest/cases/00906/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00906/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00906/l2v5/json/output.json b/latest/cases/00906/l2v5/json/output.json new file mode 100644 index 000000000..19dbee02d --- /dev/null +++ b/latest/cases/00906/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "area", + "assignments": { + "start_": "0.002" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * c * k1" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00906/l3v2/heta-code/output.heta b/latest/cases/00906/l3v2/heta-code/output.heta new file mode 100644 index 000000000..42fdc8128 --- /dev/null +++ b/latest/cases/00906/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 0.002; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := (-1) * c * k1; + +k1 @Const 'k1' { } = 1.1; + diff --git a/latest/cases/00906/l3v2/index.heta b/latest/cases/00906/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00906/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00906/l3v2/json/output.json b/latest/cases/00906/l3v2/json/output.json new file mode 100644 index 000000000..e829c3516 --- /dev/null +++ b/latest/cases/00906/l3v2/json/output.json @@ -0,0 +1,37 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre^2", + "assignments": { + "start_": "0.002" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.1 + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * c * k1" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00906/model-sbml-l2v5.xml b/latest/cases/00906/model-sbml-l2v5.xml new file mode 100644 index 000000000..3a83f421f --- /dev/null +++ b/latest/cases/00906/model-sbml-l2v5.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + -1 + c + k1 + + + + + + diff --git a/latest/cases/00906/model-sbml-l3v2.xml b/latest/cases/00906/model-sbml-l3v2.xml new file mode 100644 index 000000000..15fd72a87 --- /dev/null +++ b/latest/cases/00906/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + c + k1 + + + + + + diff --git a/latest/cases/00906/output.heta b/latest/cases/00906/output.heta new file mode 100644 index 000000000..0d7690adc --- /dev/null +++ b/latest/cases/00906/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Parameter, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c and one constant +parameter called k1. (Note that indeed c is a compartment and not +species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $-c * k1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$ 0.002$ |metre^2^ | +|Value of parameter k1 |$ 1.1$ |second^-1^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 0.002; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := (-1) * c * k1; + +k1 @Const 'k1' { } = 1.1; + diff --git a/latest/cases/00906/synopsis.txt b/latest/cases/00906/synopsis.txt new file mode 100644 index 000000000..514462e18 --- /dev/null +++ b/latest/cases/00906/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Parameter, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c and one constant +parameter called k1. (Note that indeed c is a compartment and not +species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $-c * k1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$ 0.002$ |metre^2^ | +|Value of parameter k1 |$ 1.1$ |second^-1^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00907/l2v5/heta-code/output.heta b/latest/cases/00907/l2v5/heta-code/output.heta new file mode 100644 index 000000000..facc899cd --- /dev/null +++ b/latest/cases/00907/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: length, } .= 22.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := (-1) * c / k1; + +k1 @Record 'k1' { } .= 0.175; + diff --git a/latest/cases/00907/l2v5/index.heta b/latest/cases/00907/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00907/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00907/l2v5/json/output.json b/latest/cases/00907/l2v5/json/output.json new file mode 100644 index 000000000..f77c56527 --- /dev/null +++ b/latest/cases/00907/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "length", + "assignments": { + "start_": "22.5" + } + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.175" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * c / k1" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00907/l3v2/heta-code/output.heta b/latest/cases/00907/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fc2143d49 --- /dev/null +++ b/latest/cases/00907/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 22.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := (-1) * c / k1; + +k1 @Const 'k1' { } = 0.175; + diff --git a/latest/cases/00907/l3v2/index.heta b/latest/cases/00907/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00907/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00907/l3v2/json/output.json b/latest/cases/00907/l3v2/json/output.json new file mode 100644 index 000000000..d875dd69e --- /dev/null +++ b/latest/cases/00907/l3v2/json/output.json @@ -0,0 +1,37 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre", + "assignments": { + "start_": "22.5" + } + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.175 + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-1) * c / k1" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00907/model-sbml-l2v5.xml b/latest/cases/00907/model-sbml-l2v5.xml new file mode 100644 index 000000000..8e883be23 --- /dev/null +++ b/latest/cases/00907/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + -1 + + + c + k1 + + + + + + + diff --git a/latest/cases/00907/model-sbml-l3v2.xml b/latest/cases/00907/model-sbml-l3v2.xml new file mode 100644 index 000000000..14b82da3b --- /dev/null +++ b/latest/cases/00907/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + + + c + k1 + + + + + + + diff --git a/latest/cases/00907/output.heta b/latest/cases/00907/output.heta new file mode 100644 index 000000000..349c4d6ff --- /dev/null +++ b/latest/cases/00907/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Parameter, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c and one constant +parameter called k1. (Note that indeed c is a compartment and not +species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $-c / k1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$ 22.5$ |metre | +|Value of parameter k1 |$ 0.175$ |second |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 22.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := (-1) * c / k1; + +k1 @Const 'k1' { } = 0.175; + diff --git a/latest/cases/00907/synopsis.txt b/latest/cases/00907/synopsis.txt new file mode 100644 index 000000000..de0bb7d2b --- /dev/null +++ b/latest/cases/00907/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Parameter, RateRule +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c and one constant +parameter called k1. (Note that indeed c is a compartment and not +species in this model.) + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $-c / k1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$ 22.5$ |metre | +|Value of parameter k1 |$ 0.175$ |second |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00908/l2v5/heta-code/output.heta b/latest/cases/00908/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3813f14ec --- /dev/null +++ b/latest/cases/00908/l2v5/heta-code/output.heta @@ -0,0 +1,17 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment 'C1' { units: volume, } .= 1.5; +C2 @Compartment 'C2' { units: area, } .= 0.75; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.15 * C2 - (0.2 * C1); +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.3 * C1 - (0.1 * C2); + diff --git a/latest/cases/00908/l2v5/index.heta b/latest/cases/00908/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00908/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00908/l2v5/json/output.json b/latest/cases/00908/l2v5/json/output.json new file mode 100644 index 000000000..cee04b16a --- /dev/null +++ b/latest/cases/00908/l2v5/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "title": "C1", + "units": "volume", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Compartment", + "id": "C2", + "title": "C2", + "units": "area", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Process", + "id": "C1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15 * C2 - (0.2 * C1)" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.3 * C1 - (0.1 * C2)" + }, + "actors": [ + { + "target": "C2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00908/l3v2/heta-code/output.heta b/latest/cases/00908/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2e463e57e --- /dev/null +++ b/latest/cases/00908/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { units: second, }; + +C1 @Compartment 'C1' { units: litre, } .= 1.5; +C2 @Compartment 'C2' { units: metre^2, } .= 0.75; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.15 * C2 - (0.2 * C1); +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.3 * C1 - (0.1 * C2); + diff --git a/latest/cases/00908/l3v2/index.heta b/latest/cases/00908/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00908/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00908/l3v2/json/output.json b/latest/cases/00908/l3v2/json/output.json new file mode 100644 index 000000000..f0aa60f41 --- /dev/null +++ b/latest/cases/00908/l3v2/json/output.json @@ -0,0 +1,56 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C1", + "title": "C1", + "units": "litre", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Compartment", + "id": "C2", + "title": "C2", + "units": "metre^2", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Process", + "id": "C1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15 * C2 - (0.2 * C1)" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.3 * C1 - (0.1 * C2)" + }, + "actors": [ + { + "target": "C2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00908/model-sbml-l2v5.xml b/latest/cases/00908/model-sbml-l2v5.xml new file mode 100644 index 000000000..40f23842b --- /dev/null +++ b/latest/cases/00908/model-sbml-l2v5.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + 0.15 + C2 + + + + 0.2 + C1 + + + + + + + + + + + 0.3 + C1 + + + + 0.1 + C2 + + + + + + + diff --git a/latest/cases/00908/model-sbml-l3v2.xml b/latest/cases/00908/model-sbml-l3v2.xml new file mode 100644 index 000000000..e73b347d7 --- /dev/null +++ b/latest/cases/00908/model-sbml-l3v2.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.15 + C2 + + + + 0.2 + C1 + + + + + + + + + + + 0.3 + C1 + + + + 0.1 + C2 + + + + + + + diff --git a/latest/cases/00908/output.heta b/latest/cases/00908/output.heta new file mode 100644 index 000000000..0150fecda --- /dev/null +++ b/latest/cases/00908/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two varying compartments called C1 and C2, where C2 +is 2-dimensional. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C1 | $C2 * 0.15 - C1 * 0.2$ | + | Rate | C2 | $C1 * 0.3 - C2 * 0.1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment C1 |$1.5$ |litre | +|Size of compartment C2 |$0.75$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +C1 @Compartment 'C1' { units: litre, } .= 1.5; +C2 @Compartment 'C2' { units: metre^2, } .= 0.75; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.15 * C2 - (0.2 * C1); +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.3 * C1 - (0.1 * C2); + diff --git a/latest/cases/00908/synopsis.txt b/latest/cases/00908/synopsis.txt new file mode 100644 index 000000000..58447764c --- /dev/null +++ b/latest/cases/00908/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two varying compartments called C1 and C2, where C2 +is 2-dimensional. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C1 | $C2 * 0.15 - C1 * 0.2$ | + | Rate | C2 | $C1 * 0.3 - C2 * 0.1$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment C1 |$1.5$ |litre | +|Size of compartment C2 |$0.75$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00909/l2v5/heta-code/output.heta b/latest/cases/00909/l2v5/heta-code/output.heta new file mode 100644 index 000000000..55340f8d4 --- /dev/null +++ b/latest/cases/00909/l2v5/heta-code/output.heta @@ -0,0 +1,17 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment 'C1' { units: volume, } .= 0.015; +C2 @Compartment 'C2' { units: length, } .= 0.01; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.4 * C1 + 0.25 * C2; +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.15 * C1 + 0.2 * C2; + diff --git a/latest/cases/00909/l2v5/index.heta b/latest/cases/00909/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00909/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00909/l2v5/json/output.json b/latest/cases/00909/l2v5/json/output.json new file mode 100644 index 000000000..1a92d6da7 --- /dev/null +++ b/latest/cases/00909/l2v5/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "title": "C1", + "units": "volume", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Compartment", + "id": "C2", + "title": "C2", + "units": "length", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Process", + "id": "C1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.4 * C1 + 0.25 * C2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.15 * C1 + 0.2 * C2" + }, + "actors": [ + { + "target": "C2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00909/l3v2/heta-code/output.heta b/latest/cases/00909/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c8d50cb55 --- /dev/null +++ b/latest/cases/00909/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { units: second, }; + +C1 @Compartment 'C1' { units: litre, } .= 0.015; +C2 @Compartment 'C2' { units: metre, } .= 0.01; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.4 * C1 + 0.25 * C2; +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.15 * C1 + 0.2 * C2; + diff --git a/latest/cases/00909/l3v2/index.heta b/latest/cases/00909/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00909/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00909/l3v2/json/output.json b/latest/cases/00909/l3v2/json/output.json new file mode 100644 index 000000000..88343e9da --- /dev/null +++ b/latest/cases/00909/l3v2/json/output.json @@ -0,0 +1,56 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C1", + "title": "C1", + "units": "litre", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Compartment", + "id": "C2", + "title": "C2", + "units": "metre", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Process", + "id": "C1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.4 * C1 + 0.25 * C2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.15 * C1 + 0.2 * C2" + }, + "actors": [ + { + "target": "C2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00909/model-sbml-l2v5.xml b/latest/cases/00909/model-sbml-l2v5.xml new file mode 100644 index 000000000..e11afaeee --- /dev/null +++ b/latest/cases/00909/model-sbml-l2v5.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + 0.4 + C1 + + + + 0.25 + C2 + + + + + + + + + + + 0.15 + C1 + + + + 0.2 + C2 + + + + + + + diff --git a/latest/cases/00909/model-sbml-l3v2.xml b/latest/cases/00909/model-sbml-l3v2.xml new file mode 100644 index 000000000..64212a3ed --- /dev/null +++ b/latest/cases/00909/model-sbml-l3v2.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.4 + C1 + + + + 0.25 + C2 + + + + + + + + + + + 0.15 + C1 + + + + 0.2 + C2 + + + + + + + diff --git a/latest/cases/00909/output.heta b/latest/cases/00909/output.heta new file mode 100644 index 000000000..edeee7749 --- /dev/null +++ b/latest/cases/00909/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two varying compartments called C1 and C2, where C2 +is 1-dimensional. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C1 | $C2 * 0.25 + C1 * 0.4$ | + | Rate | C2 | $C1 * 0.15 + C2 * 0.2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment C1 |$1.5 x 10^-2^$ |litre | +|Size of compartment C2 |$1.0 x 10^-2^$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +C1 @Compartment 'C1' { units: litre, } .= 0.015; +C2 @Compartment 'C2' { units: metre, } .= 0.01; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.4 * C1 + 0.25 * C2; +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.15 * C1 + 0.2 * C2; + diff --git a/latest/cases/00909/synopsis.txt b/latest/cases/00909/synopsis.txt new file mode 100644 index 000000000..7c3e58328 --- /dev/null +++ b/latest/cases/00909/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two varying compartments called C1 and C2, where C2 +is 1-dimensional. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C1 | $C2 * 0.25 + C1 * 0.4$ | + | Rate | C2 | $C1 * 0.15 + C2 * 0.2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment C1 |$1.5 x 10^-2^$ |litre | +|Size of compartment C2 |$1.0 x 10^-2^$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00910/l2v5/heta-code/output.heta b/latest/cases/00910/l2v5/heta-code/output.heta new file mode 100644 index 000000000..be239e33a --- /dev/null +++ b/latest/cases/00910/l2v5/heta-code/output.heta @@ -0,0 +1,17 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment 'C1' { units: length, } .= 0.015; +C2 @Compartment 'C2' { units: area, } .= 0.01; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.3 * C1 + 0.5 * C2; +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.1 * C1 + 0.2 * C2; + diff --git a/latest/cases/00910/l2v5/index.heta b/latest/cases/00910/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00910/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00910/l2v5/json/output.json b/latest/cases/00910/l2v5/json/output.json new file mode 100644 index 000000000..2c6f8dd6c --- /dev/null +++ b/latest/cases/00910/l2v5/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "title": "C1", + "units": "length", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Compartment", + "id": "C2", + "title": "C2", + "units": "area", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Process", + "id": "C1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.3 * C1 + 0.5 * C2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1 * C1 + 0.2 * C2" + }, + "actors": [ + { + "target": "C2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00910/l3v2/heta-code/output.heta b/latest/cases/00910/l3v2/heta-code/output.heta new file mode 100644 index 000000000..82a589e85 --- /dev/null +++ b/latest/cases/00910/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { units: second, }; + +C1 @Compartment 'C1' { units: metre, } .= 0.015; +C2 @Compartment 'C2' { units: metre^2, } .= 0.01; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.3 * C1 + 0.5 * C2; +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.1 * C1 + 0.2 * C2; + diff --git a/latest/cases/00910/l3v2/index.heta b/latest/cases/00910/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00910/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00910/l3v2/json/output.json b/latest/cases/00910/l3v2/json/output.json new file mode 100644 index 000000000..ed2d8a160 --- /dev/null +++ b/latest/cases/00910/l3v2/json/output.json @@ -0,0 +1,56 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C1", + "title": "C1", + "units": "metre", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Compartment", + "id": "C2", + "title": "C2", + "units": "metre^2", + "assignments": { + "start_": "0.01" + } + }, + { + "class": "Process", + "id": "C1_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.3 * C1 + 0.5 * C2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C2_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "0.1 * C1 + 0.2 * C2" + }, + "actors": [ + { + "target": "C2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00910/model-sbml-l2v5.xml b/latest/cases/00910/model-sbml-l2v5.xml new file mode 100644 index 000000000..4f707bc6e --- /dev/null +++ b/latest/cases/00910/model-sbml-l2v5.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + 0.3 + C1 + + + + 0.5 + C2 + + + + + + + + + + + 0.1 + C1 + + + + 0.2 + C2 + + + + + + + diff --git a/latest/cases/00910/model-sbml-l3v2.xml b/latest/cases/00910/model-sbml-l3v2.xml new file mode 100644 index 000000000..f03ace293 --- /dev/null +++ b/latest/cases/00910/model-sbml-l3v2.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.3 + C1 + + + + 0.5 + C2 + + + + + + + + + + + 0.1 + C1 + + + + 0.2 + C2 + + + + + + + diff --git a/latest/cases/00910/output.heta b/latest/cases/00910/output.heta new file mode 100644 index 000000000..7b3746900 --- /dev/null +++ b/latest/cases/00910/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two varying compartments called C1 and C2, where C1 +is 1-dimensional and C2 is 2-dimensional. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C1 | $C2 * 0.5 + C1 * 0.3$ | + | Rate | C2 | $C1 * 0.1 + C2 * 0.2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment C1 |$1.5 x 10^-2^$ |metre | +|Size of compartment C2 |$1.0 x 10^-2^$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +C1 @Compartment 'C1' { units: metre, } .= 0.015; +C2 @Compartment 'C2' { units: metre^2, } .= 0.01; + +C1_proc @Process { actors: = C1, aux: {{"metaid":"rule1"}}, }; +C1_proc := 0.3 * C1 + 0.5 * C2; +C2_proc @Process { actors: = C2, aux: {{"metaid":"rule2"}}, }; +C2_proc := 0.1 * C1 + 0.2 * C2; + diff --git a/latest/cases/00910/synopsis.txt b/latest/cases/00910/synopsis.txt new file mode 100644 index 000000000..97e1eb64a --- /dev/null +++ b/latest/cases/00910/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule +testTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two varying compartments called C1 and C2, where C1 +is 1-dimensional and C2 is 2-dimensional. + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | C1 | $C2 * 0.5 + C1 * 0.3$ | + | Rate | C2 | $C1 * 0.1 + C2 * 0.2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment C1 |$1.5 x 10^-2^$ |metre | +|Size of compartment C2 |$1.0 x 10^-2^$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00911/l2v5/heta-code/output.heta b/latest/cases/00911/l2v5/heta-code/output.heta new file mode 100644 index 000000000..aab1a9e4a --- /dev/null +++ b/latest/cases/00911/l2v5/heta-code/output.heta @@ -0,0 +1,15 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: volume, } .= 1.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := multiply(c, 0.5); + diff --git a/latest/cases/00911/l2v5/index.heta b/latest/cases/00911/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00911/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00911/l2v5/json/output.json b/latest/cases/00911/l2v5/json/output.json new file mode 100644 index 000000000..4f2b814cf --- /dev/null +++ b/latest/cases/00911/l2v5/json/output.json @@ -0,0 +1,64 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "volume", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(c, 0.5)" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00911/l3v2/heta-code/output.heta b/latest/cases/00911/l3v2/heta-code/output.heta new file mode 100644 index 000000000..28a722606 --- /dev/null +++ b/latest/cases/00911/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 1.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := multiply(c, 0.5); + diff --git a/latest/cases/00911/l3v2/index.heta b/latest/cases/00911/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00911/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00911/l3v2/json/output.json b/latest/cases/00911/l3v2/json/output.json new file mode 100644 index 000000000..e88cdb0c9 --- /dev/null +++ b/latest/cases/00911/l3v2/json/output.json @@ -0,0 +1,40 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "litre", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(c, 0.5)" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00911/model-sbml-l2v5.xml b/latest/cases/00911/model-sbml-l2v5.xml new file mode 100644 index 000000000..c2d285fd2 --- /dev/null +++ b/latest/cases/00911/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + multiply + c + 0.5 + + + + + + diff --git a/latest/cases/00911/model-sbml-l3v2.xml b/latest/cases/00911/model-sbml-l3v2.xml new file mode 100644 index 000000000..4876e438b --- /dev/null +++ b/latest/cases/00911/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + multiply + c + 0.5 + + + + + + diff --git a/latest/cases/00911/output.heta b/latest/cases/00911/output.heta new file mode 100644 index 000000000..456bce22f --- /dev/null +++ b/latest/cases/00911/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, FunctionDefinition +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $multiply(0.5, c)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$1.5$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 1.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := multiply(c, 0.5); + diff --git a/latest/cases/00911/synopsis.txt b/latest/cases/00911/synopsis.txt new file mode 100644 index 000000000..ac18c6d3d --- /dev/null +++ b/latest/cases/00911/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, FunctionDefinition +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $multiply(0.5, c)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$1.5$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00912/l2v5/heta-code/output.heta b/latest/cases/00912/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f5c1013d1 --- /dev/null +++ b/latest/cases/00912/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: volume, } .= 3 / 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.25 * c; + diff --git a/latest/cases/00912/l2v5/index.heta b/latest/cases/00912/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00912/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00912/l2v5/json/output.json b/latest/cases/00912/l2v5/json/output.json new file mode 100644 index 000000000..5a8359dea --- /dev/null +++ b/latest/cases/00912/l2v5/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "volume", + "assignments": { + "start_": "3 / 2" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00912/l3v2/heta-code/output.heta b/latest/cases/00912/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ea80e6fc3 --- /dev/null +++ b/latest/cases/00912/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 3 / 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.25 * c; + diff --git a/latest/cases/00912/l3v2/index.heta b/latest/cases/00912/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00912/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00912/l3v2/json/output.json b/latest/cases/00912/l3v2/json/output.json new file mode 100644 index 000000000..56eac777a --- /dev/null +++ b/latest/cases/00912/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "litre", + "assignments": { + "start_": "3 / 2" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00912/model-sbml-l2v5.xml b/latest/cases/00912/model-sbml-l2v5.xml new file mode 100644 index 000000000..7bfe23243 --- /dev/null +++ b/latest/cases/00912/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + 3 + 2 + + + + + + + + + + 0.25 + c + + + + + + diff --git a/latest/cases/00912/model-sbml-l3v2.xml b/latest/cases/00912/model-sbml-l3v2.xml new file mode 100644 index 000000000..93c16894a --- /dev/null +++ b/latest/cases/00912/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + 3 + 2 + + + + + + + + + + 0.25 + c + + + + + + diff --git a/latest/cases/00912/output.heta b/latest/cases/00912/output.heta new file mode 100644 index 000000000..67058cdd0 --- /dev/null +++ b/latest/cases/00912/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.25 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$undeclared$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 3 / 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.25 * c; + diff --git a/latest/cases/00912/synopsis.txt b/latest/cases/00912/synopsis.txt new file mode 100644 index 000000000..26266ced2 --- /dev/null +++ b/latest/cases/00912/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.25 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$undeclared$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00913/l2v5/heta-code/output.heta b/latest/cases/00913/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f5c1013d1 --- /dev/null +++ b/latest/cases/00913/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: volume, } .= 3 / 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.25 * c; + diff --git a/latest/cases/00913/l2v5/index.heta b/latest/cases/00913/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00913/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00913/l2v5/json/output.json b/latest/cases/00913/l2v5/json/output.json new file mode 100644 index 000000000..5a8359dea --- /dev/null +++ b/latest/cases/00913/l2v5/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "volume", + "assignments": { + "start_": "3 / 2" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00913/l3v2/heta-code/output.heta b/latest/cases/00913/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ea80e6fc3 --- /dev/null +++ b/latest/cases/00913/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 3 / 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.25 * c; + diff --git a/latest/cases/00913/l3v2/index.heta b/latest/cases/00913/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00913/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00913/l3v2/json/output.json b/latest/cases/00913/l3v2/json/output.json new file mode 100644 index 000000000..56eac777a --- /dev/null +++ b/latest/cases/00913/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "litre", + "assignments": { + "start_": "3 / 2" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00913/model-sbml-l2v5.xml b/latest/cases/00913/model-sbml-l2v5.xml new file mode 100644 index 000000000..90c111b33 --- /dev/null +++ b/latest/cases/00913/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + 3 + 2 + + + + + + + + + + 0.25 + c + + + + + + diff --git a/latest/cases/00913/model-sbml-l3v2.xml b/latest/cases/00913/model-sbml-l3v2.xml new file mode 100644 index 000000000..ca13b02e8 --- /dev/null +++ b/latest/cases/00913/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + 3 + 2 + + + + + + + + + + 0.25 + c + + + + + + diff --git a/latest/cases/00913/output.heta b/latest/cases/00913/output.heta new file mode 100644 index 000000000..bb12587bd --- /dev/null +++ b/latest/cases/00913/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.25 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$2$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 3 / 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.25 * c; + diff --git a/latest/cases/00913/synopsis.txt b/latest/cases/00913/synopsis.txt new file mode 100644 index 000000000..9afecefff --- /dev/null +++ b/latest/cases/00913/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.25 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$2$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00914/l2v5/heta-code/output.heta b/latest/cases/00914/l2v5/heta-code/output.heta new file mode 100644 index 000000000..510fb5d89 --- /dev/null +++ b/latest/cases/00914/l2v5/heta-code/output.heta @@ -0,0 +1,15 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: area, } .= 0.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := multiply(c, 0.5); + diff --git a/latest/cases/00914/l2v5/index.heta b/latest/cases/00914/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00914/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00914/l2v5/json/output.json b/latest/cases/00914/l2v5/json/output.json new file mode 100644 index 000000000..d462a8dc9 --- /dev/null +++ b/latest/cases/00914/l2v5/json/output.json @@ -0,0 +1,64 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "area", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(c, 0.5)" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00914/l3v2/heta-code/output.heta b/latest/cases/00914/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8075853c4 --- /dev/null +++ b/latest/cases/00914/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 0.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := multiply(c, 0.5); + diff --git a/latest/cases/00914/l3v2/index.heta b/latest/cases/00914/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00914/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00914/l3v2/json/output.json b/latest/cases/00914/l3v2/json/output.json new file mode 100644 index 000000000..a7e74d31b --- /dev/null +++ b/latest/cases/00914/l3v2/json/output.json @@ -0,0 +1,40 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre^2", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(c, 0.5)" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00914/model-sbml-l2v5.xml b/latest/cases/00914/model-sbml-l2v5.xml new file mode 100644 index 000000000..18d6723fb --- /dev/null +++ b/latest/cases/00914/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + multiply + c + 0.5 + + + + + + diff --git a/latest/cases/00914/model-sbml-l3v2.xml b/latest/cases/00914/model-sbml-l3v2.xml new file mode 100644 index 000000000..1cd87b411 --- /dev/null +++ b/latest/cases/00914/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + multiply + c + 0.5 + + + + + + diff --git a/latest/cases/00914/output.heta b/latest/cases/00914/output.heta new file mode 100644 index 000000000..df2067d64 --- /dev/null +++ b/latest/cases/00914/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, FunctionDefinition +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $multiply(0.5, c)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$0.5$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 0.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := multiply(c, 0.5); + diff --git a/latest/cases/00914/synopsis.txt b/latest/cases/00914/synopsis.txt new file mode 100644 index 000000000..67d1657f3 --- /dev/null +++ b/latest/cases/00914/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, FunctionDefinition +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $multiply(0.5, c)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$0.5$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00915/l2v5/heta-code/output.heta b/latest/cases/00915/l2v5/heta-code/output.heta new file mode 100644 index 000000000..03bd86df1 --- /dev/null +++ b/latest/cases/00915/l2v5/heta-code/output.heta @@ -0,0 +1,15 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: length, } .= 0.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := multiply(c, 0.15); + diff --git a/latest/cases/00915/l2v5/index.heta b/latest/cases/00915/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00915/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00915/l2v5/json/output.json b/latest/cases/00915/l2v5/json/output.json new file mode 100644 index 000000000..580ca3a25 --- /dev/null +++ b/latest/cases/00915/l2v5/json/output.json @@ -0,0 +1,64 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "length", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(c, 0.15)" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00915/l3v2/heta-code/output.heta b/latest/cases/00915/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f8ef00cf6 --- /dev/null +++ b/latest/cases/00915/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 0.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := multiply(c, 0.15); + diff --git a/latest/cases/00915/l3v2/index.heta b/latest/cases/00915/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00915/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00915/l3v2/json/output.json b/latest/cases/00915/l3v2/json/output.json new file mode 100644 index 000000000..ba68d4f6b --- /dev/null +++ b/latest/cases/00915/l3v2/json/output.json @@ -0,0 +1,40 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "multiply(c, 0.15)" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00915/model-sbml-l2v5.xml b/latest/cases/00915/model-sbml-l2v5.xml new file mode 100644 index 000000000..b4aec3de9 --- /dev/null +++ b/latest/cases/00915/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + multiply + c + 0.15 + + + + + + diff --git a/latest/cases/00915/model-sbml-l3v2.xml b/latest/cases/00915/model-sbml-l3v2.xml new file mode 100644 index 000000000..80df945db --- /dev/null +++ b/latest/cases/00915/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + multiply + c + 0.15 + + + + + + diff --git a/latest/cases/00915/output.heta b/latest/cases/00915/output.heta new file mode 100644 index 000000000..e7cf763e3 --- /dev/null +++ b/latest/cases/00915/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, FunctionDefinition +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $multiply(0.15, c)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$0.5$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 0.5; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := multiply(c, 0.15); + diff --git a/latest/cases/00915/synopsis.txt b/latest/cases/00915/synopsis.txt new file mode 100644 index 000000000..eaa261acd --- /dev/null +++ b/latest/cases/00915/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, FunctionDefinition +testTags: NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $multiply(0.15, c)$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$0.5$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00916/l2v5/heta-code/output.heta b/latest/cases/00916/l2v5/heta-code/output.heta new file mode 100644 index 000000000..eb2e8c9ee --- /dev/null +++ b/latest/cases/00916/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: area, } .= 2 / 3; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00916/l2v5/index.heta b/latest/cases/00916/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00916/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00916/l2v5/json/output.json b/latest/cases/00916/l2v5/json/output.json new file mode 100644 index 000000000..27378d12b --- /dev/null +++ b/latest/cases/00916/l2v5/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "area", + "assignments": { + "start_": "2 / 3" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00916/l3v2/heta-code/output.heta b/latest/cases/00916/l3v2/heta-code/output.heta new file mode 100644 index 000000000..871d88fce --- /dev/null +++ b/latest/cases/00916/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 2 / 3; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00916/l3v2/index.heta b/latest/cases/00916/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00916/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00916/l3v2/json/output.json b/latest/cases/00916/l3v2/json/output.json new file mode 100644 index 000000000..96b14c893 --- /dev/null +++ b/latest/cases/00916/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre^2", + "assignments": { + "start_": "2 / 3" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00916/model-sbml-l2v5.xml b/latest/cases/00916/model-sbml-l2v5.xml new file mode 100644 index 000000000..f713ef727 --- /dev/null +++ b/latest/cases/00916/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + 2 + 3 + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00916/model-sbml-l3v2.xml b/latest/cases/00916/model-sbml-l3v2.xml new file mode 100644 index 000000000..1afafa5ad --- /dev/null +++ b/latest/cases/00916/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + 2 + 3 + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00916/output.heta b/latest/cases/00916/output.heta new file mode 100644 index 000000000..11ed4d4fb --- /dev/null +++ b/latest/cases/00916/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$undeclared$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 2 / 3; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00916/synopsis.txt b/latest/cases/00916/synopsis.txt new file mode 100644 index 000000000..63f5d9d26 --- /dev/null +++ b/latest/cases/00916/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$undeclared$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00917/l2v5/heta-code/output.heta b/latest/cases/00917/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e459f71ef --- /dev/null +++ b/latest/cases/00917/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: length, } .= 2.2 / 3; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00917/l2v5/index.heta b/latest/cases/00917/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00917/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00917/l2v5/json/output.json b/latest/cases/00917/l2v5/json/output.json new file mode 100644 index 000000000..494f022d0 --- /dev/null +++ b/latest/cases/00917/l2v5/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "length", + "assignments": { + "start_": "2.2 / 3" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00917/l3v2/heta-code/output.heta b/latest/cases/00917/l3v2/heta-code/output.heta new file mode 100644 index 000000000..57f3f3e08 --- /dev/null +++ b/latest/cases/00917/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 2.2 / 3; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00917/l3v2/index.heta b/latest/cases/00917/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00917/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00917/l3v2/json/output.json b/latest/cases/00917/l3v2/json/output.json new file mode 100644 index 000000000..dd544a761 --- /dev/null +++ b/latest/cases/00917/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre", + "assignments": { + "start_": "2.2 / 3" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00917/model-sbml-l2v5.xml b/latest/cases/00917/model-sbml-l2v5.xml new file mode 100644 index 000000000..9b1265db7 --- /dev/null +++ b/latest/cases/00917/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + 2.2 + 3 + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00917/model-sbml-l3v2.xml b/latest/cases/00917/model-sbml-l3v2.xml new file mode 100644 index 000000000..4b3288511 --- /dev/null +++ b/latest/cases/00917/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + 2.2 + 3 + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00917/output.heta b/latest/cases/00917/output.heta new file mode 100644 index 000000000..8e78bfe15 --- /dev/null +++ b/latest/cases/00917/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$undeclared$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 2.2 / 3; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00917/synopsis.txt b/latest/cases/00917/synopsis.txt new file mode 100644 index 000000000..9025ce512 --- /dev/null +++ b/latest/cases/00917/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c has not been +explicitly declared and must be calculated using the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$undeclared$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00918/l2v5/heta-code/output.heta b/latest/cases/00918/l2v5/heta-code/output.heta new file mode 100644 index 000000000..271e84df0 --- /dev/null +++ b/latest/cases/00918/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: area, } .= 3.3 / 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 1.25 * c; + diff --git a/latest/cases/00918/l2v5/index.heta b/latest/cases/00918/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00918/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00918/l2v5/json/output.json b/latest/cases/00918/l2v5/json/output.json new file mode 100644 index 000000000..63d7f98f1 --- /dev/null +++ b/latest/cases/00918/l2v5/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "area", + "assignments": { + "start_": "3.3 / 2" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00918/l3v2/heta-code/output.heta b/latest/cases/00918/l3v2/heta-code/output.heta new file mode 100644 index 000000000..87a918465 --- /dev/null +++ b/latest/cases/00918/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 3.3 / 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 1.25 * c; + diff --git a/latest/cases/00918/l3v2/index.heta b/latest/cases/00918/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00918/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00918/l3v2/json/output.json b/latest/cases/00918/l3v2/json/output.json new file mode 100644 index 000000000..193977286 --- /dev/null +++ b/latest/cases/00918/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre^2", + "assignments": { + "start_": "3.3 / 2" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00918/model-sbml-l2v5.xml b/latest/cases/00918/model-sbml-l2v5.xml new file mode 100644 index 000000000..88592c12d --- /dev/null +++ b/latest/cases/00918/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + 3.3 + 2 + + + + + + + + + + 1.25 + c + + + + + + diff --git a/latest/cases/00918/model-sbml-l3v2.xml b/latest/cases/00918/model-sbml-l3v2.xml new file mode 100644 index 000000000..60cb9618e --- /dev/null +++ b/latest/cases/00918/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + 3.3 + 2 + + + + + + + + + + 1.25 + c + + + + + + diff --git a/latest/cases/00918/output.heta b/latest/cases/00918/output.heta new file mode 100644 index 000000000..bb3163887 --- /dev/null +++ b/latest/cases/00918/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $1.25 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$2$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre^2, } .= 3.3 / 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 1.25 * c; + diff --git a/latest/cases/00918/synopsis.txt b/latest/cases/00918/synopsis.txt new file mode 100644 index 000000000..5831fc5c6 --- /dev/null +++ b/latest/cases/00918/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 2-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $1.25 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$2$ |metre^2^ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00919/l2v5/heta-code/output.heta b/latest/cases/00919/l2v5/heta-code/output.heta new file mode 100644 index 000000000..01e5ff506 --- /dev/null +++ b/latest/cases/00919/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: length, } .= 2.1 / 4; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 1.25 * c; + diff --git a/latest/cases/00919/l2v5/index.heta b/latest/cases/00919/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00919/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00919/l2v5/json/output.json b/latest/cases/00919/l2v5/json/output.json new file mode 100644 index 000000000..6fc6f7b87 --- /dev/null +++ b/latest/cases/00919/l2v5/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "length", + "assignments": { + "start_": "2.1 / 4" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00919/l3v2/heta-code/output.heta b/latest/cases/00919/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7069b4c3d --- /dev/null +++ b/latest/cases/00919/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 2.1 / 4; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 1.25 * c; + diff --git a/latest/cases/00919/l3v2/index.heta b/latest/cases/00919/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00919/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00919/l3v2/json/output.json b/latest/cases/00919/l3v2/json/output.json new file mode 100644 index 000000000..057108993 --- /dev/null +++ b/latest/cases/00919/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "metre", + "assignments": { + "start_": "2.1 / 4" + } + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "1.25 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00919/model-sbml-l2v5.xml b/latest/cases/00919/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef645900a --- /dev/null +++ b/latest/cases/00919/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + 2.1 + 4 + + + + + + + + + + 1.25 + c + + + + + + diff --git a/latest/cases/00919/model-sbml-l3v2.xml b/latest/cases/00919/model-sbml-l3v2.xml new file mode 100644 index 000000000..16478f5d5 --- /dev/null +++ b/latest/cases/00919/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + 2.1 + 4 + + + + + + + + + + 1.25 + c + + + + + + diff --git a/latest/cases/00919/output.heta b/latest/cases/00919/output.heta new file mode 100644 index 000000000..8ae86c40a --- /dev/null +++ b/latest/cases/00919/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $1.25 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$2$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: metre, } .= 2.1 / 4; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 1.25 * c; + diff --git a/latest/cases/00919/synopsis.txt b/latest/cases/00919/synopsis.txt new file mode 100644 index 000000000..e457fbebc --- /dev/null +++ b/latest/cases/00919/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, RateRule, InitialAssignment +testTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying 1-dimensional compartment called c. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $1.25 * c$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | c | $3 / 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the compartment c is +inconsistent with the value returned by the InitialAssignment. + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Size of compartment c |$2$ |metre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00920/l2v5/heta-code/output.heta b/latest/cases/00920/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1c19f9f11 --- /dev/null +++ b/latest/cases/00920/l2v5/heta-code/output.heta @@ -0,0 +1,12 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +k1 @Record 'k1' { } .= 2.5 * k2; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00920/l2v5/index.heta b/latest/cases/00920/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00920/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00920/l2v5/json/output.json b/latest/cases/00920/l2v5/json/output.json new file mode 100644 index 000000000..bf0aa07f3 --- /dev/null +++ b/latest/cases/00920/l2v5/json/output.json @@ -0,0 +1,46 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "2.5 * k2" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00920/l3v2/build.log b/latest/cases/00920/l3v2/build.log new file mode 100644 index 000000000..8f063c240 --- /dev/null +++ b/latest/cases/00920/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00920/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00920/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00920/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] No required "num" property for "k1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00920/l3v2/index.heta b/latest/cases/00920/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00920/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00920/model-sbml-l2v5.xml b/latest/cases/00920/model-sbml-l2v5.xml new file mode 100644 index 000000000..de8a821d0 --- /dev/null +++ b/latest/cases/00920/model-sbml-l2v5.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 2.5 + k2 + + + + + + diff --git a/latest/cases/00920/model-sbml-l3v2.xml b/latest/cases/00920/model-sbml-l3v2.xml new file mode 100644 index 000000000..ae4900af6 --- /dev/null +++ b/latest/cases/00920/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + 2.5 + k2 + + + + + + diff --git a/latest/cases/00920/output.heta b/latest/cases/00920/output.heta new file mode 100644 index 000000000..090c7ed63 --- /dev/null +++ b/latest/cases/00920/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: Model with parameters and initialAssignments only. +componentTags: Parameter, InitialAssignment +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 * 2.5$ |] + +Note: InitialAssignments override any declared initial values. In this +case, the initial value of k1 has not been explicitly declared and must be +calculated using the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ undeclared$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +k1 @Record 'k1' { } .= 2.5 * k2; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00920/synopsis.txt b/latest/cases/00920/synopsis.txt new file mode 100644 index 000000000..f42e70de4 --- /dev/null +++ b/latest/cases/00920/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Model with parameters and initialAssignments only. +componentTags: Parameter, InitialAssignment +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 * 2.5$ |] + +Note: InitialAssignments override any declared initial values. In this +case, the initial value of k1 has not been explicitly declared and must be +calculated using the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ undeclared$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + + diff --git a/latest/cases/00921/l2v5/heta-code/output.heta b/latest/cases/00921/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ffa21af00 --- /dev/null +++ b/latest/cases/00921/l2v5/heta-code/output.heta @@ -0,0 +1,12 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +k1 @Record 'k1' { } .= 1.5 * k2; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00921/l2v5/index.heta b/latest/cases/00921/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00921/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00921/l2v5/json/output.json b/latest/cases/00921/l2v5/json/output.json new file mode 100644 index 000000000..a83b2db28 --- /dev/null +++ b/latest/cases/00921/l2v5/json/output.json @@ -0,0 +1,46 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5 * k2" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00921/l3v2/heta-code/output.heta b/latest/cases/00921/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ee75d3b83 --- /dev/null +++ b/latest/cases/00921/l3v2/heta-code/output.heta @@ -0,0 +1,7 @@ + + +t @TimeScale { units: second, }; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00921/l3v2/index.heta b/latest/cases/00921/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00921/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00921/l3v2/json/output.json b/latest/cases/00921/l3v2/json/output.json new file mode 100644 index 000000000..183cd7e63 --- /dev/null +++ b/latest/cases/00921/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00921/model-sbml-l2v5.xml b/latest/cases/00921/model-sbml-l2v5.xml new file mode 100644 index 000000000..6a64f9ff0 --- /dev/null +++ b/latest/cases/00921/model-sbml-l2v5.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 1.5 + k2 + + + + + + diff --git a/latest/cases/00921/model-sbml-l3v2.xml b/latest/cases/00921/model-sbml-l3v2.xml new file mode 100644 index 000000000..4e126a683 --- /dev/null +++ b/latest/cases/00921/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + 1.5 + k2 + + + + + + diff --git a/latest/cases/00921/output.heta b/latest/cases/00921/output.heta new file mode 100644 index 000000000..841fd0d4e --- /dev/null +++ b/latest/cases/00921/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: Model with parameters and initialAssignments only. +componentTags: Parameter, InitialAssignment +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 * 1.5$ |] + +Note: InitialAssignments override any declared initial values. In this +case, the initial value of k1 is inconsistent with the value +calculated using the initialAssignment. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ 0.5$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +k1 @Const 'k1' { } = 0.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00921/synopsis.txt b/latest/cases/00921/synopsis.txt new file mode 100644 index 000000000..2992f2ee6 --- /dev/null +++ b/latest/cases/00921/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Model with parameters and initialAssignments only. +componentTags: Parameter, InitialAssignment +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 * 1.5$ |] + +Note: InitialAssignments override any declared initial values. In this +case, the initial value of k1 is inconsistent with the value +calculated using the initialAssignment. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ 0.5$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00922/l2v5/heta-code/output.heta b/latest/cases/00922/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ae9259d50 --- /dev/null +++ b/latest/cases/00922/l2v5/heta-code/output.heta @@ -0,0 +1,12 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +k1 @Record 'k1' { } .= 2 * k2; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00922/l2v5/index.heta b/latest/cases/00922/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00922/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00922/l2v5/json/output.json b/latest/cases/00922/l2v5/json/output.json new file mode 100644 index 000000000..1bf64ef9c --- /dev/null +++ b/latest/cases/00922/l2v5/json/output.json @@ -0,0 +1,46 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "2 * k2" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00922/l3v2/heta-code/output.heta b/latest/cases/00922/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d468fc807 --- /dev/null +++ b/latest/cases/00922/l3v2/heta-code/output.heta @@ -0,0 +1,7 @@ + + +t @TimeScale { units: second, }; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00922/l3v2/index.heta b/latest/cases/00922/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00922/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00922/l3v2/json/output.json b/latest/cases/00922/l3v2/json/output.json new file mode 100644 index 000000000..1f307d5f6 --- /dev/null +++ b/latest/cases/00922/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.6 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00922/model-sbml-l2v5.xml b/latest/cases/00922/model-sbml-l2v5.xml new file mode 100644 index 000000000..12f92f7a8 --- /dev/null +++ b/latest/cases/00922/model-sbml-l2v5.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 2 + k2 + + + + + + diff --git a/latest/cases/00922/model-sbml-l3v2.xml b/latest/cases/00922/model-sbml-l3v2.xml new file mode 100644 index 000000000..74254325e --- /dev/null +++ b/latest/cases/00922/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + 2 + k2 + + + + + + diff --git a/latest/cases/00922/output.heta b/latest/cases/00922/output.heta new file mode 100644 index 000000000..da8e57b5c --- /dev/null +++ b/latest/cases/00922/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: Model with parameters and initialAssignments only. +componentTags: Parameter, InitialAssignment +testTags: +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 * 2.0$ |] + +Note: InitialAssignments override any declared initial values. In this +case, the initial value of k1 is consistent with the value +calculated using the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ 0.6$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +k1 @Const 'k1' { } = 0.6; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00922/synopsis.txt b/latest/cases/00922/synopsis.txt new file mode 100644 index 000000000..bd6fef638 --- /dev/null +++ b/latest/cases/00922/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Model with parameters and initialAssignments only. +componentTags: Parameter, InitialAssignment +testTags: +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | k1 | $k2 * 2.0$ |] + +Note: InitialAssignments override any declared initial values. In this +case, the initial value of k1 is consistent with the value +calculated using the initialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ 0.6$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00923/l2v5/heta-code/output.heta b/latest/cases/00923/l2v5/heta-code/output.heta new file mode 100644 index 000000000..93a47e9ea --- /dev/null +++ b/latest/cases/00923/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +k1 @Record 'k1' { }; +k1 := 4 * k2; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00923/l2v5/index.heta b/latest/cases/00923/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00923/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00923/l2v5/json/output.json b/latest/cases/00923/l2v5/json/output.json new file mode 100644 index 000000000..54caeade3 --- /dev/null +++ b/latest/cases/00923/l2v5/json/output.json @@ -0,0 +1,46 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "4 * k2" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00923/l3v2/heta-code/output.heta b/latest/cases/00923/l3v2/heta-code/output.heta new file mode 100644 index 000000000..718ef6c91 --- /dev/null +++ b/latest/cases/00923/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +k1 @Record 'k1' { }; +k1 := 4 * k2; + +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00923/l3v2/index.heta b/latest/cases/00923/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00923/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00923/l3v2/json/output.json b/latest/cases/00923/l3v2/json/output.json new file mode 100644 index 000000000..f4bd3edb1 --- /dev/null +++ b/latest/cases/00923/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "ode_": "4 * k2" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00923/model-sbml-l2v5.xml b/latest/cases/00923/model-sbml-l2v5.xml new file mode 100644 index 000000000..bd6f0c02d --- /dev/null +++ b/latest/cases/00923/model-sbml-l2v5.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 4 + k2 + + + + + + diff --git a/latest/cases/00923/model-sbml-l3v2.xml b/latest/cases/00923/model-sbml-l3v2.xml new file mode 100644 index 000000000..18c202bcb --- /dev/null +++ b/latest/cases/00923/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + 4 + k2 + + + + + + diff --git a/latest/cases/00923/output.heta b/latest/cases/00923/output.heta new file mode 100644 index 000000000..d466403e1 --- /dev/null +++ b/latest/cases/00923/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Model with parameters and assignmentRule only. +componentTags: Parameter, AssignmentRule +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| assignmentRule | k1 | $k2 * 4$ |] + + +Note: AssignmentRules override any declared initial values. In this +case, the initial value of k1 has not been explicitly declared and must be +calculated using the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ undeclared$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +k1 @Record 'k1' { }; +k1 := 4 * k2; + +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00923/synopsis.txt b/latest/cases/00923/synopsis.txt new file mode 100644 index 000000000..c920491f3 --- /dev/null +++ b/latest/cases/00923/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Model with parameters and assignmentRule only. +componentTags: Parameter, AssignmentRule +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| assignmentRule | k1 | $k2 * 4$ |] + + +Note: AssignmentRules override any declared initial values. In this +case, the initial value of k1 has not been explicitly declared and must be +calculated using the AssignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ undeclared$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00924/l2v5/heta-code/output.heta b/latest/cases/00924/l2v5/heta-code/output.heta new file mode 100644 index 000000000..09af30bc9 --- /dev/null +++ b/latest/cases/00924/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +k1 @Record 'k1' { } .= 1; +k1 := 3 * k2; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/00924/l2v5/index.heta b/latest/cases/00924/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00924/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00924/l2v5/json/output.json b/latest/cases/00924/l2v5/json/output.json new file mode 100644 index 000000000..a05020b17 --- /dev/null +++ b/latest/cases/00924/l2v5/json/output.json @@ -0,0 +1,47 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1", + "ode_": "3 * k2" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00924/l3v2/heta-code/output.heta b/latest/cases/00924/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0c0e6c2e5 --- /dev/null +++ b/latest/cases/00924/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +k1 @Record 'k1' { } .= 1; +k1 := 3 * k2; + +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00924/l3v2/index.heta b/latest/cases/00924/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00924/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00924/l3v2/json/output.json b/latest/cases/00924/l3v2/json/output.json new file mode 100644 index 000000000..c2d7ba8c8 --- /dev/null +++ b/latest/cases/00924/l3v2/json/output.json @@ -0,0 +1,21 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1", + "ode_": "3 * k2" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/00924/model-sbml-l2v5.xml b/latest/cases/00924/model-sbml-l2v5.xml new file mode 100644 index 000000000..adda30135 --- /dev/null +++ b/latest/cases/00924/model-sbml-l2v5.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 3 + k2 + + + + + + diff --git a/latest/cases/00924/model-sbml-l3v2.xml b/latest/cases/00924/model-sbml-l3v2.xml new file mode 100644 index 000000000..18ef0a4ea --- /dev/null +++ b/latest/cases/00924/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + 3 + k2 + + + + + + diff --git a/latest/cases/00924/output.heta b/latest/cases/00924/output.heta new file mode 100644 index 000000000..4c95ac2fe --- /dev/null +++ b/latest/cases/00924/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Model with parameters and assignmentRule only. +componentTags: Parameter, AssignmentRule +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| assignmentRule | k1 | $k2 * 3$ |] + + +Note: AssignmentRules override any declared initial values. In this +case, the initial value of k1 is inconsistent with the value +calculated using the assignmentRule. The calculated value should be used. +. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ 1.0$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +k1 @Record 'k1' { } .= 1; +k1 := 3 * k2; + +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/00924/synopsis.txt b/latest/cases/00924/synopsis.txt new file mode 100644 index 000000000..6f8eed9f8 --- /dev/null +++ b/latest/cases/00924/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Model with parameters and assignmentRule only. +componentTags: Parameter, AssignmentRule +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| assignmentRule | k1 | $k2 * 3$ |] + + +Note: AssignmentRules override any declared initial values. In this +case, the initial value of k1 is inconsistent with the value +calculated using the assignmentRule. The calculated value should be used. +. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ 1.0$ |any | +|Value of parameter k2 |$0.3$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00925/l2v5/heta-code/output.heta b/latest/cases/00925/l2v5/heta-code/output.heta new file mode 100644 index 000000000..046903b71 --- /dev/null +++ b/latest/cases/00925/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +k1 @Record 'k1' { } .= 0.6; +k1 := 3 * k2; +k2 @Record 'k2' { } .= 0.2; + diff --git a/latest/cases/00925/l2v5/index.heta b/latest/cases/00925/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00925/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00925/l2v5/json/output.json b/latest/cases/00925/l2v5/json/output.json new file mode 100644 index 000000000..33d1af43d --- /dev/null +++ b/latest/cases/00925/l2v5/json/output.json @@ -0,0 +1,47 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.6", + "ode_": "3 * k2" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00925/l3v2/heta-code/output.heta b/latest/cases/00925/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6d0471893 --- /dev/null +++ b/latest/cases/00925/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { units: second, }; + +k1 @Record 'k1' { } .= 0.6; +k1 := 3 * k2; + +k2 @Const 'k2' { } = 0.2; + diff --git a/latest/cases/00925/l3v2/index.heta b/latest/cases/00925/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00925/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00925/l3v2/json/output.json b/latest/cases/00925/l3v2/json/output.json new file mode 100644 index 000000000..a391cddbf --- /dev/null +++ b/latest/cases/00925/l3v2/json/output.json @@ -0,0 +1,21 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.6", + "ode_": "3 * k2" + } + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/00925/model-sbml-l2v5.xml b/latest/cases/00925/model-sbml-l2v5.xml new file mode 100644 index 000000000..671c0ff2c --- /dev/null +++ b/latest/cases/00925/model-sbml-l2v5.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 3 + k2 + + + + + + diff --git a/latest/cases/00925/model-sbml-l3v2.xml b/latest/cases/00925/model-sbml-l3v2.xml new file mode 100644 index 000000000..95ae81c07 --- /dev/null +++ b/latest/cases/00925/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + 3 + k2 + + + + + + diff --git a/latest/cases/00925/output.heta b/latest/cases/00925/output.heta new file mode 100644 index 000000000..95c561b2f --- /dev/null +++ b/latest/cases/00925/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Model with parameters and assignmentRule only. +componentTags: Parameter, AssignmentRule +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| assignmentRule | k1 | $k2 * 3$ |] + + +Note: AssignmentRules override any declared initial values. In this +case, the initial value of k1 is consistent with the value +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ 0.6$ |any | +|Value of parameter k2 |$0.2$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +k1 @Record 'k1' { } .= 0.6; +k1 := 3 * k2; + +k2 @Const 'k2' { } = 0.2; + diff --git a/latest/cases/00925/synopsis.txt b/latest/cases/00925/synopsis.txt new file mode 100644 index 000000000..7b8974c94 --- /dev/null +++ b/latest/cases/00925/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Model with parameters and assignmentRule only. +componentTags: Parameter, AssignmentRule +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains two constant +parameters called k1 and k2. + + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| assignmentRule | k1 | $k2 * 3$ |] + + +Note: AssignmentRules override any declared initial values. In this +case, the initial value of k1 is consistent with the value +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Value of parameter k1 |$ 0.6$ |any | +|Value of parameter k2 |$0.2$ |same as k1 |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00926/l2v5/heta-code/output.heta b/latest/cases/00926/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7fbceb54c --- /dev/null +++ b/latest/cases/00926/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: volume, } .= 1; + +s @Species 's' { units: substance/volume, compartment: c, } .= 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00926/l2v5/index.heta b/latest/cases/00926/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00926/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00926/l2v5/json/output.json b/latest/cases/00926/l2v5/json/output.json new file mode 100644 index 000000000..9ca8932d0 --- /dev/null +++ b/latest/cases/00926/l2v5/json/output.json @@ -0,0 +1,65 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "volume", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "s", + "title": "s", + "units": "substance/volume", + "assignments": { + "start_": "2" + }, + "compartment": "c" + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00926/l3v2/heta-code/output.heta b/latest/cases/00926/l3v2/heta-code/output.heta new file mode 100644 index 000000000..64bef06f1 --- /dev/null +++ b/latest/cases/00926/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 1; + +s @Species 's' { units: mole/litre, compartment: c, } .= 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00926/l3v2/index.heta b/latest/cases/00926/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00926/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00926/l3v2/json/output.json b/latest/cases/00926/l3v2/json/output.json new file mode 100644 index 000000000..c5868dd19 --- /dev/null +++ b/latest/cases/00926/l3v2/json/output.json @@ -0,0 +1,41 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "litre", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "s", + "title": "s", + "units": "mole/litre", + "assignments": { + "start_": "2" + }, + "compartment": "c" + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00926/model-sbml-l2v5.xml b/latest/cases/00926/model-sbml-l2v5.xml new file mode 100644 index 000000000..5d36de35c --- /dev/null +++ b/latest/cases/00926/model-sbml-l2v5.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00926/model-sbml-l3v2.xml b/latest/cases/00926/model-sbml-l3v2.xml new file mode 100644 index 000000000..e84379efc --- /dev/null +++ b/latest/cases/00926/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00926/output.heta b/latest/cases/00926/output.heta new file mode 100644 index 000000000..ed22e8519 --- /dev/null +++ b/latest/cases/00926/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Species, RateRule +testTags: Concentration, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c and a species +s. The species is not directly affected by anything but the concentration +will change as a result of the varying compartment size. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of s |$2$ |mole litre^-1 | +|Size of compartment c |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 1; + +s @Species 's' { units: mole/litre, compartment: c, } .= 2; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00926/synopsis.txt b/latest/cases/00926/synopsis.txt new file mode 100644 index 000000000..388d83ed5 --- /dev/null +++ b/latest/cases/00926/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Species, RateRule +testTags: Concentration, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c and a species +s. The species is not directly affected by anything but the concentration +will change as a result of the varying compartment size. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of s |$2$ |mole litre^-1 | +|Size of compartment c |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00927/l2v5/heta-code/output.heta b/latest/cases/00927/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b04b503fc --- /dev/null +++ b/latest/cases/00927/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment 'c' { units: volume, } .= 1; + +s @Species 's' { units: substance/volume, compartment: c, } .= 2 / c; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00927/l2v5/index.heta b/latest/cases/00927/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00927/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00927/l2v5/json/output.json b/latest/cases/00927/l2v5/json/output.json new file mode 100644 index 000000000..968a5ed03 --- /dev/null +++ b/latest/cases/00927/l2v5/json/output.json @@ -0,0 +1,65 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "volume", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "s", + "title": "s", + "units": "substance/volume", + "assignments": { + "start_": "2 / c" + }, + "compartment": "c" + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00927/l3v2/heta-code/output.heta b/latest/cases/00927/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6fa37f971 --- /dev/null +++ b/latest/cases/00927/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 1; + +s @Species 's' { units: mole/litre, compartment: c, } .= 2 / c; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00927/l3v2/index.heta b/latest/cases/00927/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00927/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00927/l3v2/json/output.json b/latest/cases/00927/l3v2/json/output.json new file mode 100644 index 000000000..523446f2b --- /dev/null +++ b/latest/cases/00927/l3v2/json/output.json @@ -0,0 +1,41 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "c", + "title": "c", + "units": "litre", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "s", + "title": "s", + "units": "mole/litre", + "assignments": { + "start_": "2 / c" + }, + "compartment": "c" + }, + { + "class": "Process", + "id": "c_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.5 * c" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00927/model-sbml-l2v5.xml b/latest/cases/00927/model-sbml-l2v5.xml new file mode 100644 index 000000000..d36a8a80d --- /dev/null +++ b/latest/cases/00927/model-sbml-l2v5.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00927/model-sbml-l3v2.xml b/latest/cases/00927/model-sbml-l3v2.xml new file mode 100644 index 000000000..81b46115c --- /dev/null +++ b/latest/cases/00927/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + c + + + + + + diff --git a/latest/cases/00927/output.heta b/latest/cases/00927/output.heta new file mode 100644 index 000000000..8e0a3040c --- /dev/null +++ b/latest/cases/00927/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Species, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c and a species +s. The species is not directly affected by anything but the concentration +will change as a result of the varying compartment size. However the +amount of the species will remain constant. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of s |$2$ |mole | +|Size of compartment c |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + +*/ + + + +t @TimeScale { units: second, }; + +c @Compartment 'c' { units: litre, } .= 1; + +s @Species 's' { units: mole/litre, compartment: c, } .= 2 / c; + +c_proc @Process { actors: = c, aux: {{"metaid":"rule1"}}, }; +c_proc := 0.5 * c; + diff --git a/latest/cases/00927/synopsis.txt b/latest/cases/00927/synopsis.txt new file mode 100644 index 000000000..00518199f --- /dev/null +++ b/latest/cases/00927/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Model varying compartment using rules only. +componentTags: Compartment, Species, RateRule +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one varying compartment called c and a species +s. The species is not directly affected by anything but the concentration +will change as a result of the varying compartment size. However the +amount of the species will remain constant. + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | c | $0.5 * c$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of s |$2$ |mole | +|Size of compartment c |$1$ |litre |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + + diff --git a/latest/cases/00928/l2v5/index.heta b/latest/cases/00928/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00928/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00928/l3v2/heta-code/output.heta b/latest/cases/00928/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6ac60a1a3 --- /dev/null +++ b/latest/cases/00928/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0 / C; +S1 [evt0]= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + +evt0 @DSwitcher { trigger: t >= 0, }; + diff --git a/latest/cases/00928/l3v2/index.heta b/latest/cases/00928/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00928/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00928/l3v2/json/output.json b/latest/cases/00928/l3v2/json/output.json new file mode 100644 index 000000000..660c1e123 --- /dev/null +++ b/latest/cases/00928/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "0 / C", + "evt0": "1.5e-4 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "DSwitcher", + "id": "evt0", + "trigger": "t >= 0" + } +] \ No newline at end of file diff --git a/latest/cases/00928/model-sbml-l3v2.xml b/latest/cases/00928/model-sbml-l3v2.xml new file mode 100644 index 000000000..3f2f004c8 --- /dev/null +++ b/latest/cases/00928/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + time + 0 + + + + + + + + + 0.00015 + C + + + + + + + + diff --git a/latest/cases/00928/output.heta b/latest/cases/00928/output.heta new file mode 100644 index 000000000..c93179805 --- /dev/null +++ b/latest/cases/00928/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: Compartment, CSymbolTime, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "C". There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one event that assigns value to species S1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $t >= 0$ | $-$ | $S1 = 1.5 \x 10^-4$ |] + +The initialValue of the Trigger is set to 'false'. Thus at t = 0 the Trigger +transitions from 'false' to 'true' and thus the event is fired. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment "C" |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0 / C; +S1 [evt0]= 1.5e-4 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + +evt0 @DSwitcher { trigger: t >= 0, }; + diff --git a/latest/cases/00928/synopsis.txt b/latest/cases/00928/synopsis.txt new file mode 100644 index 000000000..94676faa8 --- /dev/null +++ b/latest/cases/00928/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: Compartment, CSymbolTime, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "C". There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one event that assigns value to species S1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $t >= 0$ | $-$ | $S1 = 1.5 \x 10^-4$ |] + +The initialValue of the Trigger is set to 'false'. Thus at t = 0 the Trigger +transitions from 'false' to 'true' and thus the event is fired. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment "C" |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00929/l2v5/index.heta b/latest/cases/00929/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00929/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00929/l3v2/heta-code/output.heta b/latest/cases/00929/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3d114753d --- /dev/null +++ b/latest/cases/00929/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S1 [evt0]= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + +evt0 @DSwitcher { trigger: t >= 0, }; + diff --git a/latest/cases/00929/l3v2/index.heta b/latest/cases/00929/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00929/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00929/l3v2/json/output.json b/latest/cases/00929/l3v2/json/output.json new file mode 100644 index 000000000..a416cabdd --- /dev/null +++ b/latest/cases/00929/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1.5e-4 / C", + "evt0": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "C * k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + }, + { + "class": "DSwitcher", + "id": "evt0", + "trigger": "t >= 0" + } +] \ No newline at end of file diff --git a/latest/cases/00929/model-sbml-l3v2.xml b/latest/cases/00929/model-sbml-l3v2.xml new file mode 100644 index 000000000..87774bed9 --- /dev/null +++ b/latest/cases/00929/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + time + 0 + + + + + + + + + 1 + C + + + + + + + + diff --git a/latest/cases/00929/output.heta b/latest/cases/00929/output.heta new file mode 100644 index 000000000..fbd80ead2 --- /dev/null +++ b/latest/cases/00929/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: Compartment, CSymbolTime, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "C". There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one event that assigns value to species S1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $t >= 0$ | $-$ | $S1 = 1$ |] + +The initialValue of the Trigger is set to 'true'. Thus at t = 0 the Trigger +does not transition from 'false' to 'true' and thus the event is not fired. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment "C" |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C; +S1 [evt0]= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := C * k1 * S1; + +k1 @Const 'k1' { } = 1; + +evt0 @DSwitcher { trigger: t >= 0, }; + diff --git a/latest/cases/00929/synopsis.txt b/latest/cases/00929/synopsis.txt new file mode 100644 index 000000000..5bb5b754e --- /dev/null +++ b/latest/cases/00929/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: Compartment, CSymbolTime, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "C". There are two +species called S1 and S2 and one parameter called k1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one event that assigns value to species S1 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $t >= 0$ | $-$ | $S1 = 1$ |] + +The initialValue of the Trigger is set to 'true'. Thus at t = 0 the Trigger +does not transition from 'false' to 'true' and thus the event is not fired. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment "C" |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00930/l2v5/index.heta b/latest/cases/00930/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00930/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00930/l3v2/heta-code/output.heta b/latest/cases/00930/l3v2/heta-code/output.heta new file mode 100644 index 000000000..63a479991 --- /dev/null +++ b/latest/cases/00930/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0 / C; +S1 [_E0]= 4; +S1 [_E1]= 1; +S2 @Species { compartment: C, } .= 0 / C; +S2 [_E0]= 5; +S2 [_E1]= 2; +S3 @Species { compartment: C, } .= 0 / C; +S3 [_E0]= 6; +S3 [_E1]= 3; + +_E0 @DSwitcher { trigger: t >= 0.99, }; +_E1 @DSwitcher { trigger: t >= 0.99, }; + diff --git a/latest/cases/00930/l3v2/index.heta b/latest/cases/00930/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00930/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00930/l3v2/json/output.json b/latest/cases/00930/l3v2/json/output.json new file mode 100644 index 000000000..cebfa1b03 --- /dev/null +++ b/latest/cases/00930/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0 / C", + "_E0": "4", + "_E1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0 / C", + "_E0": "5", + "_E1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "0 / C", + "_E0": "6", + "_E1": "3" + }, + "compartment": "C" + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E1", + "trigger": "t >= 0.99" + } +] \ No newline at end of file diff --git a/latest/cases/00930/model-sbml-l3v2.xml b/latest/cases/00930/model-sbml-l3v2.xml new file mode 100644 index 000000000..232bbeab4 --- /dev/null +++ b/latest/cases/00930/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + time + 0.99 + + + + + + 1 + + + + + + 4 + + + + + 5 + + + + + 6 + + + + + + + + + + time + 0.99 + + + + + + 0 + + + + + + 1 + + + + + 2 + + + + + 3 + + + + + + + diff --git a/latest/cases/00930/output.heta b/latest/cases/00930/output.heta new file mode 100644 index 000000000..8efb5a639 --- /dev/null +++ b/latest/cases/00930/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: Compartment, CSymbolTime, Species, EventNoDelay, EventPriority +testTags: Amount +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "C". There are two +species called S1 and S2. + + +The model contains two events that assign value to species S1, S2 and S3 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Priority* | *Delay* | *Assignments* | + | Event1 | $t >= 0.99$ | $1$ | $-$ | $S1 = 4$ | + | | | | | $S2 = 5$ | + | | | | | $S3 = 6$ | + | Event2 | $t >= 0.99$ | $0$ | $-$ | $S1 = 1$ | + | | | | | $S2 = 2$ | + | | | | | $S3 = 3$ |] + +The Events will fire simultaneously and must be executed in order determined by +the Priority. Thus the assignments of Event1 will be executed followed by the +assignments for Event2. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Volume of compartment "C" |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0 / C; +S1 [_E0]= 4; +S1 [_E1]= 1; +S2 @Species { compartment: C, } .= 0 / C; +S2 [_E0]= 5; +S2 [_E1]= 2; +S3 @Species { compartment: C, } .= 0 / C; +S3 [_E0]= 6; +S3 [_E1]= 3; + +_E0 @DSwitcher { trigger: t >= 0.99, }; +_E1 @DSwitcher { trigger: t >= 0.99, }; + diff --git a/latest/cases/00930/synopsis.txt b/latest/cases/00930/synopsis.txt new file mode 100644 index 000000000..724b04e61 --- /dev/null +++ b/latest/cases/00930/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: Compartment, CSymbolTime, Species, EventNoDelay, EventPriority +testTags: Amount +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "C". There are two +species called S1 and S2. + + +The model contains two events that assign value to species S1, S2 and S3 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Priority* | *Delay* | *Assignments* | + | Event1 | $t >= 0.99$ | $1$ | $-$ | $S1 = 4$ | + | | | | | $S2 = 5$ | + | | | | | $S3 = 6$ | + | Event2 | $t >= 0.99$ | $0$ | $-$ | $S1 = 1$ | + | | | | | $S2 = 2$ | + | | | | | $S3 = 3$ |] + +The Events will fire simultaneously and must be executed in order determined by +the Priority. Thus the assignments of Event1 will be executed followed by the +assignments for Event2. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Volume of compartment "C" |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00931/l2v5/index.heta b/latest/cases/00931/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00931/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00931/l3v2/heta-code/output.heta b/latest/cases/00931/l3v2/heta-code/output.heta new file mode 100644 index 000000000..63a479991 --- /dev/null +++ b/latest/cases/00931/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0 / C; +S1 [_E0]= 4; +S1 [_E1]= 1; +S2 @Species { compartment: C, } .= 0 / C; +S2 [_E0]= 5; +S2 [_E1]= 2; +S3 @Species { compartment: C, } .= 0 / C; +S3 [_E0]= 6; +S3 [_E1]= 3; + +_E0 @DSwitcher { trigger: t >= 0.99, }; +_E1 @DSwitcher { trigger: t >= 0.99, }; + diff --git a/latest/cases/00931/l3v2/index.heta b/latest/cases/00931/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00931/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00931/l3v2/json/output.json b/latest/cases/00931/l3v2/json/output.json new file mode 100644 index 000000000..cebfa1b03 --- /dev/null +++ b/latest/cases/00931/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0 / C", + "_E0": "4", + "_E1": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0 / C", + "_E0": "5", + "_E1": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "0 / C", + "_E0": "6", + "_E1": "3" + }, + "compartment": "C" + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E1", + "trigger": "t >= 0.99" + } +] \ No newline at end of file diff --git a/latest/cases/00931/model-sbml-l3v2.xml b/latest/cases/00931/model-sbml-l3v2.xml new file mode 100644 index 000000000..0850158eb --- /dev/null +++ b/latest/cases/00931/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + time + 0.99 + + + + + + -1 + + + + + + 4 + + + + + 5 + + + + + 6 + + + + + + + + + + time + 0.99 + + + + + + 0 + + + + + + 1 + + + + + 2 + + + + + 3 + + + + + + + diff --git a/latest/cases/00931/output.heta b/latest/cases/00931/output.heta new file mode 100644 index 000000000..6c69e31f5 --- /dev/null +++ b/latest/cases/00931/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: Compartment, CSymbolTime, Species, EventNoDelay, EventPriority +testTags: Amount +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "C". There are two +species called S1 and S2. + + +The model contains two events that assign value to species S1, S2 and S3 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Priority* | *Delay* | *Assignments* | + | Event1 | $t >= 1$ | $-1$ | $-$ | $S1 = 4$ | + | | | | | $S2 = 5$ | + | | | | | $S3 = 6$ | + | Event2 | $t >= 1$ | $0$ | $-$ | $S1 = 1$ | + | | | | | $S2 = 2$ | + | | | | | $S3 = 3$ |] + +The Events will fire simultaneously and must be executed in order determined by +the Priority. Thus the assignments of Event2 will be executed followed by the +assignments for Event1. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Volume of compartment "C" |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0 / C; +S1 [_E0]= 4; +S1 [_E1]= 1; +S2 @Species { compartment: C, } .= 0 / C; +S2 [_E0]= 5; +S2 [_E1]= 2; +S3 @Species { compartment: C, } .= 0 / C; +S3 [_E0]= 6; +S3 [_E1]= 3; + +_E0 @DSwitcher { trigger: t >= 0.99, }; +_E1 @DSwitcher { trigger: t >= 0.99, }; + diff --git a/latest/cases/00931/synopsis.txt b/latest/cases/00931/synopsis.txt new file mode 100644 index 000000000..cd64221d3 --- /dev/null +++ b/latest/cases/00931/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: Compartment, CSymbolTime, Species, EventNoDelay, EventPriority +testTags: Amount +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "C". There are two +species called S1 and S2. + + +The model contains two events that assign value to species S1, S2 and S3 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Priority* | *Delay* | *Assignments* | + | Event1 | $t >= 1$ | $-1$ | $-$ | $S1 = 4$ | + | | | | | $S2 = 5$ | + | | | | | $S3 = 6$ | + | Event2 | $t >= 1$ | $0$ | $-$ | $S1 = 1$ | + | | | | | $S2 = 2$ | + | | | | | $S3 = 3$ |] + +The Events will fire simultaneously and must be executed in order determined by +the Priority. Thus the assignments of Event2 will be executed followed by the +assignments for Event1. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Volume of compartment "C" |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00932/l2v5/index.heta b/latest/cases/00932/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00932/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00932/l3v2/build.log b/latest/cases/00932/l3v2/build.log new file mode 100644 index 000000000..f339d4d1b --- /dev/null +++ b/latest/cases/00932/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00932/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00932/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00932/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00932/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00932/l3v2/index.heta b/latest/cases/00932/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00932/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00932/model-sbml-l3v2.xml b/latest/cases/00932/model-sbml-l3v2.xml new file mode 100644 index 000000000..5078d87f4 --- /dev/null +++ b/latest/cases/00932/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + S1 + 5 -5 + + + + S1 + 4 -5 + + + + + + + 3 + + + + + + 0.00025 + + + + + + + diff --git a/latest/cases/00932/synopsis.txt b/latest/cases/00932/synopsis.txt new file mode 100644 index 000000000..53c4ad59f --- /dev/null +++ b/latest/cases/00932/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic single forward reaction with two species and a delayed event. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, EventIsNotPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains one compartment called "C". There are three +species named S1, S2 and S3 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one event that assigns value to species S3 defined as: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 <= 0.00005 && S1 >= 0.00004$ | $3$ | $S3 = 2.5 \x 10^-4$ |] + +The persistent attribute of the Trigger is set to 'false'. Thus, once the event has fired, +if the trigger value reverts to 'false' before the event is executed, then execution should +not take place. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Value of parameter k1 |$1$ |second^-1^ | +|Volume of compartment "C" |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00933/l2v5/build.log b/latest/cases/00933/l2v5/build.log new file mode 100644 index 000000000..0d4827fae --- /dev/null +++ b/latest/cases/00933/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00933/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00933/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00933/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00933/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00933/l2v5/index.heta b/latest/cases/00933/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00933/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00933/l3v2/build.log b/latest/cases/00933/l3v2/build.log new file mode 100644 index 000000000..3e694cc4b --- /dev/null +++ b/latest/cases/00933/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00933/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00933/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00933/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00933/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00933/l3v2/index.heta b/latest/cases/00933/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00933/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00933/model-sbml-l2v5.xml b/latest/cases/00933/model-sbml-l2v5.xml new file mode 100644 index 000000000..6bf2a7752 --- /dev/null +++ b/latest/cases/00933/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + S1 + 0.1 + + + + S2 + 0.95 + + + + + + + 1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00933/model-sbml-l3v2.xml b/latest/cases/00933/model-sbml-l3v2.xml new file mode 100644 index 000000000..77996e766 --- /dev/null +++ b/latest/cases/00933/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + S1 + 0.1 + + + + S2 + 0.95 + + + + + + + 1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00933/synopsis.txt b/latest/cases/00933/synopsis.txt new file mode 100644 index 000000000..c81f0687c --- /dev/null +++ b/latest/cases/00933/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A simple reaction during which the species values are reset + by an event which is subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called "C". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C$ |] + +The model contains one event defined as: + +[{width:30em,margin: 1em auto}| | Trigger | Delay | Assignments | + | Event1 | $S1 < 0.1 && S2 < 0.95$ | $1$ | $S1 = 1$ |] + +The persistent attribute of the Trigger is set to 'true'. Thus, once the event has fired, +even though the trigger value reverts to 'false' before the event is executed, execution must +take place. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/00934/l2v5/index.heta b/latest/cases/00934/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00934/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00934/l3v2/heta-code/output.heta b/latest/cases/00934/l3v2/heta-code/output.heta new file mode 100644 index 000000000..19331285b --- /dev/null +++ b/latest/cases/00934/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0 / C; +S1 [A]= 1; +S1 [B]= 2; +S1 [C1]= 3; +S2 @Species { compartment: C, } .= 1 / C; +S2 [A]= 0; +S2 [B]= 1; +S2 [C1]= 2; + +A @DSwitcher { trigger: t >= 0.99, }; +B @DSwitcher { trigger: t >= 0.99, }; +C1 @DSwitcher { trigger: t >= 0.99, }; + diff --git a/latest/cases/00934/l3v2/index.heta b/latest/cases/00934/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00934/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00934/l3v2/json/output.json b/latest/cases/00934/l3v2/json/output.json new file mode 100644 index 000000000..621fdeab7 --- /dev/null +++ b/latest/cases/00934/l3v2/json/output.json @@ -0,0 +1,50 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0 / C", + "A": "1", + "B": "2", + "C1": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "1 / C", + "A": "0", + "B": "1", + "C1": "2" + }, + "compartment": "C" + }, + { + "class": "DSwitcher", + "id": "A", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "B", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "C1", + "trigger": "t >= 0.99" + } +] \ No newline at end of file diff --git a/latest/cases/00934/model-sbml-l3v2.xml b/latest/cases/00934/model-sbml-l3v2.xml new file mode 100644 index 000000000..7d41e8348 --- /dev/null +++ b/latest/cases/00934/model-sbml-l3v2.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + time + 0.99 + + + + + + 10 + + + + + + 1 + + + + + 0 + + + + + + + + + + time + 0.99 + + + + + + + + 2 + S2 + + + + + + + 2 + + + + + 1 + + + + + + + + + + time + 0.99 + + + + + + + + 2 + S1 + + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/00934/output.heta b/latest/cases/00934/output.heta new file mode 100644 index 000000000..3d0fc4cec --- /dev/null +++ b/latest/cases/00934/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Species +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The Events will execute simultaneously and must be executed in order determined by +the Priority. Since the priority of all remaining events must be re-calculated +after each event is executed, the order in which the events execute changes after +Event1. + + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There are 3 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A | $time ≥ 0.99$ | $10$ | $S1 = 1$ | +| | | | $S2 = 0$ | +| B | $time ≥ 0.99$ | $2 * S2$ | $S1 = 2$ | +| | | | $S2 = 1$ | +| C1 | $time ≥ 0.99$ | $2 * S1$ | $S1 = 3$ | +| | | | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $0$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0 / C; +S1 [A]= 1; +S1 [B]= 2; +S1 [C1]= 3; +S2 @Species { compartment: C, } .= 1 / C; +S2 [A]= 0; +S2 [B]= 1; +S2 [C1]= 2; + +A @DSwitcher { trigger: t >= 0.99, }; +B @DSwitcher { trigger: t >= 0.99, }; +C1 @DSwitcher { trigger: t >= 0.99, }; + diff --git a/latest/cases/00934/synopsis.txt b/latest/cases/00934/synopsis.txt new file mode 100644 index 000000000..9c0520507 --- /dev/null +++ b/latest/cases/00934/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Single forward reaction with two species in one compartment and an event +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Species +testTags: Amount, EventIsPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The Events will execute simultaneously and must be executed in order determined by +the Priority. Since the priority of all remaining events must be re-calculated +after each event is executed, the order in which the events execute changes after +Event1. + + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There are 3 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A | $time ≥ 0.99$ | $10$ | $S1 = 1$ | +| | | | $S2 = 0$ | +| B | $time ≥ 0.99$ | $2 * S2$ | $S1 = 2$ | +| | | | $S2 = 1$ | +| C1 | $time ≥ 0.99$ | $2 * S1$ | $S1 = 3$ | +| | | | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $0$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00935/l2v5/index.heta b/latest/cases/00935/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00935/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00935/l3v2/heta-code/output.heta b/latest/cases/00935/l3v2/heta-code/output.heta new file mode 100644 index 000000000..26cce2e00 --- /dev/null +++ b/latest/cases/00935/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0 / C; +S1 [A]= 1; +S1 [B]= 2; +S1 [C1]= 3; +S2 @Species { compartment: C, } .= 1 / C; +S2 [A]= 0; +S2 [B]= 1; +S2 [C1]= 2; + +A @DSwitcher { trigger: t >= 0.99 and S1 < 0.5, }; +B @DSwitcher { trigger: t >= 0.99 and S1 < 0.5, }; +C1 @DSwitcher { trigger: t >= 0.99 and S1 < 0.5, }; + diff --git a/latest/cases/00935/l3v2/index.heta b/latest/cases/00935/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00935/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00935/l3v2/json/output.json b/latest/cases/00935/l3v2/json/output.json new file mode 100644 index 000000000..8527b7630 --- /dev/null +++ b/latest/cases/00935/l3v2/json/output.json @@ -0,0 +1,50 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0 / C", + "A": "1", + "B": "2", + "C1": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "1 / C", + "A": "0", + "B": "1", + "C1": "2" + }, + "compartment": "C" + }, + { + "class": "DSwitcher", + "id": "A", + "trigger": "t >= 0.99 and S1 < 0.5" + }, + { + "class": "DSwitcher", + "id": "B", + "trigger": "t >= 0.99 and S1 < 0.5" + }, + { + "class": "DSwitcher", + "id": "C1", + "trigger": "t >= 0.99 and S1 < 0.5" + } +] \ No newline at end of file diff --git a/latest/cases/00935/model-sbml-l3v2.xml b/latest/cases/00935/model-sbml-l3v2.xml new file mode 100644 index 000000000..5ebe48bfd --- /dev/null +++ b/latest/cases/00935/model-sbml-l3v2.xml @@ -0,0 +1,122 @@ + + + + + + + + + + + + + + + + + + + time + 0.99 + + + + S1 + 0.5 + + + + + + + 10 + + + + + + 1 + + + + + 0 + + + + + + + + + + + + time + 0.99 + + + + S1 + 0.5 + + + + + + + 8 + + + + + + 2 + + + + + 1 + + + + + + + + + + + + time + 0.99 + + + + S1 + 0.5 + + + + + + + 9 + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/00935/output.heta b/latest/cases/00935/output.heta new file mode 100644 index 000000000..12df510cf --- /dev/null +++ b/latest/cases/00935/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Single forward reaction with two species in one compartment and three events +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Species +testTags: Amount, EventIsNotPersistent, EventIsPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains three events that assign value to species S1 and S2 defined below. + +The events will execute simultaneously and must be executed in order determined by +the Priority. However, since Event2 is not persistent, the execution of Event1 +causes the Trigger of Event2 to return to 'false'. It must therefore be removed +from the list of pending events. + + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There are 3 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| A | $and(geq(time, 0.99), lt(S1, 0.5))$ | $10$ | true | $S1 = 1$ | +| | | | | $S2 = 0$ | +| B | $and(geq(time, 0.99), lt(S1, 0.5))$ | $8$ | false | $S1 = 2$ | +| | | | | $S2 = 1$ | +| C1 | $and(geq(time, 0.99), lt(S1, 0.5))$ | $9$ | true | $S1 = 3$ | +| | | | | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $0$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0 / C; +S1 [A]= 1; +S1 [B]= 2; +S1 [C1]= 3; +S2 @Species { compartment: C, } .= 1 / C; +S2 [A]= 0; +S2 [B]= 1; +S2 [C1]= 2; + +A @DSwitcher { trigger: t >= 0.99 and S1 < 0.5, }; +B @DSwitcher { trigger: t >= 0.99 and S1 < 0.5, }; +C1 @DSwitcher { trigger: t >= 0.99 and S1 < 0.5, }; + diff --git a/latest/cases/00935/synopsis.txt b/latest/cases/00935/synopsis.txt new file mode 100644 index 000000000..282cd59ae --- /dev/null +++ b/latest/cases/00935/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Single forward reaction with two species in one compartment and three events +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Species +testTags: Amount, EventIsNotPersistent, EventIsPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains three events that assign value to species S1 and S2 defined below. + +The events will execute simultaneously and must be executed in order determined by +the Priority. However, since Event2 is not persistent, the execution of Event1 +causes the Trigger of Event2 to return to 'false'. It must therefore be removed +from the list of pending events. + + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There are 3 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| A | $and(geq(time, 0.99), lt(S1, 0.5))$ | $10$ | true | $S1 = 1$ | +| | | | | $S2 = 0$ | +| B | $and(geq(time, 0.99), lt(S1, 0.5))$ | $8$ | false | $S1 = 2$ | +| | | | | $S2 = 1$ | +| C1 | $and(geq(time, 0.99), lt(S1, 0.5))$ | $9$ | true | $S1 = 3$ | +| | | | | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $0$ | variable | +| Initial amount of species S2 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00936/l2v5/build.log b/latest/cases/00936/l2v5/build.log new file mode 100644 index 000000000..5e3274560 --- /dev/null +++ b/latest/cases/00936/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00936/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00936/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00936/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00936/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00936/l2v5/index.heta b/latest/cases/00936/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00936/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00936/l3v2/build.log b/latest/cases/00936/l3v2/build.log new file mode 100644 index 000000000..85a3d4c18 --- /dev/null +++ b/latest/cases/00936/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00936/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00936/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00936/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00936/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00936/l3v2/index.heta b/latest/cases/00936/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00936/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00936/model-sbml-l2v5.xml b/latest/cases/00936/model-sbml-l2v5.xml new file mode 100644 index 000000000..aa4064262 --- /dev/null +++ b/latest/cases/00936/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + time + 10 + + + + + time + 2 + + + + 1 + + + + + + + + + + + + S1 + 0 + + + + + + 2 + + + + + + + + S2 + 1 + + + + + + + + diff --git a/latest/cases/00936/model-sbml-l3v2.xml b/latest/cases/00936/model-sbml-l3v2.xml new file mode 100644 index 000000000..ca74081ea --- /dev/null +++ b/latest/cases/00936/model-sbml-l3v2.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + + time + 10 + + + + + time + 2 + + + + 1 + + + + + + + + + + + + S1 + 0 + + + + + + 2 + + + + + + + + S2 + 1 + + + + + + + + diff --git a/latest/cases/00936/synopsis.txt b/latest/cases/00936/synopsis.txt new file mode 100644 index 000000000..dde65d819 --- /dev/null +++ b/latest/cases/00936/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Limited-time oscillation that triggers a delayed event three times before the first one executes. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventWithDelay, Species +testTags: Concentration, BoundaryCondition, EventIsPersistent, EventUsesAssignmentTimeValues, InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + The model contains one species (S1) that oscillates (from the 'sin' function) for two seconds, then stops. During that oscillation, the single event is triggered three times with a delay of two seconds each, increasing the value of the second species (S2) by one each time. As 'useValuesFromTriggerTime' is false, this means that first S1 oscillates, then S2 steps up three times. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (default_compartment) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| _E0 | $S1 < 0$ | Assignment time | $2$ | $S2 = S2 + 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1 | $piecewise(sin(time * 10), time < 2, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $piecewise(sin(time * 10), time < 2, 1)$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00937/l2v5/build.log b/latest/cases/00937/l2v5/build.log new file mode 100644 index 000000000..ea045f0c4 --- /dev/null +++ b/latest/cases/00937/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00937/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00937/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00937/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00937/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00937/l2v5/index.heta b/latest/cases/00937/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00937/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00937/l3v2/build.log b/latest/cases/00937/l3v2/build.log new file mode 100644 index 000000000..ca02fb533 --- /dev/null +++ b/latest/cases/00937/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00937/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00937/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00937/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00937/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00937/l3v2/index.heta b/latest/cases/00937/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00937/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00937/model-sbml-l2v5.xml b/latest/cases/00937/model-sbml-l2v5.xml new file mode 100644 index 000000000..62ea1cd12 --- /dev/null +++ b/latest/cases/00937/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + 10 + time + + + + + + + + + 2 + + delay + x + 0.2 + + + + + + + diff --git a/latest/cases/00937/model-sbml-l3v2.xml b/latest/cases/00937/model-sbml-l3v2.xml new file mode 100644 index 000000000..668e4c14f --- /dev/null +++ b/latest/cases/00937/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + 10 + time + + + + + + + + + 2 + + delay + x + 0.2 + + + + + + + diff --git a/latest/cases/00937/synopsis.txt b/latest/cases/00937/synopsis.txt new file mode 100644 index 000000000..3cb1377e9 --- /dev/null +++ b/latest/cases/00937/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Two oscillators; one that echoes the first by a delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Parameter +testTags: NonConstantParameter, InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one parameter (x) that oscillates (from the 'sin' function), and a second parameter (y) that echoes the first after a 0.2 second delay. + +The model contains: +* 2 parameters (x, y) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $sin(10 * time)$ | +| Assignment | y | $2 + delay(x, 0.2)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $sin(10 * time)$ | variable | +| Initial value of parameter y | $2 + delay(x, 0.2)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00938/l2v5/build.log b/latest/cases/00938/l2v5/build.log new file mode 100644 index 000000000..aa7df2229 --- /dev/null +++ b/latest/cases/00938/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00938/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00938/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00938/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00938/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00938/l2v5/index.heta b/latest/cases/00938/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00938/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00938/l3v2/build.log b/latest/cases/00938/l3v2/build.log new file mode 100644 index 000000000..edde33bda --- /dev/null +++ b/latest/cases/00938/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00938/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00938/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00938/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00938/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00938/l3v2/index.heta b/latest/cases/00938/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00938/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00938/model-sbml-l2v5.xml b/latest/cases/00938/model-sbml-l2v5.xml new file mode 100644 index 000000000..b1fae00fa --- /dev/null +++ b/latest/cases/00938/model-sbml-l2v5.xml @@ -0,0 +1,64 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + 1 + + + + + 10 + time + + + + + + + + + + + + 2 + + delay + x + 0.2 + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/00938/model-sbml-l3v2.xml b/latest/cases/00938/model-sbml-l3v2.xml new file mode 100644 index 000000000..ade4a9e31 --- /dev/null +++ b/latest/cases/00938/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + 1 + + + + + 10 + time + + + + + + + + + + + + 2 + + delay + x + 0.2 + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/00938/synopsis.txt b/latest/cases/00938/synopsis.txt new file mode 100644 index 000000000..54e0679d0 --- /dev/null +++ b/latest/cases/00938/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A species that changes behavior between its IntialAssignment andsubsequently produced by a reaction, being echoed by a parameter viewing it through a delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter, InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains a single species S1 whose InitialAssignment claims that it has been oscillating (the sine function) up until the start of the simulation, at which point a reaction begins to create it. A parameter (y) echoes this species with a 0.2 second delay, meaning that it starts by 'seeing' the oscillations before echoing the linear increase. + +The model contains: +* 1 species (x) +* 1 parameter (y) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> x | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | y | $2 + delay(x, 0.2)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species x | $1 * sin(10 * time)$ | variable | +| Initial value of parameter y | $2 + delay(x, 0.2)$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00939/l2v5/build.log b/latest/cases/00939/l2v5/build.log new file mode 100644 index 000000000..a0bb82688 --- /dev/null +++ b/latest/cases/00939/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00939/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00939/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00939/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00939/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00939/l2v5/index.heta b/latest/cases/00939/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00939/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00939/l3v2/build.log b/latest/cases/00939/l3v2/build.log new file mode 100644 index 000000000..a1dead47e --- /dev/null +++ b/latest/cases/00939/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00939/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00939/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00939/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00939/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00939/l3v2/index.heta b/latest/cases/00939/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00939/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00939/model-sbml-l2v5.xml b/latest/cases/00939/model-sbml-l2v5.xml new file mode 100644 index 000000000..e4762cca0 --- /dev/null +++ b/latest/cases/00939/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + delay + x + 0.2 + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/00939/model-sbml-l3v2.xml b/latest/cases/00939/model-sbml-l3v2.xml new file mode 100644 index 000000000..d7f6a92a2 --- /dev/null +++ b/latest/cases/00939/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + delay + x + 0.2 + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/00939/synopsis.txt b/latest/cases/00939/synopsis.txt new file mode 100644 index 000000000..a6d3da770 --- /dev/null +++ b/latest/cases/00939/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A species that with an initial concentration set, and subsequently produced by a reaction, being echoed by a parameter viewing it through a delay. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + The model contains a single species x with an initial concentration, which at the start of the simulation increases due to a reaction. A parameter (y) echoes this species with a 0.2 second delay, meaning that it starts by 'seeing' the initial constant value before echoing the linear increase. + + +The model contains: +* 1 species (x) +* 1 parameter (y) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> x | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | y | $2 + delay(x, 0.2)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species x | $3$ | variable | +| Initial value of parameter y | $2 + delay(x, 0.2)$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00940/l2v5/build.log b/latest/cases/00940/l2v5/build.log new file mode 100644 index 000000000..466ae7d25 --- /dev/null +++ b/latest/cases/00940/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00940/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00940/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00940/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00940/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00940/l2v5/index.heta b/latest/cases/00940/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00940/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00940/l3v2/build.log b/latest/cases/00940/l3v2/build.log new file mode 100644 index 000000000..3da3da94f --- /dev/null +++ b/latest/cases/00940/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00940/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00940/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00940/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00940/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00940/l3v2/index.heta b/latest/cases/00940/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00940/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00940/model-sbml-l2v5.xml b/latest/cases/00940/model-sbml-l2v5.xml new file mode 100644 index 000000000..a44295f69 --- /dev/null +++ b/latest/cases/00940/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + 10 + time + + + + + + + + + + + + 2 + + delay + x + 0.5 + + + + + + + diff --git a/latest/cases/00940/model-sbml-l3v2.xml b/latest/cases/00940/model-sbml-l3v2.xml new file mode 100644 index 000000000..1d992749e --- /dev/null +++ b/latest/cases/00940/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + 10 + time + + + + + + + + + + + + 2 + + delay + x + 0.5 + + + + + + + diff --git a/latest/cases/00940/synopsis.txt b/latest/cases/00940/synopsis.txt new file mode 100644 index 000000000..c6949f194 --- /dev/null +++ b/latest/cases/00940/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A variable species that varies in its IntialAssignment, but is constant thereafte, being echoed by a parameter viewing it through a delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, InitialAssignment, Parameter, Species +testTags: Amount, NonConstantParameter, InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains a single species x whose InitialAssignment claims that it has been oscillating (the sine function) up until the start of the simulation, at which point it stops changing. A parameter (y) echoes this species with a 0.5 second delay, meaning that it starts by 'seeing' the oscillations before flattening out. + +The model contains: +* 1 species (x) +* 1 parameter (y) +* 1 compartment (default_compartment) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | y | $2 + delay(x, 0.5)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species x | $1 * sin(10 * time)$ | variable | +| Initial value of parameter y | $2 + delay(x, 0.5)$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00941/l2v5/build.log b/latest/cases/00941/l2v5/build.log new file mode 100644 index 000000000..2ab71053b --- /dev/null +++ b/latest/cases/00941/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00941/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00941/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00941/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00941/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00941/l2v5/index.heta b/latest/cases/00941/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00941/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00941/l3v2/build.log b/latest/cases/00941/l3v2/build.log new file mode 100644 index 000000000..9f013cbce --- /dev/null +++ b/latest/cases/00941/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00941/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00941/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00941/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00941/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00941/l3v2/index.heta b/latest/cases/00941/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00941/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00941/model-sbml-l2v5.xml b/latest/cases/00941/model-sbml-l2v5.xml new file mode 100644 index 000000000..72ff9f83f --- /dev/null +++ b/latest/cases/00941/model-sbml-l2v5.xml @@ -0,0 +1,43 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + 10 + time + + + + + + + + + + + 2 + + delay + x + 0.5 + + + + + + + diff --git a/latest/cases/00941/model-sbml-l3v2.xml b/latest/cases/00941/model-sbml-l3v2.xml new file mode 100644 index 000000000..1031a2430 --- /dev/null +++ b/latest/cases/00941/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + 10 + time + + + + + + + + + + + 2 + + delay + x + 0.5 + + + + + + + diff --git a/latest/cases/00941/synopsis.txt b/latest/cases/00941/synopsis.txt new file mode 100644 index 000000000..7ad336bd2 --- /dev/null +++ b/latest/cases/00941/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A parameter that varies in its IntialAssignment, but is constant thereafter, being echoed by a second parameter viewing it through a delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, InitialAssignment, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + The model contains a parameter x whose InitialAssignment claims that it has been oscillating (the sine function) up until the start of the simulation, at which point it stops changing. A second parameter (y) echoes this species with a 0.5 second delay, meaning that it starts by 'seeing' the oscillations before flattening out. + +The model contains: +* 2 parameters (y, x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | y | $2 + delay(x, 0.5)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $sin(10 * time)$ | constant | +| Initial value of parameter y | $2 + delay(x, 0.5)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00942/l2v5/build.log b/latest/cases/00942/l2v5/build.log new file mode 100644 index 000000000..5c021224c --- /dev/null +++ b/latest/cases/00942/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00942/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00942/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00942/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00942/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00942/l2v5/index.heta b/latest/cases/00942/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00942/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00942/l3v2/build.log b/latest/cases/00942/l3v2/build.log new file mode 100644 index 000000000..054cd38a6 --- /dev/null +++ b/latest/cases/00942/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00942/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00942/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00942/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00942/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00942/l3v2/index.heta b/latest/cases/00942/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00942/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00942/model-sbml-l2v5.xml b/latest/cases/00942/model-sbml-l2v5.xml new file mode 100644 index 000000000..b2de60b58 --- /dev/null +++ b/latest/cases/00942/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + 10 + time + + + + + + + + + + + + 2 + + delay + x + 0.5 + + + + + + + diff --git a/latest/cases/00942/model-sbml-l3v2.xml b/latest/cases/00942/model-sbml-l3v2.xml new file mode 100644 index 000000000..bf031fbfd --- /dev/null +++ b/latest/cases/00942/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + 10 + time + + + + + + + + + + + + 2 + + delay + x + 0.5 + + + + + + + diff --git a/latest/cases/00942/synopsis.txt b/latest/cases/00942/synopsis.txt new file mode 100644 index 000000000..18fc8b1eb --- /dev/null +++ b/latest/cases/00942/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A constant species that nevertheless varies in its IntialAssignment, but is constant thereafter, being echoed by a parameter viewing it through a delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, InitialAssignment, Parameter, Species +testTags: Amount, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +This model has a single constant species x whose InitialAssignment claims that it has been oscillating (the sine function) up until the start of the simulation, at which point it stops changing. A parameter (y) echoes this species with a 0.5 second delay, meaning that it starts by 'seeing' the oscillations before flattening out. + +The model contains: +* 1 species (x) +* 1 parameter (y) +* 1 compartment (default_compartment) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | y | $2 + delay(x, 0.5)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species x | $1 * sin(10 * time)$ | constant | +| Initial value of parameter y | $2 + delay(x, 0.5)$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00943/l2v5/build.log b/latest/cases/00943/l2v5/build.log new file mode 100644 index 000000000..67cdd0871 --- /dev/null +++ b/latest/cases/00943/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00943/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00943/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00943/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00943/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00943/l2v5/index.heta b/latest/cases/00943/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00943/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00943/l3v2/build.log b/latest/cases/00943/l3v2/build.log new file mode 100644 index 000000000..8c7df4986 --- /dev/null +++ b/latest/cases/00943/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00943/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00943/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00943/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00943/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00943/l3v2/index.heta b/latest/cases/00943/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00943/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00943/model-sbml-l2v5.xml b/latest/cases/00943/model-sbml-l2v5.xml new file mode 100644 index 000000000..7e3d47c0e --- /dev/null +++ b/latest/cases/00943/model-sbml-l2v5.xml @@ -0,0 +1,55 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + 10 + time + + + + + + + + + + + 2 + + delay + x + 0.5 + + + + + + + diff --git a/latest/cases/00943/model-sbml-l3v2.xml b/latest/cases/00943/model-sbml-l3v2.xml new file mode 100644 index 000000000..38cd0c2f4 --- /dev/null +++ b/latest/cases/00943/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + +

Originally created by libAntimony 1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + 10 + time + + + + + + + + + + + 2 + + delay + x + 0.5 + + + + + + + diff --git a/latest/cases/00943/synopsis.txt b/latest/cases/00943/synopsis.txt new file mode 100644 index 000000000..81689f3c5 --- /dev/null +++ b/latest/cases/00943/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A constant parameter that nonetheless varies in its IntialAssignment, but is constant thereafter, being echoed by a second parameter viewing it through a delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, InitialAssignment, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + The model contains a constant parameter x whose InitialAssignment claims that it has been oscillating (the sine function) up until the start of the simulation, at which point it stops changing. A second parameter (y) echoes this species with a 0.5 second delay, meaning that it starts by 'seeing' the oscillations before flattening out. + +The model contains: +* 2 parameters (y, x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | y | $2 + delay(x, 0.5)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $sin(10 * time)$ | constant | +| Initial value of parameter y | $2 + delay(x, 0.5)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00944/l2v5/heta-code/output.heta b/latest/cases/00944/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d3ea2fa61 --- /dev/null +++ b/latest/cases/00944/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +k1 @Record { } .= 1; +k1 [event1]= 10; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00944/l2v5/index.heta b/latest/cases/00944/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00944/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00944/l2v5/json/output.json b/latest/cases/00944/l2v5/json/output.json new file mode 100644 index 000000000..9424910d9 --- /dev/null +++ b/latest/cases/00944/l2v5/json/output.json @@ -0,0 +1,73 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00944/l3v2/heta-code/output.heta b/latest/cases/00944/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e5c5bcd9d --- /dev/null +++ b/latest/cases/00944/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +k1 @Record { } .= 1; +k1 [event1]= 10; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00944/l3v2/index.heta b/latest/cases/00944/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00944/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00944/l3v2/json/output.json b/latest/cases/00944/l3v2/json/output.json new file mode 100644 index 000000000..c6a0d0ce1 --- /dev/null +++ b/latest/cases/00944/l3v2/json/output.json @@ -0,0 +1,48 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + } +] \ No newline at end of file diff --git a/latest/cases/00944/model-sbml-l2v5.xml b/latest/cases/00944/model-sbml-l2v5.xml new file mode 100644 index 000000000..aea55f510 --- /dev/null +++ b/latest/cases/00944/model-sbml-l2v5.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00944/model-sbml-l3v2.xml b/latest/cases/00944/model-sbml-l3v2.xml new file mode 100644 index 000000000..f1e64d810 --- /dev/null +++ b/latest/cases/00944/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00944/output.heta b/latest/cases/00944/output.heta new file mode 100644 index 000000000..19d5647e1 --- /dev/null +++ b/latest/cases/00944/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +This model tests when an event changes a parameter involved in a kinetic law. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $k1 = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +k1 @Record { } .= 1; +k1 [event1]= 10; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00944/synopsis.txt b/latest/cases/00944/synopsis.txt new file mode 100644 index 000000000..d88b07519 --- /dev/null +++ b/latest/cases/00944/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +This model tests when an event changes a parameter involved in a kinetic law. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $k1 = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00945/l2v5/heta-code/output.heta b/latest/cases/00945/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7d457f494 --- /dev/null +++ b/latest/cases/00945/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { } .= 1; +C [event1]= 10; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +k1 @Record { } .= 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00945/l2v5/index.heta b/latest/cases/00945/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00945/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00945/l2v5/json/output.json b/latest/cases/00945/l2v5/json/output.json new file mode 100644 index 000000000..302f8c2e9 --- /dev/null +++ b/latest/cases/00945/l2v5/json/output.json @@ -0,0 +1,72 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00945/l3v2/heta-code/output.heta b/latest/cases/00945/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8a4a45de7 --- /dev/null +++ b/latest/cases/00945/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { } .= 1; +C [event1]= 10; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +k1 @Const { } = 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00945/l3v2/index.heta b/latest/cases/00945/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00945/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00945/l3v2/json/output.json b/latest/cases/00945/l3v2/json/output.json new file mode 100644 index 000000000..f2fdc455a --- /dev/null +++ b/latest/cases/00945/l3v2/json/output.json @@ -0,0 +1,45 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "num": 1 + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + } +] \ No newline at end of file diff --git a/latest/cases/00945/model-sbml-l2v5.xml b/latest/cases/00945/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef6b46735 --- /dev/null +++ b/latest/cases/00945/model-sbml-l2v5.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00945/model-sbml-l3v2.xml b/latest/cases/00945/model-sbml-l3v2.xml new file mode 100644 index 000000000..92ba10aab --- /dev/null +++ b/latest/cases/00945/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00945/output.heta b/latest/cases/00945/output.heta new file mode 100644 index 000000000..9db84a24e --- /dev/null +++ b/latest/cases/00945/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic one reaction with one species in one compartment and one event that changes the size of the compartment. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +This model tests that a reaction behaves properly when a compartment size is changed by an event. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $C = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { } .= 1; +C [event1]= 10; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +k1 @Const { } = 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00945/synopsis.txt b/latest/cases/00945/synopsis.txt new file mode 100644 index 000000000..014afb66f --- /dev/null +++ b/latest/cases/00945/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic one reaction with one species in one compartment and one event that changes the size of the compartment. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +This model tests that a reaction behaves properly when a compartment size is changed by an event. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $C = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00946/l2v5/heta-code/output.heta b/latest/cases/00946/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7ef35e6a7 --- /dev/null +++ b/latest/cases/00946/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { }; +C := fakeC; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +fakeC @Record { } .= 1; +fakeC [event1]= 10; +k1 @Record { } .= 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00946/l2v5/index.heta b/latest/cases/00946/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00946/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00946/l2v5/json/output.json b/latest/cases/00946/l2v5/json/output.json new file mode 100644 index 000000000..c7d6e27fa --- /dev/null +++ b/latest/cases/00946/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "ode_": "fakeC" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "fakeC", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00946/l3v2/heta-code/output.heta b/latest/cases/00946/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f46d1cd2c --- /dev/null +++ b/latest/cases/00946/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C @Compartment { }; +C := fakeC; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +fakeC @Record { } .= 1; +fakeC [event1]= 10; + +k1 @Const { } = 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00946/l3v2/index.heta b/latest/cases/00946/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00946/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00946/l3v2/json/output.json b/latest/cases/00946/l3v2/json/output.json new file mode 100644 index 000000000..37be734f2 --- /dev/null +++ b/latest/cases/00946/l3v2/json/output.json @@ -0,0 +1,52 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "ode_": "fakeC" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "fakeC", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "Const", + "id": "k1", + "num": 1 + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + } +] \ No newline at end of file diff --git a/latest/cases/00946/model-sbml-l2v5.xml b/latest/cases/00946/model-sbml-l2v5.xml new file mode 100644 index 000000000..1ae830212 --- /dev/null +++ b/latest/cases/00946/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + fakeC + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00946/model-sbml-l3v2.xml b/latest/cases/00946/model-sbml-l3v2.xml new file mode 100644 index 000000000..239304979 --- /dev/null +++ b/latest/cases/00946/model-sbml-l3v2.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + fakeC + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00946/output.heta b/latest/cases/00946/output.heta new file mode 100644 index 000000000..a62188080 --- /dev/null +++ b/latest/cases/00946/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter. +componentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There is one species called S1 and two parameters, k1 and fakeC. It is identical in design and expected output to model 00945, except that instead of the event assigning to a compartment directly, it assigns to a temporary variable 'fakeC' which is then assigned to compartment C through an assignment rule. + +The model contains one reaction defined as: + + +The model contains: +* 1 species (S1) +* 2 parameters (fakeC, k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +The model contains one event that assigns a value to the temporary parameter fakeC: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $fakeC = 10$ |] + + +And the model contains one assignment rule that assigns the value of fakeC to compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | C | $fakeC$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter fakeC | $1$ | variable | +| Initial volume of compartment 'C' | $fakeC$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { }; +C := fakeC; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +fakeC @Record { } .= 1; +fakeC [event1]= 10; + +k1 @Const { } = 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00946/synopsis.txt b/latest/cases/00946/synopsis.txt new file mode 100644 index 000000000..c52ededae --- /dev/null +++ b/latest/cases/00946/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter. +componentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There is one species called S1 and two parameters, k1 and fakeC. It is identical in design and expected output to model 00945, except that instead of the event assigning to a compartment directly, it assigns to a temporary variable 'fakeC' which is then assigned to compartment C through an assignment rule. + +The model contains one reaction defined as: + + +The model contains: +* 1 species (S1) +* 2 parameters (fakeC, k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +The model contains one event that assigns a value to the temporary parameter fakeC: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $fakeC = 10$ |] + + +And the model contains one assignment rule that assigns the value of fakeC to compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | C | $fakeC$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter fakeC | $1$ | variable | +| Initial volume of compartment 'C' | $fakeC$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00947/l2v5/heta-code/output.heta b/latest/cases/00947/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7d457f494 --- /dev/null +++ b/latest/cases/00947/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { } .= 1; +C [event1]= 10; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +k1 @Record { } .= 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00947/l2v5/index.heta b/latest/cases/00947/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00947/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00947/l2v5/json/output.json b/latest/cases/00947/l2v5/json/output.json new file mode 100644 index 000000000..302f8c2e9 --- /dev/null +++ b/latest/cases/00947/l2v5/json/output.json @@ -0,0 +1,72 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00947/l3v2/heta-code/output.heta b/latest/cases/00947/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8a4a45de7 --- /dev/null +++ b/latest/cases/00947/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { } .= 1; +C [event1]= 10; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +k1 @Const { } = 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00947/l3v2/index.heta b/latest/cases/00947/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00947/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00947/l3v2/json/output.json b/latest/cases/00947/l3v2/json/output.json new file mode 100644 index 000000000..f2fdc455a --- /dev/null +++ b/latest/cases/00947/l3v2/json/output.json @@ -0,0 +1,45 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "num": 1 + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + } +] \ No newline at end of file diff --git a/latest/cases/00947/model-sbml-l2v5.xml b/latest/cases/00947/model-sbml-l2v5.xml new file mode 100644 index 000000000..63c77e370 --- /dev/null +++ b/latest/cases/00947/model-sbml-l2v5.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00947/model-sbml-l3v2.xml b/latest/cases/00947/model-sbml-l3v2.xml new file mode 100644 index 000000000..a6d3e258c --- /dev/null +++ b/latest/cases/00947/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00947/output.heta b/latest/cases/00947/output.heta new file mode 100644 index 000000000..5b1123791 --- /dev/null +++ b/latest/cases/00947/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Concentration, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Test of an event changing the size of a compartment. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +The model contains one event that assigns a value to the compartment C: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $C = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { } .= 1; +C [event1]= 10; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +k1 @Const { } = 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00947/synopsis.txt b/latest/cases/00947/synopsis.txt new file mode 100644 index 000000000..742e280de --- /dev/null +++ b/latest/cases/00947/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Concentration, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Test of an event changing the size of a compartment. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +The model contains one event that assigns a value to the compartment C: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $C = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00948/l2v5/heta-code/output.heta b/latest/cases/00948/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7ef35e6a7 --- /dev/null +++ b/latest/cases/00948/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { }; +C := fakeC; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +fakeC @Record { } .= 1; +fakeC [event1]= 10; +k1 @Record { } .= 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00948/l2v5/index.heta b/latest/cases/00948/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00948/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00948/l2v5/json/output.json b/latest/cases/00948/l2v5/json/output.json new file mode 100644 index 000000000..c7d6e27fa --- /dev/null +++ b/latest/cases/00948/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "ode_": "fakeC" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "fakeC", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00948/l3v2/heta-code/output.heta b/latest/cases/00948/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f46d1cd2c --- /dev/null +++ b/latest/cases/00948/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C @Compartment { }; +C := fakeC; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +fakeC @Record { } .= 1; +fakeC [event1]= 10; + +k1 @Const { } = 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00948/l3v2/index.heta b/latest/cases/00948/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00948/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00948/l3v2/json/output.json b/latest/cases/00948/l3v2/json/output.json new file mode 100644 index 000000000..37be734f2 --- /dev/null +++ b/latest/cases/00948/l3v2/json/output.json @@ -0,0 +1,52 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "ode_": "fakeC" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "assignments": { + "ode_": "(C * k1) / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "fakeC", + "assignments": { + "start_": "1", + "event1": "10" + } + }, + { + "class": "Const", + "id": "k1", + "num": 1 + }, + { + "class": "DSwitcher", + "id": "event1", + "trigger": "S1 > 2.1" + } +] \ No newline at end of file diff --git a/latest/cases/00948/model-sbml-l2v5.xml b/latest/cases/00948/model-sbml-l2v5.xml new file mode 100644 index 000000000..490c2cc26 --- /dev/null +++ b/latest/cases/00948/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + fakeC + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00948/model-sbml-l3v2.xml b/latest/cases/00948/model-sbml-l3v2.xml new file mode 100644 index 000000000..c5afed9a9 --- /dev/null +++ b/latest/cases/00948/model-sbml-l3v2.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + fakeC + + + + + + + + + + + + + + + C + k1 + + S1 + + + + + + + + + + + + S1 + 2.1 + + + + + + + 10 + + + + + + + diff --git a/latest/cases/00948/output.heta b/latest/cases/00948/output.heta new file mode 100644 index 000000000..de8b07bf4 --- /dev/null +++ b/latest/cases/00948/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter. +componentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Concentration, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There is one species called S1 and two parameters, k1 and fakeC. It is identical in design and expected output to model 00945, except that instead of the event assigning to a compartment directly, it assigns to a temporary variable 'fakeC' which is then assigned to compartment C through an assignment rule. + +The model contains: +* 1 species (S1) +* 2 parameters (fakeC, k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +The model contains one event that assigns a value to the temporary parameter fakeC: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $fakeC = 10$ |] + + +And the model contains one assignment rule that assigns the value of fakeC to compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | C | $fakeC$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter fakeC | $1$ | variable | +| Initial volume of compartment 'C' | $fakeC$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { }; +C := fakeC; + +S1 @Species { compartment: C, } .= 1 / C; + +reaction1 @Reaction { actors: = S1, reversible: false, }; +reaction1 := (C * k1) / S1; + +fakeC @Record { } .= 1; +fakeC [event1]= 10; + +k1 @Const { } = 1; + +event1 @DSwitcher { trigger: S1 > 2.1, }; + diff --git a/latest/cases/00948/synopsis.txt b/latest/cases/00948/synopsis.txt new file mode 100644 index 000000000..ad99e46bb --- /dev/null +++ b/latest/cases/00948/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter. +componentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Concentration, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The model contains one compartment called C. There is one species called S1 and two parameters, k1 and fakeC. It is identical in design and expected output to model 00945, except that instead of the event assigning to a compartment directly, it assigns to a temporary variable 'fakeC' which is then assigned to compartment C through an assignment rule. + +The model contains: +* 1 species (S1) +* 2 parameters (fakeC, k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $C * k1 / S1$ |] + + +The model contains one event that assigns a value to the temporary parameter fakeC: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| event1 | $S1 > 2.1$ | $fakeC = 10$ |] + + +And the model contains one assignment rule that assigns the value of fakeC to compartment C: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | C | $fakeC$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter fakeC | $1$ | variable | +| Initial volume of compartment 'C' | $fakeC$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00949/l2v5/heta-code/output.heta b/latest/cases/00949/l2v5/heta-code/output.heta new file mode 100644 index 000000000..829a50658 --- /dev/null +++ b/latest/cases/00949/l2v5/heta-code/output.heta @@ -0,0 +1,11 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +P @Record { } .= 3.7; + diff --git a/latest/cases/00949/l2v5/index.heta b/latest/cases/00949/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00949/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00949/l2v5/json/output.json b/latest/cases/00949/l2v5/json/output.json new file mode 100644 index 000000000..7948b66cb --- /dev/null +++ b/latest/cases/00949/l2v5/json/output.json @@ -0,0 +1,37 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P", + "assignments": { + "start_": "3.7" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00949/l3v2/heta-code/output.heta b/latest/cases/00949/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2bbd0606c --- /dev/null +++ b/latest/cases/00949/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +P @Const { } = 3.7; + diff --git a/latest/cases/00949/l3v2/index.heta b/latest/cases/00949/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00949/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00949/l3v2/json/output.json b/latest/cases/00949/l3v2/json/output.json new file mode 100644 index 000000000..dc70975d6 --- /dev/null +++ b/latest/cases/00949/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "P", + "num": 3.7 + } +] \ No newline at end of file diff --git a/latest/cases/00949/model-sbml-l2v5.xml b/latest/cases/00949/model-sbml-l2v5.xml new file mode 100644 index 000000000..a88e38c9e --- /dev/null +++ b/latest/cases/00949/model-sbml-l2v5.xml @@ -0,0 +1,13 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + diff --git a/latest/cases/00949/model-sbml-l3v2.xml b/latest/cases/00949/model-sbml-l3v2.xml new file mode 100644 index 000000000..a0b061281 --- /dev/null +++ b/latest/cases/00949/model-sbml-l3v2.xml @@ -0,0 +1,13 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + diff --git a/latest/cases/00949/output.heta b/latest/cases/00949/output.heta new file mode 100644 index 000000000..cb49ebd6f --- /dev/null +++ b/latest/cases/00949/output.heta @@ -0,0 +1,31 @@ +/* +category: Test +synopsis: One constant parameter. +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one parameter P. It doesn't change. + +There are no rules, reactions or events. + +The model contains: +* 1 parameter (P) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P | $3.7$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P @Const { } = 3.7; + diff --git a/latest/cases/00949/synopsis.txt b/latest/cases/00949/synopsis.txt new file mode 100644 index 000000000..96e04f75e --- /dev/null +++ b/latest/cases/00949/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: One constant parameter. +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model contains one parameter P. It doesn't change. + +There are no rules, reactions or events. + +The model contains: +* 1 parameter (P) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P | $3.7$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00950/l2v5/heta-code/output.heta b/latest/cases/00950/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2d55a8536 --- /dev/null +++ b/latest/cases/00950/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +P @Record { } .= Infinity; +Q @Record { } .= (-Infinity); +R @Record { } .= NaN; + diff --git a/latest/cases/00950/l2v5/index.heta b/latest/cases/00950/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00950/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00950/l2v5/json/output.json b/latest/cases/00950/l2v5/json/output.json new file mode 100644 index 000000000..93499f20a --- /dev/null +++ b/latest/cases/00950/l2v5/json/output.json @@ -0,0 +1,51 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P", + "assignments": { + "start_": "Infinity" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "(-Infinity)" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "NaN" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00950/l3v2/heta-code/output.heta b/latest/cases/00950/l3v2/heta-code/output.heta new file mode 100644 index 000000000..daaaeab49 --- /dev/null +++ b/latest/cases/00950/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +P @Const { } = 0; +Q @Const { } = 0; +R @Const { } = 0; + diff --git a/latest/cases/00950/l3v2/index.heta b/latest/cases/00950/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00950/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00950/l3v2/json/output.json b/latest/cases/00950/l3v2/json/output.json new file mode 100644 index 000000000..b912c737e --- /dev/null +++ b/latest/cases/00950/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "P", + "num": 0 + }, + { + "class": "Const", + "id": "Q", + "num": 0 + }, + { + "class": "Const", + "id": "R", + "num": 0 + } +] \ No newline at end of file diff --git a/latest/cases/00950/model-sbml-l2v5.xml b/latest/cases/00950/model-sbml-l2v5.xml new file mode 100644 index 000000000..14b7e567e --- /dev/null +++ b/latest/cases/00950/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/00950/model-sbml-l3v2.xml b/latest/cases/00950/model-sbml-l3v2.xml new file mode 100644 index 000000000..437b790f0 --- /dev/null +++ b/latest/cases/00950/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/00950/output.heta b/latest/cases/00950/output.heta new file mode 100644 index 000000000..2a0e854e0 --- /dev/null +++ b/latest/cases/00950/output.heta @@ -0,0 +1,33 @@ +/* +category: Test +synopsis: Three constant parameters, with initialassignments to inf, -inf, and nan. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model tests the 'INF' and 'NaN' constructs with initial assignments. + +The model contains: +* 3 parameters (P, Q, R) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P | $INF$ | constant | +| Initial value of parameter Q | $-INF$ | constant | +| Initial value of parameter R | $NaN$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P @Const { } = 0; +Q @Const { } = 0; +R @Const { } = 0; + diff --git a/latest/cases/00950/synopsis.txt b/latest/cases/00950/synopsis.txt new file mode 100644 index 000000000..5009f3f57 --- /dev/null +++ b/latest/cases/00950/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: Three constant parameters, with initialassignments to inf, -inf, and nan. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model tests the 'INF' and 'NaN' constructs with initial assignments. + +The model contains: +* 3 parameters (P, Q, R) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P | $INF$ | constant | +| Initial value of parameter Q | $-INF$ | constant | +| Initial value of parameter R | $NaN$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00951/l2v5/heta-code/output.heta b/latest/cases/00951/l2v5/heta-code/output.heta new file mode 100644 index 000000000..16a610a9c --- /dev/null +++ b/latest/cases/00951/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +P @Record { } .= Infinity; +Q @Record { } .= -Infinity; +R @Record { } .= NaN; + diff --git a/latest/cases/00951/l2v5/index.heta b/latest/cases/00951/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00951/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00951/l2v5/json/output.json b/latest/cases/00951/l2v5/json/output.json new file mode 100644 index 000000000..78dd0d928 --- /dev/null +++ b/latest/cases/00951/l2v5/json/output.json @@ -0,0 +1,51 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P", + "assignments": { + "start_": "Infinity" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "-Infinity" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "NaN" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00951/l3v2/heta-code/output.heta b/latest/cases/00951/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0a70d6c8c --- /dev/null +++ b/latest/cases/00951/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { units: second, }; + +P @Const { } = Infinity; +Q @Const { } = -Infinity; +R @Const { } = NaN; + diff --git a/latest/cases/00951/l3v2/index.heta b/latest/cases/00951/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00951/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00951/l3v2/json/output.json b/latest/cases/00951/l3v2/json/output.json new file mode 100644 index 000000000..8be7156d6 --- /dev/null +++ b/latest/cases/00951/l3v2/json/output.json @@ -0,0 +1,21 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Const", + "id": "P", + "num": null + }, + { + "class": "Const", + "id": "Q", + "num": null + }, + { + "class": "Const", + "id": "R", + "num": null + } +] \ No newline at end of file diff --git a/latest/cases/00951/model-sbml-l2v5.xml b/latest/cases/00951/model-sbml-l2v5.xml new file mode 100644 index 000000000..fef04fd77 --- /dev/null +++ b/latest/cases/00951/model-sbml-l2v5.xml @@ -0,0 +1,27 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/00951/model-sbml-l3v2.xml b/latest/cases/00951/model-sbml-l3v2.xml new file mode 100644 index 000000000..a20997b0c --- /dev/null +++ b/latest/cases/00951/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/00951/output.heta b/latest/cases/00951/output.heta new file mode 100644 index 000000000..3b71b2b25 --- /dev/null +++ b/latest/cases/00951/output.heta @@ -0,0 +1,33 @@ +/* +category: Test +synopsis: Three constant parameters, with initial values of inf, -inf, and NaN. +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +This model tests the INF and NaN constructs. + +The model contains: +* 3 parameters (P, Q, R) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P | $INF$ | constant | +| Initial value of parameter Q | $-INF$ | constant | +| Initial value of parameter R | $NaN$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +P @Const { } = Infinity; +Q @Const { } = -Infinity; +R @Const { } = NaN; + diff --git a/latest/cases/00951/synopsis.txt b/latest/cases/00951/synopsis.txt new file mode 100644 index 000000000..1e740f1b2 --- /dev/null +++ b/latest/cases/00951/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: Three constant parameters, with initial values of inf, -inf, and NaN. +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +This model tests the INF and NaN constructs. + +The model contains: +* 3 parameters (P, Q, R) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P | $INF$ | constant | +| Initial value of parameter Q | $-INF$ | constant | +| Initial value of parameter R | $NaN$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00952/l2v5/index.heta b/latest/cases/00952/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00952/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00952/l3v2/heta-code/output.heta b/latest/cases/00952/l3v2/heta-code/output.heta new file mode 100644 index 000000000..67b281346 --- /dev/null +++ b/latest/cases/00952/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +error @Record { } .= 0; +error [error_check]= 1; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +error_check @DSwitcher { trigger: abs(Q - R) >= 4, }; + diff --git a/latest/cases/00952/l3v2/index.heta b/latest/cases/00952/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00952/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00952/l3v2/json/output.json b/latest/cases/00952/l3v2/json/output.json new file mode 100644 index 000000000..ed2a871f0 --- /dev/null +++ b/latest/cases/00952/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S", + "assignments": { + "start_": "0", + "ode_": "Q + R" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "0", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "0", + "Rinc": "R + 0.01" + } + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Qinc": "t", + "Rinc": "t" + } + }, + { + "class": "Record", + "id": "error", + "assignments": { + "start_": "0", + "error_check": "1" + } + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "error_check", + "trigger": "abs(Q - R) >= 4" + } +] \ No newline at end of file diff --git a/latest/cases/00952/model-sbml-l3v2.xml b/latest/cases/00952/model-sbml-l3v2.xml new file mode 100644 index 000000000..9d8f218a9 --- /dev/null +++ b/latest/cases/00952/model-sbml-l3v2.xml @@ -0,0 +1,122 @@ + + + + + + + + + + + + + + + + Q + R + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 1 + + + + + + time + + + + + + + Q + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 1 + + + + + + time + + + + + + + R + 0.01 + + + + + + + + + + + + + + + Q + R + + + 4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00952/output.heta b/latest/cases/00952/output.heta new file mode 100644 index 000000000..f46ea01a7 --- /dev/null +++ b/latest/cases/00952/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure one event doesn't severly out-compete the other. NOTE: STOCHASTIC TEST. This test is designed to fail only one time in a million, but it still may happen. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 4, it triggers. In our simulations, this happened less often than one time in a million, so if you see it happen in your simulator more often than once, there's a good chance something is wrong. + +The model contains: +* 5 parameters (S, Q, R, reset, error) + +There are 3 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ | +| error_check | $geq(abs(Q - R), 4)$ | (unset) | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +error @Record { } .= 0; +error [error_check]= 1; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +error_check @DSwitcher { trigger: abs(Q - R) >= 4, }; + diff --git a/latest/cases/00952/synopsis.txt b/latest/cases/00952/synopsis.txt new file mode 100644 index 000000000..29537d29b --- /dev/null +++ b/latest/cases/00952/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure one event doesn't severly out-compete the other. NOTE: STOCHASTIC TEST. This test is designed to fail only one time in a million, but it still may happen. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 4, it triggers. In our simulations, this happened less often than one time in a million, so if you see it happen in your simulator more often than once, there's a good chance something is wrong. + +The model contains: +* 5 parameters (S, Q, R, reset, error) + +There are 3 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ | +| error_check | $geq(abs(Q - R), 4)$ | (unset) | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00953/l2v5/index.heta b/latest/cases/00953/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00953/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00953/l3v2/heta-code/output.heta b/latest/cases/00953/l3v2/heta-code/output.heta new file mode 100644 index 000000000..21fbaf450 --- /dev/null +++ b/latest/cases/00953/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +S @Record { }; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +error @Record { } .= 0; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; + diff --git a/latest/cases/00953/l3v2/index.heta b/latest/cases/00953/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00953/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00953/l3v2/json/output.json b/latest/cases/00953/l3v2/json/output.json new file mode 100644 index 000000000..4f52f6f09 --- /dev/null +++ b/latest/cases/00953/l3v2/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "S", + "assignments": { + "ode_": "Q + R" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "0", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "0", + "Rinc": "R + 0.01" + } + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Qinc": "t", + "Rinc": "t" + } + }, + { + "class": "Record", + "id": "error", + "assignments": { + "start_": "0" + } + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "(t - reset) >= 0.01" + } +] \ No newline at end of file diff --git a/latest/cases/00953/model-sbml-l3v2.xml b/latest/cases/00953/model-sbml-l3v2.xml new file mode 100644 index 000000000..1c44f5cb5 --- /dev/null +++ b/latest/cases/00953/model-sbml-l3v2.xml @@ -0,0 +1,104 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + Q + R + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + + time + + + + + + + Q + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + + time + + + + + + + R + 0.01 + + + + + + + + diff --git a/latest/cases/00953/output.heta b/latest/cases/00953/output.heta new file mode 100644 index 000000000..a96687355 --- /dev/null +++ b/latest/cases/00953/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Competing events without priorities, jointly causing a parameter to monotonically increase. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter, EventIsNotPersistent, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events with the same trigger, no priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. This model is identical to 952, except that there are no priorities, so Qinc and Rinc do not have to be chosen between at random, but can be chosen in any ratio. + +The model contains: +* 5 parameters (S, Q, R, reset, error) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | false | $reset = time$ | +| | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | false | $reset = time$ | +| | | | $R = R + 0.01$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +S @Record { }; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +error @Record { } .= 0; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; + diff --git a/latest/cases/00953/synopsis.txt b/latest/cases/00953/synopsis.txt new file mode 100644 index 000000000..7e0c504af --- /dev/null +++ b/latest/cases/00953/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Competing events without priorities, jointly causing a parameter to monotonically increase. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter, EventIsNotPersistent, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events with the same trigger, no priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. This model is identical to 952, except that there are no priorities, so Qinc and Rinc do not have to be chosen between at random, but can be chosen in any ratio. + +The model contains: +* 5 parameters (S, Q, R, reset, error) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | false | $reset = time$ | +| | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | false | $reset = time$ | +| | | | $R = R + 0.01$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00954/l2v5/heta-code/output.heta b/latest/cases/00954/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6ecdfee7f --- /dev/null +++ b/latest/cases/00954/l2v5/heta-code/output.heta @@ -0,0 +1,89 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +P1 @Record { } .= 3.7; +P2 @Record { }; +P2 := abs((-1)); +P3 @Record { }; +P3 := abs(1); +P4 @Record { }; +P4 := acos((-1)); +P5 @Record { }; +P5 := acos(0.5); +P6 @Record { }; +P6 := asin(1); +P7 @Record { }; +P7 := asin((-0.5)); +P8 @Record { }; +P8 := atan(2.8); +P9 @Record { }; +P9 := atan((-7.09)); +P10 @Record { }; +P10 := ceil(0.5); +P11 @Record { }; +P11 := ceil(3.55); +P12 @Record { }; +P12 := ceil((-4.6)); +P13 @Record { }; +P13 := cos(9.1); +P14 @Record { }; +P14 := cos((-0.22)); +P15 @Record { }; +P15 := exp(0); +P16 @Record { }; +P16 := exp(1); +P17 @Record { }; +P17 := exp(0.77); +P18 @Record { }; +P18 := floor((-4.6)); +P19 @Record { }; +P19 := floor(9.1); +P20 @Record { }; +P20 := ln(0.2); +P21 @Record { }; +P21 := ln(1); +P22 @Record { }; +P22 := logbase(0.2, 10); +P23 @Record { }; +P23 := logbase(1, 10); +P24 @Record { }; +P24 := pow(1, 2); +P25 @Record { }; +P25 := pow(2, 2); +P26 @Record { }; +P26 := pow(1.4, 5.1); +P27 @Record { }; +P27 := pow(4, 2); +P28 @Record { }; +P28 := pow(3.1, 2); +P29 @Record { }; +P29 := pow(4, 1 / 2); +P30 @Record { }; +P30 := pow(7.4, 1 / 2); +P31 @Record { }; +P31 := sin(2.1); +P32 @Record { }; +P32 := sin(0); +P33 @Record { }; +P33 := sin((-5.9)); +P34 @Record { }; +P34 := tan(0); +P35 @Record { }; +P35 := tan(1.11); +P36 @Record { }; +P36 := tan((-6)); +P37 @Record { }; +P37 := 1 + 2; +P38 @Record { }; +P38 := 1 - 2; +P39 @Record { }; +P39 := 5 / 2; +P40 @Record { }; +P40 := 8 * 3; + diff --git a/latest/cases/00954/l2v5/index.heta b/latest/cases/00954/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00954/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00954/l2v5/json/output.json b/latest/cases/00954/l2v5/json/output.json new file mode 100644 index 000000000..e51e8d656 --- /dev/null +++ b/latest/cases/00954/l2v5/json/output.json @@ -0,0 +1,310 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "3.7" + } + }, + { + "class": "Record", + "id": "P2", + "assignments": { + "ode_": "abs((-1))" + } + }, + { + "class": "Record", + "id": "P3", + "assignments": { + "ode_": "abs(1)" + } + }, + { + "class": "Record", + "id": "P4", + "assignments": { + "ode_": "acos((-1))" + } + }, + { + "class": "Record", + "id": "P5", + "assignments": { + "ode_": "acos(0.5)" + } + }, + { + "class": "Record", + "id": "P6", + "assignments": { + "ode_": "asin(1)" + } + }, + { + "class": "Record", + "id": "P7", + "assignments": { + "ode_": "asin((-0.5))" + } + }, + { + "class": "Record", + "id": "P8", + "assignments": { + "ode_": "atan(2.8)" + } + }, + { + "class": "Record", + "id": "P9", + "assignments": { + "ode_": "atan((-7.09))" + } + }, + { + "class": "Record", + "id": "P10", + "assignments": { + "ode_": "ceil(0.5)" + } + }, + { + "class": "Record", + "id": "P11", + "assignments": { + "ode_": "ceil(3.55)" + } + }, + { + "class": "Record", + "id": "P12", + "assignments": { + "ode_": "ceil((-4.6))" + } + }, + { + "class": "Record", + "id": "P13", + "assignments": { + "ode_": "cos(9.1)" + } + }, + { + "class": "Record", + "id": "P14", + "assignments": { + "ode_": "cos((-0.22))" + } + }, + { + "class": "Record", + "id": "P15", + "assignments": { + "ode_": "exp(0)" + } + }, + { + "class": "Record", + "id": "P16", + "assignments": { + "ode_": "exp(1)" + } + }, + { + "class": "Record", + "id": "P17", + "assignments": { + "ode_": "exp(0.77)" + } + }, + { + "class": "Record", + "id": "P18", + "assignments": { + "ode_": "floor((-4.6))" + } + }, + { + "class": "Record", + "id": "P19", + "assignments": { + "ode_": "floor(9.1)" + } + }, + { + "class": "Record", + "id": "P20", + "assignments": { + "ode_": "ln(0.2)" + } + }, + { + "class": "Record", + "id": "P21", + "assignments": { + "ode_": "ln(1)" + } + }, + { + "class": "Record", + "id": "P22", + "assignments": { + "ode_": "logbase(0.2, 10)" + } + }, + { + "class": "Record", + "id": "P23", + "assignments": { + "ode_": "logbase(1, 10)" + } + }, + { + "class": "Record", + "id": "P24", + "assignments": { + "ode_": "pow(1, 2)" + } + }, + { + "class": "Record", + "id": "P25", + "assignments": { + "ode_": "pow(2, 2)" + } + }, + { + "class": "Record", + "id": "P26", + "assignments": { + "ode_": "pow(1.4, 5.1)" + } + }, + { + "class": "Record", + "id": "P27", + "assignments": { + "ode_": "pow(4, 2)" + } + }, + { + "class": "Record", + "id": "P28", + "assignments": { + "ode_": "pow(3.1, 2)" + } + }, + { + "class": "Record", + "id": "P29", + "assignments": { + "ode_": "pow(4, 1 / 2)" + } + }, + { + "class": "Record", + "id": "P30", + "assignments": { + "ode_": "pow(7.4, 1 / 2)" + } + }, + { + "class": "Record", + "id": "P31", + "assignments": { + "ode_": "sin(2.1)" + } + }, + { + "class": "Record", + "id": "P32", + "assignments": { + "ode_": "sin(0)" + } + }, + { + "class": "Record", + "id": "P33", + "assignments": { + "ode_": "sin((-5.9))" + } + }, + { + "class": "Record", + "id": "P34", + "assignments": { + "ode_": "tan(0)" + } + }, + { + "class": "Record", + "id": "P35", + "assignments": { + "ode_": "tan(1.11)" + } + }, + { + "class": "Record", + "id": "P36", + "assignments": { + "ode_": "tan((-6))" + } + }, + { + "class": "Record", + "id": "P37", + "assignments": { + "ode_": "1 + 2" + } + }, + { + "class": "Record", + "id": "P38", + "assignments": { + "ode_": "1 - 2" + } + }, + { + "class": "Record", + "id": "P39", + "assignments": { + "ode_": "5 / 2" + } + }, + { + "class": "Record", + "id": "P40", + "assignments": { + "ode_": "8 * 3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00954/l3v2/heta-code/output.heta b/latest/cases/00954/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f14481219 --- /dev/null +++ b/latest/cases/00954/l3v2/heta-code/output.heta @@ -0,0 +1,85 @@ + + +t @TimeScale { units: second, }; + +P2 @Record { }; +P2 := abs((-1)); +P3 @Record { }; +P3 := abs(1); +P4 @Record { }; +P4 := acos((-1)); +P5 @Record { }; +P5 := acos(0.5); +P6 @Record { }; +P6 := asin(1); +P7 @Record { }; +P7 := asin((-0.5)); +P8 @Record { }; +P8 := atan(2.8); +P9 @Record { }; +P9 := atan((-7.09)); +P10 @Record { }; +P10 := ceil(0.5); +P11 @Record { }; +P11 := ceil(3.55); +P12 @Record { }; +P12 := ceil((-4.6)); +P13 @Record { }; +P13 := cos(9.1); +P14 @Record { }; +P14 := cos((-0.22)); +P15 @Record { }; +P15 := exp(0); +P16 @Record { }; +P16 := exp(1); +P17 @Record { }; +P17 := exp(0.77); +P18 @Record { }; +P18 := floor((-4.6)); +P19 @Record { }; +P19 := floor(9.1); +P20 @Record { }; +P20 := ln(0.2); +P21 @Record { }; +P21 := ln(1); +P22 @Record { }; +P22 := logbase(0.2, 10); +P23 @Record { }; +P23 := logbase(1, 10); +P24 @Record { }; +P24 := pow(1, 2); +P25 @Record { }; +P25 := pow(2, 2); +P26 @Record { }; +P26 := pow(1.4, 5.1); +P27 @Record { }; +P27 := pow(4, 2); +P28 @Record { }; +P28 := pow(3.1, 2); +P29 @Record { }; +P29 := pow(4, 1 / 2); +P30 @Record { }; +P30 := pow(7.4, 1 / 2); +P31 @Record { }; +P31 := sin(2.1); +P32 @Record { }; +P32 := sin(0); +P33 @Record { }; +P33 := sin((-5.9)); +P34 @Record { }; +P34 := tan(0); +P35 @Record { }; +P35 := tan(1.11); +P36 @Record { }; +P36 := tan((-6)); +P37 @Record { }; +P37 := 1 + 2; +P38 @Record { }; +P38 := 1 - 2; +P39 @Record { }; +P39 := 5 / 2; +P40 @Record { }; +P40 := 8 * 3; + +P1 @Const { } = 3.7; + diff --git a/latest/cases/00954/l3v2/index.heta b/latest/cases/00954/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00954/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00954/l3v2/json/output.json b/latest/cases/00954/l3v2/json/output.json new file mode 100644 index 000000000..f9e561cdb --- /dev/null +++ b/latest/cases/00954/l3v2/json/output.json @@ -0,0 +1,284 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Const", + "id": "P1", + "num": 3.7 + }, + { + "class": "Record", + "id": "P2", + "assignments": { + "ode_": "abs((-1))" + } + }, + { + "class": "Record", + "id": "P3", + "assignments": { + "ode_": "abs(1)" + } + }, + { + "class": "Record", + "id": "P4", + "assignments": { + "ode_": "acos((-1))" + } + }, + { + "class": "Record", + "id": "P5", + "assignments": { + "ode_": "acos(0.5)" + } + }, + { + "class": "Record", + "id": "P6", + "assignments": { + "ode_": "asin(1)" + } + }, + { + "class": "Record", + "id": "P7", + "assignments": { + "ode_": "asin((-0.5))" + } + }, + { + "class": "Record", + "id": "P8", + "assignments": { + "ode_": "atan(2.8)" + } + }, + { + "class": "Record", + "id": "P9", + "assignments": { + "ode_": "atan((-7.09))" + } + }, + { + "class": "Record", + "id": "P10", + "assignments": { + "ode_": "ceil(0.5)" + } + }, + { + "class": "Record", + "id": "P11", + "assignments": { + "ode_": "ceil(3.55)" + } + }, + { + "class": "Record", + "id": "P12", + "assignments": { + "ode_": "ceil((-4.6))" + } + }, + { + "class": "Record", + "id": "P13", + "assignments": { + "ode_": "cos(9.1)" + } + }, + { + "class": "Record", + "id": "P14", + "assignments": { + "ode_": "cos((-0.22))" + } + }, + { + "class": "Record", + "id": "P15", + "assignments": { + "ode_": "exp(0)" + } + }, + { + "class": "Record", + "id": "P16", + "assignments": { + "ode_": "exp(1)" + } + }, + { + "class": "Record", + "id": "P17", + "assignments": { + "ode_": "exp(0.77)" + } + }, + { + "class": "Record", + "id": "P18", + "assignments": { + "ode_": "floor((-4.6))" + } + }, + { + "class": "Record", + "id": "P19", + "assignments": { + "ode_": "floor(9.1)" + } + }, + { + "class": "Record", + "id": "P20", + "assignments": { + "ode_": "ln(0.2)" + } + }, + { + "class": "Record", + "id": "P21", + "assignments": { + "ode_": "ln(1)" + } + }, + { + "class": "Record", + "id": "P22", + "assignments": { + "ode_": "logbase(0.2, 10)" + } + }, + { + "class": "Record", + "id": "P23", + "assignments": { + "ode_": "logbase(1, 10)" + } + }, + { + "class": "Record", + "id": "P24", + "assignments": { + "ode_": "pow(1, 2)" + } + }, + { + "class": "Record", + "id": "P25", + "assignments": { + "ode_": "pow(2, 2)" + } + }, + { + "class": "Record", + "id": "P26", + "assignments": { + "ode_": "pow(1.4, 5.1)" + } + }, + { + "class": "Record", + "id": "P27", + "assignments": { + "ode_": "pow(4, 2)" + } + }, + { + "class": "Record", + "id": "P28", + "assignments": { + "ode_": "pow(3.1, 2)" + } + }, + { + "class": "Record", + "id": "P29", + "assignments": { + "ode_": "pow(4, 1 / 2)" + } + }, + { + "class": "Record", + "id": "P30", + "assignments": { + "ode_": "pow(7.4, 1 / 2)" + } + }, + { + "class": "Record", + "id": "P31", + "assignments": { + "ode_": "sin(2.1)" + } + }, + { + "class": "Record", + "id": "P32", + "assignments": { + "ode_": "sin(0)" + } + }, + { + "class": "Record", + "id": "P33", + "assignments": { + "ode_": "sin((-5.9))" + } + }, + { + "class": "Record", + "id": "P34", + "assignments": { + "ode_": "tan(0)" + } + }, + { + "class": "Record", + "id": "P35", + "assignments": { + "ode_": "tan(1.11)" + } + }, + { + "class": "Record", + "id": "P36", + "assignments": { + "ode_": "tan((-6))" + } + }, + { + "class": "Record", + "id": "P37", + "assignments": { + "ode_": "1 + 2" + } + }, + { + "class": "Record", + "id": "P38", + "assignments": { + "ode_": "1 - 2" + } + }, + { + "class": "Record", + "id": "P39", + "assignments": { + "ode_": "5 / 2" + } + }, + { + "class": "Record", + "id": "P40", + "assignments": { + "ode_": "8 * 3" + } + } +] \ No newline at end of file diff --git a/latest/cases/00954/model-sbml-l2v5.xml b/latest/cases/00954/model-sbml-l2v5.xml new file mode 100644 index 000000000..caf659986 --- /dev/null +++ b/latest/cases/00954/model-sbml-l2v5.xml @@ -0,0 +1,399 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + + + 1 + + + + + + + + -1 + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + -0.5 + + + + + + + + 2.8 + + + + + + + + -7.09 + + + + + + + + 0.5 + + + + + + + + 3.55 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + -0.22 + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + 0.77 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + 10 + + 0.2 + + + + + + + + + 10 + + 1 + + + + + + + + 1 + 2 + + + + + + + + 2 + 2 + + + + + + + + 1.4 + 5.1 + + + + + + + + 4 + 2 + + + + + + + + 3.1 + 2 + + + + + + + + + 2 + + 4 + + + + + + + + + 2 + + 7.4 + + + + + + + + 2.1 + + + + + + + + 0 + + + + + + + + -5.9 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + 1 + 2 + + + + + + + + 1 + 2 + + + + + + + + 5 + 2 + + + + + + + + 8 + 3 + + + + + + diff --git a/latest/cases/00954/model-sbml-l3v2.xml b/latest/cases/00954/model-sbml-l3v2.xml new file mode 100644 index 000000000..a5de4645d --- /dev/null +++ b/latest/cases/00954/model-sbml-l3v2.xml @@ -0,0 +1,399 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + + + 1 + + + + + + + + -1 + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + -0.5 + + + + + + + + 2.8 + + + + + + + + -7.09 + + + + + + + + 0.5 + + + + + + + + 3.55 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + -0.22 + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + 0.77 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + 10 + + 0.2 + + + + + + + + + 10 + + 1 + + + + + + + + 1 + 2 + + + + + + + + 2 + 2 + + + + + + + + 1.4 + 5.1 + + + + + + + + 4 + 2 + + + + + + + + 3.1 + 2 + + + + + + + + + 2 + + 4 + + + + + + + + + 2 + + 7.4 + + + + + + + + 2.1 + + + + + + + + 0 + + + + + + + + -5.9 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + 1 + 2 + + + + + + + + 1 + 2 + + + + + + + + 5 + 2 + + + + + + + + 8 + 3 + + + + + + diff --git a/latest/cases/00954/output.heta b/latest/cases/00954/output.heta new file mode 100644 index 000000000..afda68f3a --- /dev/null +++ b/latest/cases/00954/output.heta @@ -0,0 +1,191 @@ +/* +category: Test +synopsis: Several parameters with assignment rules, testing various L1 built-in functions acting on constants. +componentTags: AssignmentRule, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model tests the various mathematical constructs present in L1. + +The model contains: +* 40 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40) + +There are 39 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P2 | $abs(-1)$ | +| Assignment | P3 | $abs(1)$ | +| Assignment | P4 | $acos(-1)$ | +| Assignment | P5 | $acos(0.5)$ | +| Assignment | P6 | $asin(1)$ | +| Assignment | P7 | $asin(-0.5)$ | +| Assignment | P8 | $atan(2.8)$ | +| Assignment | P9 | $atan(-7.09)$ | +| Assignment | P10 | $ceil(0.5)$ | +| Assignment | P11 | $ceil(3.55)$ | +| Assignment | P12 | $ceil(-4.6)$ | +| Assignment | P13 | $cos(9.1)$ | +| Assignment | P14 | $cos(-0.22)$ | +| Assignment | P15 | $exp(0)$ | +| Assignment | P16 | $exp(1)$ | +| Assignment | P17 | $exp(0.77)$ | +| Assignment | P18 | $floor(-4.6)$ | +| Assignment | P19 | $floor(9.1)$ | +| Assignment | P20 | $log(0.2)$ | +| Assignment | P21 | $log(1)$ | +| Assignment | P22 | $log10(0.2)$ | +| Assignment | P23 | $log10(1)$ | +| Assignment | P24 | $pow(1, 2)$ | +| Assignment | P25 | $pow(2, 2)$ | +| Assignment | P26 | $pow(1.4, 5.1)$ | +| Assignment | P27 | $pow(4, 2)$ | +| Assignment | P28 | $pow(3.1, 2)$ | +| Assignment | P29 | $sqrt(4)$ | +| Assignment | P30 | $sqrt(7.4)$ | +| Assignment | P31 | $sin(2.1)$ | +| Assignment | P32 | $sin(0)$ | +| Assignment | P33 | $sin(-5.9)$ | +| Assignment | P34 | $tan(0)$ | +| Assignment | P35 | $tan(1.11)$ | +| Assignment | P36 | $tan(-6)$ | +| Assignment | P37 | $1 + 2$ | +| Assignment | P38 | $1 - 2$ | +| Assignment | P39 | $5 / 2$ | +| Assignment | P40 | $8 * 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $3.7$ | constant | +| Initial value of parameter P2 | $abs(-1)$ | variable | +| Initial value of parameter P3 | $abs(1)$ | variable | +| Initial value of parameter P4 | $acos(-1)$ | variable | +| Initial value of parameter P5 | $acos(0.5)$ | variable | +| Initial value of parameter P6 | $asin(1)$ | variable | +| Initial value of parameter P7 | $asin(-0.5)$ | variable | +| Initial value of parameter P8 | $atan(2.8)$ | variable | +| Initial value of parameter P9 | $atan(-7.09)$ | variable | +| Initial value of parameter P10 | $ceil(0.5)$ | variable | +| Initial value of parameter P11 | $ceil(3.55)$ | variable | +| Initial value of parameter P12 | $ceil(-4.6)$ | variable | +| Initial value of parameter P13 | $cos(9.1)$ | variable | +| Initial value of parameter P14 | $cos(-0.22)$ | variable | +| Initial value of parameter P15 | $exp(0)$ | variable | +| Initial value of parameter P16 | $exp(1)$ | variable | +| Initial value of parameter P17 | $exp(0.77)$ | variable | +| Initial value of parameter P18 | $floor(-4.6)$ | variable | +| Initial value of parameter P19 | $floor(9.1)$ | variable | +| Initial value of parameter P20 | $log(0.2)$ | variable | +| Initial value of parameter P21 | $log(1)$ | variable | +| Initial value of parameter P22 | $log10(0.2)$ | variable | +| Initial value of parameter P23 | $log10(1)$ | variable | +| Initial value of parameter P24 | $pow(1, 2)$ | variable | +| Initial value of parameter P25 | $pow(2, 2)$ | variable | +| Initial value of parameter P26 | $pow(1.4, 5.1)$ | variable | +| Initial value of parameter P27 | $pow(4, 2)$ | variable | +| Initial value of parameter P28 | $pow(3.1, 2)$ | variable | +| Initial value of parameter P29 | $sqrt(4)$ | variable | +| Initial value of parameter P30 | $sqrt(7.4)$ | variable | +| Initial value of parameter P31 | $sin(2.1)$ | variable | +| Initial value of parameter P32 | $sin(0)$ | variable | +| Initial value of parameter P33 | $sin(-5.9)$ | variable | +| Initial value of parameter P34 | $tan(0)$ | variable | +| Initial value of parameter P35 | $tan(1.11)$ | variable | +| Initial value of parameter P36 | $tan(-6)$ | variable | +| Initial value of parameter P37 | $1 + 2$ | variable | +| Initial value of parameter P38 | $1 - 2$ | variable | +| Initial value of parameter P39 | $5 / 2$ | variable | +| Initial value of parameter P40 | $8 * 3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +P2 @Record { }; +P2 := abs((-1)); +P3 @Record { }; +P3 := abs(1); +P4 @Record { }; +P4 := acos((-1)); +P5 @Record { }; +P5 := acos(0.5); +P6 @Record { }; +P6 := asin(1); +P7 @Record { }; +P7 := asin((-0.5)); +P8 @Record { }; +P8 := atan(2.8); +P9 @Record { }; +P9 := atan((-7.09)); +P10 @Record { }; +P10 := ceil(0.5); +P11 @Record { }; +P11 := ceil(3.55); +P12 @Record { }; +P12 := ceil((-4.6)); +P13 @Record { }; +P13 := cos(9.1); +P14 @Record { }; +P14 := cos((-0.22)); +P15 @Record { }; +P15 := exp(0); +P16 @Record { }; +P16 := exp(1); +P17 @Record { }; +P17 := exp(0.77); +P18 @Record { }; +P18 := floor((-4.6)); +P19 @Record { }; +P19 := floor(9.1); +P20 @Record { }; +P20 := ln(0.2); +P21 @Record { }; +P21 := ln(1); +P22 @Record { }; +P22 := logbase(0.2, 10); +P23 @Record { }; +P23 := logbase(1, 10); +P24 @Record { }; +P24 := pow(1, 2); +P25 @Record { }; +P25 := pow(2, 2); +P26 @Record { }; +P26 := pow(1.4, 5.1); +P27 @Record { }; +P27 := pow(4, 2); +P28 @Record { }; +P28 := pow(3.1, 2); +P29 @Record { }; +P29 := pow(4, 1 / 2); +P30 @Record { }; +P30 := pow(7.4, 1 / 2); +P31 @Record { }; +P31 := sin(2.1); +P32 @Record { }; +P32 := sin(0); +P33 @Record { }; +P33 := sin((-5.9)); +P34 @Record { }; +P34 := tan(0); +P35 @Record { }; +P35 := tan(1.11); +P36 @Record { }; +P36 := tan((-6)); +P37 @Record { }; +P37 := 1 + 2; +P38 @Record { }; +P38 := 1 - 2; +P39 @Record { }; +P39 := 5 / 2; +P40 @Record { }; +P40 := 8 * 3; + +P1 @Const { } = 3.7; + diff --git a/latest/cases/00954/synopsis.txt b/latest/cases/00954/synopsis.txt new file mode 100644 index 000000000..e7fea1ff8 --- /dev/null +++ b/latest/cases/00954/synopsis.txt @@ -0,0 +1,104 @@ + +category: Test +synopsis: Several parameters with assignment rules, testing various L1 built-in functions acting on constants. +componentTags: AssignmentRule, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model tests the various mathematical constructs present in L1. + +The model contains: +* 40 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40) + +There are 39 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P2 | $abs(-1)$ | +| Assignment | P3 | $abs(1)$ | +| Assignment | P4 | $acos(-1)$ | +| Assignment | P5 | $acos(0.5)$ | +| Assignment | P6 | $asin(1)$ | +| Assignment | P7 | $asin(-0.5)$ | +| Assignment | P8 | $atan(2.8)$ | +| Assignment | P9 | $atan(-7.09)$ | +| Assignment | P10 | $ceil(0.5)$ | +| Assignment | P11 | $ceil(3.55)$ | +| Assignment | P12 | $ceil(-4.6)$ | +| Assignment | P13 | $cos(9.1)$ | +| Assignment | P14 | $cos(-0.22)$ | +| Assignment | P15 | $exp(0)$ | +| Assignment | P16 | $exp(1)$ | +| Assignment | P17 | $exp(0.77)$ | +| Assignment | P18 | $floor(-4.6)$ | +| Assignment | P19 | $floor(9.1)$ | +| Assignment | P20 | $log(0.2)$ | +| Assignment | P21 | $log(1)$ | +| Assignment | P22 | $log10(0.2)$ | +| Assignment | P23 | $log10(1)$ | +| Assignment | P24 | $pow(1, 2)$ | +| Assignment | P25 | $pow(2, 2)$ | +| Assignment | P26 | $pow(1.4, 5.1)$ | +| Assignment | P27 | $pow(4, 2)$ | +| Assignment | P28 | $pow(3.1, 2)$ | +| Assignment | P29 | $sqrt(4)$ | +| Assignment | P30 | $sqrt(7.4)$ | +| Assignment | P31 | $sin(2.1)$ | +| Assignment | P32 | $sin(0)$ | +| Assignment | P33 | $sin(-5.9)$ | +| Assignment | P34 | $tan(0)$ | +| Assignment | P35 | $tan(1.11)$ | +| Assignment | P36 | $tan(-6)$ | +| Assignment | P37 | $1 + 2$ | +| Assignment | P38 | $1 - 2$ | +| Assignment | P39 | $5 / 2$ | +| Assignment | P40 | $8 * 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $3.7$ | constant | +| Initial value of parameter P2 | $abs(-1)$ | variable | +| Initial value of parameter P3 | $abs(1)$ | variable | +| Initial value of parameter P4 | $acos(-1)$ | variable | +| Initial value of parameter P5 | $acos(0.5)$ | variable | +| Initial value of parameter P6 | $asin(1)$ | variable | +| Initial value of parameter P7 | $asin(-0.5)$ | variable | +| Initial value of parameter P8 | $atan(2.8)$ | variable | +| Initial value of parameter P9 | $atan(-7.09)$ | variable | +| Initial value of parameter P10 | $ceil(0.5)$ | variable | +| Initial value of parameter P11 | $ceil(3.55)$ | variable | +| Initial value of parameter P12 | $ceil(-4.6)$ | variable | +| Initial value of parameter P13 | $cos(9.1)$ | variable | +| Initial value of parameter P14 | $cos(-0.22)$ | variable | +| Initial value of parameter P15 | $exp(0)$ | variable | +| Initial value of parameter P16 | $exp(1)$ | variable | +| Initial value of parameter P17 | $exp(0.77)$ | variable | +| Initial value of parameter P18 | $floor(-4.6)$ | variable | +| Initial value of parameter P19 | $floor(9.1)$ | variable | +| Initial value of parameter P20 | $log(0.2)$ | variable | +| Initial value of parameter P21 | $log(1)$ | variable | +| Initial value of parameter P22 | $log10(0.2)$ | variable | +| Initial value of parameter P23 | $log10(1)$ | variable | +| Initial value of parameter P24 | $pow(1, 2)$ | variable | +| Initial value of parameter P25 | $pow(2, 2)$ | variable | +| Initial value of parameter P26 | $pow(1.4, 5.1)$ | variable | +| Initial value of parameter P27 | $pow(4, 2)$ | variable | +| Initial value of parameter P28 | $pow(3.1, 2)$ | variable | +| Initial value of parameter P29 | $sqrt(4)$ | variable | +| Initial value of parameter P30 | $sqrt(7.4)$ | variable | +| Initial value of parameter P31 | $sin(2.1)$ | variable | +| Initial value of parameter P32 | $sin(0)$ | variable | +| Initial value of parameter P33 | $sin(-5.9)$ | variable | +| Initial value of parameter P34 | $tan(0)$ | variable | +| Initial value of parameter P35 | $tan(1.11)$ | variable | +| Initial value of parameter P36 | $tan(-6)$ | variable | +| Initial value of parameter P37 | $1 + 2$ | variable | +| Initial value of parameter P38 | $1 - 2$ | variable | +| Initial value of parameter P39 | $5 / 2$ | variable | +| Initial value of parameter P40 | $8 * 3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00955/l2v5/heta-code/output.heta b/latest/cases/00955/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e0e3bdde5 --- /dev/null +++ b/latest/cases/00955/l2v5/heta-code/output.heta @@ -0,0 +1,80 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +P1 @Record { }; +P1 := t; +P2 @Record { }; +P2 := abs(t); +P3 @Record { }; +P3 := abs((-t)); +P4 @Record { }; +P4 := acos(t); +P5 @Record { }; +P5 := acos((-t)); +P6 @Record { }; +P6 := asin(t); +P7 @Record { }; +P7 := asin((-t)); +P8 @Record { }; +P8 := atan(t); +P9 @Record { }; +P9 := atan((-t)); +P10 @Record { }; +P10 := ceil(t - 0.001); +P11 @Record { }; +P11 := ceil((-t) - 0.001); +P13 @Record { }; +P13 := cos(t); +P14 @Record { }; +P14 := cos((-t)); +P15 @Record { }; +P15 := exp(t); +P16 @Record { }; +P16 := exp((-t)); +P18 @Record { }; +P18 := floor(t + 0.001); +P19 @Record { }; +P19 := floor((-t) + 0.001); +P20 @Record { }; +P20 := ln(t + 1); +P22 @Record { }; +P22 := logbase(t + 1, 10); +P24 @Record { }; +P24 := pow(t, 2); +P25 @Record { }; +P25 := pow(2, t); +P26 @Record { }; +P26 := pow(t, t); +P29 @Record { }; +P29 := pow(t, 1 / 2); +P31 @Record { }; +P31 := sin(t); +P32 @Record { }; +P32 := sin((-t)); +P34 @Record { }; +P34 := tan(t); +P35 @Record { }; +P35 := tan((-t)); +P37 @Record { }; +P37 := t + 2; +P38 @Record { }; +P38 := t - 2; +P39 @Record { }; +P39 := t / 2; +P40 @Record { }; +P40 := t * 3; +P41 @Record { }; +P41 := 2 + t; +P42 @Record { }; +P42 := 2 - t; +P43 @Record { }; +P43 := 2 / (t + 1); +P44 @Record { }; +P44 := 3 * t; + diff --git a/latest/cases/00955/l2v5/index.heta b/latest/cases/00955/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00955/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00955/l2v5/json/output.json b/latest/cases/00955/l2v5/json/output.json new file mode 100644 index 000000000..feb0af693 --- /dev/null +++ b/latest/cases/00955/l2v5/json/output.json @@ -0,0 +1,275 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "ode_": "t" + } + }, + { + "class": "Record", + "id": "P2", + "assignments": { + "ode_": "abs(t)" + } + }, + { + "class": "Record", + "id": "P3", + "assignments": { + "ode_": "abs((-t))" + } + }, + { + "class": "Record", + "id": "P4", + "assignments": { + "ode_": "acos(t)" + } + }, + { + "class": "Record", + "id": "P5", + "assignments": { + "ode_": "acos((-t))" + } + }, + { + "class": "Record", + "id": "P6", + "assignments": { + "ode_": "asin(t)" + } + }, + { + "class": "Record", + "id": "P7", + "assignments": { + "ode_": "asin((-t))" + } + }, + { + "class": "Record", + "id": "P8", + "assignments": { + "ode_": "atan(t)" + } + }, + { + "class": "Record", + "id": "P9", + "assignments": { + "ode_": "atan((-t))" + } + }, + { + "class": "Record", + "id": "P10", + "assignments": { + "ode_": "ceil(t - 0.001)" + } + }, + { + "class": "Record", + "id": "P11", + "assignments": { + "ode_": "ceil((-t) - 0.001)" + } + }, + { + "class": "Record", + "id": "P13", + "assignments": { + "ode_": "cos(t)" + } + }, + { + "class": "Record", + "id": "P14", + "assignments": { + "ode_": "cos((-t))" + } + }, + { + "class": "Record", + "id": "P15", + "assignments": { + "ode_": "exp(t)" + } + }, + { + "class": "Record", + "id": "P16", + "assignments": { + "ode_": "exp((-t))" + } + }, + { + "class": "Record", + "id": "P18", + "assignments": { + "ode_": "floor(t + 0.001)" + } + }, + { + "class": "Record", + "id": "P19", + "assignments": { + "ode_": "floor((-t) + 0.001)" + } + }, + { + "class": "Record", + "id": "P20", + "assignments": { + "ode_": "ln(t + 1)" + } + }, + { + "class": "Record", + "id": "P22", + "assignments": { + "ode_": "logbase(t + 1, 10)" + } + }, + { + "class": "Record", + "id": "P24", + "assignments": { + "ode_": "pow(t, 2)" + } + }, + { + "class": "Record", + "id": "P25", + "assignments": { + "ode_": "pow(2, t)" + } + }, + { + "class": "Record", + "id": "P26", + "assignments": { + "ode_": "pow(t, t)" + } + }, + { + "class": "Record", + "id": "P29", + "assignments": { + "ode_": "pow(t, 1 / 2)" + } + }, + { + "class": "Record", + "id": "P31", + "assignments": { + "ode_": "sin(t)" + } + }, + { + "class": "Record", + "id": "P32", + "assignments": { + "ode_": "sin((-t))" + } + }, + { + "class": "Record", + "id": "P34", + "assignments": { + "ode_": "tan(t)" + } + }, + { + "class": "Record", + "id": "P35", + "assignments": { + "ode_": "tan((-t))" + } + }, + { + "class": "Record", + "id": "P37", + "assignments": { + "ode_": "t + 2" + } + }, + { + "class": "Record", + "id": "P38", + "assignments": { + "ode_": "t - 2" + } + }, + { + "class": "Record", + "id": "P39", + "assignments": { + "ode_": "t / 2" + } + }, + { + "class": "Record", + "id": "P40", + "assignments": { + "ode_": "t * 3" + } + }, + { + "class": "Record", + "id": "P41", + "assignments": { + "ode_": "2 + t" + } + }, + { + "class": "Record", + "id": "P42", + "assignments": { + "ode_": "2 - t" + } + }, + { + "class": "Record", + "id": "P43", + "assignments": { + "ode_": "2 / (t + 1)" + } + }, + { + "class": "Record", + "id": "P44", + "assignments": { + "ode_": "3 * t" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00955/l3v2/heta-code/output.heta b/latest/cases/00955/l3v2/heta-code/output.heta new file mode 100644 index 000000000..955ba2738 --- /dev/null +++ b/latest/cases/00955/l3v2/heta-code/output.heta @@ -0,0 +1,75 @@ + + +t @TimeScale { }; + +P1 @Record { }; +P1 := t; +P2 @Record { }; +P2 := abs(t); +P3 @Record { }; +P3 := abs((-t)); +P4 @Record { }; +P4 := acos(t); +P5 @Record { }; +P5 := acos((-t)); +P6 @Record { }; +P6 := asin(t); +P7 @Record { }; +P7 := asin((-t)); +P8 @Record { }; +P8 := atan(t); +P9 @Record { }; +P9 := atan((-t)); +P10 @Record { }; +P10 := ceil(t - 0.001); +P11 @Record { }; +P11 := ceil((-t) - 0.001); +P13 @Record { }; +P13 := cos(t); +P14 @Record { }; +P14 := cos((-t)); +P15 @Record { }; +P15 := exp(t); +P16 @Record { }; +P16 := exp((-t)); +P18 @Record { }; +P18 := floor(t + 0.001); +P19 @Record { }; +P19 := floor((-t) + 0.001); +P20 @Record { }; +P20 := ln(t + 1); +P22 @Record { }; +P22 := logbase(t + 1, 10); +P24 @Record { }; +P24 := pow(t, 2); +P25 @Record { }; +P25 := pow(2, t); +P26 @Record { }; +P26 := pow(t, t); +P29 @Record { }; +P29 := pow(t, 1 / 2); +P31 @Record { }; +P31 := sin(t); +P32 @Record { }; +P32 := sin((-t)); +P34 @Record { }; +P34 := tan(t); +P35 @Record { }; +P35 := tan((-t)); +P37 @Record { }; +P37 := t + 2; +P38 @Record { }; +P38 := t - 2; +P39 @Record { }; +P39 := t / 2; +P40 @Record { }; +P40 := t * 3; +P41 @Record { }; +P41 := 2 + t; +P42 @Record { }; +P42 := 2 - t; +P43 @Record { }; +P43 := 2 / (t + 1); +P44 @Record { }; +P44 := 3 * t; + diff --git a/latest/cases/00955/l3v2/index.heta b/latest/cases/00955/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00955/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00955/l3v2/json/output.json b/latest/cases/00955/l3v2/json/output.json new file mode 100644 index 000000000..4cb6c6482 --- /dev/null +++ b/latest/cases/00955/l3v2/json/output.json @@ -0,0 +1,250 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "ode_": "t" + } + }, + { + "class": "Record", + "id": "P2", + "assignments": { + "ode_": "abs(t)" + } + }, + { + "class": "Record", + "id": "P3", + "assignments": { + "ode_": "abs((-t))" + } + }, + { + "class": "Record", + "id": "P4", + "assignments": { + "ode_": "acos(t)" + } + }, + { + "class": "Record", + "id": "P5", + "assignments": { + "ode_": "acos((-t))" + } + }, + { + "class": "Record", + "id": "P6", + "assignments": { + "ode_": "asin(t)" + } + }, + { + "class": "Record", + "id": "P7", + "assignments": { + "ode_": "asin((-t))" + } + }, + { + "class": "Record", + "id": "P8", + "assignments": { + "ode_": "atan(t)" + } + }, + { + "class": "Record", + "id": "P9", + "assignments": { + "ode_": "atan((-t))" + } + }, + { + "class": "Record", + "id": "P10", + "assignments": { + "ode_": "ceil(t - 0.001)" + } + }, + { + "class": "Record", + "id": "P11", + "assignments": { + "ode_": "ceil((-t) - 0.001)" + } + }, + { + "class": "Record", + "id": "P13", + "assignments": { + "ode_": "cos(t)" + } + }, + { + "class": "Record", + "id": "P14", + "assignments": { + "ode_": "cos((-t))" + } + }, + { + "class": "Record", + "id": "P15", + "assignments": { + "ode_": "exp(t)" + } + }, + { + "class": "Record", + "id": "P16", + "assignments": { + "ode_": "exp((-t))" + } + }, + { + "class": "Record", + "id": "P18", + "assignments": { + "ode_": "floor(t + 0.001)" + } + }, + { + "class": "Record", + "id": "P19", + "assignments": { + "ode_": "floor((-t) + 0.001)" + } + }, + { + "class": "Record", + "id": "P20", + "assignments": { + "ode_": "ln(t + 1)" + } + }, + { + "class": "Record", + "id": "P22", + "assignments": { + "ode_": "logbase(t + 1, 10)" + } + }, + { + "class": "Record", + "id": "P24", + "assignments": { + "ode_": "pow(t, 2)" + } + }, + { + "class": "Record", + "id": "P25", + "assignments": { + "ode_": "pow(2, t)" + } + }, + { + "class": "Record", + "id": "P26", + "assignments": { + "ode_": "pow(t, t)" + } + }, + { + "class": "Record", + "id": "P29", + "assignments": { + "ode_": "pow(t, 1 / 2)" + } + }, + { + "class": "Record", + "id": "P31", + "assignments": { + "ode_": "sin(t)" + } + }, + { + "class": "Record", + "id": "P32", + "assignments": { + "ode_": "sin((-t))" + } + }, + { + "class": "Record", + "id": "P34", + "assignments": { + "ode_": "tan(t)" + } + }, + { + "class": "Record", + "id": "P35", + "assignments": { + "ode_": "tan((-t))" + } + }, + { + "class": "Record", + "id": "P37", + "assignments": { + "ode_": "t + 2" + } + }, + { + "class": "Record", + "id": "P38", + "assignments": { + "ode_": "t - 2" + } + }, + { + "class": "Record", + "id": "P39", + "assignments": { + "ode_": "t / 2" + } + }, + { + "class": "Record", + "id": "P40", + "assignments": { + "ode_": "t * 3" + } + }, + { + "class": "Record", + "id": "P41", + "assignments": { + "ode_": "2 + t" + } + }, + { + "class": "Record", + "id": "P42", + "assignments": { + "ode_": "2 - t" + } + }, + { + "class": "Record", + "id": "P43", + "assignments": { + "ode_": "2 / (t + 1)" + } + }, + { + "class": "Record", + "id": "P44", + "assignments": { + "ode_": "3 * t" + } + } +] \ No newline at end of file diff --git a/latest/cases/00955/model-sbml-l2v5.xml b/latest/cases/00955/model-sbml-l2v5.xml new file mode 100644 index 000000000..666430a90 --- /dev/null +++ b/latest/cases/00955/model-sbml-l2v5.xml @@ -0,0 +1,396 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + + + time + 0.001 + + + + + + + + + + + + + time + + 0.001 + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + + + time + 0.001 + + + + + + + + + + + + + time + + 0.001 + + + + + + + + + + + time + 1 + + + + + + + + + + 10 + + + + time + 1 + + + + + + + + + time + 2 + + + + + + + + 2 + time + + + + + + + + time + time + + + + + + + + + 2 + + time + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + 2 + + + + + + + + time + 2 + + + + + + + + time + 2 + + + + + + + + time + 3 + + + + + + + + 2 + time + + + + + + + + 2 + time + + + + + + + + 2 + + + time + 1 + + + + + + + + + 3 + time + + + + + + diff --git a/latest/cases/00955/model-sbml-l3v2.xml b/latest/cases/00955/model-sbml-l3v2.xml new file mode 100644 index 000000000..79ac11dd9 --- /dev/null +++ b/latest/cases/00955/model-sbml-l3v2.xml @@ -0,0 +1,397 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + + + time + 0.001 + + + + + + + + + + + + + time + + 0.001 + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + + + time + 0.001 + + + + + + + + + + + + + time + + 0.001 + + + + + + + + + + + time + 1 + + + + + + + + + + 10 + + + + time + 1 + + + + + + + + + time + 2 + + + + + + + + 2 + time + + + + + + + + time + time + + + + + + + + + 2 + + time + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + 2 + + + + + + + + time + 2 + + + + + + + + time + 2 + + + + + + + + time + 3 + + + + + + + + 2 + time + + + + + + + + 2 + time + + + + + + + + 2 + + + time + 1 + + + + + + + + + 3 + time + + + + + + diff --git a/latest/cases/00955/output.heta b/latest/cases/00955/output.heta new file mode 100644 index 000000000..788d434a0 --- /dev/null +++ b/latest/cases/00955/output.heta @@ -0,0 +1,173 @@ +/* +category: Test +synopsis: Several parameters with assignment rules involving time, testing various L1 built-in functions. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various mathematical constructs present in L1, as applied to the time variable. Ironically, this doesn't work in L1, since time isn't present, but hey. + +The model contains: +* 35 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P13, P14, P15, P16, P18, P19, P20, P22, P24, P25, P26, P29, P31, P32, P34, P35, P37, P38, P39, P40, P41, P42, P43, P44) + +There are 35 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $time$ | +| Assignment | P2 | $abs(time)$ | +| Assignment | P3 | $abs(-time)$ | +| Assignment | P4 | $acos(time)$ | +| Assignment | P5 | $acos(-time)$ | +| Assignment | P6 | $asin(time)$ | +| Assignment | P7 | $asin(-time)$ | +| Assignment | P8 | $atan(time)$ | +| Assignment | P9 | $atan(-time)$ | +| Assignment | P10 | $ceil(time - 0.001)$ | +| Assignment | P11 | $ceil(-time - 0.001)$ | +| Assignment | P13 | $cos(time)$ | +| Assignment | P14 | $cos(-time)$ | +| Assignment | P15 | $exp(time)$ | +| Assignment | P16 | $exp(-time)$ | +| Assignment | P18 | $floor(time + 0.001)$ | +| Assignment | P19 | $floor(-time + 0.001)$ | +| Assignment | P20 | $ln(time + 1)$ | +| Assignment | P22 | $log10(time + 1)$ | +| Assignment | P24 | $time^2$ | +| Assignment | P25 | $2^time$ | +| Assignment | P26 | $time^time$ | +| Assignment | P29 | $sqrt(time)$ | +| Assignment | P31 | $sin(time)$ | +| Assignment | P32 | $sin(-time)$ | +| Assignment | P34 | $tan(time)$ | +| Assignment | P35 | $tan(-time)$ | +| Assignment | P37 | $time + 2$ | +| Assignment | P38 | $time - 2$ | +| Assignment | P39 | $time / 2$ | +| Assignment | P40 | $time * 3$ | +| Assignment | P41 | $2 + time$ | +| Assignment | P42 | $2 - time$ | +| Assignment | P43 | $2 / (time + 1)$ | +| Assignment | P44 | $3 * time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $time$ | variable | +| Initial value of parameter P2 | $abs(time)$ | variable | +| Initial value of parameter P3 | $abs(-time)$ | variable | +| Initial value of parameter P4 | $acos(time)$ | variable | +| Initial value of parameter P5 | $acos(-time)$ | variable | +| Initial value of parameter P6 | $asin(time)$ | variable | +| Initial value of parameter P7 | $asin(-time)$ | variable | +| Initial value of parameter P8 | $atan(time)$ | variable | +| Initial value of parameter P9 | $atan(-time)$ | variable | +| Initial value of parameter P10 | $ceil(time - 0.001)$ | variable | +| Initial value of parameter P11 | $ceil(-time - 0.001)$ | variable | +| Initial value of parameter P13 | $cos(time)$ | variable | +| Initial value of parameter P14 | $cos(-time)$ | variable | +| Initial value of parameter P15 | $exp(time)$ | variable | +| Initial value of parameter P16 | $exp(-time)$ | variable | +| Initial value of parameter P18 | $floor(time + 0.001)$ | variable | +| Initial value of parameter P19 | $floor(-time + 0.001)$ | variable | +| Initial value of parameter P20 | $ln(time + 1)$ | variable | +| Initial value of parameter P22 | $log10(time + 1)$ | variable | +| Initial value of parameter P24 | $time^2$ | variable | +| Initial value of parameter P25 | $2^time$ | variable | +| Initial value of parameter P26 | $time^time$ | variable | +| Initial value of parameter P29 | $sqrt(time)$ | variable | +| Initial value of parameter P31 | $sin(time)$ | variable | +| Initial value of parameter P32 | $sin(-time)$ | variable | +| Initial value of parameter P34 | $tan(time)$ | variable | +| Initial value of parameter P35 | $tan(-time)$ | variable | +| Initial value of parameter P37 | $time + 2$ | variable | +| Initial value of parameter P38 | $time - 2$ | variable | +| Initial value of parameter P39 | $time / 2$ | variable | +| Initial value of parameter P40 | $time * 3$ | variable | +| Initial value of parameter P41 | $2 + time$ | variable | +| Initial value of parameter P42 | $2 - time$ | variable | +| Initial value of parameter P43 | $2 / (time + 1)$ | variable | +| Initial value of parameter P44 | $3 * time$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P1 @Record { }; +P1 := t; +P2 @Record { }; +P2 := abs(t); +P3 @Record { }; +P3 := abs((-t)); +P4 @Record { }; +P4 := acos(t); +P5 @Record { }; +P5 := acos((-t)); +P6 @Record { }; +P6 := asin(t); +P7 @Record { }; +P7 := asin((-t)); +P8 @Record { }; +P8 := atan(t); +P9 @Record { }; +P9 := atan((-t)); +P10 @Record { }; +P10 := ceil(t - 0.001); +P11 @Record { }; +P11 := ceil((-t) - 0.001); +P13 @Record { }; +P13 := cos(t); +P14 @Record { }; +P14 := cos((-t)); +P15 @Record { }; +P15 := exp(t); +P16 @Record { }; +P16 := exp((-t)); +P18 @Record { }; +P18 := floor(t + 0.001); +P19 @Record { }; +P19 := floor((-t) + 0.001); +P20 @Record { }; +P20 := ln(t + 1); +P22 @Record { }; +P22 := logbase(t + 1, 10); +P24 @Record { }; +P24 := pow(t, 2); +P25 @Record { }; +P25 := pow(2, t); +P26 @Record { }; +P26 := pow(t, t); +P29 @Record { }; +P29 := pow(t, 1 / 2); +P31 @Record { }; +P31 := sin(t); +P32 @Record { }; +P32 := sin((-t)); +P34 @Record { }; +P34 := tan(t); +P35 @Record { }; +P35 := tan((-t)); +P37 @Record { }; +P37 := t + 2; +P38 @Record { }; +P38 := t - 2; +P39 @Record { }; +P39 := t / 2; +P40 @Record { }; +P40 := t * 3; +P41 @Record { }; +P41 := 2 + t; +P42 @Record { }; +P42 := 2 - t; +P43 @Record { }; +P43 := 2 / (t + 1); +P44 @Record { }; +P44 := 3 * t; + diff --git a/latest/cases/00955/synopsis.txt b/latest/cases/00955/synopsis.txt new file mode 100644 index 000000000..107a1f899 --- /dev/null +++ b/latest/cases/00955/synopsis.txt @@ -0,0 +1,96 @@ + +category: Test +synopsis: Several parameters with assignment rules involving time, testing various L1 built-in functions. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various mathematical constructs present in L1, as applied to the time variable. Ironically, this doesn't work in L1, since time isn't present, but hey. + +The model contains: +* 35 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P13, P14, P15, P16, P18, P19, P20, P22, P24, P25, P26, P29, P31, P32, P34, P35, P37, P38, P39, P40, P41, P42, P43, P44) + +There are 35 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $time$ | +| Assignment | P2 | $abs(time)$ | +| Assignment | P3 | $abs(-time)$ | +| Assignment | P4 | $acos(time)$ | +| Assignment | P5 | $acos(-time)$ | +| Assignment | P6 | $asin(time)$ | +| Assignment | P7 | $asin(-time)$ | +| Assignment | P8 | $atan(time)$ | +| Assignment | P9 | $atan(-time)$ | +| Assignment | P10 | $ceil(time - 0.001)$ | +| Assignment | P11 | $ceil(-time - 0.001)$ | +| Assignment | P13 | $cos(time)$ | +| Assignment | P14 | $cos(-time)$ | +| Assignment | P15 | $exp(time)$ | +| Assignment | P16 | $exp(-time)$ | +| Assignment | P18 | $floor(time + 0.001)$ | +| Assignment | P19 | $floor(-time + 0.001)$ | +| Assignment | P20 | $ln(time + 1)$ | +| Assignment | P22 | $log10(time + 1)$ | +| Assignment | P24 | $time^2$ | +| Assignment | P25 | $2^time$ | +| Assignment | P26 | $time^time$ | +| Assignment | P29 | $sqrt(time)$ | +| Assignment | P31 | $sin(time)$ | +| Assignment | P32 | $sin(-time)$ | +| Assignment | P34 | $tan(time)$ | +| Assignment | P35 | $tan(-time)$ | +| Assignment | P37 | $time + 2$ | +| Assignment | P38 | $time - 2$ | +| Assignment | P39 | $time / 2$ | +| Assignment | P40 | $time * 3$ | +| Assignment | P41 | $2 + time$ | +| Assignment | P42 | $2 - time$ | +| Assignment | P43 | $2 / (time + 1)$ | +| Assignment | P44 | $3 * time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $time$ | variable | +| Initial value of parameter P2 | $abs(time)$ | variable | +| Initial value of parameter P3 | $abs(-time)$ | variable | +| Initial value of parameter P4 | $acos(time)$ | variable | +| Initial value of parameter P5 | $acos(-time)$ | variable | +| Initial value of parameter P6 | $asin(time)$ | variable | +| Initial value of parameter P7 | $asin(-time)$ | variable | +| Initial value of parameter P8 | $atan(time)$ | variable | +| Initial value of parameter P9 | $atan(-time)$ | variable | +| Initial value of parameter P10 | $ceil(time - 0.001)$ | variable | +| Initial value of parameter P11 | $ceil(-time - 0.001)$ | variable | +| Initial value of parameter P13 | $cos(time)$ | variable | +| Initial value of parameter P14 | $cos(-time)$ | variable | +| Initial value of parameter P15 | $exp(time)$ | variable | +| Initial value of parameter P16 | $exp(-time)$ | variable | +| Initial value of parameter P18 | $floor(time + 0.001)$ | variable | +| Initial value of parameter P19 | $floor(-time + 0.001)$ | variable | +| Initial value of parameter P20 | $ln(time + 1)$ | variable | +| Initial value of parameter P22 | $log10(time + 1)$ | variable | +| Initial value of parameter P24 | $time^2$ | variable | +| Initial value of parameter P25 | $2^time$ | variable | +| Initial value of parameter P26 | $time^time$ | variable | +| Initial value of parameter P29 | $sqrt(time)$ | variable | +| Initial value of parameter P31 | $sin(time)$ | variable | +| Initial value of parameter P32 | $sin(-time)$ | variable | +| Initial value of parameter P34 | $tan(time)$ | variable | +| Initial value of parameter P35 | $tan(-time)$ | variable | +| Initial value of parameter P37 | $time + 2$ | variable | +| Initial value of parameter P38 | $time - 2$ | variable | +| Initial value of parameter P39 | $time / 2$ | variable | +| Initial value of parameter P40 | $time * 3$ | variable | +| Initial value of parameter P41 | $2 + time$ | variable | +| Initial value of parameter P42 | $2 - time$ | variable | +| Initial value of parameter P43 | $2 / (time + 1)$ | variable | +| Initial value of parameter P44 | $3 * time$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00956/l2v5/heta-code/output.heta b/latest/cases/00956/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cac1e182c --- /dev/null +++ b/latest/cases/00956/l2v5/heta-code/output.heta @@ -0,0 +1,50 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +P1 @Record { } .= 3.7; +P2 @Record { } .= abs((-1)); +P3 @Record { } .= abs(1); +P4 @Record { } .= acos((-1)); +P5 @Record { } .= acos(0.5); +P6 @Record { } .= asin(1); +P7 @Record { } .= asin((-0.5)); +P8 @Record { } .= atan(2.8); +P9 @Record { } .= atan((-7.09)); +P10 @Record { } .= ceil(0.5); +P11 @Record { } .= ceil(3.55); +P12 @Record { } .= ceil((-4.6)); +P13 @Record { } .= cos(9.1); +P14 @Record { } .= cos((-0.22)); +P15 @Record { } .= exp(0); +P16 @Record { } .= exp(1); +P17 @Record { } .= exp(0.77); +P18 @Record { } .= floor((-4.6)); +P19 @Record { } .= floor(9.1); +P20 @Record { } .= ln(0.2); +P21 @Record { } .= ln(1); +P22 @Record { } .= logbase(0.2, 10); +P23 @Record { } .= logbase(1, 10); +P24 @Record { } .= pow(1, 2); +P25 @Record { } .= pow(2, 2); +P26 @Record { } .= pow(1.4, 5.1); +P27 @Record { } .= pow(4, 2); +P28 @Record { } .= pow(3.1, 2); +P29 @Record { } .= pow(4, 1 / 2); +P30 @Record { } .= pow(7.4, 1 / 2); +P31 @Record { } .= sin(2.1); +P32 @Record { } .= sin(0); +P33 @Record { } .= sin((-5.9)); +P34 @Record { } .= tan(0); +P35 @Record { } .= tan(1.11); +P36 @Record { } .= tan((-6)); +P37 @Record { } .= 1 + 2; +P38 @Record { } .= 1 - 2; +P39 @Record { } .= 5 / 2; +P40 @Record { } .= 8 * 3; + diff --git a/latest/cases/00956/l2v5/index.heta b/latest/cases/00956/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00956/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00956/l2v5/json/output.json b/latest/cases/00956/l2v5/json/output.json new file mode 100644 index 000000000..1cdf7ad48 --- /dev/null +++ b/latest/cases/00956/l2v5/json/output.json @@ -0,0 +1,310 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "3.7" + } + }, + { + "class": "Record", + "id": "P2", + "assignments": { + "start_": "abs((-1))" + } + }, + { + "class": "Record", + "id": "P3", + "assignments": { + "start_": "abs(1)" + } + }, + { + "class": "Record", + "id": "P4", + "assignments": { + "start_": "acos((-1))" + } + }, + { + "class": "Record", + "id": "P5", + "assignments": { + "start_": "acos(0.5)" + } + }, + { + "class": "Record", + "id": "P6", + "assignments": { + "start_": "asin(1)" + } + }, + { + "class": "Record", + "id": "P7", + "assignments": { + "start_": "asin((-0.5))" + } + }, + { + "class": "Record", + "id": "P8", + "assignments": { + "start_": "atan(2.8)" + } + }, + { + "class": "Record", + "id": "P9", + "assignments": { + "start_": "atan((-7.09))" + } + }, + { + "class": "Record", + "id": "P10", + "assignments": { + "start_": "ceil(0.5)" + } + }, + { + "class": "Record", + "id": "P11", + "assignments": { + "start_": "ceil(3.55)" + } + }, + { + "class": "Record", + "id": "P12", + "assignments": { + "start_": "ceil((-4.6))" + } + }, + { + "class": "Record", + "id": "P13", + "assignments": { + "start_": "cos(9.1)" + } + }, + { + "class": "Record", + "id": "P14", + "assignments": { + "start_": "cos((-0.22))" + } + }, + { + "class": "Record", + "id": "P15", + "assignments": { + "start_": "exp(0)" + } + }, + { + "class": "Record", + "id": "P16", + "assignments": { + "start_": "exp(1)" + } + }, + { + "class": "Record", + "id": "P17", + "assignments": { + "start_": "exp(0.77)" + } + }, + { + "class": "Record", + "id": "P18", + "assignments": { + "start_": "floor((-4.6))" + } + }, + { + "class": "Record", + "id": "P19", + "assignments": { + "start_": "floor(9.1)" + } + }, + { + "class": "Record", + "id": "P20", + "assignments": { + "start_": "ln(0.2)" + } + }, + { + "class": "Record", + "id": "P21", + "assignments": { + "start_": "ln(1)" + } + }, + { + "class": "Record", + "id": "P22", + "assignments": { + "start_": "logbase(0.2, 10)" + } + }, + { + "class": "Record", + "id": "P23", + "assignments": { + "start_": "logbase(1, 10)" + } + }, + { + "class": "Record", + "id": "P24", + "assignments": { + "start_": "pow(1, 2)" + } + }, + { + "class": "Record", + "id": "P25", + "assignments": { + "start_": "pow(2, 2)" + } + }, + { + "class": "Record", + "id": "P26", + "assignments": { + "start_": "pow(1.4, 5.1)" + } + }, + { + "class": "Record", + "id": "P27", + "assignments": { + "start_": "pow(4, 2)" + } + }, + { + "class": "Record", + "id": "P28", + "assignments": { + "start_": "pow(3.1, 2)" + } + }, + { + "class": "Record", + "id": "P29", + "assignments": { + "start_": "pow(4, 1 / 2)" + } + }, + { + "class": "Record", + "id": "P30", + "assignments": { + "start_": "pow(7.4, 1 / 2)" + } + }, + { + "class": "Record", + "id": "P31", + "assignments": { + "start_": "sin(2.1)" + } + }, + { + "class": "Record", + "id": "P32", + "assignments": { + "start_": "sin(0)" + } + }, + { + "class": "Record", + "id": "P33", + "assignments": { + "start_": "sin((-5.9))" + } + }, + { + "class": "Record", + "id": "P34", + "assignments": { + "start_": "tan(0)" + } + }, + { + "class": "Record", + "id": "P35", + "assignments": { + "start_": "tan(1.11)" + } + }, + { + "class": "Record", + "id": "P36", + "assignments": { + "start_": "tan((-6))" + } + }, + { + "class": "Record", + "id": "P37", + "assignments": { + "start_": "1 + 2" + } + }, + { + "class": "Record", + "id": "P38", + "assignments": { + "start_": "1 - 2" + } + }, + { + "class": "Record", + "id": "P39", + "assignments": { + "start_": "5 / 2" + } + }, + { + "class": "Record", + "id": "P40", + "assignments": { + "start_": "8 * 3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00956/l3v2/build.log b/latest/cases/00956/l3v2/build.log new file mode 100644 index 000000000..957fb1c88 --- /dev/null +++ b/latest/cases/00956/l3v2/build.log @@ -0,0 +1,48 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00956/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00956/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00956/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 119 +[error] No required "num" property for "P1" of Const. +[error] No required "num" property for "P2" of Const. +[error] No required "num" property for "P3" of Const. +[error] No required "num" property for "P4" of Const. +[error] No required "num" property for "P5" of Const. +[error] No required "num" property for "P6" of Const. +[error] No required "num" property for "P7" of Const. +[error] No required "num" property for "P8" of Const. +[error] No required "num" property for "P9" of Const. +[error] No required "num" property for "P10" of Const. +[error] No required "num" property for "P11" of Const. +[error] No required "num" property for "P12" of Const. +[error] No required "num" property for "P13" of Const. +[error] No required "num" property for "P14" of Const. +[error] No required "num" property for "P15" of Const. +[error] No required "num" property for "P16" of Const. +[error] No required "num" property for "P17" of Const. +[error] No required "num" property for "P18" of Const. +[error] No required "num" property for "P19" of Const. +[error] No required "num" property for "P20" of Const. +[error] No required "num" property for "P21" of Const. +[error] No required "num" property for "P22" of Const. +[error] No required "num" property for "P23" of Const. +[error] No required "num" property for "P24" of Const. +[error] No required "num" property for "P25" of Const. +[error] No required "num" property for "P26" of Const. +[error] No required "num" property for "P27" of Const. +[error] No required "num" property for "P28" of Const. +[error] No required "num" property for "P29" of Const. +[error] No required "num" property for "P30" of Const. +[error] No required "num" property for "P31" of Const. +[error] No required "num" property for "P32" of Const. +[error] No required "num" property for "P33" of Const. +[error] No required "num" property for "P34" of Const. +[error] No required "num" property for "P35" of Const. +[error] No required "num" property for "P36" of Const. +[error] No required "num" property for "P37" of Const. +[error] No required "num" property for "P38" of Const. +[error] No required "num" property for "P39" of Const. +[error] No required "num" property for "P40" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00956/l3v2/index.heta b/latest/cases/00956/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00956/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00956/model-sbml-l2v5.xml b/latest/cases/00956/model-sbml-l2v5.xml new file mode 100644 index 000000000..8a22e0407 --- /dev/null +++ b/latest/cases/00956/model-sbml-l2v5.xml @@ -0,0 +1,404 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 3.7 + + + + + + + -1 + + + + + + + + 1 + + + + + + + + -1 + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + -0.5 + + + + + + + + 2.8 + + + + + + + + -7.09 + + + + + + + + 0.5 + + + + + + + + 3.55 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + -0.22 + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + 0.77 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + 10 + + 0.2 + + + + + + + + + 10 + + 1 + + + + + + + + 1 + 2 + + + + + + + + 2 + 2 + + + + + + + + 1.4 + 5.1 + + + + + + + + 4 + 2 + + + + + + + + 3.1 + 2 + + + + + + + + + 2 + + 4 + + + + + + + + + 2 + + 7.4 + + + + + + + + 2.1 + + + + + + + + 0 + + + + + + + + -5.9 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + 1 + 2 + + + + + + + + 1 + 2 + + + + + + + + 5 + 2 + + + + + + + + 8 + 3 + + + + + + diff --git a/latest/cases/00956/model-sbml-l3v2.xml b/latest/cases/00956/model-sbml-l3v2.xml new file mode 100644 index 000000000..bb0a51ee9 --- /dev/null +++ b/latest/cases/00956/model-sbml-l3v2.xml @@ -0,0 +1,404 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 3.7 + + + + + + + -1 + + + + + + + + 1 + + + + + + + + -1 + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + -0.5 + + + + + + + + 2.8 + + + + + + + + -7.09 + + + + + + + + 0.5 + + + + + + + + 3.55 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + -0.22 + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + 0.77 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + 10 + + 0.2 + + + + + + + + + 10 + + 1 + + + + + + + + 1 + 2 + + + + + + + + 2 + 2 + + + + + + + + 1.4 + 5.1 + + + + + + + + 4 + 2 + + + + + + + + 3.1 + 2 + + + + + + + + + 2 + + 4 + + + + + + + + + 2 + + 7.4 + + + + + + + + 2.1 + + + + + + + + 0 + + + + + + + + -5.9 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + 1 + 2 + + + + + + + + 1 + 2 + + + + + + + + 5 + 2 + + + + + + + + 8 + 3 + + + + + + diff --git a/latest/cases/00956/output.heta b/latest/cases/00956/output.heta new file mode 100644 index 000000000..e6fa0b031 --- /dev/null +++ b/latest/cases/00956/output.heta @@ -0,0 +1,112 @@ +/* +category: Test +synopsis: Several parameters with initial assignment rules, testing various L1 built-in functions acting on constants. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + The model tests the various mathematical constructs present in L1, used in InitialAssignments. + +The model contains: +* 40 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $3.7$ | constant | +| Initial value of parameter P2 | $abs(-1)$ | constant | +| Initial value of parameter P3 | $abs(1)$ | constant | +| Initial value of parameter P4 | $acos(-1)$ | constant | +| Initial value of parameter P5 | $acos(0.5)$ | constant | +| Initial value of parameter P6 | $asin(1)$ | constant | +| Initial value of parameter P7 | $asin(-0.5)$ | constant | +| Initial value of parameter P8 | $atan(2.8)$ | constant | +| Initial value of parameter P9 | $atan(-7.09)$ | constant | +| Initial value of parameter P10 | $ceil(0.5)$ | constant | +| Initial value of parameter P11 | $ceil(3.55)$ | constant | +| Initial value of parameter P12 | $ceil(-4.6)$ | constant | +| Initial value of parameter P13 | $cos(9.1)$ | constant | +| Initial value of parameter P14 | $cos(-0.22)$ | constant | +| Initial value of parameter P15 | $exp(0)$ | constant | +| Initial value of parameter P16 | $exp(1)$ | constant | +| Initial value of parameter P17 | $exp(0.77)$ | constant | +| Initial value of parameter P18 | $floor(-4.6)$ | constant | +| Initial value of parameter P19 | $floor(9.1)$ | constant | +| Initial value of parameter P20 | $log(0.2)$ | constant | +| Initial value of parameter P21 | $log(1)$ | constant | +| Initial value of parameter P22 | $log10(0.2)$ | constant | +| Initial value of parameter P23 | $log10(1)$ | constant | +| Initial value of parameter P24 | $pow(1, 2)$ | constant | +| Initial value of parameter P25 | $pow(2, 2)$ | constant | +| Initial value of parameter P26 | $pow(1.4, 5.1)$ | constant | +| Initial value of parameter P27 | $pow(4, 2)$ | constant | +| Initial value of parameter P28 | $pow(3.1, 2)$ | constant | +| Initial value of parameter P29 | $sqrt(4)$ | constant | +| Initial value of parameter P30 | $sqrt(7.4)$ | constant | +| Initial value of parameter P31 | $sin(2.1)$ | constant | +| Initial value of parameter P32 | $sin(0)$ | constant | +| Initial value of parameter P33 | $sin(-5.9)$ | constant | +| Initial value of parameter P34 | $tan(0)$ | constant | +| Initial value of parameter P35 | $tan(1.11)$ | constant | +| Initial value of parameter P36 | $tan(-6)$ | constant | +| Initial value of parameter P37 | $1 + 2$ | constant | +| Initial value of parameter P38 | $1 - 2$ | constant | +| Initial value of parameter P39 | $5 / 2$ | constant | +| Initial value of parameter P40 | $8 * 3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +P1 @Record { } .= 3.7; +P2 @Record { } .= abs((-1)); +P3 @Record { } .= abs(1); +P4 @Record { } .= acos((-1)); +P5 @Record { } .= acos(0.5); +P6 @Record { } .= asin(1); +P7 @Record { } .= asin((-0.5)); +P8 @Record { } .= atan(2.8); +P9 @Record { } .= atan((-7.09)); +P10 @Record { } .= ceil(0.5); +P11 @Record { } .= ceil(3.55); +P12 @Record { } .= ceil((-4.6)); +P13 @Record { } .= cos(9.1); +P14 @Record { } .= cos((-0.22)); +P15 @Record { } .= exp(0); +P16 @Record { } .= exp(1); +P17 @Record { } .= exp(0.77); +P18 @Record { } .= floor((-4.6)); +P19 @Record { } .= floor(9.1); +P20 @Record { } .= ln(0.2); +P21 @Record { } .= ln(1); +P22 @Record { } .= logbase(0.2, 10); +P23 @Record { } .= logbase(1, 10); +P24 @Record { } .= pow(1, 2); +P25 @Record { } .= pow(2, 2); +P26 @Record { } .= pow(1.4, 5.1); +P27 @Record { } .= pow(4, 2); +P28 @Record { } .= pow(3.1, 2); +P29 @Record { } .= pow(4, 1 / 2); +P30 @Record { } .= pow(7.4, 1 / 2); +P31 @Record { } .= sin(2.1); +P32 @Record { } .= sin(0); +P33 @Record { } .= sin((-5.9)); +P34 @Record { } .= tan(0); +P35 @Record { } .= tan(1.11); +P36 @Record { } .= tan((-6)); +P37 @Record { } .= 1 + 2; +P38 @Record { } .= 1 - 2; +P39 @Record { } .= 5 / 2; +P40 @Record { } .= 8 * 3; + diff --git a/latest/cases/00956/synopsis.txt b/latest/cases/00956/synopsis.txt new file mode 100644 index 000000000..8d5ef66db --- /dev/null +++ b/latest/cases/00956/synopsis.txt @@ -0,0 +1,60 @@ + +category: Test +synopsis: Several parameters with initial assignment rules, testing various L1 built-in functions acting on constants. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + The model tests the various mathematical constructs present in L1, used in InitialAssignments. + +The model contains: +* 40 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $3.7$ | constant | +| Initial value of parameter P2 | $abs(-1)$ | constant | +| Initial value of parameter P3 | $abs(1)$ | constant | +| Initial value of parameter P4 | $acos(-1)$ | constant | +| Initial value of parameter P5 | $acos(0.5)$ | constant | +| Initial value of parameter P6 | $asin(1)$ | constant | +| Initial value of parameter P7 | $asin(-0.5)$ | constant | +| Initial value of parameter P8 | $atan(2.8)$ | constant | +| Initial value of parameter P9 | $atan(-7.09)$ | constant | +| Initial value of parameter P10 | $ceil(0.5)$ | constant | +| Initial value of parameter P11 | $ceil(3.55)$ | constant | +| Initial value of parameter P12 | $ceil(-4.6)$ | constant | +| Initial value of parameter P13 | $cos(9.1)$ | constant | +| Initial value of parameter P14 | $cos(-0.22)$ | constant | +| Initial value of parameter P15 | $exp(0)$ | constant | +| Initial value of parameter P16 | $exp(1)$ | constant | +| Initial value of parameter P17 | $exp(0.77)$ | constant | +| Initial value of parameter P18 | $floor(-4.6)$ | constant | +| Initial value of parameter P19 | $floor(9.1)$ | constant | +| Initial value of parameter P20 | $log(0.2)$ | constant | +| Initial value of parameter P21 | $log(1)$ | constant | +| Initial value of parameter P22 | $log10(0.2)$ | constant | +| Initial value of parameter P23 | $log10(1)$ | constant | +| Initial value of parameter P24 | $pow(1, 2)$ | constant | +| Initial value of parameter P25 | $pow(2, 2)$ | constant | +| Initial value of parameter P26 | $pow(1.4, 5.1)$ | constant | +| Initial value of parameter P27 | $pow(4, 2)$ | constant | +| Initial value of parameter P28 | $pow(3.1, 2)$ | constant | +| Initial value of parameter P29 | $sqrt(4)$ | constant | +| Initial value of parameter P30 | $sqrt(7.4)$ | constant | +| Initial value of parameter P31 | $sin(2.1)$ | constant | +| Initial value of parameter P32 | $sin(0)$ | constant | +| Initial value of parameter P33 | $sin(-5.9)$ | constant | +| Initial value of parameter P34 | $tan(0)$ | constant | +| Initial value of parameter P35 | $tan(1.11)$ | constant | +| Initial value of parameter P36 | $tan(-6)$ | constant | +| Initial value of parameter P37 | $1 + 2$ | constant | +| Initial value of parameter P38 | $1 - 2$ | constant | +| Initial value of parameter P39 | $5 / 2$ | constant | +| Initial value of parameter P40 | $8 * 3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00957/l2v5/build.log b/latest/cases/00957/l2v5/build.log new file mode 100644 index 000000000..284401eff --- /dev/null +++ b/latest/cases/00957/l2v5/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00957/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00957/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00957/model-sbml-l2v5.xml"... +[info] Setting references in elements, total length 112 +[error] FunctionDef "sinh" is not found as expected here: P17 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: P18 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: P22 { math: undefined }; +[error] FunctionDef "acosh" is not found as expected here: P23 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: P24 { math: undefined }; +[error] FunctionDef "asech" is not found as expected here: P25 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: P26 { math: undefined }; +[error] FunctionDef "acoth" is not found as expected here: P27 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00957/l2v5/index.heta b/latest/cases/00957/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00957/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00957/l3v2/build.log b/latest/cases/00957/l3v2/build.log new file mode 100644 index 000000000..7e818b766 --- /dev/null +++ b/latest/cases/00957/l3v2/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00957/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00957/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00957/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 107 +[error] FunctionDef "sinh" is not found as expected here: P17 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: P18 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: P22 { math: undefined }; +[error] FunctionDef "acosh" is not found as expected here: P23 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: P24 { math: undefined }; +[error] FunctionDef "asech" is not found as expected here: P25 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: P26 { math: undefined }; +[error] FunctionDef "acoth" is not found as expected here: P27 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00957/l3v2/index.heta b/latest/cases/00957/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00957/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00957/model-sbml-l2v5.xml b/latest/cases/00957/model-sbml-l2v5.xml new file mode 100644 index 000000000..678dc224c --- /dev/null +++ b/latest/cases/00957/model-sbml-l2v5.xml @@ -0,0 +1,361 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + P1 + + + + + 3 + + + + + + + + + 2 + + + P1 + + + + + 3 + + + + + + + + + 4 + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + 3 + + + + + + + + + 0.5 + + + + + + + + 4.5 + + + + + + + + 0.2 + + + + + + + + 0.3 + + + + + + + + 1.7 + + + + + + + + 2.3 + + + + + + + + 1.1 + + + + + + + + -0.1 + + + + + + + + 99 + + + + + + + + 1.34 + + + + + + + + -0.7 + + + + + + + + 0.42 + + + + + + + + 0.01 + + + + + + + + 8.2 + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/00957/model-sbml-l3v2.xml b/latest/cases/00957/model-sbml-l3v2.xml new file mode 100644 index 000000000..8a51a3a80 --- /dev/null +++ b/latest/cases/00957/model-sbml-l3v2.xml @@ -0,0 +1,361 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + P1 + + + + + 3 + + + + + + + + + 2 + + + P1 + + + + + 3 + + + + + + + + + 4 + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + 3 + + + + + + + + + 0.5 + + + + + + + + 4.5 + + + + + + + + 0.2 + + + + + + + + 0.3 + + + + + + + + 1.7 + + + + + + + + 2.3 + + + + + + + + 1.1 + + + + + + + + -0.1 + + + + + + + + 99 + + + + + + + + 1.34 + + + + + + + + -0.7 + + + + + + + + 0.42 + + + + + + + + 0.01 + + + + + + + + 8.2 + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/00957/synopsis.txt b/latest/cases/00957/synopsis.txt new file mode 100644 index 000000000..78e4adf53 --- /dev/null +++ b/latest/cases/00957/synopsis.txt @@ -0,0 +1,81 @@ + +category: Test +synopsis: Several parameters with assignment rules, testing various L2v1 built-in functions acting on constants. +componentTags: AssignmentRule, Parameter +testTags: NonConstantParameter, InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +The model tests the various mathematical constructs added in the L2v1 specification. + +The model contains: +* 28 parameters (P1, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29) + +There are 28 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $pi$ | +| Assignment | P3 | $piecewise(2, gt(1, 0.5), 3)$ | +| Assignment | P4 | $piecewise(2, geq(1, 0.5), 3)$ | +| Assignment | P5 | $piecewise(2, lt(1, 0.5), 3)$ | +| Assignment | P6 | $piecewise(2, leq(1, 0.5), 3)$ | +| Assignment | P7 | $piecewise(2, eq(P1, pi), 3)$ | +| Assignment | P8 | $piecewise(2, neq(P1, pi), 3)$ | +| Assignment | P9 | $factorial(4)$ | +| Assignment | P10 | $piecewise(2, and(true, false), 3)$ | +| Assignment | P11 | $piecewise(2, or(true, false), 3)$ | +| Assignment | P12 | $piecewise(2, xor(true, false), 3)$ | +| Assignment | P13 | $piecewise(2, not(false), 3)$ | +| Assignment | P14 | $sec(0.5)$ | +| Assignment | P15 | $csc(4.5)$ | +| Assignment | P16 | $cot(0.2)$ | +| Assignment | P17 | $sinh(0.3)$ | +| Assignment | P18 | $cosh(1.7)$ | +| Assignment | P19 | $arcsec(2.3)$ | +| Assignment | P20 | $arccsc(1.1)$ | +| Assignment | P21 | $arccot(-0.1)$ | +| Assignment | P22 | $arcsinh(99)$ | +| Assignment | P23 | $arccosh(1.34)$ | +| Assignment | P24 | $arctanh(-0.7)$ | +| Assignment | P25 | $arcsech(0.42)$ | +| Assignment | P26 | $arccsch(0.01)$ | +| Assignment | P27 | $arccoth(8.2)$ | +| Assignment | P28 | $exponentiale$ | +| Assignment | P29 | $exp(exponentiale)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $pi$ | variable | +| Initial value of parameter P3 | $piecewise(2, gt(1, 0.5), 3)$ | variable | +| Initial value of parameter P4 | $piecewise(2, geq(1, 0.5), 3)$ | variable | +| Initial value of parameter P5 | $piecewise(2, lt(1, 0.5), 3)$ | variable | +| Initial value of parameter P6 | $piecewise(2, leq(1, 0.5), 3)$ | variable | +| Initial value of parameter P7 | $piecewise(2, eq(P1, pi), 3)$ | variable | +| Initial value of parameter P8 | $piecewise(2, neq(P1, pi), 3)$ | variable | +| Initial value of parameter P9 | $factorial(4)$ | variable | +| Initial value of parameter P10 | $piecewise(2, and(true, false), 3)$ | variable | +| Initial value of parameter P11 | $piecewise(2, or(true, false), 3)$ | variable | +| Initial value of parameter P12 | $piecewise(2, xor(true, false), 3)$ | variable | +| Initial value of parameter P13 | $piecewise(2, not(false), 3)$ | variable | +| Initial value of parameter P14 | $sec(0.5)$ | variable | +| Initial value of parameter P15 | $csc(4.5)$ | variable | +| Initial value of parameter P16 | $cot(0.2)$ | variable | +| Initial value of parameter P17 | $sinh(0.3)$ | variable | +| Initial value of parameter P18 | $cosh(1.7)$ | variable | +| Initial value of parameter P19 | $arcsec(2.3)$ | variable | +| Initial value of parameter P20 | $arccsc(1.1)$ | variable | +| Initial value of parameter P21 | $arccot(-0.1)$ | variable | +| Initial value of parameter P22 | $arcsinh(99)$ | variable | +| Initial value of parameter P23 | $arccosh(1.34)$ | variable | +| Initial value of parameter P24 | $arctanh(-0.7)$ | variable | +| Initial value of parameter P25 | $arcsech(0.42)$ | variable | +| Initial value of parameter P26 | $arccsch(0.01)$ | variable | +| Initial value of parameter P27 | $arccoth(8.2)$ | variable | +| Initial value of parameter P28 | $exponentiale$ | variable | +| Initial value of parameter P29 | $exp(exponentiale)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00958/l2v5/build.log b/latest/cases/00958/l2v5/build.log new file mode 100644 index 000000000..77fb4a23b --- /dev/null +++ b/latest/cases/00958/l2v5/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00958/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00958/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00958/model-sbml-l2v5.xml"... +[info] Setting references in elements, total length 112 +[error] FunctionDef "sinh" is not found as expected here: P17 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: P18 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: P22 { math: undefined }; +[error] FunctionDef "acosh" is not found as expected here: P23 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: P24 { math: undefined }; +[error] FunctionDef "asech" is not found as expected here: P25 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: P26 { math: undefined }; +[error] FunctionDef "acoth" is not found as expected here: P27 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00958/l2v5/index.heta b/latest/cases/00958/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00958/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00958/l3v2/build.log b/latest/cases/00958/l3v2/build.log new file mode 100644 index 000000000..38b980a51 --- /dev/null +++ b/latest/cases/00958/l3v2/build.log @@ -0,0 +1,36 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00958/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00958/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00958/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 107 +[error] No required "num" property for "P1" of Const. +[error] No required "num" property for "P3" of Const. +[error] No required "num" property for "P4" of Const. +[error] No required "num" property for "P5" of Const. +[error] No required "num" property for "P6" of Const. +[error] No required "num" property for "P7" of Const. +[error] No required "num" property for "P8" of Const. +[error] No required "num" property for "P9" of Const. +[error] No required "num" property for "P10" of Const. +[error] No required "num" property for "P11" of Const. +[error] No required "num" property for "P12" of Const. +[error] No required "num" property for "P13" of Const. +[error] No required "num" property for "P14" of Const. +[error] No required "num" property for "P15" of Const. +[error] No required "num" property for "P16" of Const. +[error] No required "num" property for "P17" of Const. +[error] No required "num" property for "P18" of Const. +[error] No required "num" property for "P19" of Const. +[error] No required "num" property for "P20" of Const. +[error] No required "num" property for "P21" of Const. +[error] No required "num" property for "P22" of Const. +[error] No required "num" property for "P23" of Const. +[error] No required "num" property for "P24" of Const. +[error] No required "num" property for "P25" of Const. +[error] No required "num" property for "P26" of Const. +[error] No required "num" property for "P27" of Const. +[error] No required "num" property for "P28" of Const. +[error] No required "num" property for "P29" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00958/l3v2/index.heta b/latest/cases/00958/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00958/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00958/model-sbml-l2v5.xml b/latest/cases/00958/model-sbml-l2v5.xml new file mode 100644 index 000000000..f2fef1095 --- /dev/null +++ b/latest/cases/00958/model-sbml-l2v5.xml @@ -0,0 +1,361 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + P1 + + + + + 3 + + + + + + + + + 2 + + + P1 + + + + + 3 + + + + + + + + + 4 + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + 3 + + + + + + + + + 0.5 + + + + + + + + 4.5 + + + + + + + + 0.2 + + + + + + + + 0.3 + + + + + + + + 1.7 + + + + + + + + 2.3 + + + + + + + + 1.1 + + + + + + + + -0.1 + + + + + + + + 99 + + + + + + + + 1.34 + + + + + + + + -0.7 + + + + + + + + 0.42 + + + + + + + + 0.01 + + + + + + + + 8.2 + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/00958/model-sbml-l3v2.xml b/latest/cases/00958/model-sbml-l3v2.xml new file mode 100644 index 000000000..2df0affb4 --- /dev/null +++ b/latest/cases/00958/model-sbml-l3v2.xml @@ -0,0 +1,361 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + 1 + 0.5 + + + + 3 + + + + + + + + + 2 + + + P1 + + + + + 3 + + + + + + + + + 2 + + + P1 + + + + + 3 + + + + + + + + + 4 + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + + 3 + + + + + + + + + 2 + + + + + + + 3 + + + + + + + + + 0.5 + + + + + + + + 4.5 + + + + + + + + 0.2 + + + + + + + + 0.3 + + + + + + + + 1.7 + + + + + + + + 2.3 + + + + + + + + 1.1 + + + + + + + + -0.1 + + + + + + + + 99 + + + + + + + + 1.34 + + + + + + + + -0.7 + + + + + + + + 0.42 + + + + + + + + 0.01 + + + + + + + + 8.2 + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/00958/synopsis.txt b/latest/cases/00958/synopsis.txt new file mode 100644 index 000000000..6986264b6 --- /dev/null +++ b/latest/cases/00958/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Several parameters with initial assignments, testing various L2v1 built-in functions acting on constants. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + The model tests the various mathematical constructs added in L2v1, as initial assignments. As such, the results are identical to case 957. + +The model contains: +* 28 parameters (P1, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $pi$ | constant | +| Initial value of parameter P3 | $piecewise(2, gt(1, 0.5), 3)$ | constant | +| Initial value of parameter P4 | $piecewise(2, geq(1, 0.5), 3)$ | constant | +| Initial value of parameter P5 | $piecewise(2, lt(1, 0.5), 3)$ | constant | +| Initial value of parameter P6 | $piecewise(2, leq(1, 0.5), 3)$ | constant | +| Initial value of parameter P7 | $piecewise(2, eq(P1, pi), 3)$ | constant | +| Initial value of parameter P8 | $piecewise(2, neq(P1, pi), 3)$ | constant | +| Initial value of parameter P9 | $factorial(4)$ | constant | +| Initial value of parameter P10 | $piecewise(2, and(true, false), 3)$ | constant | +| Initial value of parameter P11 | $piecewise(2, or(true, false), 3)$ | constant | +| Initial value of parameter P12 | $piecewise(2, xor(true, false), 3)$ | constant | +| Initial value of parameter P13 | $piecewise(2, not(false), 3)$ | constant | +| Initial value of parameter P14 | $sec(0.5)$ | constant | +| Initial value of parameter P15 | $csc(4.5)$ | constant | +| Initial value of parameter P16 | $cot(0.2)$ | constant | +| Initial value of parameter P17 | $sinh(0.3)$ | constant | +| Initial value of parameter P18 | $cosh(1.7)$ | constant | +| Initial value of parameter P19 | $arcsec(2.3)$ | constant | +| Initial value of parameter P20 | $arccsc(1.1)$ | constant | +| Initial value of parameter P21 | $arccot(-0.1)$ | constant | +| Initial value of parameter P22 | $arcsinh(99)$ | constant | +| Initial value of parameter P23 | $arccosh(1.34)$ | constant | +| Initial value of parameter P24 | $arctanh(-0.7)$ | constant | +| Initial value of parameter P25 | $arcsech(0.42)$ | constant | +| Initial value of parameter P26 | $arccsch(0.01)$ | constant | +| Initial value of parameter P27 | $arccoth(8.2)$ | constant | +| Initial value of parameter P28 | $exponentiale$ | constant | +| Initial value of parameter P29 | $exp(exponentiale)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00959/l2v5/build.log b/latest/cases/00959/l2v5/build.log new file mode 100644 index 000000000..32c4033aa --- /dev/null +++ b/latest/cases/00959/l2v5/build.log @@ -0,0 +1,22 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00959/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00959/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00959/model-sbml-l2v5.xml"... +[info] Setting references in elements, total length 110 +[error] FunctionDef "sinh" is not found as expected here: P7 { math: undefined }; +[error] FunctionDef "sinh" is not found as expected here: P8 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: P9 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: P10 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: P17 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: P18 { math: undefined }; +[error] FunctionDef "acosh" is not found as expected here: P19 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: P20 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: P21 { math: undefined }; +[error] FunctionDef "asech" is not found as expected here: P22 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: P23 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: P24 { math: undefined }; +[error] FunctionDef "acoth" is not found as expected here: P25 { math: undefined }; +[error] FunctionDef "acoth" is not found as expected here: P26 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00959/l2v5/index.heta b/latest/cases/00959/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00959/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00959/l3v2/build.log b/latest/cases/00959/l3v2/build.log new file mode 100644 index 000000000..ad90bb5bd --- /dev/null +++ b/latest/cases/00959/l3v2/build.log @@ -0,0 +1,22 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00959/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00959/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00959/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 105 +[error] FunctionDef "sinh" is not found as expected here: P7 { math: undefined }; +[error] FunctionDef "sinh" is not found as expected here: P8 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: P9 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: P10 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: P17 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: P18 { math: undefined }; +[error] FunctionDef "acosh" is not found as expected here: P19 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: P20 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: P21 { math: undefined }; +[error] FunctionDef "asech" is not found as expected here: P22 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: P23 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: P24 { math: undefined }; +[error] FunctionDef "acoth" is not found as expected here: P25 { math: undefined }; +[error] FunctionDef "acoth" is not found as expected here: P26 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00959/l3v2/index.heta b/latest/cases/00959/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00959/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00959/model-sbml-l2v5.xml b/latest/cases/00959/model-sbml-l2v5.xml new file mode 100644 index 000000000..278820cea --- /dev/null +++ b/latest/cases/00959/model-sbml-l2v5.xml @@ -0,0 +1,396 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + 1.001 + + + + + + + + + + + time + 1.001 + + + + + + + + + + + + + time + + 1 + + + + + + + + + + + time + 1 + + + + + + + + + 0 + + + + + time + 0 + + + + time + 1 + + + + + + + time + + + + + + + + + + + + + + time + + + + + time + 1 + + + + -10 + + + + + + + + + + + time + + + + time + 1 + + + + 10 + + + + + + + + + + + time + 1 + + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + + + time + + 0.001 + + + + + + + + + + + time + 0.001 + + + + + + + + + + + + + time + + 1 + + + + + + + + + + + time + 1 + + + + + + + + + + + + + time + + 1 + + + + + + + + + + + time + 1 + + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + + + time + + 0.001 + + + + + + + + + + + time + 0.001 + + + + + + + + + + + + + time + + 0.001 + + + + + + + + + + + time + 0.001 + + + + + + + + + + + time + + + + + + + + + time + + + + + + diff --git a/latest/cases/00959/model-sbml-l3v2.xml b/latest/cases/00959/model-sbml-l3v2.xml new file mode 100644 index 000000000..88c38945b --- /dev/null +++ b/latest/cases/00959/model-sbml-l3v2.xml @@ -0,0 +1,395 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + 1.001 + + + + + + + + + + + time + 1.001 + + + + + + + + + + + + + time + + 1 + + + + + + + + + + + time + 1 + + + + + + + + + 0 + + + + + time + 0 + + + + time + 1 + + + + + + + time + + + + + + + + + + + + + + time + + + + + time + 1 + + + + -10 + + + + + + + + + + + time + + + + time + 1 + + + + 10 + + + + + + + + + + + time + 1 + + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + + + time + + 0.001 + + + + + + + + + + + time + 0.001 + + + + + + + + + + + + + time + + 1 + + + + + + + + + + + time + 1 + + + + + + + + + + + + + time + + 1 + + + + + + + + + + + time + 1 + + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + time + + + + + + + + + time + + + + + + + + + + + + time + + 0.001 + + + + + + + + + + + time + 0.001 + + + + + + + + + + + + + time + + 0.001 + + + + + + + + + + + time + 0.001 + + + + + + + + + + + time + + + + + + + + + time + + + + + + diff --git a/latest/cases/00959/synopsis.txt b/latest/cases/00959/synopsis.txt new file mode 100644 index 000000000..e6d0e52b0 --- /dev/null +++ b/latest/cases/00959/synopsis.txt @@ -0,0 +1,78 @@ + +category: Test +synopsis: Several parameters with trigonometric assignment rules, testing various L2v1 built-in functions acting on parameters. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various trigonometrical constructs added in L2v1, as assignment rules with time. Some functions with weird boundary conditions have been set up with the 'piecewise' function so that the results are never 'inf', or 'nan'. + +The model contains: +* 26 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26) + +There are 26 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $sec(time)$ | +| Assignment | P2 | $sec(-time)$ | +| Assignment | P3 | $csc(time + 0.001)$ | +| Assignment | P4 | $csc(-time - 0.001)$ | +| Assignment | P5 | $cot(time + 0.001)$ | +| Assignment | P6 | $cot(-time - 0.001)$ | +| Assignment | P7 | $sinh(time)$ | +| Assignment | P8 | $sinh(-time)$ | +| Assignment | P9 | $cosh(time)$ | +| Assignment | P10 | $cosh(-time)$ | +| Assignment | P11 | $arcsec(time + 1)$ | +| Assignment | P12 | $arcsec(-time - 1)$ | +| Assignment | P13 | $arccsc(time + 1)$ | +| Assignment | P14 | $arccsc(-time - 1)$ | +| Assignment | P15 | $arccot(time + 0.001)$ | +| Assignment | P16 | $arccot(-time - 0.001)$ | +| Assignment | P17 | $arcsinh(time)$ | +| Assignment | P18 | $arcsinh(-time)$ | +| Assignment | P19 | $arccosh(time + 1)$ | +| Assignment | P20 | $piecewise(arctanh(time), lt(time, 1), 10)$ | +| Assignment | P21 | $piecewise(arctanh(-time), lt(time, 1), -10)$ | +| Assignment | P22 | $piecewise(0, or(leq(time, 0), geq(time, 1)), arcsech(time))$ | +| Assignment | P23 | $arccsch(time + 1)$ | +| Assignment | P24 | $arccsch(-time - 1)$ | +| Assignment | P25 | $arccoth(time + 1.001)$ | +| Assignment | P26 | $arccoth(-time - 1.001)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $sec(time)$ | variable | +| Initial value of parameter P2 | $sec(-time)$ | variable | +| Initial value of parameter P3 | $csc(time + 0.001)$ | variable | +| Initial value of parameter P4 | $csc(-time - 0.001)$ | variable | +| Initial value of parameter P5 | $cot(time + 0.001)$ | variable | +| Initial value of parameter P6 | $cot(-time - 0.001)$ | variable | +| Initial value of parameter P7 | $sinh(time)$ | variable | +| Initial value of parameter P8 | $sinh(-time)$ | variable | +| Initial value of parameter P9 | $cosh(time)$ | variable | +| Initial value of parameter P10 | $cosh(-time)$ | variable | +| Initial value of parameter P11 | $arcsec(time + 1)$ | variable | +| Initial value of parameter P12 | $arcsec(-time - 1)$ | variable | +| Initial value of parameter P13 | $arccsc(time + 1)$ | variable | +| Initial value of parameter P14 | $arccsc(-time - 1)$ | variable | +| Initial value of parameter P15 | $arccot(time + 0.001)$ | variable | +| Initial value of parameter P16 | $arccot(-time - 0.001)$ | variable | +| Initial value of parameter P17 | $arcsinh(time)$ | variable | +| Initial value of parameter P18 | $arcsinh(-time)$ | variable | +| Initial value of parameter P19 | $arccosh(time + 1)$ | variable | +| Initial value of parameter P20 | $piecewise(arctanh(time), time < 1, 10)$ | variable | +| Initial value of parameter P21 | $piecewise(arctanh(-time), time < 1, -10)$ | variable | +| Initial value of parameter P22 | $piecewise(0, (time <= 0) || (time >= 1), arcsech(time))$ | variable | +| Initial value of parameter P23 | $arccsch(time + 1)$ | variable | +| Initial value of parameter P24 | $arccsch(-time - 1)$ | variable | +| Initial value of parameter P25 | $arccoth(time + 1.001)$ | variable | +| Initial value of parameter P26 | $arccoth(-time - 1.001)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00960/l2v5/index.heta b/latest/cases/00960/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00960/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00960/l3v2/build.log b/latest/cases/00960/l3v2/build.log new file mode 100644 index 000000000..b95e960cf --- /dev/null +++ b/latest/cases/00960/l3v2/build.log @@ -0,0 +1,13 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00960/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00960/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00960/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 84 +[error] No required "num" property for "P1" of Const. +[error] No required "num" property for "P2" of Const. +[error] No required "num" property for "P3" of Const. +[error] No required "num" property for "P4" of Const. +[error] No required "num" property for "P5" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00960/l3v2/index.heta b/latest/cases/00960/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00960/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00960/model-sbml-l3v2.xml b/latest/cases/00960/model-sbml-l3v2.xml new file mode 100644 index 000000000..5ca7728a0 --- /dev/null +++ b/latest/cases/00960/model-sbml-l3v2.xml @@ -0,0 +1,60 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + avogadro + + + + + time + + + + + delay + + + + + + + + + + + + avogadro + 6.0221 23 + + + + + + diff --git a/latest/cases/00960/synopsis.txt b/latest/cases/00960/synopsis.txt new file mode 100644 index 000000000..10ffd44b7 --- /dev/null +++ b/latest/cases/00960/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Four different ways of writing the avogadro number in an initial assignment. +componentTags: CSymbolAvogadro, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model assigns avogadro's number as a csymbol to four parameters. It tries to fool you by calling two of them 'time' and 'delay', and by not giving one a name at all. + +To test that the value of avogadro is the same as is in the specification without requiring that you write out all 9 digits of precision, a fifth parameter is added with the value (avogadro - 6.0221e+23). + +The model contains: +* 5 parameters (P1, P2, P3, P4, P5) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $avogadro$ | constant | +| Initial value of parameter P2 | $time$ | constant | +| Initial value of parameter P3 | $delay$ | constant | +| Initial value of parameter P4 | $$ | constant | +| Initial value of parameter P5 | $avogadro - 6.022100e+023$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00961/l2v5/index.heta b/latest/cases/00961/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00961/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00961/l3v2/heta-code/output.heta b/latest/cases/00961/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a65908e4f --- /dev/null +++ b/latest/cases/00961/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +P1 @Record { }; +P1 := 6.02214076e+23; +P2 @Record { }; +P2 := 6.02214076e+23; +P3 @Record { }; +P3 := 6.02214076e+23; +P4 @Record { }; +P4 := 6.02214076e+23; +P5 @Record { }; +P5 := 6.02214076e+23 - (6.0221e+23); + diff --git a/latest/cases/00961/l3v2/index.heta b/latest/cases/00961/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00961/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00961/l3v2/json/output.json b/latest/cases/00961/l3v2/json/output.json new file mode 100644 index 000000000..b67935310 --- /dev/null +++ b/latest/cases/00961/l3v2/json/output.json @@ -0,0 +1,40 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "ode_": "6.02214076e+23" + } + }, + { + "class": "Record", + "id": "P2", + "assignments": { + "ode_": "6.02214076e+23" + } + }, + { + "class": "Record", + "id": "P3", + "assignments": { + "ode_": "6.02214076e+23" + } + }, + { + "class": "Record", + "id": "P4", + "assignments": { + "ode_": "6.02214076e+23" + } + }, + { + "class": "Record", + "id": "P5", + "assignments": { + "ode_": "6.02214076e+23 - (6.0221e+23)" + } + } +] \ No newline at end of file diff --git a/latest/cases/00961/model-sbml-l3v2.xml b/latest/cases/00961/model-sbml-l3v2.xml new file mode 100644 index 000000000..e479597c1 --- /dev/null +++ b/latest/cases/00961/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + avogadro + + + + + time + + + + + delay + + + + + + + + + + + + avogadro + 6.0221 23 + + + + + + diff --git a/latest/cases/00961/output.heta b/latest/cases/00961/output.heta new file mode 100644 index 000000000..5a5c42f9f --- /dev/null +++ b/latest/cases/00961/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Four different ways of writing the avogadro number in an assignment rule. +componentTags: AssignmentRule, CSymbolAvogadro, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model assigns avogadro's number as a csymbol to four parameters in an assignment rule. It tries to fool you by calling two of them 'time' and 'delay', and by not giving one a name at all. + +To test that the value of avogadro is the same as is in the specification without requiring that you write out all 9 digits of precision, a fifth parameter is added with the value (avogadro - 6.0221e+23). + +The model contains: +* 5 parameters (P1, P2, P3, P4, P5) + +There are 5 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $avogadro$ | +| Assignment | P2 | $time$ | +| Assignment | P3 | $delay$ | +| Assignment | P4 | $$ | +| Assignment | P5 | $avogadro - 6.022100e+023$ |] + + Note: All parameters actually assigned the CSymbol 'avogadro', but the text is different for the first four cases. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $avogadro$ | variable | +| Initial value of parameter P2 | $time$ | variable | +| Initial value of parameter P3 | $delay$ | variable | +| Initial value of parameter P4 | $$ | variable | +| Initial value of parameter P5 | $avogadro - 6.022100e+023$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P1 @Record { }; +P1 := 6.02214076e+23; +P2 @Record { }; +P2 := 6.02214076e+23; +P3 @Record { }; +P3 := 6.02214076e+23; +P4 @Record { }; +P4 := 6.02214076e+23; +P5 @Record { }; +P5 := 6.02214076e+23 - (6.0221e+23); + diff --git a/latest/cases/00961/synopsis.txt b/latest/cases/00961/synopsis.txt new file mode 100644 index 000000000..f75a5863e --- /dev/null +++ b/latest/cases/00961/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Four different ways of writing the avogadro number in an assignment rule. +componentTags: AssignmentRule, CSymbolAvogadro, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model assigns avogadro's number as a csymbol to four parameters in an assignment rule. It tries to fool you by calling two of them 'time' and 'delay', and by not giving one a name at all. + +To test that the value of avogadro is the same as is in the specification without requiring that you write out all 9 digits of precision, a fifth parameter is added with the value (avogadro - 6.0221e+23). + +The model contains: +* 5 parameters (P1, P2, P3, P4, P5) + +There are 5 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $avogadro$ | +| Assignment | P2 | $time$ | +| Assignment | P3 | $delay$ | +| Assignment | P4 | $$ | +| Assignment | P5 | $avogadro - 6.022100e+023$ |] + + Note: All parameters actually assigned the CSymbol 'avogadro', but the text is different for the first four cases. + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $avogadro$ | variable | +| Initial value of parameter P2 | $time$ | variable | +| Initial value of parameter P3 | $delay$ | variable | +| Initial value of parameter P4 | $$ | variable | +| Initial value of parameter P5 | $avogadro - 6.022100e+023$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00962/l2v5/index.heta b/latest/cases/00962/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00962/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00962/l3v2/heta-code/output.heta b/latest/cases/00962/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5c7740237 --- /dev/null +++ b/latest/cases/00962/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +maxdiff @Record { } .= 0; +maxdiff [maxcheck]= abs(Q - R); +error @Record { } .= 0; +error [error_check]= 1; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +maxcheck @DSwitcher { trigger: abs(Q - R) > maxdiff, }; +error_check @DSwitcher { trigger: t >= 99 and maxdiff < 0.2, }; + diff --git a/latest/cases/00962/l3v2/index.heta b/latest/cases/00962/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00962/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00962/l3v2/json/output.json b/latest/cases/00962/l3v2/json/output.json new file mode 100644 index 000000000..9b2bcb939 --- /dev/null +++ b/latest/cases/00962/l3v2/json/output.json @@ -0,0 +1,74 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S", + "assignments": { + "start_": "0", + "ode_": "Q + R" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "0", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "0", + "Rinc": "R + 0.01" + } + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Qinc": "t", + "Rinc": "t" + } + }, + { + "class": "Record", + "id": "maxdiff", + "assignments": { + "start_": "0", + "maxcheck": "abs(Q - R)" + } + }, + { + "class": "Record", + "id": "error", + "assignments": { + "start_": "0", + "error_check": "1" + } + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "maxcheck", + "trigger": "abs(Q - R) > maxdiff" + }, + { + "class": "DSwitcher", + "id": "error_check", + "trigger": "t >= 99 and maxdiff < 0.2" + } +] \ No newline at end of file diff --git a/latest/cases/00962/model-sbml-l3v2.xml b/latest/cases/00962/model-sbml-l3v2.xml new file mode 100644 index 000000000..2009a2bc9 --- /dev/null +++ b/latest/cases/00962/model-sbml-l3v2.xml @@ -0,0 +1,156 @@ + + + + + + + + + + + + + + + + + Q + R + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 1 + + + + + + time + + + + + + + Q + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 1 + + + + + + time + + + + + + + R + 0.01 + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00962/output.heta b/latest/cases/00962/output.heta new file mode 100644 index 000000000..6230501b4 --- /dev/null +++ b/latest/cases/00962/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. + + Note: The 'error' parameter is a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The value of '0.2' was chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events exactly evenly. + +The model contains: +* 6 parameters (S, Q, R, reset, maxdiff, error) + +There are 4 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ | +| maxcheck | $gt(abs(Q - R), maxdiff)$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $and(geq(time, 99), lt(maxdiff, 0.2))$ | (unset) | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +maxdiff @Record { } .= 0; +maxdiff [maxcheck]= abs(Q - R); +error @Record { } .= 0; +error [error_check]= 1; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +maxcheck @DSwitcher { trigger: abs(Q - R) > maxdiff, }; +error_check @DSwitcher { trigger: t >= 99 and maxdiff < 0.2, }; + diff --git a/latest/cases/00962/synopsis.txt b/latest/cases/00962/synopsis.txt new file mode 100644 index 000000000..e0f9b6731 --- /dev/null +++ b/latest/cases/00962/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. + + Note: The 'error' parameter is a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The value of '0.2' was chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events exactly evenly. + +The model contains: +* 6 parameters (S, Q, R, reset, maxdiff, error) + +There are 4 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ | +| maxcheck | $gt(abs(Q - R), maxdiff)$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $and(geq(time, 99), lt(maxdiff, 0.2))$ | (unset) | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00963/l2v5/index.heta b/latest/cases/00963/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00963/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00963/l3v2/heta-code/output.heta b/latest/cases/00963/l3v2/heta-code/output.heta new file mode 100644 index 000000000..82218d7bf --- /dev/null +++ b/latest/cases/00963/l3v2/heta-code/output.heta @@ -0,0 +1,24 @@ + + +t @TimeScale { units: second, }; + +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +Q2 @Record { } .= 0; +Q2 [Qinc2]= Q2 + 0.01; +R2 @Record { } .= 0; +R2 [Rinc2]= R2 + 0.01; +reset2 @Record { } .= 0; +reset2 [Qinc2]= t; +reset2 [Rinc2]= t; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Qinc2 @DSwitcher { trigger: (t - reset2) >= 0.01, }; +Rinc2 @DSwitcher { trigger: (t - reset2) >= 0.01, }; + diff --git a/latest/cases/00963/l3v2/index.heta b/latest/cases/00963/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00963/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00963/l3v2/json/output.json b/latest/cases/00963/l3v2/json/output.json new file mode 100644 index 000000000..218709ded --- /dev/null +++ b/latest/cases/00963/l3v2/json/output.json @@ -0,0 +1,76 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "0", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "0", + "Rinc": "R + 0.01" + } + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Qinc": "t", + "Rinc": "t" + } + }, + { + "class": "Record", + "id": "Q2", + "assignments": { + "start_": "0", + "Qinc2": "Q2 + 0.01" + } + }, + { + "class": "Record", + "id": "R2", + "assignments": { + "start_": "0", + "Rinc2": "R2 + 0.01" + } + }, + { + "class": "Record", + "id": "reset2", + "assignments": { + "start_": "0", + "Qinc2": "t", + "Rinc2": "t" + } + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Qinc2", + "trigger": "(t - reset2) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc2", + "trigger": "(t - reset2) >= 0.01" + } +] \ No newline at end of file diff --git a/latest/cases/00963/model-sbml-l3v2.xml b/latest/cases/00963/model-sbml-l3v2.xml new file mode 100644 index 000000000..b7a4174ab --- /dev/null +++ b/latest/cases/00963/model-sbml-l3v2.xml @@ -0,0 +1,176 @@ + + + + + +

Originally created by libAntimony v1.4 (using libSBML 5.0.0-a1)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 1 + + + + + + time + + + + + + + Q + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + -1 + + + + + + time + + + + + + + R + 0.01 + + + + + + + + + + + + + time + reset2 + + 0.01 + + + + + + -1 + + + + + + time + + + + + + + Q2 + 0.01 + + + + + + + + + + + + + time + reset2 + + 0.01 + + + + + + 1 + + + + + + time + + + + + + + R2 + 0.01 + + + + + + + + diff --git a/latest/cases/00963/output.heta b/latest/cases/00963/output.heta new file mode 100644 index 000000000..09e403cd4 --- /dev/null +++ b/latest/cases/00963/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Competing events with different priorities, meaning one always fires and the other does not. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + + This model contains two pairs of events with the same two triggers and different priorities, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, and the higher-priority event is the one that always wins. Just to make sure that simulators don't accidentally do what was designed to happen here, the two pairs of events come in the same order alphabetically and within the file, but the priorities are reversed, so if you always pick the first event instead of looking at the priority, you will fail one of the tests. + +The model contains: +* 6 parameters (Q, R, reset, Q2, R2, reset2) + +There are 4 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | $-1$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ | +| Qinc2 | $geq(time - reset2, 0.01)$ | $-1$ | false | $reset2 = time$ | +| | | | | $Q2 = Q2 + 0.01$ | +| Rinc2 | $geq(time - reset2, 0.01)$ | $1$ | false | $reset2 = time$ | +| | | | | $R2 = R2 + 0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter Q2 | $0$ | variable | +| Initial value of parameter R2 | $0$ | variable | +| Initial value of parameter reset2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +Q2 @Record { } .= 0; +Q2 [Qinc2]= Q2 + 0.01; +R2 @Record { } .= 0; +R2 [Rinc2]= R2 + 0.01; +reset2 @Record { } .= 0; +reset2 [Qinc2]= t; +reset2 [Rinc2]= t; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Qinc2 @DSwitcher { trigger: (t - reset2) >= 0.01, }; +Rinc2 @DSwitcher { trigger: (t - reset2) >= 0.01, }; + diff --git a/latest/cases/00963/synopsis.txt b/latest/cases/00963/synopsis.txt new file mode 100644 index 000000000..0b141b851 --- /dev/null +++ b/latest/cases/00963/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Competing events with different priorities, meaning one always fires and the other does not. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + + This model contains two pairs of events with the same two triggers and different priorities, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, and the higher-priority event is the one that always wins. Just to make sure that simulators don't accidentally do what was designed to happen here, the two pairs of events come in the same order alphabetically and within the file, but the priorities are reversed, so if you always pick the first event instead of looking at the priority, you will fail one of the tests. + +The model contains: +* 6 parameters (Q, R, reset, Q2, R2, reset2) + +There are 4 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | $-1$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ | +| Qinc2 | $geq(time - reset2, 0.01)$ | $-1$ | false | $reset2 = time$ | +| | | | | $Q2 = Q2 + 0.01$ | +| Rinc2 | $geq(time - reset2, 0.01)$ | $1$ | false | $reset2 = time$ | +| | | | | $R2 = R2 + 0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter Q2 | $0$ | variable | +| Initial value of parameter R2 | $0$ | variable | +| Initial value of parameter reset2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00964/l2v5/index.heta b/latest/cases/00964/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00964/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00964/l3v2/heta-code/output.heta b/latest/cases/00964/l3v2/heta-code/output.heta new file mode 100644 index 000000000..525f6e561 --- /dev/null +++ b/latest/cases/00964/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R + T; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +T @Record { } .= 0; +T [Tinc]= T + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +reset [Tinc]= t; +error @Record { } .= 0; +error [error_check]= 1; + +tolerance @Const { } = 5; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Tinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +error_check @DSwitcher { trigger: abs(Q - R) >= tolerance or abs(Q - T) >= tolerance or abs(T - R) >= tolerance, }; + diff --git a/latest/cases/00964/l3v2/index.heta b/latest/cases/00964/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00964/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00964/l3v2/json/output.json b/latest/cases/00964/l3v2/json/output.json new file mode 100644 index 000000000..8379eaef6 --- /dev/null +++ b/latest/cases/00964/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S", + "assignments": { + "start_": "0", + "ode_": "Q + R + T" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "0", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "0", + "Rinc": "R + 0.01" + } + }, + { + "class": "Record", + "id": "T", + "assignments": { + "start_": "0", + "Tinc": "T + 0.01" + } + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Qinc": "t", + "Rinc": "t", + "Tinc": "t" + } + }, + { + "class": "Const", + "id": "tolerance", + "num": 5 + }, + { + "class": "Record", + "id": "error", + "assignments": { + "start_": "0", + "error_check": "1" + } + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Tinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "error_check", + "trigger": "abs(Q - R) >= tolerance or abs(Q - T) >= tolerance or abs(T - R) >= tolerance" + } +] \ No newline at end of file diff --git a/latest/cases/00964/model-sbml-l3v2.xml b/latest/cases/00964/model-sbml-l3v2.xml new file mode 100644 index 000000000..8e8d0a3ea --- /dev/null +++ b/latest/cases/00964/model-sbml-l3v2.xml @@ -0,0 +1,188 @@ + + + + + + + + + + + + + + + + + + Q + R + T + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 1 + + + + + + time + + + + + + + Q + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 1 + + + + + + time + + + + + + + R + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 1 + + + + + + time + + + + + + + T + 0.01 + + + + + + + + + + + + + + + + + Q + R + + + tolerance + + + + + + + + Q + T + + + tolerance + + + + + + + + T + R + + + tolerance + + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00964/output.heta b/latest/cases/00964/output.heta new file mode 100644 index 000000000..a96b57c01 --- /dev/null +++ b/latest/cases/00964/output.heta @@ -0,0 +1,74 @@ +/* +category: Test +synopsis: Three competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure one event doesn't severely out-compete the other two. NOTE: STOCHASTIC TEST. This test is designed to fail only one time in a million, but it still may happen. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains three events with the same trigger, the same priority, and all set 'persistent=false', and all of which disable the trigger of the others. This means that every .01 seconds, one fires and the others do not, at random, and increases the parameters Q, R, and T, respectively. A fourth parameter, S, is assigned the value of Q+R+T, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure none of the three parameters are chosen more frequently than the other two--if the difference gets higher than 5, it triggers. From our simulations, this should happen less often than one time in a million, so if you see it happen in your simulator more often than once, there's a good chance something is wrong. + + +The model contains: +* 7 parameters (S, Q, R, T, reset, tolerance, error) + +There are 4 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ | +| Tinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $T = T + 0.01$ | +| error_check | $or(geq(abs(Q - R), tolerance), geq(abs(Q - T), tolerance), geq(abs(T - R), tolerance))$ | (unset) | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R + T$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter tolerance | $5$ | constant | +| Initial value of parameter S | $Q + R + T$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter T | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R + T; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +T @Record { } .= 0; +T [Tinc]= T + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +reset [Tinc]= t; +error @Record { } .= 0; +error [error_check]= 1; + +tolerance @Const { } = 5; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Tinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +error_check @DSwitcher { trigger: abs(Q - R) >= tolerance or abs(Q - T) >= tolerance or abs(T - R) >= tolerance, }; + diff --git a/latest/cases/00964/synopsis.txt b/latest/cases/00964/synopsis.txt new file mode 100644 index 000000000..cc0038f5a --- /dev/null +++ b/latest/cases/00964/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Three competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure one event doesn't severely out-compete the other two. NOTE: STOCHASTIC TEST. This test is designed to fail only one time in a million, but it still may happen. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains three events with the same trigger, the same priority, and all set 'persistent=false', and all of which disable the trigger of the others. This means that every .01 seconds, one fires and the others do not, at random, and increases the parameters Q, R, and T, respectively. A fourth parameter, S, is assigned the value of Q+R+T, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure none of the three parameters are chosen more frequently than the other two--if the difference gets higher than 5, it triggers. From our simulations, this should happen less often than one time in a million, so if you see it happen in your simulator more often than once, there's a good chance something is wrong. + + +The model contains: +* 7 parameters (S, Q, R, T, reset, tolerance, error) + +There are 4 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ | +| Tinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ | +| | | | | $T = T + 0.01$ | +| error_check | $or(geq(abs(Q - R), tolerance), geq(abs(Q - T), tolerance), geq(abs(T - R), tolerance))$ | (unset) | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R + T$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter tolerance | $5$ | constant | +| Initial value of parameter S | $Q + R + T$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter T | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00965/l2v5/index.heta b/latest/cases/00965/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00965/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00965/l3v2/heta-code/output.heta b/latest/cases/00965/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6292312f7 --- /dev/null +++ b/latest/cases/00965/l3v2/heta-code/output.heta @@ -0,0 +1,31 @@ + + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +Qrun @Record { } .= 0; +Qrun [Qinc]= Qrun + 1; +Qrun [Rinc]= 0; +Rrun @Record { } .= 0; +Rrun [Qinc]= 0; +Rrun [Rinc]= Rrun + 1; +maxrun @Record { } .= 0; +maxrun [maxrun_check1]= Qrun; +maxrun [maxrun_check2]= Rrun; +error @Record { } .= 0; +error [error_check]= 1; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +maxrun_check1 @DSwitcher { trigger: Qrun > maxrun, }; +maxrun_check2 @DSwitcher { trigger: Rrun > maxrun, }; +error_check @DSwitcher { trigger: maxrun > 300, }; + diff --git a/latest/cases/00965/l3v2/index.heta b/latest/cases/00965/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00965/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00965/l3v2/json/output.json b/latest/cases/00965/l3v2/json/output.json new file mode 100644 index 000000000..caf40097b --- /dev/null +++ b/latest/cases/00965/l3v2/json/output.json @@ -0,0 +1,98 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S", + "assignments": { + "start_": "0", + "ode_": "Q + R" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "0", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "0", + "Rinc": "R + 0.01" + } + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Qinc": "t", + "Rinc": "t" + } + }, + { + "class": "Record", + "id": "Qrun", + "assignments": { + "start_": "0", + "Qinc": "Qrun + 1", + "Rinc": "0" + } + }, + { + "class": "Record", + "id": "Rrun", + "assignments": { + "start_": "0", + "Qinc": "0", + "Rinc": "Rrun + 1" + } + }, + { + "class": "Record", + "id": "maxrun", + "assignments": { + "start_": "0", + "maxrun_check1": "Qrun", + "maxrun_check2": "Rrun" + } + }, + { + "class": "Record", + "id": "error", + "assignments": { + "start_": "0", + "error_check": "1" + } + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "maxrun_check1", + "trigger": "Qrun > maxrun" + }, + { + "class": "DSwitcher", + "id": "maxrun_check2", + "trigger": "Rrun > maxrun" + }, + { + "class": "DSwitcher", + "id": "error_check", + "trigger": "maxrun > 300" + } +] \ No newline at end of file diff --git a/latest/cases/00965/model-sbml-l3v2.xml b/latest/cases/00965/model-sbml-l3v2.xml new file mode 100644 index 000000000..d3194f7fe --- /dev/null +++ b/latest/cases/00965/model-sbml-l3v2.xml @@ -0,0 +1,197 @@ + + + + + + + + + + + + + + + + + + + Q + R + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 10 + + + + + + time + + + + + 0 + + + + + + + Qrun + 1 + + + + + + + + Q + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 10 + + + + + + time + + + + + 0 + + + + + + + Rrun + 1 + + + + + + + + R + 0.01 + + + + + + + + + + + Qrun + maxrun + + + + + + 9 + + + + + + Qrun + + + + + + + + + + Rrun + maxrun + + + + + + 8 + + + + + + Rrun + + + + + + + + + + maxrun + 300 + + + + + + 7 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00965/output.heta b/latest/cases/00965/output.heta new file mode 100644 index 000000000..f1f4f47bd --- /dev/null +++ b/latest/cases/00965/output.heta @@ -0,0 +1,118 @@ +/* +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure one event doesn't happen too many times in a row. NOTE: STOCHASTIC TEST. This test is designed to fail only one time in a million, but it still may happen. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, EventIsPersistent, EventUsesTriggerTimeValues, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model (the same basic model as 952) contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. + +In this test, we also keep track of how many times in a row either Q or R have been chosen, through the parameters Qrun and Rrun. Another parameter, maxrun, is set by its own events to be max(maxrun, Qrun, Rrun). A final event checks to see if maxrun has exceeded 20; if so, it is set to 1. In our simulations, in 1,000,000 runs, maxrun had an average of 13.25, and never exceeded 15 at all, so exceeding 300 is an occurrence that should happen much less than one time in a million. While this doesn't mean that your simulator will never have a run where maxrun exceeds 300, it does mean that this is a very rare event, and almost certainly means that something is wrong with your simulator: it may be that the same random number is being chosen multiple times. + +The model contains: +* 8 parameters (S, Q, R, reset, Qrun, Rrun, maxrun, error) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $(time - reset) ≥ 0.01$ | $10$ | false | $reset = time$ | +| | | | | $Rrun = 0$ | +| | | | | $Qrun = Qrun + 1$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $(time - reset) ≥ 0.01$ | $10$ | false | $reset = time$ | +| | | | | $Qrun = 0$ | +| | | | | $Rrun = Rrun + 1$ | +| | | | | $R = R + 0.01$ | +| maxrun_check1 | $Qrun > maxrun$ | $9$ | true | $maxrun = Qrun$ | +| maxrun_check2 | $Rrun > maxrun$ | $8$ | true | $maxrun = Rrun$ | +| error_check | $maxrun > 300$ | $7$ | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter Qrun | $0$ | variable | +| Initial value of parameter Rrun | $0$ | variable | +| Initial value of parameter maxrun | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*) +(* + +category: Test +componentTags: Parameter, EventNoDelay, EventPriority, AssignmentRule, CSymbolTime +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The events are: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Qinc | $time - reset >= 0.01$ | $-$ | $Q = Q + 0.01, Qrun = Qrun + 1, Rrun = 0, reset = time$ | + | Rinc | $time - reset >= 0.01$ | $-$ | $R = R + 0.01, Rrun = Rrun + 1, Qrun = 0, reset = time$ | + | maxrun_check1 | $Qrun > maxrun$ | $-$ | $maxrun = Qrun$ | + | maxrun_check2 | $Rrun > maxrun$ | $-$ | $maxrun = Rrun$ | + | error_check | $maxrun > 300$ | $-$ | $error = 1$ |] + + + The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value*| +|Value of parameter Q |$0$ | +|Value of parameter R |$0$ | +|Value of parameter S |$0$ | +|Value of parameter reset |$0$ | +|Value of parameter Qrun |$0$ | +|Value of parameter Rrun |$0$ | +|Value of parameter maxrun |$0$ | +|Value of parameter error |$0$ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. +*/ + + + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +Qrun @Record { } .= 0; +Qrun [Qinc]= Qrun + 1; +Qrun [Rinc]= 0; +Rrun @Record { } .= 0; +Rrun [Qinc]= 0; +Rrun [Rinc]= Rrun + 1; +maxrun @Record { } .= 0; +maxrun [maxrun_check1]= Qrun; +maxrun [maxrun_check2]= Rrun; +error @Record { } .= 0; +error [error_check]= 1; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +maxrun_check1 @DSwitcher { trigger: Qrun > maxrun, }; +maxrun_check2 @DSwitcher { trigger: Rrun > maxrun, }; +error_check @DSwitcher { trigger: maxrun > 300, }; + diff --git a/latest/cases/00965/synopsis.txt b/latest/cases/00965/synopsis.txt new file mode 100644 index 000000000..3d08df5d8 --- /dev/null +++ b/latest/cases/00965/synopsis.txt @@ -0,0 +1,85 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure one event doesn't happen too many times in a row. NOTE: STOCHASTIC TEST. This test is designed to fail only one time in a million, but it still may happen. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, EventIsPersistent, EventUsesTriggerTimeValues, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model (the same basic model as 952) contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. + +In this test, we also keep track of how many times in a row either Q or R have been chosen, through the parameters Qrun and Rrun. Another parameter, maxrun, is set by its own events to be max(maxrun, Qrun, Rrun). A final event checks to see if maxrun has exceeded 20; if so, it is set to 1. In our simulations, in 1,000,000 runs, maxrun had an average of 13.25, and never exceeded 15 at all, so exceeding 300 is an occurrence that should happen much less than one time in a million. While this doesn't mean that your simulator will never have a run where maxrun exceeds 300, it does mean that this is a very rare event, and almost certainly means that something is wrong with your simulator: it may be that the same random number is being chosen multiple times. + +The model contains: +* 8 parameters (S, Q, R, reset, Qrun, Rrun, maxrun, error) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $(time - reset) ≥ 0.01$ | $10$ | false | $reset = time$ | +| | | | | $Rrun = 0$ | +| | | | | $Qrun = Qrun + 1$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $(time - reset) ≥ 0.01$ | $10$ | false | $reset = time$ | +| | | | | $Qrun = 0$ | +| | | | | $Rrun = Rrun + 1$ | +| | | | | $R = R + 0.01$ | +| maxrun_check1 | $Qrun > maxrun$ | $9$ | true | $maxrun = Qrun$ | +| maxrun_check2 | $Rrun > maxrun$ | $8$ | true | $maxrun = Rrun$ | +| error_check | $maxrun > 300$ | $7$ | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter Qrun | $0$ | variable | +| Initial value of parameter Rrun | $0$ | variable | +| Initial value of parameter maxrun | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*) +(* + +category: Test +componentTags: Parameter, EventNoDelay, EventPriority, AssignmentRule, CSymbolTime +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The events are: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Qinc | $time - reset >= 0.01$ | $-$ | $Q = Q + 0.01, Qrun = Qrun + 1, Rrun = 0, reset = time$ | + | Rinc | $time - reset >= 0.01$ | $-$ | $R = R + 0.01, Rrun = Rrun + 1, Qrun = 0, reset = time$ | + | maxrun_check1 | $Qrun > maxrun$ | $-$ | $maxrun = Qrun$ | + | maxrun_check2 | $Rrun > maxrun$ | $-$ | $maxrun = Rrun$ | + | error_check | $maxrun > 300$ | $-$ | $error = 1$ |] + + + The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value*| +|Value of parameter Q |$0$ | +|Value of parameter R |$0$ | +|Value of parameter S |$0$ | +|Value of parameter reset |$0$ | +|Value of parameter Qrun |$0$ | +|Value of parameter Rrun |$0$ | +|Value of parameter maxrun |$0$ | +|Value of parameter error |$0$ |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. diff --git a/latest/cases/00966/l2v5/index.heta b/latest/cases/00966/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00966/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00966/l3v2/heta-code/output.heta b/latest/cases/00966/l3v2/heta-code/output.heta new file mode 100644 index 000000000..48f54e764 --- /dev/null +++ b/latest/cases/00966/l3v2/heta-code/output.heta @@ -0,0 +1,89 @@ + +calculateerror #defineFunction { arguments: [x0, x1, x2, x3, x4, x5, x6, x7, x8, x9, x10, x11, x12, x13, x14, x15, x16], math: pow(x0 - 0.0952, 2) / 0.0952 + pow(x1 - 1.523, 2) / 1.523 + pow(x2 - 11.428, 2) / 11.428 + pow(x3 - 53.32, 2) / 53.32 + pow(x4 - 173.29, 2) / 173.29 + pow(x5 - 415.898, 2) / 415.898 + pow(x6 - 762.48, 2) / 762.48 + pow(x7 - 1089.26, 2) / 1089.26 + pow(x8 - 1225.415, 2) / 1225.415 + pow(x9 - 1089.26, 2) / 1089.26 + pow(x10 - 762.48, 2) / 762.48 + pow(x11 - 415.898, 2) / 415.898 + pow(x12 - 173.29, 2) / 173.29 + pow(x13 - 53.32, 2) / 53.32 + pow(x14 - 11.428, 2) / 11.428 + pow(x15 - 1.523, 2) / 1.523 + pow(x16 - 0.0952, 2) / 0.0952, }; + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Rinc]= t; +reset [Qinc]= t; +chicount @Record { } .= 0; +chicount [Rinc]= chicount + 1; +chicount [Qinc]= chicount + 1; +chicount [repeat]= 0; +chitest @Record { } .= 0; +chitest [Qinc]= chitest + 1; +chitest [_E17]= 0; +assemble @Record { } .= 0; +assemble [repeat]= 1.5; +assemble [_E17]= 0; +chi0 @Record { } .= 0; +chi0 [_E0]= chi0 + 1; +chi1 @Record { } .= 0; +chi1 [_E1]= chi1 + 1; +chi2 @Record { } .= 0; +chi2 [_E2]= chi2 + 1; +chi3 @Record { } .= 0; +chi3 [_E3]= chi3 + 1; +chi4 @Record { } .= 0; +chi4 [_E4]= chi4 + 1; +chi5 @Record { } .= 0; +chi5 [_E5]= chi5 + 1; +chi6 @Record { } .= 0; +chi6 [_E6]= chi6 + 1; +chi7 @Record { } .= 0; +chi7 [_E7]= chi7 + 1; +chi8 @Record { } .= 0; +chi8 [_E8]= chi8 + 1; +chi9 @Record { } .= 0; +chi9 [_E9]= chi9 + 1; +chi10 @Record { } .= 0; +chi10 [_E10]= chi10 + 1; +chi11 @Record { } .= 0; +chi11 [_E11]= chi11 + 1; +chi12 @Record { } .= 0; +chi12 [_E12]= chi12 + 1; +chi13 @Record { } .= 0; +chi13 [_E13]= chi13 + 1; +chi14 @Record { } .= 0; +chi14 [_E14]= chi14 + 1; +chi15 @Record { } .= 0; +chi15 [_E15]= chi15 + 1; +chi16 @Record { } .= 0; +chi16 [_E16]= chi16 + 1; +tests @Record { } .= 0; +tests [_E17]= tests + 1; +finalchi @Record { } .= 0; +finalchi [_E18]= calculateerror(chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16); +error @Record { } .= 0; +error [error_check]= 1; + +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +repeat @DSwitcher { trigger: floor(chicount / 16) >= 1, }; +_E0 @DSwitcher { trigger: assemble >= 1 and chitest == 0, }; +_E1 @DSwitcher { trigger: assemble >= 1 and chitest == 1, }; +_E2 @DSwitcher { trigger: assemble >= 1 and chitest == 2, }; +_E3 @DSwitcher { trigger: assemble >= 1 and chitest == 3, }; +_E4 @DSwitcher { trigger: assemble >= 1 and chitest == 4, }; +_E5 @DSwitcher { trigger: assemble >= 1 and chitest == 5, }; +_E6 @DSwitcher { trigger: assemble >= 1 and chitest == 6, }; +_E7 @DSwitcher { trigger: assemble >= 1 and chitest == 7, }; +_E8 @DSwitcher { trigger: assemble >= 1 and chitest == 8, }; +_E9 @DSwitcher { trigger: assemble >= 1 and chitest == 9, }; +_E10 @DSwitcher { trigger: assemble >= 1 and chitest == 10, }; +_E11 @DSwitcher { trigger: assemble >= 1 and chitest == 11, }; +_E12 @DSwitcher { trigger: assemble >= 1 and chitest == 12, }; +_E13 @DSwitcher { trigger: assemble >= 1 and chitest == 13, }; +_E14 @DSwitcher { trigger: assemble >= 1 and chitest == 14, }; +_E15 @DSwitcher { trigger: assemble >= 1 and chitest == 15, }; +_E16 @DSwitcher { trigger: assemble >= 1 and chitest == 16, }; +_E17 @DSwitcher { trigger: assemble >= 1, }; +_E18 @DSwitcher { trigger: tests >= 6240 and finalchi == 0, }; +error_check @DSwitcher { trigger: finalchi > 50, }; + diff --git a/latest/cases/00966/l3v2/index.heta b/latest/cases/00966/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00966/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00966/l3v2/json/output.json b/latest/cases/00966/l3v2/json/output.json new file mode 100644 index 000000000..2c7ee8cfb --- /dev/null +++ b/latest/cases/00966/l3v2/json/output.json @@ -0,0 +1,365 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S", + "assignments": { + "start_": "0", + "ode_": "Q + R" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "0", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "0", + "Rinc": "R + 0.01" + } + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Rinc": "t", + "Qinc": "t" + } + }, + { + "class": "Record", + "id": "chicount", + "assignments": { + "start_": "0", + "Rinc": "chicount + 1", + "Qinc": "chicount + 1", + "repeat": "0" + } + }, + { + "class": "Record", + "id": "chitest", + "assignments": { + "start_": "0", + "Qinc": "chitest + 1", + "_E17": "0" + } + }, + { + "class": "Record", + "id": "assemble", + "assignments": { + "start_": "0", + "repeat": "1.5", + "_E17": "0" + } + }, + { + "class": "Record", + "id": "chi0", + "assignments": { + "start_": "0", + "_E0": "chi0 + 1" + } + }, + { + "class": "Record", + "id": "chi1", + "assignments": { + "start_": "0", + "_E1": "chi1 + 1" + } + }, + { + "class": "Record", + "id": "chi2", + "assignments": { + "start_": "0", + "_E2": "chi2 + 1" + } + }, + { + "class": "Record", + "id": "chi3", + "assignments": { + "start_": "0", + "_E3": "chi3 + 1" + } + }, + { + "class": "Record", + "id": "chi4", + "assignments": { + "start_": "0", + "_E4": "chi4 + 1" + } + }, + { + "class": "Record", + "id": "chi5", + "assignments": { + "start_": "0", + "_E5": "chi5 + 1" + } + }, + { + "class": "Record", + "id": "chi6", + "assignments": { + "start_": "0", + "_E6": "chi6 + 1" + } + }, + { + "class": "Record", + "id": "chi7", + "assignments": { + "start_": "0", + "_E7": "chi7 + 1" + } + }, + { + "class": "Record", + "id": "chi8", + "assignments": { + "start_": "0", + "_E8": "chi8 + 1" + } + }, + { + "class": "Record", + "id": "chi9", + "assignments": { + "start_": "0", + "_E9": "chi9 + 1" + } + }, + { + "class": "Record", + "id": "chi10", + "assignments": { + "start_": "0", + "_E10": "chi10 + 1" + } + }, + { + "class": "Record", + "id": "chi11", + "assignments": { + "start_": "0", + "_E11": "chi11 + 1" + } + }, + { + "class": "Record", + "id": "chi12", + "assignments": { + "start_": "0", + "_E12": "chi12 + 1" + } + }, + { + "class": "Record", + "id": "chi13", + "assignments": { + "start_": "0", + "_E13": "chi13 + 1" + } + }, + { + "class": "Record", + "id": "chi14", + "assignments": { + "start_": "0", + "_E14": "chi14 + 1" + } + }, + { + "class": "Record", + "id": "chi15", + "assignments": { + "start_": "0", + "_E15": "chi15 + 1" + } + }, + { + "class": "Record", + "id": "chi16", + "assignments": { + "start_": "0", + "_E16": "chi16 + 1" + } + }, + { + "class": "Record", + "id": "tests", + "assignments": { + "start_": "0", + "_E17": "tests + 1" + } + }, + { + "class": "Record", + "id": "finalchi", + "assignments": { + "start_": "0", + "_E18": "calculateerror(chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16)" + } + }, + { + "class": "Record", + "id": "error", + "assignments": { + "start_": "0", + "error_check": "1" + } + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "repeat", + "trigger": "floor(chicount / 16) >= 1" + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "assemble >= 1 and chitest == 0" + }, + { + "class": "DSwitcher", + "id": "_E1", + "trigger": "assemble >= 1 and chitest == 1" + }, + { + "class": "DSwitcher", + "id": "_E2", + "trigger": "assemble >= 1 and chitest == 2" + }, + { + "class": "DSwitcher", + "id": "_E3", + "trigger": "assemble >= 1 and chitest == 3" + }, + { + "class": "DSwitcher", + "id": "_E4", + "trigger": "assemble >= 1 and chitest == 4" + }, + { + "class": "DSwitcher", + "id": "_E5", + "trigger": "assemble >= 1 and chitest == 5" + }, + { + "class": "DSwitcher", + "id": "_E6", + "trigger": "assemble >= 1 and chitest == 6" + }, + { + "class": "DSwitcher", + "id": "_E7", + "trigger": "assemble >= 1 and chitest == 7" + }, + { + "class": "DSwitcher", + "id": "_E8", + "trigger": "assemble >= 1 and chitest == 8" + }, + { + "class": "DSwitcher", + "id": "_E9", + "trigger": "assemble >= 1 and chitest == 9" + }, + { + "class": "DSwitcher", + "id": "_E10", + "trigger": "assemble >= 1 and chitest == 10" + }, + { + "class": "DSwitcher", + "id": "_E11", + "trigger": "assemble >= 1 and chitest == 11" + }, + { + "class": "DSwitcher", + "id": "_E12", + "trigger": "assemble >= 1 and chitest == 12" + }, + { + "class": "DSwitcher", + "id": "_E13", + "trigger": "assemble >= 1 and chitest == 13" + }, + { + "class": "DSwitcher", + "id": "_E14", + "trigger": "assemble >= 1 and chitest == 14" + }, + { + "class": "DSwitcher", + "id": "_E15", + "trigger": "assemble >= 1 and chitest == 15" + }, + { + "class": "DSwitcher", + "id": "_E16", + "trigger": "assemble >= 1 and chitest == 16" + }, + { + "class": "DSwitcher", + "id": "_E17", + "trigger": "assemble >= 1" + }, + { + "class": "DSwitcher", + "id": "_E18", + "trigger": "tests >= 6240 and finalchi == 0" + }, + { + "class": "DSwitcher", + "id": "error_check", + "trigger": "finalchi > 50" + }, + { + "id": "calculateerror", + "arguments": [ + "x0", + "x1", + "x2", + "x3", + "x4", + "x5", + "x6", + "x7", + "x8", + "x9", + "x10", + "x11", + "x12", + "x13", + "x14", + "x15", + "x16" + ], + "math": "pow(x0 - 0.0952, 2) / 0.0952 + pow(x1 - 1.523, 2) / 1.523 + pow(x2 - 11.428, 2) / 11.428 + pow(x3 - 53.32, 2) / 53.32 + pow(x4 - 173.29, 2) / 173.29 + pow(x5 - 415.898, 2) / 415.898 + pow(x6 - 762.48, 2) / 762.48 + pow(x7 - 1089.26, 2) / 1089.26 + pow(x8 - 1225.415, 2) / 1225.415 + pow(x9 - 1089.26, 2) / 1089.26 + pow(x10 - 762.48, 2) / 762.48 + pow(x11 - 415.898, 2) / 415.898 + pow(x12 - 173.29, 2) / 173.29 + pow(x13 - 53.32, 2) / 53.32 + pow(x14 - 11.428, 2) / 11.428 + pow(x15 - 1.523, 2) / 1.523 + pow(x16 - 0.0952, 2) / 0.0952", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/00966/model-sbml-l3v2.xml b/latest/cases/00966/model-sbml-l3v2.xml new file mode 100644 index 000000000..372d061e9 --- /dev/null +++ b/latest/cases/00966/model-sbml-l3v2.xml @@ -0,0 +1,1169 @@ + + + + + + + + + x0 + + + x1 + + + x2 + + + x3 + + + x4 + + + x5 + + + x6 + + + x7 + + + x8 + + + x9 + + + x10 + + + x11 + + + x12 + + + x13 + + + x14 + + + x15 + + + x16 + + + + + + + + + + x0 + 0.0952 + + 2 + + 0.0952 + + + + + + + + x1 + 1.523 + + 2 + + 1.523 + + + + + + + + x2 + 11.428 + + 2 + + 11.428 + + + + + + + + x3 + 53.32 + + 2 + + 53.32 + + + + + + + + x4 + 173.29 + + 2 + + 173.29 + + + + + + + + x5 + 415.898 + + 2 + + 415.898 + + + + + + + + x6 + 762.48 + + 2 + + 762.48 + + + + + + + + x7 + 1089.26 + + 2 + + 1089.26 + + + + + + + + x8 + 1225.415 + + 2 + + 1225.415 + + + + + + + + x9 + 1089.26 + + 2 + + 1089.26 + + + + + + + + x10 + 762.48 + + 2 + + 762.48 + + + + + + + + x11 + 415.898 + + 2 + + 415.898 + + + + + + + + x12 + 173.29 + + 2 + + 173.29 + + + + + + + + x13 + 53.32 + + 2 + + 53.32 + + + + + + + + x14 + 11.428 + + 2 + + 11.428 + + + + + + + + x15 + 1.523 + + 2 + + 1.523 + + + + + + + + x16 + 0.0952 + + 2 + + 0.0952 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Q + R + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 10 + + + + + + time + + + + + + + chicount + 1 + + + + + + + + R + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 10 + + + + + + time + + + + + + + chitest + 1 + + + + + + + + chicount + 1 + + + + + + + + Q + 0.01 + + + + + + + + + + + + + + + chicount + 16 + + + 1 + + + + + + 5 + + + + + + 1.5 + + + + + 0 + + + + + + + + + + + + assemble + 1 + + + + chitest + 0 + + + + + + + 3 + + + + + + + + chi0 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 1 + + + + + + + 3 + + + + + + + + chi1 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 2 + + + + + + + 3 + + + + + + + + chi2 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 3 + + + + + + + 3 + + + + + + + + chi3 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 4 + + + + + + + 3 + + + + + + + + chi4 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 5 + + + + + + + 3 + + + + + + + + chi5 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 6 + + + + + + + 3 + + + + + + + + chi6 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 7 + + + + + + + 3 + + + + + + + + chi7 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 8 + + + + + + + 3 + + + + + + + + chi8 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 9 + + + + + + + 3 + + + + + + + + chi9 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 10 + + + + + + + 3 + + + + + + + + chi10 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 11 + + + + + + + 3 + + + + + + + + chi11 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 12 + + + + + + + 3 + + + + + + + + chi12 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 13 + + + + + + + 3 + + + + + + + + chi13 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 14 + + + + + + + 3 + + + + + + + + chi14 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 15 + + + + + + + 3 + + + + + + + + chi15 + 1 + + + + + + + + + + + + + assemble + 1 + + + + chitest + 16 + + + + + + + 3 + + + + + + + + chi16 + 1 + + + + + + + + + + + assemble + 1 + + + + + + 1 + + + + + + + + tests + 1 + + + + + + 0 + + + + + 0 + + + + + + + + + + + + tests + 6240 + + + + finalchi + 0 + + + + + + + 0 + + + + + + + calculateerror + chi0 + chi1 + chi2 + chi3 + chi4 + chi5 + chi6 + chi7 + chi8 + chi9 + chi10 + chi11 + chi12 + chi13 + chi14 + chi15 + chi16 + + + + + + + + + + + finalchi + 50 + + + + + + -1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/00966/output.heta b/latest/cases/00966/output.heta new file mode 100644 index 000000000..6cb9a3e4a --- /dev/null +++ b/latest/cases/00966/output.heta @@ -0,0 +1,188 @@ +/* +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, calculating a chi-squared statistic to ensure randomness. NOTE: STOCHASTIC TEST. This test is designed to fail with a frequency of 0.00002, but it still may happen. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, FunctionDefinition, Parameter +testTags: EventIsNotPersistent, EventIsPersistent, EventUsesTriggerTimeValues, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model (the same basic model as 952) contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. + +In this test, we also keep track of each run of 16 tests in a row, calculating the sum of Q during that run, and incrementing the appropriate frequency (chi0 -> chi16). At the end of 6,420 tests, the chi-square value is calculated from the observed and the pre-calculated expected frequencies of the 17 possible values. If this value is greater than 50, an error is triggered. The liklihood of the error being triggered is 0.00002, so it is quite unlikely (though possible) that a simulator would trigger it with a working random number generator, and almost impossible for this to happen twice in a row. + +This model has a number of events, so it's probably best to look at the antimony file for more details: 00966-antimony.txt + + +The model contains: +* 27 parameters (S, Q, R, reset, chicount, chitest, assemble, chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16, tests, finalchi, error) + +It also contains 1 function definition(s): +; calculateerror: $pow(x0 - 0.0952, 2) / 0.0952 + pow(x1 - 1.523, 2) / 1.523 + pow(x2 - 11.428, 2) / 11.428 + pow(x3 - 53.32, 2) / 53.32 + pow(x4 - 173.29, 2) / 173.29 + pow(x5 - 415.898, 2) / 415.898 + pow(x6 - 762.48, 2) / 762.48 + pow(x7 - 1089.26, 2) / 1089.26 + pow(x8 - 1225.415, 2) / 1225.415 + pow(x9 - 1089.26, 2) / 1089.26 + pow(x10 - 762.48, 2) / 762.48 + pow(x11 - 415.898, 2) / 415.898 + pow(x12 - 173.29, 2) / 173.29 + pow(x13 - 53.32, 2) / 53.32 + pow(x14 - 11.428, 2) / 11.428 + pow(x15 - 1.523, 2) / 1.523 + pow(x16 - 0.0952, 2) / 0.0952$ + +There are 23 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Rinc | $geq(time - reset, 0.01)$ | $10$ | false | $reset = time$ | +| | | | | $chicount = chicount + 1$ | +| | | | | $R = R + 0.01$ | +| Qinc | $geq(time - reset, 0.01)$ | $10$ | false | $reset = time$ | +| | | | | $chitest = chitest + 1$ | +| | | | | $chicount = chicount + 1$ | +| | | | | $Q = Q + 0.01$ | +| repeat | $geq(floor(chicount / 16), 1)$ | $5$ | true | $assemble = 1.5$ | +| | | | | $chicount = 0$ | +| _E0 | $and(geq(assemble, 1), eq(chitest, 0))$ | $3$ | true | $chi0 = chi0 + 1$ | +| _E1 | $and(geq(assemble, 1), eq(chitest, 1))$ | $3$ | true | $chi1 = chi1 + 1$ | +| _E2 | $and(geq(assemble, 1), eq(chitest, 2))$ | $3$ | true | $chi2 = chi2 + 1$ | +| _E3 | $and(geq(assemble, 1), eq(chitest, 3))$ | $3$ | true | $chi3 = chi3 + 1$ | +| _E4 | $and(geq(assemble, 1), eq(chitest, 4))$ | $3$ | true | $chi4 = chi4 + 1$ | +| _E5 | $and(geq(assemble, 1), eq(chitest, 5))$ | $3$ | true | $chi5 = chi5 + 1$ | +| _E6 | $and(geq(assemble, 1), eq(chitest, 6))$ | $3$ | true | $chi6 = chi6 + 1$ | +| _E7 | $and(geq(assemble, 1), eq(chitest, 7))$ | $3$ | true | $chi7 = chi7 + 1$ | +| _E8 | $and(geq(assemble, 1), eq(chitest, 8))$ | $3$ | true | $chi8 = chi8 + 1$ | +| _E9 | $and(geq(assemble, 1), eq(chitest, 9))$ | $3$ | true | $chi9 = chi9 + 1$ | +| _E10 | $and(geq(assemble, 1), eq(chitest, 10))$ | $3$ | true | $chi10 = chi10 + 1$ | +| _E11 | $and(geq(assemble, 1), eq(chitest, 11))$ | $3$ | true | $chi11 = chi11 + 1$ | +| _E12 | $and(geq(assemble, 1), eq(chitest, 12))$ | $3$ | true | $chi12 = chi12 + 1$ | +| _E13 | $and(geq(assemble, 1), eq(chitest, 13))$ | $3$ | true | $chi13 = chi13 + 1$ | +| _E14 | $and(geq(assemble, 1), eq(chitest, 14))$ | $3$ | true | $chi14 = chi14 + 1$ | +| _E15 | $and(geq(assemble, 1), eq(chitest, 15))$ | $3$ | true | $chi15 = chi15 + 1$ | +| _E16 | $and(geq(assemble, 1), eq(chitest, 16))$ | $3$ | true | $chi16 = chi16 + 1$ | +| _E17 | $geq(assemble, 1)$ | $1$ | true | $tests = tests + 1$ | +| | | | | $chitest = 0$ | +| | | | | $assemble = 0$ | +| _E18 | $and(geq(tests, 6240), eq(finalchi, 0))$ | $0$ | true | $finalchi = calculateerror(chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16)$ | +| error_check | $gt(finalchi, 50)$ | $-1$ | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter chicount | $0$ | variable | +| Initial value of parameter chitest | $0$ | variable | +| Initial value of parameter assemble | $0$ | variable | +| Initial value of parameter chi0 | $0$ | variable | +| Initial value of parameter chi1 | $0$ | variable | +| Initial value of parameter chi2 | $0$ | variable | +| Initial value of parameter chi3 | $0$ | variable | +| Initial value of parameter chi4 | $0$ | variable | +| Initial value of parameter chi5 | $0$ | variable | +| Initial value of parameter chi6 | $0$ | variable | +| Initial value of parameter chi7 | $0$ | variable | +| Initial value of parameter chi8 | $0$ | variable | +| Initial value of parameter chi9 | $0$ | variable | +| Initial value of parameter chi10 | $0$ | variable | +| Initial value of parameter chi11 | $0$ | variable | +| Initial value of parameter chi12 | $0$ | variable | +| Initial value of parameter chi13 | $0$ | variable | +| Initial value of parameter chi14 | $0$ | variable | +| Initial value of parameter chi15 | $0$ | variable | +| Initial value of parameter chi16 | $0$ | variable | +| Initial value of parameter tests | $0$ | variable | +| Initial value of parameter finalchi | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +calculateerror #defineFunction { arguments: [x0, x1, x2, x3, x4, x5, x6, x7, x8, x9, x10, x11, x12, x13, x14, x15, x16], math: pow(x0 - 0.0952, 2) / 0.0952 + pow(x1 - 1.523, 2) / 1.523 + pow(x2 - 11.428, 2) / 11.428 + pow(x3 - 53.32, 2) / 53.32 + pow(x4 - 173.29, 2) / 173.29 + pow(x5 - 415.898, 2) / 415.898 + pow(x6 - 762.48, 2) / 762.48 + pow(x7 - 1089.26, 2) / 1089.26 + pow(x8 - 1225.415, 2) / 1225.415 + pow(x9 - 1089.26, 2) / 1089.26 + pow(x10 - 762.48, 2) / 762.48 + pow(x11 - 415.898, 2) / 415.898 + pow(x12 - 173.29, 2) / 173.29 + pow(x13 - 53.32, 2) / 53.32 + pow(x14 - 11.428, 2) / 11.428 + pow(x15 - 1.523, 2) / 1.523 + pow(x16 - 0.0952, 2) / 0.0952, }; + +t @TimeScale { }; + +S @Record { } .= 0; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Rinc]= t; +reset [Qinc]= t; +chicount @Record { } .= 0; +chicount [Rinc]= chicount + 1; +chicount [Qinc]= chicount + 1; +chicount [repeat]= 0; +chitest @Record { } .= 0; +chitest [Qinc]= chitest + 1; +chitest [_E17]= 0; +assemble @Record { } .= 0; +assemble [repeat]= 1.5; +assemble [_E17]= 0; +chi0 @Record { } .= 0; +chi0 [_E0]= chi0 + 1; +chi1 @Record { } .= 0; +chi1 [_E1]= chi1 + 1; +chi2 @Record { } .= 0; +chi2 [_E2]= chi2 + 1; +chi3 @Record { } .= 0; +chi3 [_E3]= chi3 + 1; +chi4 @Record { } .= 0; +chi4 [_E4]= chi4 + 1; +chi5 @Record { } .= 0; +chi5 [_E5]= chi5 + 1; +chi6 @Record { } .= 0; +chi6 [_E6]= chi6 + 1; +chi7 @Record { } .= 0; +chi7 [_E7]= chi7 + 1; +chi8 @Record { } .= 0; +chi8 [_E8]= chi8 + 1; +chi9 @Record { } .= 0; +chi9 [_E9]= chi9 + 1; +chi10 @Record { } .= 0; +chi10 [_E10]= chi10 + 1; +chi11 @Record { } .= 0; +chi11 [_E11]= chi11 + 1; +chi12 @Record { } .= 0; +chi12 [_E12]= chi12 + 1; +chi13 @Record { } .= 0; +chi13 [_E13]= chi13 + 1; +chi14 @Record { } .= 0; +chi14 [_E14]= chi14 + 1; +chi15 @Record { } .= 0; +chi15 [_E15]= chi15 + 1; +chi16 @Record { } .= 0; +chi16 [_E16]= chi16 + 1; +tests @Record { } .= 0; +tests [_E17]= tests + 1; +finalchi @Record { } .= 0; +finalchi [_E18]= calculateerror(chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16); +error @Record { } .= 0; +error [error_check]= 1; + +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +repeat @DSwitcher { trigger: floor(chicount / 16) >= 1, }; +_E0 @DSwitcher { trigger: assemble >= 1 and chitest == 0, }; +_E1 @DSwitcher { trigger: assemble >= 1 and chitest == 1, }; +_E2 @DSwitcher { trigger: assemble >= 1 and chitest == 2, }; +_E3 @DSwitcher { trigger: assemble >= 1 and chitest == 3, }; +_E4 @DSwitcher { trigger: assemble >= 1 and chitest == 4, }; +_E5 @DSwitcher { trigger: assemble >= 1 and chitest == 5, }; +_E6 @DSwitcher { trigger: assemble >= 1 and chitest == 6, }; +_E7 @DSwitcher { trigger: assemble >= 1 and chitest == 7, }; +_E8 @DSwitcher { trigger: assemble >= 1 and chitest == 8, }; +_E9 @DSwitcher { trigger: assemble >= 1 and chitest == 9, }; +_E10 @DSwitcher { trigger: assemble >= 1 and chitest == 10, }; +_E11 @DSwitcher { trigger: assemble >= 1 and chitest == 11, }; +_E12 @DSwitcher { trigger: assemble >= 1 and chitest == 12, }; +_E13 @DSwitcher { trigger: assemble >= 1 and chitest == 13, }; +_E14 @DSwitcher { trigger: assemble >= 1 and chitest == 14, }; +_E15 @DSwitcher { trigger: assemble >= 1 and chitest == 15, }; +_E16 @DSwitcher { trigger: assemble >= 1 and chitest == 16, }; +_E17 @DSwitcher { trigger: assemble >= 1, }; +_E18 @DSwitcher { trigger: tests >= 6240 and finalchi == 0, }; +error_check @DSwitcher { trigger: finalchi > 50, }; + diff --git a/latest/cases/00966/synopsis.txt b/latest/cases/00966/synopsis.txt new file mode 100644 index 000000000..3678663d7 --- /dev/null +++ b/latest/cases/00966/synopsis.txt @@ -0,0 +1,97 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, calculating a chi-squared statistic to ensure randomness. NOTE: STOCHASTIC TEST. This test is designed to fail with a frequency of 0.00002, but it still may happen. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, FunctionDefinition, Parameter +testTags: EventIsNotPersistent, EventIsPersistent, EventUsesTriggerTimeValues, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model (the same basic model as 952) contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. + +In this test, we also keep track of each run of 16 tests in a row, calculating the sum of Q during that run, and incrementing the appropriate frequency (chi0 -> chi16). At the end of 6,420 tests, the chi-square value is calculated from the observed and the pre-calculated expected frequencies of the 17 possible values. If this value is greater than 50, an error is triggered. The liklihood of the error being triggered is 0.00002, so it is quite unlikely (though possible) that a simulator would trigger it with a working random number generator, and almost impossible for this to happen twice in a row. + +This model has a number of events, so it's probably best to look at the antimony file for more details: 00966-antimony.txt + + +The model contains: +* 27 parameters (S, Q, R, reset, chicount, chitest, assemble, chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16, tests, finalchi, error) + +It also contains 1 function definition(s): +; calculateerror: $pow(x0 - 0.0952, 2) / 0.0952 + pow(x1 - 1.523, 2) / 1.523 + pow(x2 - 11.428, 2) / 11.428 + pow(x3 - 53.32, 2) / 53.32 + pow(x4 - 173.29, 2) / 173.29 + pow(x5 - 415.898, 2) / 415.898 + pow(x6 - 762.48, 2) / 762.48 + pow(x7 - 1089.26, 2) / 1089.26 + pow(x8 - 1225.415, 2) / 1225.415 + pow(x9 - 1089.26, 2) / 1089.26 + pow(x10 - 762.48, 2) / 762.48 + pow(x11 - 415.898, 2) / 415.898 + pow(x12 - 173.29, 2) / 173.29 + pow(x13 - 53.32, 2) / 53.32 + pow(x14 - 11.428, 2) / 11.428 + pow(x15 - 1.523, 2) / 1.523 + pow(x16 - 0.0952, 2) / 0.0952$ + +There are 23 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Rinc | $geq(time - reset, 0.01)$ | $10$ | false | $reset = time$ | +| | | | | $chicount = chicount + 1$ | +| | | | | $R = R + 0.01$ | +| Qinc | $geq(time - reset, 0.01)$ | $10$ | false | $reset = time$ | +| | | | | $chitest = chitest + 1$ | +| | | | | $chicount = chicount + 1$ | +| | | | | $Q = Q + 0.01$ | +| repeat | $geq(floor(chicount / 16), 1)$ | $5$ | true | $assemble = 1.5$ | +| | | | | $chicount = 0$ | +| _E0 | $and(geq(assemble, 1), eq(chitest, 0))$ | $3$ | true | $chi0 = chi0 + 1$ | +| _E1 | $and(geq(assemble, 1), eq(chitest, 1))$ | $3$ | true | $chi1 = chi1 + 1$ | +| _E2 | $and(geq(assemble, 1), eq(chitest, 2))$ | $3$ | true | $chi2 = chi2 + 1$ | +| _E3 | $and(geq(assemble, 1), eq(chitest, 3))$ | $3$ | true | $chi3 = chi3 + 1$ | +| _E4 | $and(geq(assemble, 1), eq(chitest, 4))$ | $3$ | true | $chi4 = chi4 + 1$ | +| _E5 | $and(geq(assemble, 1), eq(chitest, 5))$ | $3$ | true | $chi5 = chi5 + 1$ | +| _E6 | $and(geq(assemble, 1), eq(chitest, 6))$ | $3$ | true | $chi6 = chi6 + 1$ | +| _E7 | $and(geq(assemble, 1), eq(chitest, 7))$ | $3$ | true | $chi7 = chi7 + 1$ | +| _E8 | $and(geq(assemble, 1), eq(chitest, 8))$ | $3$ | true | $chi8 = chi8 + 1$ | +| _E9 | $and(geq(assemble, 1), eq(chitest, 9))$ | $3$ | true | $chi9 = chi9 + 1$ | +| _E10 | $and(geq(assemble, 1), eq(chitest, 10))$ | $3$ | true | $chi10 = chi10 + 1$ | +| _E11 | $and(geq(assemble, 1), eq(chitest, 11))$ | $3$ | true | $chi11 = chi11 + 1$ | +| _E12 | $and(geq(assemble, 1), eq(chitest, 12))$ | $3$ | true | $chi12 = chi12 + 1$ | +| _E13 | $and(geq(assemble, 1), eq(chitest, 13))$ | $3$ | true | $chi13 = chi13 + 1$ | +| _E14 | $and(geq(assemble, 1), eq(chitest, 14))$ | $3$ | true | $chi14 = chi14 + 1$ | +| _E15 | $and(geq(assemble, 1), eq(chitest, 15))$ | $3$ | true | $chi15 = chi15 + 1$ | +| _E16 | $and(geq(assemble, 1), eq(chitest, 16))$ | $3$ | true | $chi16 = chi16 + 1$ | +| _E17 | $geq(assemble, 1)$ | $1$ | true | $tests = tests + 1$ | +| | | | | $chitest = 0$ | +| | | | | $assemble = 0$ | +| _E18 | $and(geq(tests, 6240), eq(finalchi, 0))$ | $0$ | true | $finalchi = calculateerror(chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16)$ | +| error_check | $gt(finalchi, 50)$ | $-1$ | true | $error = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter chicount | $0$ | variable | +| Initial value of parameter chitest | $0$ | variable | +| Initial value of parameter assemble | $0$ | variable | +| Initial value of parameter chi0 | $0$ | variable | +| Initial value of parameter chi1 | $0$ | variable | +| Initial value of parameter chi2 | $0$ | variable | +| Initial value of parameter chi3 | $0$ | variable | +| Initial value of parameter chi4 | $0$ | variable | +| Initial value of parameter chi5 | $0$ | variable | +| Initial value of parameter chi6 | $0$ | variable | +| Initial value of parameter chi7 | $0$ | variable | +| Initial value of parameter chi8 | $0$ | variable | +| Initial value of parameter chi9 | $0$ | variable | +| Initial value of parameter chi10 | $0$ | variable | +| Initial value of parameter chi11 | $0$ | variable | +| Initial value of parameter chi12 | $0$ | variable | +| Initial value of parameter chi13 | $0$ | variable | +| Initial value of parameter chi14 | $0$ | variable | +| Initial value of parameter chi15 | $0$ | variable | +| Initial value of parameter chi16 | $0$ | variable | +| Initial value of parameter tests | $0$ | variable | +| Initial value of parameter finalchi | $0$ | variable | +| Initial value of parameter error | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00967/l2v5/index.heta b/latest/cases/00967/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00967/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00967/l3v2/heta-code/output.heta b/latest/cases/00967/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6d25124be --- /dev/null +++ b/latest/cases/00967/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; + diff --git a/latest/cases/00967/l3v2/index.heta b/latest/cases/00967/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00967/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00967/l3v2/json/output.json b/latest/cases/00967/l3v2/json/output.json new file mode 100644 index 000000000..771104769 --- /dev/null +++ b/latest/cases/00967/l3v2/json/output.json @@ -0,0 +1,40 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Qinc": "t", + "Rinc": "t" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "0", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "0", + "Rinc": "R + 0.01" + } + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "(t - reset) >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "(t - reset) >= 0.01" + } +] \ No newline at end of file diff --git a/latest/cases/00967/model-sbml-l3v2.xml b/latest/cases/00967/model-sbml-l3v2.xml new file mode 100644 index 000000000..1b4b93754 --- /dev/null +++ b/latest/cases/00967/model-sbml-l3v2.xml @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + time + + + + + + time + + + + + + + Q + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 5.001 + + + + + + time + + + + + + + R + 0.01 + + + + + + + + diff --git a/latest/cases/00967/output.heta b/latest/cases/00967/output.heta new file mode 100644 index 000000000..8e22ff3e7 --- /dev/null +++ b/latest/cases/00967/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Competing events with alternating priorities, so one fires for 5 seconds, then the other fires for the next 5 seconds. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NonConstantParameter, EventIsNotPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events with the same trigger, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not. One has the priority 'time' and the other the priority '5.001', meaning that for the first 5 seconds, one fires, and for the next 5 seconds, the other fires. + + +The model contains: +* 3 parameters (reset, Q, R) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $(time - reset) ≥ 0.01$ | $time$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $(time - reset) ≥ 0.01$ | $5.001$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +reset @Record { } .= 0; +reset [Qinc]= t; +reset [Rinc]= t; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; + +Qinc @DSwitcher { trigger: (t - reset) >= 0.01, }; +Rinc @DSwitcher { trigger: (t - reset) >= 0.01, }; + diff --git a/latest/cases/00967/synopsis.txt b/latest/cases/00967/synopsis.txt new file mode 100644 index 000000000..884cb413a --- /dev/null +++ b/latest/cases/00967/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Competing events with alternating priorities, so one fires for 5 seconds, then the other fires for the next 5 seconds. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NonConstantParameter, EventIsNotPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events with the same trigger, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not. One has the priority 'time' and the other the priority '5.001', meaning that for the first 5 seconds, one fires, and for the next 5 seconds, the other fires. + + +The model contains: +* 3 parameters (reset, Q, R) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $(time - reset) ≥ 0.01$ | $time$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $(time - reset) ≥ 0.01$ | $5.001$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00968/l2v5/build.log b/latest/cases/00968/l2v5/build.log new file mode 100644 index 000000000..57d1292b7 --- /dev/null +++ b/latest/cases/00968/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00968/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00968/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00968/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00968/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00968/l2v5/index.heta b/latest/cases/00968/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00968/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00968/l3v2/index.heta b/latest/cases/00968/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00968/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00968/model-sbml-l2v5.xml b/latest/cases/00968/model-sbml-l2v5.xml new file mode 100644 index 000000000..10b5c6d35 --- /dev/null +++ b/latest/cases/00968/model-sbml-l2v5.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + 3 + + + + + + + k1 + + + + + + diff --git a/latest/cases/00968/synopsis.txt b/latest/cases/00968/synopsis.txt new file mode 100644 index 000000000..787b32079 --- /dev/null +++ b/latest/cases/00968/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A very simple reaction with stoichiometry set by an initialAssignment. +componentTags: StoichiometryMath, Compartment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The speciesReference ('Xref') is set with stoichiometryMath in the L2 models. No 'stoichiometry' value is provided in the speciesReference in the reaction itself. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species X | $0$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00969/l2v5/index.heta b/latest/cases/00969/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00969/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00027/l3v2/build.log b/latest/cases/00969/l3v2/build.log similarity index 62% rename from latest/cases/00027/l3v2/build.log rename to latest/cases/00969/l3v2/build.log index 5760f2aad..6c8428edf 100644 --- a/latest/cases/00027/l3v2/build.log +++ b/latest/cases/00969/l3v2/build.log @@ -1,9 +1,9 @@ [info] Namespace "nameless" was set as "concrete" -[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00027/l3v2". +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00969/l3v2". [info] Compilation of module "index.heta" of type "heta"... -[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00027/l3v2/index.heta"... -[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00027/model-sbml-l3v2.xml"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00969/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00969/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. [info] Setting references in elements, total length 83 -[error] Component "k" is not found in space "nameless" as expected in expression: reaction1 [ode_]= compartment * k * S1; [info] Checking for circular references in Records. [warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00969/l3v2/index.heta b/latest/cases/00969/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00969/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00969/model-sbml-l3v2.xml b/latest/cases/00969/model-sbml-l3v2.xml new file mode 100644 index 000000000..defba8c3e --- /dev/null +++ b/latest/cases/00969/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + 3 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/00969/synopsis.txt b/latest/cases/00969/synopsis.txt new file mode 100644 index 000000000..d608413f6 --- /dev/null +++ b/latest/cases/00969/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A very simple reaction with stoichiometry set by an initialAssignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The speciesReference ('Xref') is set with an initialAssignment of 3. A 'stoichiometry' value is provided in the speciesReference in the reaction itself of '1'. This should be replaced by the value in the initialAssignment. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species X | $0$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00970/l2v5/index.heta b/latest/cases/00970/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00970/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00970/l3v2/build.log b/latest/cases/00970/l3v2/build.log new file mode 100644 index 000000000..220644289 --- /dev/null +++ b/latest/cases/00970/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00970/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00970/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00970/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00970/l3v2/index.heta b/latest/cases/00970/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00970/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00970/model-sbml-l3v2.xml b/latest/cases/00970/model-sbml-l3v2.xml new file mode 100644 index 000000000..80b0c86d8 --- /dev/null +++ b/latest/cases/00970/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + 3 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/00970/synopsis.txt b/latest/cases/00970/synopsis.txt new file mode 100644 index 000000000..e5648822d --- /dev/null +++ b/latest/cases/00970/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A very simple reaction with stoichiometry set by an initialAssignment. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The speciesReference ('Xref') is set with an initialAssignment of 3. No 'stoichiometry' value is provided in the speciesReference in the reaction itself. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $0$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00971/l2v5/index.heta b/latest/cases/00971/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00971/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00971/l3v2/build.log b/latest/cases/00971/l3v2/build.log new file mode 100644 index 000000000..47bc56ab0 --- /dev/null +++ b/latest/cases/00971/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00971/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00971/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00971/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00971/l3v2/index.heta b/latest/cases/00971/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00971/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00971/model-sbml-l3v2.xml b/latest/cases/00971/model-sbml-l3v2.xml new file mode 100644 index 000000000..d3d46c657 --- /dev/null +++ b/latest/cases/00971/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + 3 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/00971/synopsis.txt b/latest/cases/00971/synopsis.txt new file mode 100644 index 000000000..0c4059f5d --- /dev/null +++ b/latest/cases/00971/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A very simple reaction with stoichiometry set by an assignmentRule. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The speciesReference ('Xref') is set with an assignmentRule of 3. A 'stoichiometry' value of '1' is provided in the speciesReference in the reaction itself, which should be overridden by the assignment rule. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $0$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00972/l2v5/index.heta b/latest/cases/00972/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00972/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00972/l3v2/build.log b/latest/cases/00972/l3v2/build.log new file mode 100644 index 000000000..f690994b5 --- /dev/null +++ b/latest/cases/00972/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00972/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00972/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00972/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00972/l3v2/index.heta b/latest/cases/00972/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00972/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00972/model-sbml-l3v2.xml b/latest/cases/00972/model-sbml-l3v2.xml new file mode 100644 index 000000000..99c45a6d5 --- /dev/null +++ b/latest/cases/00972/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + X + 5 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/00972/synopsis.txt b/latest/cases/00972/synopsis.txt new file mode 100644 index 000000000..f3c6fd7e5 --- /dev/null +++ b/latest/cases/00972/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A very simple reaction with stoichiometry changed by an event. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +An event watches to see when X goes above 5. When it does, the stoichiometry of the reaction producing X jumps to 3, increasing X production. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $X ≥ 5$ | $Xref = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $0$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00973/l2v5/build.log b/latest/cases/00973/l2v5/build.log new file mode 100644 index 000000000..ee3f79790 --- /dev/null +++ b/latest/cases/00973/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00973/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00973/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00973/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00973/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00973/l2v5/index.heta b/latest/cases/00973/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00973/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00973/l3v2/index.heta b/latest/cases/00973/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00973/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00973/model-sbml-l2v5.xml b/latest/cases/00973/model-sbml-l2v5.xml new file mode 100644 index 000000000..f624a1e70 --- /dev/null +++ b/latest/cases/00973/model-sbml-l2v5.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + parameterId_0 + + + + + + + k1 + + + + + + diff --git a/latest/cases/00973/synopsis.txt b/latest/cases/00973/synopsis.txt new file mode 100644 index 000000000..71b1c51b0 --- /dev/null +++ b/latest/cases/00973/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: A very simple reaction with stoichiometry changed by a rate rule. +componentTags: StoichiometryMath, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +Over the course of the simulation, the stoichiometry 'Xref' changes at a rate of 0.01/time, so the effective rate of synthesis increases as well, identically to the same model with k1 changing instead of Xref. The Level 2 versions of this test create a new parameter 'parameterId_0'. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | Xref | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00974/l2v5/index.heta b/latest/cases/00974/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00974/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00974/l3v2/build.log b/latest/cases/00974/l3v2/build.log new file mode 100644 index 000000000..7e8ae0f73 --- /dev/null +++ b/latest/cases/00974/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00974/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00974/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00974/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 87 +[error] Component "Xref" is not found in space "nameless" as expected in expression: Z [ode_]= Xref; +[error] Component "Xref" is not found in space "nameless" as expected in expression: Y_proc [ode_]= Xref; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00974/l3v2/index.heta b/latest/cases/00974/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00974/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00974/model-sbml-l3v2.xml b/latest/cases/00974/model-sbml-l3v2.xml new file mode 100644 index 000000000..50c36f90c --- /dev/null +++ b/latest/cases/00974/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + Xref + + + + + + + Xref + + + + + Xref + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/00974/synopsis.txt b/latest/cases/00974/synopsis.txt new file mode 100644 index 000000000..564f99cd5 --- /dev/null +++ b/latest/cases/00974/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A very simple reaction whose stoichiometry is referenced in other math. +componentTags: AssignmentRule, Compartment, InitialAssignment, Parameter, RateRule, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The reaction in this model has a speciesReference which doesn't change, but is used in various other equations and rules in the model. + +The model contains: +* 1 species (X) +* 4 parameters (Y, Z, Q, k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> X | $k1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | Y | $Xref$ | +| Assignment | Z | $Xref$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $0$ | variable | +| Initial value of parameter Q | $Xref$ | constant | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter Y | $Xref$ | variable | +| Initial value of parameter Z | $Xref$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00975/l2v5/index.heta b/latest/cases/00975/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00975/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00975/l3v2/heta-code/output.heta b/latest/cases/00975/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e48da6aa8 --- /dev/null +++ b/latest/cases/00975/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { }; + +default_compartment @Compartment { boundary: true, aux: {{"sboTerm":"SBO:0000410"}}, } .= 1; + +S1 @Species { compartment: default_compartment, } .= 0 / default_compartment; +S2 @Species { compartment: default_compartment, } .= 0.001 / default_compartment; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; +_J1 @Reaction { actors: 2*S1 = 3*S2, }; +_J1 := (k2 * S1) / S2; +_J2 @Reaction { actors: S2 = , }; +_J2 := k3 * S2; + +k1 @Const { } = 1; +k2 @Const { } = 3; +k3 @Const { } = 1.4; +S1conv @Const { } = 3; +modelconv @Const { } = 4; + diff --git a/latest/cases/00975/l3v2/index.heta b/latest/cases/00975/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00975/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00975/l3v2/json/output.json b/latest/cases/00975/l3v2/json/output.json new file mode 100644 index 000000000..879c31111 --- /dev/null +++ b/latest/cases/00975/l3v2/json/output.json @@ -0,0 +1,100 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "default_compartment", + "aux": { + "sboTerm": "SBO:0000410" + }, + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0 / default_compartment" + }, + "compartment": "default_compartment" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0.001 / default_compartment" + }, + "compartment": "default_compartment" + }, + { + "class": "Reaction", + "id": "_J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "_J1", + "assignments": { + "ode_": "(k2 * S1) / S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 3 + }, + { + "target": "S1", + "stoichiometry": -2 + } + ] + }, + { + "class": "Reaction", + "id": "_J2", + "assignments": { + "ode_": "k3 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "num": 3 + }, + { + "class": "Const", + "id": "k3", + "num": 1.4 + }, + { + "class": "Const", + "id": "S1conv", + "num": 3 + }, + { + "class": "Const", + "id": "modelconv", + "num": 4 + } +] \ No newline at end of file diff --git a/latest/cases/00975/model-sbml-l3v2.xml b/latest/cases/00975/model-sbml-l3v2.xml new file mode 100644 index 000000000..d5d8a9aac --- /dev/null +++ b/latest/cases/00975/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + + + + + + + k2 + S1 + + S2 + + + + + + + + + + + + + k3 + S2 + + + + + + + diff --git a/latest/cases/00975/output.heta b/latest/cases/00975/output.heta new file mode 100644 index 000000000..4b79643fb --- /dev/null +++ b/latest/cases/00975/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: A three-step reaction scheme with a model conversion factor. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +This model tests conversion factors through a system of three reactions. There is a conversion factor ('modelconv') on the model of 4. This changes how S1 and S2 change in time, but not how S1 and S2 are interpreted in the reaction rates. + +The model contains: +* 2 species (S1, S2) +* 5 parameters (k1, k2, k3, S1conv, modelconv) +* 1 compartment (default_compartment) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $k1$ | +| 2S1 -> 3S2 | $k2 * S1 / S2$ | +| S2 -> | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $0$ | variable | +| Initial amount of species S2 | $0.001$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter k2 | $3$ | constant | +| Initial value of parameter k3 | $1.4$ | constant | +| Initial value of parameter S1conv | $3$ | constant | +| Initial value of parameter modelconv | $4$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +default_compartment @Compartment { boundary: true, aux: {{"sboTerm":"SBO:0000410"}}, } .= 1; + +S1 @Species { compartment: default_compartment, } .= 0 / default_compartment; +S2 @Species { compartment: default_compartment, } .= 0.001 / default_compartment; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; +_J1 @Reaction { actors: 2*S1 = 3*S2, }; +_J1 := (k2 * S1) / S2; +_J2 @Reaction { actors: S2 = , }; +_J2 := k3 * S2; + +k1 @Const { } = 1; +k2 @Const { } = 3; +k3 @Const { } = 1.4; +S1conv @Const { } = 3; +modelconv @Const { } = 4; + diff --git a/latest/cases/00975/synopsis.txt b/latest/cases/00975/synopsis.txt new file mode 100644 index 000000000..196bc93cb --- /dev/null +++ b/latest/cases/00975/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A three-step reaction scheme with a model conversion factor. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +This model tests conversion factors through a system of three reactions. There is a conversion factor ('modelconv') on the model of 4. This changes how S1 and S2 change in time, but not how S1 and S2 are interpreted in the reaction rates. + +The model contains: +* 2 species (S1, S2) +* 5 parameters (k1, k2, k3, S1conv, modelconv) +* 1 compartment (default_compartment) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $k1$ | +| 2S1 -> 3S2 | $k2 * S1 / S2$ | +| S2 -> | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $0$ | variable | +| Initial amount of species S2 | $0.001$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter k2 | $3$ | constant | +| Initial value of parameter k3 | $1.4$ | constant | +| Initial value of parameter S1conv | $3$ | constant | +| Initial value of parameter modelconv | $4$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/00976/l2v5/index.heta b/latest/cases/00976/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00976/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00976/l3v2/heta-code/output.heta b/latest/cases/00976/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4fa9631f3 --- /dev/null +++ b/latest/cases/00976/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { }; + +default_compartment @Compartment { boundary: true, aux: {{"sboTerm":"SBO:0000410"}}, } .= 1; + +S1 @Species { compartment: default_compartment, } .= 0; +S2 @Species { compartment: default_compartment, } .= 0.001; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; +_J1 @Reaction { actors: 2*S1 = 3*S2, }; +_J1 := (k2 * S1) / S2; +_J2 @Reaction { actors: S2 = , }; +_J2 := k3 * S2; + +k1 @Const { } = 1; +k2 @Const { } = 3; +k3 @Const { } = 1.4; +S1conv @Const { } = 3; +modelconv @Const { } = 4; + diff --git a/latest/cases/00976/l3v2/index.heta b/latest/cases/00976/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00976/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00976/l3v2/json/output.json b/latest/cases/00976/l3v2/json/output.json new file mode 100644 index 000000000..357ea4d26 --- /dev/null +++ b/latest/cases/00976/l3v2/json/output.json @@ -0,0 +1,100 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "default_compartment", + "aux": { + "sboTerm": "SBO:0000410" + }, + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "default_compartment" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0.001" + }, + "compartment": "default_compartment" + }, + { + "class": "Reaction", + "id": "_J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "_J1", + "assignments": { + "ode_": "(k2 * S1) / S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 3 + }, + { + "target": "S1", + "stoichiometry": -2 + } + ] + }, + { + "class": "Reaction", + "id": "_J2", + "assignments": { + "ode_": "k3 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "num": 3 + }, + { + "class": "Const", + "id": "k3", + "num": 1.4 + }, + { + "class": "Const", + "id": "S1conv", + "num": 3 + }, + { + "class": "Const", + "id": "modelconv", + "num": 4 + } +] \ No newline at end of file diff --git a/latest/cases/00976/model-sbml-l3v2.xml b/latest/cases/00976/model-sbml-l3v2.xml new file mode 100644 index 000000000..c0d20b0ef --- /dev/null +++ b/latest/cases/00976/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + + + + + + + k2 + S1 + + S2 + + + + + + + + + + + + + k3 + S2 + + + + + + + diff --git a/latest/cases/00976/output.heta b/latest/cases/00976/output.heta new file mode 100644 index 000000000..310c52d4f --- /dev/null +++ b/latest/cases/00976/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: A three-step reaction scheme with a model conversion factor and a species conversion factor. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +This model tests conversion factors through a system of three reactions. There is a conversion factor ('modelconv') on the model of 4, and a second conversion factor ('S1conv') on species S1. This means that S1 is converted according to S1conv, and S2 is converted according to modelconv. Together, this changes how S1 and S2 change in time, but not how S1 and S2 are interpreted in the reaction rates. + + +The model contains: +* 2 species (S1, S2) +* 5 parameters (k1, k2, k3, S1conv, modelconv) +* 1 compartment (default_compartment) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $k1$ | +| 2S1 -> 3S2 | $k2 * S1 / S2$ | +| S2 -> | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0.001$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter k2 | $3$ | constant | +| Initial value of parameter k3 | $1.4$ | constant | +| Initial value of parameter S1conv | $3$ | constant | +| Initial value of parameter modelconv | $4$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +default_compartment @Compartment { boundary: true, aux: {{"sboTerm":"SBO:0000410"}}, } .= 1; + +S1 @Species { compartment: default_compartment, } .= 0; +S2 @Species { compartment: default_compartment, } .= 0.001; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; +_J1 @Reaction { actors: 2*S1 = 3*S2, }; +_J1 := (k2 * S1) / S2; +_J2 @Reaction { actors: S2 = , }; +_J2 := k3 * S2; + +k1 @Const { } = 1; +k2 @Const { } = 3; +k3 @Const { } = 1.4; +S1conv @Const { } = 3; +modelconv @Const { } = 4; + diff --git a/latest/cases/00976/synopsis.txt b/latest/cases/00976/synopsis.txt new file mode 100644 index 000000000..15a01f440 --- /dev/null +++ b/latest/cases/00976/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A three-step reaction scheme with a model conversion factor and a species conversion factor. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +This model tests conversion factors through a system of three reactions. There is a conversion factor ('modelconv') on the model of 4, and a second conversion factor ('S1conv') on species S1. This means that S1 is converted according to S1conv, and S2 is converted according to modelconv. Together, this changes how S1 and S2 change in time, but not how S1 and S2 are interpreted in the reaction rates. + + +The model contains: +* 2 species (S1, S2) +* 5 parameters (k1, k2, k3, S1conv, modelconv) +* 1 compartment (default_compartment) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $k1$ | +| 2S1 -> 3S2 | $k2 * S1 / S2$ | +| S2 -> | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0.001$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter k2 | $3$ | constant | +| Initial value of parameter k3 | $1.4$ | constant | +| Initial value of parameter S1conv | $3$ | constant | +| Initial value of parameter modelconv | $4$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/00977/l2v5/index.heta b/latest/cases/00977/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00977/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00977/l3v2/heta-code/output.heta b/latest/cases/00977/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4fa9631f3 --- /dev/null +++ b/latest/cases/00977/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { }; + +default_compartment @Compartment { boundary: true, aux: {{"sboTerm":"SBO:0000410"}}, } .= 1; + +S1 @Species { compartment: default_compartment, } .= 0; +S2 @Species { compartment: default_compartment, } .= 0.001; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; +_J1 @Reaction { actors: 2*S1 = 3*S2, }; +_J1 := (k2 * S1) / S2; +_J2 @Reaction { actors: S2 = , }; +_J2 := k3 * S2; + +k1 @Const { } = 1; +k2 @Const { } = 3; +k3 @Const { } = 1.4; +S1conv @Const { } = 3; +modelconv @Const { } = 4; + diff --git a/latest/cases/00977/l3v2/index.heta b/latest/cases/00977/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00977/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00977/l3v2/json/output.json b/latest/cases/00977/l3v2/json/output.json new file mode 100644 index 000000000..357ea4d26 --- /dev/null +++ b/latest/cases/00977/l3v2/json/output.json @@ -0,0 +1,100 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "default_compartment", + "aux": { + "sboTerm": "SBO:0000410" + }, + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "default_compartment" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0.001" + }, + "compartment": "default_compartment" + }, + { + "class": "Reaction", + "id": "_J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "_J1", + "assignments": { + "ode_": "(k2 * S1) / S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 3 + }, + { + "target": "S1", + "stoichiometry": -2 + } + ] + }, + { + "class": "Reaction", + "id": "_J2", + "assignments": { + "ode_": "k3 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "num": 1 + }, + { + "class": "Const", + "id": "k2", + "num": 3 + }, + { + "class": "Const", + "id": "k3", + "num": 1.4 + }, + { + "class": "Const", + "id": "S1conv", + "num": 3 + }, + { + "class": "Const", + "id": "modelconv", + "num": 4 + } +] \ No newline at end of file diff --git a/latest/cases/00977/model-sbml-l3v2.xml b/latest/cases/00977/model-sbml-l3v2.xml new file mode 100644 index 000000000..9ba40faf9 --- /dev/null +++ b/latest/cases/00977/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + + + + + + + k2 + S1 + + S2 + + + + + + + + + + + + + k3 + S2 + + + + + + + diff --git a/latest/cases/00977/output.heta b/latest/cases/00977/output.heta new file mode 100644 index 000000000..189d9d4c8 --- /dev/null +++ b/latest/cases/00977/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: A three-step reaction scheme with a species conversion factor. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +This model tests conversion factors through a system of three reactions. There is a conversion factor ('S1conv') on species S1. This means that S1 is converted according to S1conv, and S2 is not converted. This changes how S1 change in time, but not how S1 is interpreted in the reaction rates. + + +The model contains: +* 2 species (S1, S2) +* 5 parameters (k1, k2, k3, S1conv, modelconv) +* 1 compartment (default_compartment) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $k1$ | +| 2S1 -> 3S2 | $k2 * S1 / S2$ | +| S2 -> | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0.001$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter k2 | $3$ | constant | +| Initial value of parameter k3 | $1.4$ | constant | +| Initial value of parameter S1conv | $3$ | constant | +| Initial value of parameter modelconv | $4$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +default_compartment @Compartment { boundary: true, aux: {{"sboTerm":"SBO:0000410"}}, } .= 1; + +S1 @Species { compartment: default_compartment, } .= 0; +S2 @Species { compartment: default_compartment, } .= 0.001; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; +_J1 @Reaction { actors: 2*S1 = 3*S2, }; +_J1 := (k2 * S1) / S2; +_J2 @Reaction { actors: S2 = , }; +_J2 := k3 * S2; + +k1 @Const { } = 1; +k2 @Const { } = 3; +k3 @Const { } = 1.4; +S1conv @Const { } = 3; +modelconv @Const { } = 4; + diff --git a/latest/cases/00977/synopsis.txt b/latest/cases/00977/synopsis.txt new file mode 100644 index 000000000..76a608ac2 --- /dev/null +++ b/latest/cases/00977/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A three-step reaction scheme with a species conversion factor. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +This model tests conversion factors through a system of three reactions. There is a conversion factor ('S1conv') on species S1. This means that S1 is converted according to S1conv, and S2 is not converted. This changes how S1 change in time, but not how S1 is interpreted in the reaction rates. + + +The model contains: +* 2 species (S1, S2) +* 5 parameters (k1, k2, k3, S1conv, modelconv) +* 1 compartment (default_compartment) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $k1$ | +| 2S1 -> 3S2 | $k2 * S1 / S2$ | +| S2 -> | $k3 * S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0.001$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter k2 | $3$ | constant | +| Initial value of parameter k3 | $1.4$ | constant | +| Initial value of parameter S1conv | $3$ | constant | +| Initial value of parameter modelconv | $4$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/00978/l2v5/index.heta b/latest/cases/00978/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00978/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00978/l3v2/heta-code/output.heta b/latest/cases/00978/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b55914621 --- /dev/null +++ b/latest/cases/00978/l3v2/heta-code/output.heta @@ -0,0 +1,34 @@ + + +t @TimeScale { }; + +multitrig @Record { } .= 0; +multitrig [_E0]= 2; +multitrig [_E1]= 0; +multitrig [_E2]= 2; +multitrig [_E3]= 0; +multitrig [_E4]= 2; +multitrig [_E5]= 0; +multitrig [_E6]= 2; +multitrig [_E7]= 0; +multitrig [_E8]= 2; +x @Record { } .= 0; +x [_E9]= x + 1; +y @Record { } .= 0; +y [_E10]= y + 1; +z @Record { } .= 0; +z [_E11]= z + 3; + +_E0 @DSwitcher { trigger: t >= 0.99, }; +_E1 @DSwitcher { trigger: t >= 0.99, }; +_E2 @DSwitcher { trigger: t >= 0.99, }; +_E3 @DSwitcher { trigger: t >= 0.99, }; +_E4 @DSwitcher { trigger: t >= 0.99, }; +_E5 @DSwitcher { trigger: t >= 0.99, }; +_E6 @DSwitcher { trigger: t >= 0.99, }; +_E7 @DSwitcher { trigger: t >= 0.99, }; +_E8 @DSwitcher { trigger: t >= 0.99, }; +_E9 @DSwitcher { trigger: multitrig > 1, }; +_E10 @DSwitcher { trigger: multitrig > 1, }; +_E11 @DSwitcher { trigger: multitrig > 1, }; + diff --git a/latest/cases/00978/l3v2/index.heta b/latest/cases/00978/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00978/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00978/l3v2/json/output.json b/latest/cases/00978/l3v2/json/output.json new file mode 100644 index 000000000..e5445d857 --- /dev/null +++ b/latest/cases/00978/l3v2/json/output.json @@ -0,0 +1,105 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "multitrig", + "assignments": { + "start_": "0", + "_E0": "2", + "_E1": "0", + "_E2": "2", + "_E3": "0", + "_E4": "2", + "_E5": "0", + "_E6": "2", + "_E7": "0", + "_E8": "2" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0", + "_E9": "x + 1" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "0", + "_E10": "y + 1" + } + }, + { + "class": "Record", + "id": "z", + "assignments": { + "start_": "0", + "_E11": "z + 3" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E1", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E2", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E3", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E4", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E5", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E6", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E7", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E8", + "trigger": "t >= 0.99" + }, + { + "class": "DSwitcher", + "id": "_E9", + "trigger": "multitrig > 1" + }, + { + "class": "DSwitcher", + "id": "_E10", + "trigger": "multitrig > 1" + }, + { + "class": "DSwitcher", + "id": "_E11", + "trigger": "multitrig > 1" + } +] \ No newline at end of file diff --git a/latest/cases/00978/model-sbml-l3v2.xml b/latest/cases/00978/model-sbml-l3v2.xml new file mode 100644 index 000000000..f54eaeaf7 --- /dev/null +++ b/latest/cases/00978/model-sbml-l3v2.xml @@ -0,0 +1,301 @@ + + + + + + + + + + + + + + + + time + 0.99 + + + + + + 10 + + + + + + 2 + + + + + + + + + + time + 0.99 + + + + + + 9 + + + + + + 0 + + + + + + + + + + time + 0.99 + + + + + + 8 + + + + + + 2 + + + + + + + + + + time + 0.99 + + + + + + 7 + + + + + + 0 + + + + + + + + + + time + 0.99 + + + + + + 6 + + + + + + 2 + + + + + + + + + + time + 0.99 + + + + + + 5 + + + + + + 0 + + + + + + + + + + time + 0.99 + + + + + + 4 + + + + + + 2 + + + + + + + + + + time + 0.99 + + + + + + 3 + + + + + + 0 + + + + + + + + + + time + 0.99 + + + + + + 2 + + + + + + 2 + + + + + + + + + + multitrig + 1 + + + + + + 1 + + + + + + + + x + 1 + + + + + + + + + + + multitrig + 1 + + + + + + 1 + + + + + + + + y + 1 + + + + + + + + + + + multitrig + 1 + + + + + + 1 + + + + + + + + z + 3 + + + + + + + + diff --git a/latest/cases/00978/output.heta b/latest/cases/00978/output.heta new file mode 100644 index 000000000..7cf302761 --- /dev/null +++ b/latest/cases/00978/output.heta @@ -0,0 +1,98 @@ +/* +category: Test +synopsis: Several events conspire within the same time step to trigger three events multiple times, with different outcomes. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, EventIsPersistent, EventUsesAssignmentTimeValues, EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events that trigger when the parameter multitrig increases to +above 1. The first is set 'persistent=true' and 'useValuesFromTriggerTime=false', and sets x=x+1, meaning that every time +it triggers, it ends up increasing x by one. + +The second is set 'persistent=true' but 'useValuesFromTriggerTime=true', meaning that it executes +multiple times, but each time uses the value of y from the time it first triggered, meaning +that y gets reset to one four times. + +The third is set 'persistent=false' and 'useValuesFromTriggerTime=false', +and sets z=z+3, meaning that every time it triggers, it has the potential to increase z +by three, but if multitrig drops below 1 again, it will not actually do so. In the end, +it only executes a single time. + +The model also contains nine events with the same trigger and with decreasing priorities +that alternate setting the value of the parameter 'multitrig' from zero to 2, then to +zero, then back again, etc. The priorities of all these events are higher than the first +two, meaning that at a single time point, the first two events are triggered five times, +and 'de-triggered' four times. Since the first event was persistent, x should increase +from zero to five, and since the second event was not persistent, y should increase from +zero to one. + +For a different view of this model, see 00978-antimony.txt + +The model contains: +* 4 parameters (multitrig, x, y, z) + +There are 12 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Use values from:* | *Event Assignments* | +| _E0 | $time ≥ 0.99$ | $10$ | true | Trigger time | $multitrig = 2$ | +| _E1 | $time ≥ 0.99$ | $9$ | true | Trigger time | $multitrig = 0$ | +| _E2 | $time ≥ 0.99$ | $8$ | true | Trigger time | $multitrig = 2$ | +| _E3 | $time ≥ 0.99$ | $7$ | true | Trigger time | $multitrig = 0$ | +| _E4 | $time ≥ 0.99$ | $6$ | true | Trigger time | $multitrig = 2$ | +| _E5 | $time ≥ 0.99$ | $5$ | true | Trigger time | $multitrig = 0$ | +| _E6 | $time ≥ 0.99$ | $4$ | true | Trigger time | $multitrig = 2$ | +| _E7 | $time ≥ 0.99$ | $3$ | true | Trigger time | $multitrig = 0$ | +| _E8 | $time ≥ 0.99$ | $2$ | true | Trigger time | $multitrig = 2$ | +| _E9 | $multitrig > 1$ | $1$ | true | Assignment time | $x = x + 1$ | +| _E10 | $multitrig > 1$ | $1$ | true | Trigger time | $y = y + 1$ | +| _E11 | $multitrig > 1$ | $1$ | false | Assignment time | $z = z + 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter multitrig | $0$ | variable | +| Initial value of parameter x | $0$ | variable | +| Initial value of parameter y | $0$ | variable | +| Initial value of parameter z | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +multitrig @Record { } .= 0; +multitrig [_E0]= 2; +multitrig [_E1]= 0; +multitrig [_E2]= 2; +multitrig [_E3]= 0; +multitrig [_E4]= 2; +multitrig [_E5]= 0; +multitrig [_E6]= 2; +multitrig [_E7]= 0; +multitrig [_E8]= 2; +x @Record { } .= 0; +x [_E9]= x + 1; +y @Record { } .= 0; +y [_E10]= y + 1; +z @Record { } .= 0; +z [_E11]= z + 3; + +_E0 @DSwitcher { trigger: t >= 0.99, }; +_E1 @DSwitcher { trigger: t >= 0.99, }; +_E2 @DSwitcher { trigger: t >= 0.99, }; +_E3 @DSwitcher { trigger: t >= 0.99, }; +_E4 @DSwitcher { trigger: t >= 0.99, }; +_E5 @DSwitcher { trigger: t >= 0.99, }; +_E6 @DSwitcher { trigger: t >= 0.99, }; +_E7 @DSwitcher { trigger: t >= 0.99, }; +_E8 @DSwitcher { trigger: t >= 0.99, }; +_E9 @DSwitcher { trigger: multitrig > 1, }; +_E10 @DSwitcher { trigger: multitrig > 1, }; +_E11 @DSwitcher { trigger: multitrig > 1, }; + diff --git a/latest/cases/00978/synopsis.txt b/latest/cases/00978/synopsis.txt new file mode 100644 index 000000000..4e712378d --- /dev/null +++ b/latest/cases/00978/synopsis.txt @@ -0,0 +1,62 @@ + +category: Test +synopsis: Several events conspire within the same time step to trigger three events multiple times, with different outcomes. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, EventIsPersistent, EventUsesAssignmentTimeValues, EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +This model contains two events that trigger when the parameter multitrig increases to +above 1. The first is set 'persistent=true' and 'useValuesFromTriggerTime=false', and sets x=x+1, meaning that every time +it triggers, it ends up increasing x by one. + +The second is set 'persistent=true' but 'useValuesFromTriggerTime=true', meaning that it executes +multiple times, but each time uses the value of y from the time it first triggered, meaning +that y gets reset to one four times. + +The third is set 'persistent=false' and 'useValuesFromTriggerTime=false', +and sets z=z+3, meaning that every time it triggers, it has the potential to increase z +by three, but if multitrig drops below 1 again, it will not actually do so. In the end, +it only executes a single time. + +The model also contains nine events with the same trigger and with decreasing priorities +that alternate setting the value of the parameter 'multitrig' from zero to 2, then to +zero, then back again, etc. The priorities of all these events are higher than the first +two, meaning that at a single time point, the first two events are triggered five times, +and 'de-triggered' four times. Since the first event was persistent, x should increase +from zero to five, and since the second event was not persistent, y should increase from +zero to one. + +For a different view of this model, see 00978-antimony.txt + +The model contains: +* 4 parameters (multitrig, x, y, z) + +There are 12 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Use values from:* | *Event Assignments* | +| _E0 | $time ≥ 0.99$ | $10$ | true | Trigger time | $multitrig = 2$ | +| _E1 | $time ≥ 0.99$ | $9$ | true | Trigger time | $multitrig = 0$ | +| _E2 | $time ≥ 0.99$ | $8$ | true | Trigger time | $multitrig = 2$ | +| _E3 | $time ≥ 0.99$ | $7$ | true | Trigger time | $multitrig = 0$ | +| _E4 | $time ≥ 0.99$ | $6$ | true | Trigger time | $multitrig = 2$ | +| _E5 | $time ≥ 0.99$ | $5$ | true | Trigger time | $multitrig = 0$ | +| _E6 | $time ≥ 0.99$ | $4$ | true | Trigger time | $multitrig = 2$ | +| _E7 | $time ≥ 0.99$ | $3$ | true | Trigger time | $multitrig = 0$ | +| _E8 | $time ≥ 0.99$ | $2$ | true | Trigger time | $multitrig = 2$ | +| _E9 | $multitrig > 1$ | $1$ | true | Assignment time | $x = x + 1$ | +| _E10 | $multitrig > 1$ | $1$ | true | Trigger time | $y = y + 1$ | +| _E11 | $multitrig > 1$ | $1$ | false | Assignment time | $z = z + 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter multitrig | $0$ | variable | +| Initial value of parameter x | $0$ | variable | +| Initial value of parameter y | $0$ | variable | +| Initial value of parameter z | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00979/l2v5/heta-code/output.heta b/latest/cases/00979/l2v5/heta-code/output.heta new file mode 100644 index 000000000..86ebb4272 --- /dev/null +++ b/latest/cases/00979/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x @Record { } .= 0; +x [_E0]= 2; +y @Record { } .= 0; +y [_E0]= y + x; +p @Record { } .= 0; +p [_E1]= 3; +q @Record { } .= 0; +q [_E1]= p + 1; + +_E0 @DSwitcher { trigger: t >= 0.98, }; +_E1 @DSwitcher { trigger: t >= 0.99, }; + diff --git a/latest/cases/00979/l2v5/index.heta b/latest/cases/00979/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00979/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00979/l2v5/json/output.json b/latest/cases/00979/l2v5/json/output.json new file mode 100644 index 000000000..14dfa79d0 --- /dev/null +++ b/latest/cases/00979/l2v5/json/output.json @@ -0,0 +1,72 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0", + "_E0": "2" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "0", + "_E0": "y + x" + } + }, + { + "class": "Record", + "id": "p", + "assignments": { + "start_": "0", + "_E1": "3" + } + }, + { + "class": "Record", + "id": "q", + "assignments": { + "start_": "0", + "_E1": "p + 1" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t >= 0.98" + }, + { + "class": "DSwitcher", + "id": "_E1", + "trigger": "t >= 0.99" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00979/l3v2/heta-code/output.heta b/latest/cases/00979/l3v2/heta-code/output.heta new file mode 100644 index 000000000..af1da05a8 --- /dev/null +++ b/latest/cases/00979/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +x @Record { } .= 0; +x [_E0]= 2; +y @Record { } .= 0; +y [_E0]= y + x; +p @Record { } .= 0; +p [_E1]= 3; +q @Record { } .= 0; +q [_E1]= p + 1; + +_E0 @DSwitcher { trigger: t >= 0.98, }; +_E1 @DSwitcher { trigger: t >= 0.99, }; + diff --git a/latest/cases/00979/l3v2/index.heta b/latest/cases/00979/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00979/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00979/l3v2/json/output.json b/latest/cases/00979/l3v2/json/output.json new file mode 100644 index 000000000..1a470f3db --- /dev/null +++ b/latest/cases/00979/l3v2/json/output.json @@ -0,0 +1,47 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0", + "_E0": "2" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "0", + "_E0": "y + x" + } + }, + { + "class": "Record", + "id": "p", + "assignments": { + "start_": "0", + "_E1": "3" + } + }, + { + "class": "Record", + "id": "q", + "assignments": { + "start_": "0", + "_E1": "p + 1" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t >= 0.98" + }, + { + "class": "DSwitcher", + "id": "_E1", + "trigger": "t >= 0.99" + } +] \ No newline at end of file diff --git a/latest/cases/00979/model-sbml-l2v5.xml b/latest/cases/00979/model-sbml-l2v5.xml new file mode 100644 index 000000000..1f88884ef --- /dev/null +++ b/latest/cases/00979/model-sbml-l2v5.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + time + 0.98 + + + + + + + + + y + x + + + + + + 2 + + + + + + + + + + time + 0.99 + + + + + + + 3 + + + + + + + p + 1 + + + + + + + + diff --git a/latest/cases/00979/model-sbml-l3v2.xml b/latest/cases/00979/model-sbml-l3v2.xml new file mode 100644 index 000000000..71f096268 --- /dev/null +++ b/latest/cases/00979/model-sbml-l3v2.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + time + 0.98 + + + + + + + + + y + x + + + + + + 2 + + + + + + + + + + time + 0.99 + + + + + + + 3 + + + + + + + p + 1 + + + + + + + + diff --git a/latest/cases/00979/output.heta b/latest/cases/00979/output.heta new file mode 100644 index 000000000..709e71267 --- /dev/null +++ b/latest/cases/00979/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Two event where the two event assignments should not interfere with each other. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model contains two events that trigger when time > 0.98 and 0.99. In each, there is on event assignment that changes the value of a parameter, and a second event assignment that uses that parameter to change the value of a second parameter. However, the second event assignment should not use the changed value from the first parameter, but rather the value it had at the beginning of event assignment. (This is true regardless of the value of 'useValuesFromTriggerTime', but the value of that flag here happens to be true.) + +The model contains: +* 4 parameters (x, y, p, q) + +There are 2 events: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time ≥ 0.98$ | $y = y + x$ | +| | | $x = 2$ | +| _E1 | $time ≥ 0.99$ | $p = 3$ | +| | | $q = p + 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $0$ | variable | +| Initial value of parameter y | $0$ | variable | +| Initial value of parameter p | $0$ | variable | +| Initial value of parameter q | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 0; +x [_E0]= 2; +y @Record { } .= 0; +y [_E0]= y + x; +p @Record { } .= 0; +p [_E1]= 3; +q @Record { } .= 0; +q [_E1]= p + 1; + +_E0 @DSwitcher { trigger: t >= 0.98, }; +_E1 @DSwitcher { trigger: t >= 0.99, }; + diff --git a/latest/cases/00979/synopsis.txt b/latest/cases/00979/synopsis.txt new file mode 100644 index 000000000..13be362eb --- /dev/null +++ b/latest/cases/00979/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Two event where the two event assignments should not interfere with each other. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model contains two events that trigger when time > 0.98 and 0.99. In each, there is on event assignment that changes the value of a parameter, and a second event assignment that uses that parameter to change the value of a second parameter. However, the second event assignment should not use the changed value from the first parameter, but rather the value it had at the beginning of event assignment. (This is true regardless of the value of 'useValuesFromTriggerTime', but the value of that flag here happens to be true.) + +The model contains: +* 4 parameters (x, y, p, q) + +There are 2 events: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time ≥ 0.98$ | $y = y + x$ | +| | | $x = 2$ | +| _E1 | $time ≥ 0.99$ | $p = 3$ | +| | | $q = p + 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $0$ | variable | +| Initial value of parameter y | $0$ | variable | +| Initial value of parameter p | $0$ | variable | +| Initial value of parameter q | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00980/l2v5/build.log b/latest/cases/00980/l2v5/build.log new file mode 100644 index 000000000..7393a0224 --- /dev/null +++ b/latest/cases/00980/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00980/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00980/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00980/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00980/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00980/l2v5/index.heta b/latest/cases/00980/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00980/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00980/l3v2/build.log b/latest/cases/00980/l3v2/build.log new file mode 100644 index 000000000..739d85ad2 --- /dev/null +++ b/latest/cases/00980/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00980/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00980/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00980/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00980/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00980/l3v2/index.heta b/latest/cases/00980/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00980/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00980/model-sbml-l2v5.xml b/latest/cases/00980/model-sbml-l2v5.xml new file mode 100644 index 000000000..82c1d37a9 --- /dev/null +++ b/latest/cases/00980/model-sbml-l2v5.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + time + 0.98 + + + + + + 0.1 + + + + + + + + y + x + + + + + + 2 + + + + + + + + + + time + 0.99 + + + + + + 0.1 + + + + + + 3 + + + + + + + p + 1 + + + + + + + + diff --git a/latest/cases/00980/model-sbml-l3v2.xml b/latest/cases/00980/model-sbml-l3v2.xml new file mode 100644 index 000000000..ee4b44037 --- /dev/null +++ b/latest/cases/00980/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + time + 0.98 + + + + + + 0.1 + + + + + + + + y + x + + + + + + 2 + + + + + + + + + + time + 0.99 + + + + + + 0.1 + + + + + + 3 + + + + + + + p + 1 + + + + + + + + diff --git a/latest/cases/00980/synopsis.txt b/latest/cases/00980/synopsis.txt new file mode 100644 index 000000000..cd3a4e411 --- /dev/null +++ b/latest/cases/00980/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Two event where the two event assignments should not interfere with each other. +componentTags: CSymbolTime, EventWithDelay, Parameter +testTags: EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model contains two events that trigger when time > 0.98 and 0.99. In each, there is one event assignment that changes the value of a parameter, and a second event assignment that uses that parameter to change the value of a second parameter. However, the second event assignment should not use the changed value from the first parameter, but rather the value it had at the beginning of event assignment. (This is true regardless of the value of 'useValuesFromTriggerTime', but the value of that flag here happens to be false. In order to test this in l2v4 and l2v5, there had to be a delay.) + +The model contains: +* 4 parameters (x, y, p, q) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| _E0 | $time ≥ 0.98$ | Assignment time | $0.1$ | $y = y + x$ | +| | | | | $x = 2$ | +| _E1 | $time ≥ 0.99$ | Assignment time | $0.1$ | $p = 3$ | +| | | | | $q = p + 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $0$ | variable | +| Initial value of parameter y | $0$ | variable | +| Initial value of parameter p | $0$ | variable | +| Initial value of parameter q | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00981/l2v5/build.log b/latest/cases/00981/l2v5/build.log new file mode 100644 index 000000000..89941a558 --- /dev/null +++ b/latest/cases/00981/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00981/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00981/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00981/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00981/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00981/l2v5/index.heta b/latest/cases/00981/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00981/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00981/l3v2/build.log b/latest/cases/00981/l3v2/build.log new file mode 100644 index 000000000..58be225d6 --- /dev/null +++ b/latest/cases/00981/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00981/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00981/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00981/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00981/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00981/l3v2/index.heta b/latest/cases/00981/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00981/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00981/model-sbml-l2v5.xml b/latest/cases/00981/model-sbml-l2v5.xml new file mode 100644 index 000000000..b6c82aae4 --- /dev/null +++ b/latest/cases/00981/model-sbml-l2v5.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + 1 + + + + + + delay + x + + + time + 2 + + + + + + + diff --git a/latest/cases/00981/model-sbml-l3v2.xml b/latest/cases/00981/model-sbml-l3v2.xml new file mode 100644 index 000000000..ae45354fb --- /dev/null +++ b/latest/cases/00981/model-sbml-l3v2.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + 1 + + + + + + delay + x + + + time + 2 + + + + + + + diff --git a/latest/cases/00981/synopsis.txt b/latest/cases/00981/synopsis.txt new file mode 100644 index 000000000..238f439c3 --- /dev/null +++ b/latest/cases/00981/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: An assignment rule with a continually-changing delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, Parameter, RateRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model contains a single parameter x changing at a constant rate, and a second parameter y with a continually-changing delay for an assignment rule: it takes the value of x at time/2 ago. Effectively, this means that y changes at half the rate of x. + +The model contains: +* 2 parameters (x, y) +* 1 compartment (default_compartment) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $1$ | +| Assignment | y | $delay(x, time / 2)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $1$ | variable | +| Initial value of parameter y | $delay(x, time / 2)$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00982/l2v5/build.log b/latest/cases/00982/l2v5/build.log new file mode 100644 index 000000000..31c6e93ab --- /dev/null +++ b/latest/cases/00982/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00982/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00982/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00982/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00982/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00982/l2v5/index.heta b/latest/cases/00982/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00982/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00982/l3v2/build.log b/latest/cases/00982/l3v2/build.log new file mode 100644 index 000000000..d9908e665 --- /dev/null +++ b/latest/cases/00982/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00982/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00982/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00982/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00982/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00982/l3v2/index.heta b/latest/cases/00982/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00982/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00982/model-sbml-l2v5.xml b/latest/cases/00982/model-sbml-l2v5.xml new file mode 100644 index 000000000..de148b27f --- /dev/null +++ b/latest/cases/00982/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + 1 + + + + + + + time + 2 + + + + + + + delay + x + temp + + + + + + diff --git a/latest/cases/00982/model-sbml-l3v2.xml b/latest/cases/00982/model-sbml-l3v2.xml new file mode 100644 index 000000000..1906ac7fa --- /dev/null +++ b/latest/cases/00982/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + 1 + + + + + + + time + 2 + + + + + + + delay + x + temp + + + + + + diff --git a/latest/cases/00982/synopsis.txt b/latest/cases/00982/synopsis.txt new file mode 100644 index 000000000..c83ddb78a --- /dev/null +++ b/latest/cases/00982/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: An assignment rule with a continually-changing delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Parameter, RateRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model contains a single parameter x changing at a constant rate, and a second parameter y with a continually-changing delay for an assignment rule: it takes the value of x at 'temp' time ago, which in turn is assigned the value of time/2. Effectively, this means that y changes at half the rate of x. + +The model contains: +* 3 parameters (x, temp, y) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $1$ | +| Assignment | temp | $time / 2$ | +| Assignment | y | $delay(x, temp)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $1$ | variable | +| Initial value of parameter temp | $time / 2$ | variable | +| Initial value of parameter y | $delay(x, temp)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00983/l2v5/build.log b/latest/cases/00983/l2v5/build.log new file mode 100644 index 000000000..cc4a34094 --- /dev/null +++ b/latest/cases/00983/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00983/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00983/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00983/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00983/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00983/l2v5/index.heta b/latest/cases/00983/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00983/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00983/l3v2/build.log b/latest/cases/00983/l3v2/build.log new file mode 100644 index 000000000..96e09cf58 --- /dev/null +++ b/latest/cases/00983/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00983/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00983/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00983/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00983/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00983/l3v2/index.heta b/latest/cases/00983/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00983/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00983/model-sbml-l2v5.xml b/latest/cases/00983/model-sbml-l2v5.xml new file mode 100644 index 000000000..f76cb940d --- /dev/null +++ b/latest/cases/00983/model-sbml-l2v5.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + 1 + + + + + + + + + -1 + temp + + + + time + 2 + + + + + + + + delay + x + temp + + + + + + diff --git a/latest/cases/00983/model-sbml-l3v2.xml b/latest/cases/00983/model-sbml-l3v2.xml new file mode 100644 index 000000000..a8fa080e3 --- /dev/null +++ b/latest/cases/00983/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + 1 + + + + + + + + + -1 + temp + + + + time + 2 + + + + + + + + delay + x + temp + + + + + + diff --git a/latest/cases/00983/synopsis.txt b/latest/cases/00983/synopsis.txt new file mode 100644 index 000000000..06d0e3912 --- /dev/null +++ b/latest/cases/00983/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: An assignment rule with a continually-changing delay from an algebraic rule. +componentTags: AlgebraicRule, AssignmentRule, CSymbolDelay, CSymbolTime, Parameter, RateRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model contains a single parameter x changing at a constant rate, and a second parameter y with a continually-changing delay for an assignment rule: it takes the value of x at 'temp' time ago, which in turn is assigned the value of time/2 via an algebraic rule. Effectively, this means that y changes at half the rate of x. + +The model contains: +* 3 parameters (x, temp, y) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $1$ | +| Algebraic | $0$ | $-1 * temp + time / 2$ | +| Assignment | y | $delay(x, temp)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $1$ | variable | +| Initial value of parameter temp | $time / 2$ | variable | +| Initial value of parameter y | $delay(x, temp)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00984/l2v5/build.log b/latest/cases/00984/l2v5/build.log new file mode 100644 index 000000000..1fb503012 --- /dev/null +++ b/latest/cases/00984/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00984/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00984/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00984/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00984/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00984/l2v5/index.heta b/latest/cases/00984/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00984/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00984/l3v2/build.log b/latest/cases/00984/l3v2/build.log new file mode 100644 index 000000000..5ba7d32d2 --- /dev/null +++ b/latest/cases/00984/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00984/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00984/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00984/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00984/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00984/l3v2/index.heta b/latest/cases/00984/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00984/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00984/model-sbml-l2v5.xml b/latest/cases/00984/model-sbml-l2v5.xml new file mode 100644 index 000000000..28c155801 --- /dev/null +++ b/latest/cases/00984/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + delay + x + temp + + + + + + 1 + + + + + + + + + + time + 0.99 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00984/model-sbml-l3v2.xml b/latest/cases/00984/model-sbml-l3v2.xml new file mode 100644 index 000000000..c9e69ae88 --- /dev/null +++ b/latest/cases/00984/model-sbml-l3v2.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + delay + x + temp + + + + + + 1 + + + + + + + + + + time + 0.99 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00984/synopsis.txt b/latest/cases/00984/synopsis.txt new file mode 100644 index 000000000..8f8fbabe7 --- /dev/null +++ b/latest/cases/00984/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: An assignment rule with a continually-changing delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model contains a single parameter x changing at a constant rate, and a second parameter y that follows x with no delay at first, but then switching to a delay of 1 at time 1 through an event. + +The model contains: +* 3 parameters (y, x, temp) +* 1 compartment (default_compartment) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time ≥ 0.99$ | $temp = 1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | y | $delay(x, temp)$ | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter y | $delay(x, temp)$ | variable | +| Initial value of parameter x | $1$ | variable | +| Initial value of parameter temp | $0$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00985/l2v5/build.log b/latest/cases/00985/l2v5/build.log new file mode 100644 index 000000000..34a4f9946 --- /dev/null +++ b/latest/cases/00985/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00985/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00985/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00985/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00985/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00985/l2v5/index.heta b/latest/cases/00985/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00985/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00985/l3v2/build.log b/latest/cases/00985/l3v2/build.log new file mode 100644 index 000000000..3fb59598b --- /dev/null +++ b/latest/cases/00985/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00985/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00985/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00985/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00985/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00985/l3v2/index.heta b/latest/cases/00985/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00985/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00985/model-sbml-l2v5.xml b/latest/cases/00985/model-sbml-l2v5.xml new file mode 100644 index 000000000..04a6430bd --- /dev/null +++ b/latest/cases/00985/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + delay + x + 1 + + + + + + 1 + + + + + + delay + x + z + + + + + + diff --git a/latest/cases/00985/model-sbml-l3v2.xml b/latest/cases/00985/model-sbml-l3v2.xml new file mode 100644 index 000000000..67388b012 --- /dev/null +++ b/latest/cases/00985/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + delay + x + 1 + + + + + + 1 + + + + + + delay + x + z + + + + + + diff --git a/latest/cases/00985/synopsis.txt b/latest/cases/00985/synopsis.txt new file mode 100644 index 000000000..03330ee85 --- /dev/null +++ b/latest/cases/00985/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: An assignment rule with a continually-changing delay. +componentTags: AssignmentRule, CSymbolDelay, Parameter, RateRule +testTags: NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +This model contains a single parameter x changing at a constant rate, and a second parameter z that follows x with a delay of 1, and a third parameter y that follows x with a delay of z. + +The model contains: +* 3 parameters (z, x, y) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $delay(x, 1)$ | +| Rate | x | $1$ | +| Assignment | y | $delay(x, z)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $delay(x, 1)$ | variable | +| Initial value of parameter x | $1$ | variable | +| Initial value of parameter y | $delay(x, z)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00986/l2v5/build.log b/latest/cases/00986/l2v5/build.log new file mode 100644 index 000000000..7e6565423 --- /dev/null +++ b/latest/cases/00986/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00986/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00986/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00986/model-sbml-l2v5.xml"... +[error] "fast" reactions "fast" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00986/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00986/l2v5/index.heta b/latest/cases/00986/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00986/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00986/l3v2/index.heta b/latest/cases/00986/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00986/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00986/model-sbml-l2v5.xml b/latest/cases/00986/model-sbml-l2v5.xml new file mode 100644 index 000000000..7d803245b --- /dev/null +++ b/latest/cases/00986/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + 1 + A + + + + + + + + + + + + + + + + 1 + B + + + + + + + diff --git a/latest/cases/00986/synopsis.txt b/latest/cases/00986/synopsis.txt new file mode 100644 index 000000000..46be68004 --- /dev/null +++ b/latest/cases/00986/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A fast and slow reaction, the first of which feeds into the second. +componentTags: Compartment, Reaction, Species +testTags: Amount, FastReaction, HasOnlySubstanceUnits +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic + +The 'fast' reaction should go to completion instantly, converting all of A to B. Then B converts to C normally. + +The model contains: +* 3 species (A, B, C) +* 1 compartment (default_compartment) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| A -> B | $1 * A$ | fast | +| B -> C | $1 * B$ | slow |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species A | $1$ | variable | +| Initial amount of species B | $0$ | variable | +| Initial amount of species C | $0$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00987/l2v5/build.log b/latest/cases/00987/l2v5/build.log new file mode 100644 index 000000000..918da1bfc --- /dev/null +++ b/latest/cases/00987/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00987/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00987/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00987/model-sbml-l2v5.xml"... +[error] "fast" reactions "fast" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00987/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00987/l2v5/index.heta b/latest/cases/00987/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00987/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00987/l3v2/index.heta b/latest/cases/00987/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00987/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00987/model-sbml-l2v5.xml b/latest/cases/00987/model-sbml-l2v5.xml new file mode 100644 index 000000000..03783850d --- /dev/null +++ b/latest/cases/00987/model-sbml-l2v5.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + A + + + + + + + + + + + + + + + + k1 + B + + + + + + + + + + + + time + 0.99 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00987/synopsis.txt b/latest/cases/00987/synopsis.txt new file mode 100644 index 000000000..c049c36e5 --- /dev/null +++ b/latest/cases/00987/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A fast and slow reaction, the first of which feeds into the second, triggered by an event. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, FastReaction, NonConstantParameter, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic + +After the event fires, the 'fast' reaction should go to completion instantly, converting all of A to B. Then B converts to C normally. + +The model contains: +* 3 species (A, B, C) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| A -> B | $k1 * A$ | fast | +| B -> C | $k1 * B$ | slow |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 0.99$ | $k1 = 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species A | $1$ | variable | +| Initial amount of species B | $0$ | variable | +| Initial amount of species C | $0$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00988/l2v5/build.log b/latest/cases/00988/l2v5/build.log new file mode 100644 index 000000000..1fdac94a4 --- /dev/null +++ b/latest/cases/00988/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00988/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00988/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00988/model-sbml-l2v5.xml"... +[error] "fast" reactions "fast" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00988/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00988/l2v5/index.heta b/latest/cases/00988/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00988/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00988/l3v2/index.heta b/latest/cases/00988/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00988/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00988/model-sbml-l2v5.xml b/latest/cases/00988/model-sbml-l2v5.xml new file mode 100644 index 000000000..f36e7439a --- /dev/null +++ b/latest/cases/00988/model-sbml-l2v5.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + + + + + k2 + A + + + + + + + + + + + + A + 0.99 + + + + + + + 1 + + + + + + + + + + A + 0.99 + + + + + + 0.1 + + + + + + 0 + + + + + + + diff --git a/latest/cases/00988/synopsis.txt b/latest/cases/00988/synopsis.txt new file mode 100644 index 000000000..033faf815 --- /dev/null +++ b/latest/cases/00988/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: A fast and slow reaction, working against each other, with the fast reaction turned on and off by Events. +componentTags: Compartment, EventWithDelay, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, EventIsPersistent, FastReaction, NonConstantParameter, HasOnlySubstanceUnits +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic + + After B is converted to A by the slow reaction for a while, eventually the two events trigger, setting the reaction rate of the fast reaction to 1*A--consuming all of A and turning it back into B. Then it turns back off, and B is once again slowly converted to A. This would cycle again, but we only test one cycle. + + +The model contains: +* 2 species (A, B) +* 2 parameters (k1, k2) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| B -> A | $k1$ | slow | +| A -> B | $k2 * A$ | fast |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $A ≥ 0.99$ | $0$ | $k2 = 1$ | +| E1 | $A ≥ 0.99$ | $0.1$ | $k2 = 0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species A | $0$ | variable | +| Initial amount of species B | $2$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial value of parameter k2 | $0$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00989/l2v5/build.log b/latest/cases/00989/l2v5/build.log new file mode 100644 index 000000000..6df582613 --- /dev/null +++ b/latest/cases/00989/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00989/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00989/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00989/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00989/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00989/l2v5/index.heta b/latest/cases/00989/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00989/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00989/l3v2/index.heta b/latest/cases/00989/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00989/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00989/model-sbml-l2v5.xml b/latest/cases/00989/model-sbml-l2v5.xml new file mode 100644 index 000000000..f96e88874 --- /dev/null +++ b/latest/cases/00989/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + X + + + + + + + k1 + + + + + + + + + + + + k1 + Y + + + + + + + diff --git a/latest/cases/00989/synopsis.txt b/latest/cases/00989/synopsis.txt new file mode 100644 index 000000000..eb4d1c736 --- /dev/null +++ b/latest/cases/00989/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: A simple reaction with stoichiometry the same as its species. For convenience, another reaction is present with the same kinetics, as the species is used in the kinetic law instead. +componentTags: StoichiometryMath, Compartment, Parameter, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, HasOnlySubstanceUnits, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +This model contains two reactions that do the same thing, one by having a kinetic law that varies with the produced species, and the other by having a variable stoichiometry set to equal the produced species, for a sort of auto-catalytic reaction. + + +The model contains: +* 2 species (X, Y) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ | +| -> Y | $k1 * Y$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $X$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species X | $1$ | variable | +| Initial amount of species Y | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/00990/l2v5/build.log b/latest/cases/00990/l2v5/build.log new file mode 100644 index 000000000..2434c16fc --- /dev/null +++ b/latest/cases/00990/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00990/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00990/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00990/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00990/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00990/l2v5/index.heta b/latest/cases/00990/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00990/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00990/l3v2/index.heta b/latest/cases/00990/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00990/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00990/model-sbml-l2v5.xml b/latest/cases/00990/model-sbml-l2v5.xml new file mode 100644 index 000000000..bbe5a05c1 --- /dev/null +++ b/latest/cases/00990/model-sbml-l2v5.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + p1 + + + + + + + k1 + + + + + + diff --git a/latest/cases/00990/synopsis.txt b/latest/cases/00990/synopsis.txt new file mode 100644 index 000000000..856d8947e --- /dev/null +++ b/latest/cases/00990/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to a parameter that varies due to a rate law. +componentTags: StoichiometryMath, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, NonUnityStoichiometry, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: earlier versions of the test suite contained a 3.1 version of this test. +That model was moved to its own test, because it did not have the 'StoichiometryMath' +component. + +The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that starts at 1 and increases at a rate of 1. + +The model contains: +* 1 species (X) +* 2 parameters (p1, k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $p1$ | +| Rate | p1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter p1 | $1$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/00991/l2v5/build.log b/latest/cases/00991/l2v5/build.log new file mode 100644 index 000000000..7575e2386 --- /dev/null +++ b/latest/cases/00991/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00991/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00991/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00991/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00991/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00991/l2v5/index.heta b/latest/cases/00991/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00991/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00991/l3v2/index.heta b/latest/cases/00991/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00991/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00991/model-sbml-l2v5.xml b/latest/cases/00991/model-sbml-l2v5.xml new file mode 100644 index 000000000..787572dfc --- /dev/null +++ b/latest/cases/00991/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + p1 + + + + + + + k1 + + + + + + + + + + + X + 2 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/00991/synopsis.txt b/latest/cases/00991/synopsis.txt new file mode 100644 index 000000000..26c2b7320 --- /dev/null +++ b/latest/cases/00991/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to a parameter that varies from an Event. +componentTags: StoichiometryMath, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, NonUnityStoichiometry, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that starts at 1 and switches to 2 due to an event. + +The equivalent model using Level 3 constructs is present as +test 1106. + +The model contains: +* 1 species (X) +* 2 parameters (p1, k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $X ≥ 2$ | $p1 = 2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter p1 | $1$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/00992/l2v5/build.log b/latest/cases/00992/l2v5/build.log new file mode 100644 index 000000000..1c1819488 --- /dev/null +++ b/latest/cases/00992/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00992/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00992/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00992/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00992/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00992/l2v5/index.heta b/latest/cases/00992/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00992/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00992/l3v2/index.heta b/latest/cases/00992/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00992/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00992/model-sbml-l2v5.xml b/latest/cases/00992/model-sbml-l2v5.xml new file mode 100644 index 000000000..b5da03138 --- /dev/null +++ b/latest/cases/00992/model-sbml-l2v5.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + X + + + + + + + + + + p1 + + + + + + + k1 + + + + + + diff --git a/latest/cases/00992/synopsis.txt b/latest/cases/00992/synopsis.txt new file mode 100644 index 000000000..123b3e7cc --- /dev/null +++ b/latest/cases/00992/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to a parameter, which in turn is set to be the same as its species. +componentTags: StoichiometryMath, AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, HasOnlySubstanceUnits, InitialValueReassigned, NonUnityStoichiometry, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that is set by an assignment rule to be equal to X. + +The equivalent model using Level 3 constructs is present as +test 1107. + +The model contains: +* 1 species (X) +* 2 parameters (p1, k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $p1$ | +| Assignment | p1 | $X$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter p1 | $X$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/00993/l2v5/build.log b/latest/cases/00993/l2v5/build.log new file mode 100644 index 000000000..a839e8f4d --- /dev/null +++ b/latest/cases/00993/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00993/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00993/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00993/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00993/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00993/l2v5/index.heta b/latest/cases/00993/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00993/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00993/l3v2/index.heta b/latest/cases/00993/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00993/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00993/model-sbml-l2v5.xml b/latest/cases/00993/model-sbml-l2v5.xml new file mode 100644 index 000000000..0e29368c0 --- /dev/null +++ b/latest/cases/00993/model-sbml-l2v5.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + X + p1 + + + + + + + + + + + p1 + + + + + + + k1 + + + + + + diff --git a/latest/cases/00993/synopsis.txt b/latest/cases/00993/synopsis.txt new file mode 100644 index 000000000..0181af4b6 --- /dev/null +++ b/latest/cases/00993/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to a parameter, which in turn is set to be the same as its species via an algebraic rule. +componentTags: StoichiometryMath, AlgebraicRule, Compartment, Parameter, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that is set by an algebraic rule to be equal to X. + +The equivalent model using Level 3 constructs is present as +test 1108. + +The model contains: +* 1 species (X) +* 2 parameters (p1, k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $X - p1$ | +| Assignment | Xref | $p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter p1 | $unknown$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/00994/l2v5/build.log b/latest/cases/00994/l2v5/build.log new file mode 100644 index 000000000..2bface829 --- /dev/null +++ b/latest/cases/00994/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00994/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00994/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00994/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/00994/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/00994/l2v5/index.heta b/latest/cases/00994/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00994/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00994/l3v2/index.heta b/latest/cases/00994/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00994/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00994/model-sbml-l2v5.xml b/latest/cases/00994/model-sbml-l2v5.xml new file mode 100644 index 000000000..13da27fbb --- /dev/null +++ b/latest/cases/00994/model-sbml-l2v5.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + time + + + + + + + k1 + + + + + + diff --git a/latest/cases/00994/synopsis.txt b/latest/cases/00994/synopsis.txt new file mode 100644 index 000000000..713174be1 --- /dev/null +++ b/latest/cases/00994/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to be equal to 'time'. +componentTags: StoichiometryMath, CSymbolTime, Compartment, Parameter, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Variable stoichiometry: the stoichiometry is literally 'time'. + +The equivalent model using Level 3 constructs is present as +test 1109. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/00995/l2v5/index.heta b/latest/cases/00995/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00995/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00995/l3v2/heta-code/output.heta b/latest/cases/00995/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a8c4452bd --- /dev/null +++ b/latest/cases/00995/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +p2 @Record { } .= 0; +p2 [E0]= 1; +p3 @Record { } .= 0; +p3 [E1]= 1; + +p1 @Const { } = 1; + +E0 @DSwitcher { trigger: p1 > 0, }; +E1 @DSwitcher { trigger: p1 > 0, }; + diff --git a/latest/cases/00995/l3v2/index.heta b/latest/cases/00995/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00995/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00995/l3v2/json/output.json b/latest/cases/00995/l3v2/json/output.json new file mode 100644 index 000000000..c947167a8 --- /dev/null +++ b/latest/cases/00995/l3v2/json/output.json @@ -0,0 +1,36 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "p1", + "num": 1 + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "start_": "0", + "E0": "1" + } + }, + { + "class": "Record", + "id": "p3", + "assignments": { + "start_": "0", + "E1": "1" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "p1 > 0" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "p1 > 0" + } +] \ No newline at end of file diff --git a/latest/cases/00995/model-sbml-l3v2.xml b/latest/cases/00995/model-sbml-l3v2.xml new file mode 100644 index 000000000..1377ee969 --- /dev/null +++ b/latest/cases/00995/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + p1 + 0 + + + + + + + 1 + + + + + + + + + + p1 + 0 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00995/output.heta b/latest/cases/00995/output.heta new file mode 100644 index 000000000..aef52abfb --- /dev/null +++ b/latest/cases/00995/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Two events with different 'initialValue's, causing one to fire and one to not fire. +componentTags: EventNoDelay, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains two events, one that assigns '1' to parameter p2, and one that assigns '1' to parameter p3. Both have the same trigger, p1>0, which is true the entire time, but the first trigger is set 'initialValue="false"' and the second 'initialValue="true"'. This causes the first to trigger at t0 and the second to not trigger. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $p1 > 0$ | false | $p2 = 1$ | +| E1 | $p1 > 0$ | true | $p3 = 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | constant | +| Initial value of parameter p2 | $0$ | variable | +| Initial value of parameter p3 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p2 @Record { } .= 0; +p2 [E0]= 1; +p3 @Record { } .= 0; +p3 [E1]= 1; + +p1 @Const { } = 1; + +E0 @DSwitcher { trigger: p1 > 0, }; +E1 @DSwitcher { trigger: p1 > 0, }; + diff --git a/latest/cases/00995/synopsis.txt b/latest/cases/00995/synopsis.txt new file mode 100644 index 000000000..087cf9acc --- /dev/null +++ b/latest/cases/00995/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Two events with different 'initialValue's, causing one to fire and one to not fire. +componentTags: EventNoDelay, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains two events, one that assigns '1' to parameter p2, and one that assigns '1' to parameter p3. Both have the same trigger, p1>0, which is true the entire time, but the first trigger is set 'initialValue="false"' and the second 'initialValue="true"'. This causes the first to trigger at t0 and the second to not trigger. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $p1 > 0$ | false | $p2 = 1$ | +| E1 | $p1 > 0$ | true | $p3 = 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | constant | +| Initial value of parameter p2 | $0$ | variable | +| Initial value of parameter p3 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00996/l2v5/index.heta b/latest/cases/00996/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00996/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00996/l3v2/heta-code/output.heta b/latest/cases/00996/l3v2/heta-code/output.heta new file mode 100644 index 000000000..dcb28ac83 --- /dev/null +++ b/latest/cases/00996/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +p1_proc @Process { actors: = p1, }; +p1_proc := (-1); + +p1 @Record { } .= 1; +p2 @Record { } .= 0; +p2 [E0]= 1; +p3 @Record { } .= 0; +p3 [E1]= 1; + +E0 @DSwitcher { trigger: p1 >= 1, }; +E1 @DSwitcher { trigger: p1 >= 1, }; + diff --git a/latest/cases/00996/l3v2/index.heta b/latest/cases/00996/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00996/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00996/l3v2/json/output.json b/latest/cases/00996/l3v2/json/output.json new file mode 100644 index 000000000..3a25c2c9b --- /dev/null +++ b/latest/cases/00996/l3v2/json/output.json @@ -0,0 +1,51 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "start_": "0", + "E0": "1" + } + }, + { + "class": "Record", + "id": "p3", + "assignments": { + "start_": "0", + "E1": "1" + } + }, + { + "class": "Process", + "id": "p1_proc", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "p1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "p1 >= 1" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "p1 >= 1" + } +] \ No newline at end of file diff --git a/latest/cases/00996/model-sbml-l3v2.xml b/latest/cases/00996/model-sbml-l3v2.xml new file mode 100644 index 000000000..4ac959b82 --- /dev/null +++ b/latest/cases/00996/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + -1 + + + + + + + + + + p1 + 1 + + + + + + + 1 + + + + + + + + + + p1 + 1 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/00996/output.heta b/latest/cases/00996/output.heta new file mode 100644 index 000000000..ed253eef3 --- /dev/null +++ b/latest/cases/00996/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Two events with different 'initialValue's, causing one to fire and one to not fire. +componentTags: EventNoDelay, Parameter, RateRule +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains two events, one that assigns '1' to parameter p2, and one that assigns '1' to parameter p3. Both have the same trigger, p1>=1, which is true at t0, but is false thereafter due to a rate rule. The first trigger is set 'initialValue="false"' and the second 'initialValue="true"'. This causes the first to trigger at t0 and the second to not trigger. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $p1 ≥ 1$ | false | $p2 = 1$ | +| E1 | $p1 ≥ 1$ | true | $p3 = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $-1$ | variable | +| Initial value of parameter p2 | $0$ | variable | +| Initial value of parameter p3 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p1_proc @Process { actors: = p1, }; +p1_proc := (-1); + +p1 @Record { } .= 1; +p2 @Record { } .= 0; +p2 [E0]= 1; +p3 @Record { } .= 0; +p3 [E1]= 1; + +E0 @DSwitcher { trigger: p1 >= 1, }; +E1 @DSwitcher { trigger: p1 >= 1, }; + diff --git a/latest/cases/00996/synopsis.txt b/latest/cases/00996/synopsis.txt new file mode 100644 index 000000000..072ac69aa --- /dev/null +++ b/latest/cases/00996/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Two events with different 'initialValue's, causing one to fire and one to not fire. +componentTags: EventNoDelay, Parameter, RateRule +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +The model contains two events, one that assigns '1' to parameter p2, and one that assigns '1' to parameter p3. Both have the same trigger, p1>=1, which is true at t0, but is false thereafter due to a rate rule. The first trigger is set 'initialValue="false"' and the second 'initialValue="true"'. This causes the first to trigger at t0 and the second to not trigger. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $p1 ≥ 1$ | false | $p2 = 1$ | +| E1 | $p1 ≥ 1$ | true | $p3 = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $-1$ | variable | +| Initial value of parameter p2 | $0$ | variable | +| Initial value of parameter p3 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00997/l2v5/index.heta b/latest/cases/00997/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00997/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00997/l3v2/heta-code/output.heta b/latest/cases/00997/l3v2/heta-code/output.heta new file mode 100644 index 000000000..72c002d63 --- /dev/null +++ b/latest/cases/00997/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [E2]= 0; +p2 @Record { } .= 0; +p2 [E0]= 1; +p3 @Record { } .= 0; +p3 [E1]= 1; + +E0 @DSwitcher { trigger: p1 >= 1, }; +E1 @DSwitcher { trigger: p1 >= 1, }; +E2 @DSwitcher { trigger: p1 >= 1, }; + diff --git a/latest/cases/00997/l3v2/index.heta b/latest/cases/00997/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00997/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00997/l3v2/json/output.json b/latest/cases/00997/l3v2/json/output.json new file mode 100644 index 000000000..0148792e0 --- /dev/null +++ b/latest/cases/00997/l3v2/json/output.json @@ -0,0 +1,44 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "1", + "E2": "0" + } + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "start_": "0", + "E0": "1" + } + }, + { + "class": "Record", + "id": "p3", + "assignments": { + "start_": "0", + "E1": "1" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "p1 >= 1" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "p1 >= 1" + }, + { + "class": "DSwitcher", + "id": "E2", + "trigger": "p1 >= 1" + } +] \ No newline at end of file diff --git a/latest/cases/00997/model-sbml-l3v2.xml b/latest/cases/00997/model-sbml-l3v2.xml new file mode 100644 index 000000000..f418eb28a --- /dev/null +++ b/latest/cases/00997/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + p1 + 1 + + + + + + 2 + + + + + + 1 + + + + + + + + + + p1 + 1 + + + + + + 2 + + + + + + 1 + + + + + + + + + + p1 + 1 + + + + + + 1 + + + + + + 0 + + + + + + + diff --git a/latest/cases/00997/output.heta b/latest/cases/00997/output.heta new file mode 100644 index 000000000..a25cb7346 --- /dev/null +++ b/latest/cases/00997/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Two events with different 'initialValue's, causing one to fire and one to not fire. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + + The model contains two events, one that assigns '1' to parameter p2, and one that assigns '1' to parameter p3. Both have the same trigger, p1>=1, which is true at t0, but is false thereafter due to a third event. The first trigger is set 'initialValue="false"' and the second 'initialValue="true"'. This causes the first to trigger at t0 and the second to not trigger. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 3 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* | +| E0 | $p1 ≥ 1$ | $2$ | false | $p2 = 1$ | +| E1 | $p1 ≥ 1$ | $2$ | true | $p3 = 1$ | +| E2 | $p1 ≥ 1$ | $1$ | false | $p1 = 0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $0$ | variable | +| Initial value of parameter p3 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [E2]= 0; +p2 @Record { } .= 0; +p2 [E0]= 1; +p3 @Record { } .= 0; +p3 [E1]= 1; + +E0 @DSwitcher { trigger: p1 >= 1, }; +E1 @DSwitcher { trigger: p1 >= 1, }; +E2 @DSwitcher { trigger: p1 >= 1, }; + diff --git a/latest/cases/00997/synopsis.txt b/latest/cases/00997/synopsis.txt new file mode 100644 index 000000000..ec8315779 --- /dev/null +++ b/latest/cases/00997/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Two events with different 'initialValue's, causing one to fire and one to not fire. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + + The model contains two events, one that assigns '1' to parameter p2, and one that assigns '1' to parameter p3. Both have the same trigger, p1>=1, which is true at t0, but is false thereafter due to a third event. The first trigger is set 'initialValue="false"' and the second 'initialValue="true"'. This causes the first to trigger at t0 and the second to not trigger. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 3 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* | +| E0 | $p1 ≥ 1$ | $2$ | false | $p2 = 1$ | +| E1 | $p1 ≥ 1$ | $2$ | true | $p3 = 1$ | +| E2 | $p1 ≥ 1$ | $1$ | false | $p1 = 0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $0$ | variable | +| Initial value of parameter p3 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/00998/l2v5/heta-code/output.heta b/latest/cases/00998/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d51982a5a --- /dev/null +++ b/latest/cases/00998/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 5; + +S1 @Species { compartment: comp, isAmount: true, } .= 1 * comp; + +J0 @Reaction { actors: = S1, }; +J0 := 10 / S1; + diff --git a/latest/cases/00998/l2v5/index.heta b/latest/cases/00998/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00998/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00998/l2v5/json/output.json b/latest/cases/00998/l2v5/json/output.json new file mode 100644 index 000000000..497205c3c --- /dev/null +++ b/latest/cases/00998/l2v5/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 * comp" + }, + "compartment": "comp", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "10 / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00998/l3v2/heta-code/output.heta b/latest/cases/00998/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c37c8ab0a --- /dev/null +++ b/latest/cases/00998/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 5; + +S1 @Species { compartment: comp, isAmount: true, } .= 1 * comp; + +J0 @Reaction { actors: = S1, }; +J0 := 10 / S1; + diff --git a/latest/cases/00998/l3v2/index.heta b/latest/cases/00998/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00998/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00998/l3v2/json/output.json b/latest/cases/00998/l3v2/json/output.json new file mode 100644 index 000000000..00a966529 --- /dev/null +++ b/latest/cases/00998/l3v2/json/output.json @@ -0,0 +1,35 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 * comp" + }, + "compartment": "comp", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "10 / S1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00998/model-sbml-l2v5.xml b/latest/cases/00998/model-sbml-l2v5.xml new file mode 100644 index 000000000..6dc9055fe --- /dev/null +++ b/latest/cases/00998/model-sbml-l2v5.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + 10 + S1 + + + + + + + diff --git a/latest/cases/00998/model-sbml-l3v2.xml b/latest/cases/00998/model-sbml-l3v2.xml new file mode 100644 index 000000000..d4a939eb2 --- /dev/null +++ b/latest/cases/00998/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + 10 + S1 + + + + + + + diff --git a/latest/cases/00998/output.heta b/latest/cases/00998/output.heta new file mode 100644 index 000000000..9dfa08cc7 --- /dev/null +++ b/latest/cases/00998/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: Species with an initialConcentration but hasOnlySubstanceUnits="true". +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The single species in this model has an initial concentration of '1', but lives in a compartment of size 5, giving it an initial amount of 5. Since 'hasOnlySubstanceUnits' is 'true', this amount is what is used for the rate rule of the reaction (10/S1). + +For comparison, if the initialConcentration of the species is changed to an initialAmount of '5', the same numerical results should be obtained. + +The model contains: +* 1 species (S1) +* 1 compartment (comp) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $10 / S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | variable | +| Initial volume of compartment 'comp' | $5$ | constant |] + +*/ + + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 5; + +S1 @Species { compartment: comp, isAmount: true, } .= 1 * comp; + +J0 @Reaction { actors: = S1, }; +J0 := 10 / S1; + diff --git a/latest/cases/00998/synopsis.txt b/latest/cases/00998/synopsis.txt new file mode 100644 index 000000000..5880d6235 --- /dev/null +++ b/latest/cases/00998/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Species with an initialConcentration but hasOnlySubstanceUnits="true". +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +The single species in this model has an initial concentration of '1', but lives in a compartment of size 5, giving it an initial amount of 5. Since 'hasOnlySubstanceUnits' is 'true', this amount is what is used for the rate rule of the reaction (10/S1). + +For comparison, if the initialConcentration of the species is changed to an initialAmount of '5', the same numerical results should be obtained. + +The model contains: +* 1 species (S1) +* 1 compartment (comp) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> S1 | $10 / S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | variable | +| Initial volume of compartment 'comp' | $5$ | constant |] + diff --git a/latest/cases/00999/l2v5/heta-code/output.heta b/latest/cases/00999/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3e97edd66 --- /dev/null +++ b/latest/cases/00999/l2v5/heta-code/output.heta @@ -0,0 +1,41 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +comp1 @Compartment { boundary: true, } .= 10; +comp2 @Compartment { } .= 10; + +S1 @Species { compartment: comp1, } .= 1; +S2 @Species { compartment: comp1, isAmount: true, } .= 2 * comp1; +S3 @Species { compartment: comp1, } .= 3 / comp1; +S4 @Species { compartment: comp1, isAmount: true, } .= 4; +S5 @Species { compartment: comp2, } .= 5; +S6 @Species { compartment: comp2, isAmount: true, } .= 6 * comp2; +S7 @Species { compartment: comp2, } .= 7 / comp2; +S8 @Species { compartment: comp2, isAmount: true, } .= 8; + +comp2_proc @Process { actors: = comp2, }; +comp2_proc := 1; + +p1 @Record { }; +p1 := S1; +p2 @Record { }; +p2 := S2; +p3 @Record { }; +p3 := S3; +p4 @Record { }; +p4 := S4; +p5 @Record { }; +p5 := S5; +p6 @Record { }; +p6 := S6; +p7 @Record { }; +p7 := S7; +p8 @Record { }; +p8 := S8; + diff --git a/latest/cases/00999/l2v5/index.heta b/latest/cases/00999/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/00999/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00999/l2v5/json/output.json b/latest/cases/00999/l2v5/json/output.json new file mode 100644 index 000000000..24ea4b2b8 --- /dev/null +++ b/latest/cases/00999/l2v5/json/output.json @@ -0,0 +1,182 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp1", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "comp2", + "assignments": { + "start_": "10" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "compartment": "comp1" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "2 * comp1" + }, + "compartment": "comp1", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "3 / comp1" + }, + "compartment": "comp1" + }, + { + "class": "Species", + "id": "S4", + "assignments": { + "start_": "4" + }, + "compartment": "comp1", + "isAmount": true + }, + { + "class": "Species", + "id": "S5", + "assignments": { + "start_": "5" + }, + "compartment": "comp2" + }, + { + "class": "Species", + "id": "S6", + "assignments": { + "start_": "6 * comp2" + }, + "compartment": "comp2", + "isAmount": true + }, + { + "class": "Species", + "id": "S7", + "assignments": { + "start_": "7 / comp2" + }, + "compartment": "comp2" + }, + { + "class": "Species", + "id": "S8", + "assignments": { + "start_": "8" + }, + "compartment": "comp2", + "isAmount": true + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "ode_": "S2" + } + }, + { + "class": "Record", + "id": "p3", + "assignments": { + "ode_": "S3" + } + }, + { + "class": "Record", + "id": "p4", + "assignments": { + "ode_": "S4" + } + }, + { + "class": "Record", + "id": "p5", + "assignments": { + "ode_": "S5" + } + }, + { + "class": "Record", + "id": "p6", + "assignments": { + "ode_": "S6" + } + }, + { + "class": "Record", + "id": "p7", + "assignments": { + "ode_": "S7" + } + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "ode_": "S8" + } + }, + { + "class": "Process", + "id": "comp2_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "comp2", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/00999/l3v2/heta-code/output.heta b/latest/cases/00999/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bb57e9c06 --- /dev/null +++ b/latest/cases/00999/l3v2/heta-code/output.heta @@ -0,0 +1,36 @@ + + +t @TimeScale { }; + +comp1 @Compartment { boundary: true, } .= 10; +comp2 @Compartment { } .= 10; + +S1 @Species { compartment: comp1, } .= 1; +S2 @Species { compartment: comp1, isAmount: true, } .= 2 * comp1; +S3 @Species { compartment: comp1, } .= 3 / comp1; +S4 @Species { compartment: comp1, isAmount: true, } .= 4; +S5 @Species { compartment: comp2, } .= 5; +S6 @Species { compartment: comp2, isAmount: true, } .= 6 * comp2; +S7 @Species { compartment: comp2, } .= 7 / comp2; +S8 @Species { compartment: comp2, isAmount: true, } .= 8; + +comp2_proc @Process { actors: = comp2, }; +comp2_proc := 1; + +p1 @Record { }; +p1 := S1; +p2 @Record { }; +p2 := S2; +p3 @Record { }; +p3 := S3; +p4 @Record { }; +p4 := S4; +p5 @Record { }; +p5 := S5; +p6 @Record { }; +p6 := S6; +p7 @Record { }; +p7 := S7; +p8 @Record { }; +p8 := S8; + diff --git a/latest/cases/00999/l3v2/index.heta b/latest/cases/00999/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/00999/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/00999/l3v2/json/output.json b/latest/cases/00999/l3v2/json/output.json new file mode 100644 index 000000000..cb7a53439 --- /dev/null +++ b/latest/cases/00999/l3v2/json/output.json @@ -0,0 +1,157 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp1", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "comp2", + "assignments": { + "start_": "10" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "compartment": "comp1" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "2 * comp1" + }, + "compartment": "comp1", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "3 / comp1" + }, + "compartment": "comp1" + }, + { + "class": "Species", + "id": "S4", + "assignments": { + "start_": "4" + }, + "compartment": "comp1", + "isAmount": true + }, + { + "class": "Species", + "id": "S5", + "assignments": { + "start_": "5" + }, + "compartment": "comp2" + }, + { + "class": "Species", + "id": "S6", + "assignments": { + "start_": "6 * comp2" + }, + "compartment": "comp2", + "isAmount": true + }, + { + "class": "Species", + "id": "S7", + "assignments": { + "start_": "7 / comp2" + }, + "compartment": "comp2" + }, + { + "class": "Species", + "id": "S8", + "assignments": { + "start_": "8" + }, + "compartment": "comp2", + "isAmount": true + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "ode_": "S2" + } + }, + { + "class": "Record", + "id": "p3", + "assignments": { + "ode_": "S3" + } + }, + { + "class": "Record", + "id": "p4", + "assignments": { + "ode_": "S4" + } + }, + { + "class": "Record", + "id": "p5", + "assignments": { + "ode_": "S5" + } + }, + { + "class": "Record", + "id": "p6", + "assignments": { + "ode_": "S6" + } + }, + { + "class": "Record", + "id": "p7", + "assignments": { + "ode_": "S7" + } + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "ode_": "S8" + } + }, + { + "class": "Process", + "id": "comp2_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "comp2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/00999/model-sbml-l2v5.xml b/latest/cases/00999/model-sbml-l2v5.xml new file mode 100644 index 000000000..dfefa72d7 --- /dev/null +++ b/latest/cases/00999/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + S1 + + + + + S2 + + + + + S3 + + + + + S4 + + + + + S5 + + + + + S6 + + + + + S7 + + + + + S8 + + + + + diff --git a/latest/cases/00999/model-sbml-l3v2.xml b/latest/cases/00999/model-sbml-l3v2.xml new file mode 100644 index 000000000..d8cae8bd6 --- /dev/null +++ b/latest/cases/00999/model-sbml-l3v2.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + S1 + + + + + S2 + + + + + S3 + + + + + S4 + + + + + S5 + + + + + S6 + + + + + S7 + + + + + S8 + + + + + diff --git a/latest/cases/00999/output.heta b/latest/cases/00999/output.heta new file mode 100644 index 000000000..99d43a11b --- /dev/null +++ b/latest/cases/00999/output.heta @@ -0,0 +1,92 @@ +/* +category: Test +synopsis: Testing different versions of initialAmount vs. initialConcentration with hasOnlySubstanceUnits=true/false, in a constant and varying compartment. +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, HasOnlySubstanceUnits, MultiCompartment, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model has four species in a constant (non-unity) compartment with the four different combinations of being set by initialAmount or initialConcentration, and being set 'hasOnlySubstanceUnits' equal to true or false. It also has another four species with the same spread, in a different compartment whose volume changes over time. Each of these eight species is assigned to a parameter, to catch the 'hasOnlySubstanceUnits' differences (every other parameter has units of amount or concentration, respectively). + +The model contains: +* 8 species (S1, S2, S3, S4, S5, S6, S7, S8) +* 8 parameters (p1, p2, p3, p4, p5, p6, p7, p8) +* 2 compartments (comp1, comp2) + +There are 9 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | comp2 | $1$ | +| Assignment | p1 | $S1$ | +| Assignment | p2 | $S2$ | +| Assignment | p3 | $S3$ | +| Assignment | p4 | $S4$ | +| Assignment | p5 | $S5$ | +| Assignment | p6 | $S6$ | +| Assignment | p7 | $S7$ | +| Assignment | p8 | $S8$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial concentration of species S2 | $2$ | variable | +| Initial amount of species S3 | $3$ | variable | +| Initial amount of species S4 | $4$ | variable | +| Initial concentration of species S5 | $5$ | variable | +| Initial concentration of species S6 | $6$ | variable | +| Initial amount of species S7 | $7$ | variable | +| Initial amount of species S8 | $8$ | variable | +| Initial value of parameter p1 | $S1$ | variable | +| Initial value of parameter p2 | $S2$ | variable | +| Initial value of parameter p3 | $S3$ | variable | +| Initial value of parameter p4 | $S4$ | variable | +| Initial value of parameter p5 | $S5$ | variable | +| Initial value of parameter p6 | $S6$ | variable | +| Initial value of parameter p7 | $S7$ | variable | +| Initial value of parameter p8 | $S8$ | variable | +| Initial volume of compartment 'comp1' | $10$ | constant | +| Initial volume of compartment 'comp2' | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +comp1 @Compartment { boundary: true, } .= 10; +comp2 @Compartment { } .= 10; + +S1 @Species { compartment: comp1, } .= 1; +S2 @Species { compartment: comp1, isAmount: true, } .= 2 * comp1; +S3 @Species { compartment: comp1, } .= 3 / comp1; +S4 @Species { compartment: comp1, isAmount: true, } .= 4; +S5 @Species { compartment: comp2, } .= 5; +S6 @Species { compartment: comp2, isAmount: true, } .= 6 * comp2; +S7 @Species { compartment: comp2, } .= 7 / comp2; +S8 @Species { compartment: comp2, isAmount: true, } .= 8; + +comp2_proc @Process { actors: = comp2, }; +comp2_proc := 1; + +p1 @Record { }; +p1 := S1; +p2 @Record { }; +p2 := S2; +p3 @Record { }; +p3 := S3; +p4 @Record { }; +p4 := S4; +p5 @Record { }; +p5 := S5; +p6 @Record { }; +p6 := S6; +p7 @Record { }; +p7 := S7; +p8 @Record { }; +p8 := S8; + diff --git a/latest/cases/00999/synopsis.txt b/latest/cases/00999/synopsis.txt new file mode 100644 index 000000000..5f342d577 --- /dev/null +++ b/latest/cases/00999/synopsis.txt @@ -0,0 +1,54 @@ + +category: Test +synopsis: Testing different versions of initialAmount vs. initialConcentration with hasOnlySubstanceUnits=true/false, in a constant and varying compartment. +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, HasOnlySubstanceUnits, MultiCompartment, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model has four species in a constant (non-unity) compartment with the four different combinations of being set by initialAmount or initialConcentration, and being set 'hasOnlySubstanceUnits' equal to true or false. It also has another four species with the same spread, in a different compartment whose volume changes over time. Each of these eight species is assigned to a parameter, to catch the 'hasOnlySubstanceUnits' differences (every other parameter has units of amount or concentration, respectively). + +The model contains: +* 8 species (S1, S2, S3, S4, S5, S6, S7, S8) +* 8 parameters (p1, p2, p3, p4, p5, p6, p7, p8) +* 2 compartments (comp1, comp2) + +There are 9 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | comp2 | $1$ | +| Assignment | p1 | $S1$ | +| Assignment | p2 | $S2$ | +| Assignment | p3 | $S3$ | +| Assignment | p4 | $S4$ | +| Assignment | p5 | $S5$ | +| Assignment | p6 | $S6$ | +| Assignment | p7 | $S7$ | +| Assignment | p8 | $S8$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial concentration of species S2 | $2$ | variable | +| Initial amount of species S3 | $3$ | variable | +| Initial amount of species S4 | $4$ | variable | +| Initial concentration of species S5 | $5$ | variable | +| Initial concentration of species S6 | $6$ | variable | +| Initial amount of species S7 | $7$ | variable | +| Initial amount of species S8 | $8$ | variable | +| Initial value of parameter p1 | $S1$ | variable | +| Initial value of parameter p2 | $S2$ | variable | +| Initial value of parameter p3 | $S3$ | variable | +| Initial value of parameter p4 | $S4$ | variable | +| Initial value of parameter p5 | $S5$ | variable | +| Initial value of parameter p6 | $S6$ | variable | +| Initial value of parameter p7 | $S7$ | variable | +| Initial value of parameter p8 | $S8$ | variable | +| Initial volume of compartment 'comp1' | $10$ | constant | +| Initial volume of compartment 'comp2' | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01000/l2v5/index.heta b/latest/cases/01000/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01000/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01000/l3v2/build.log b/latest/cases/01000/l3v2/build.log new file mode 100644 index 000000000..4ee1454e3 --- /dev/null +++ b/latest/cases/01000/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01000/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01000/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01000/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01000/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01000/l3v2/index.heta b/latest/cases/01000/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01000/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01000/model-sbml-l3v2.xml b/latest/cases/01000/model-sbml-l3v2.xml new file mode 100644 index 000000000..6af007414 --- /dev/null +++ b/latest/cases/01000/model-sbml-l3v2.xml @@ -0,0 +1,376 @@ + + + + + + + + + a + + + b + + + c + + + d + + + e + + + f + + + g + + + h + + + i + + + j + + + + + + + + a + + b + c + d + e + f + g + h + i + j + + 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + avogadro + 6.022 23 + + + + + + k1 + + + + + + + 1 + + + + + k4 + + + + + time + + + + + + + k1 + S1 + + + + + + + + + + + + + + + + + + + + kinetics + k1 + k2 + k3 + k4 + k5 + S1 + S1ref + S3 + S4 + S2 + + + + + + + + + + + + + + + time + 0.5 + + + + + + + 0.1 + + + + + + + + + + time + 1 + + + + + + 2 + + + + + 1 + + + + + + 4 + + + + + + + + + + time + 1 + + + + + + 2 + + + + + 2 + + + + + + k3 + + + + + + + + + + time + 1 + + + + + + 2 + + + + + 3 + + + + + + k4 + + + + + + + + + + time + 1 + + + + + + 2 + + + + + 4 + + + + + + k5 + + + + + + + + + + comp + 5.1 + + + + + + 1 + + + + + + 4 + + + + + + + + + + + + time + 1 + + + + time + 4 + + + + + + + 4.995 + + + + + + 14.5 + + + + + + + + + + + + time + 1 + + + + time + 4 + + + + + + + 4.995 + + + + + + 0 + + + + + + + diff --git a/latest/cases/01000/synopsis.txt b/latest/cases/01000/synopsis.txt new file mode 100644 index 000000000..b3e392112 --- /dev/null +++ b/latest/cases/01000/synopsis.txt @@ -0,0 +1,66 @@ + +category: Test +synopsis: A 'kitchen sink' model with 34 tags. Woo-hoo! +componentTags: AssignmentRule, CSymbolAvogadro, CSymbolTime, Compartment, EventNoDelay, EventPriority, EventWithDelay, FunctionDefinition, InitialAssignment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, AssignedVariableStoichiometry, BoundaryCondition, ConstantSpecies, ConversionFactors, EventIsNotPersistent, EventIsPersistent, EventT0Firing, EventUsesAssignmentTimeValues, EventUsesTriggerTimeValues, HasOnlySubstanceUnits, InitialValueReassigned, LocalParameters, MultiCompartment, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, ReversibleReaction, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + This is a 'kitchen sink' model with almost everything in it. It's a RoadRunner-friendly model in that it only doesn't have bits that RoadRunner can't handle: AlgebraicRules, CSymbolDelays, and FastReactions. It also does not test RandomEventExecution because those tests are fundamentally difficult to put together, and inherently non-precise in their output. It is, frankly, a fairly ridiculous model with things thrown in willy-nilly with no regard to unit correctness in the interest of simply testing everything together. The canonical results were taken from RoadRunner output. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 8 parameters (kavo, k1, k3, k4, k5, k2, conversion1, conversion2) +* 2 compartments (comp, comp2) + +It also contains 1 function definition(s): +; kinetics: $(-a + b + c + d + e + f + g + h + i + j) / 10$ + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: S3 + S1ref S1 -> S2ref S2 | $kinetics(k1, k2, k3, k4, k5, S1, S1ref, S3, S4, S2)$ |] +Note: the following stoichiometries are set separately: S1ref, S2ref + + +There are 8 events: + +[{width:55em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *initialValue* | *Use values from:* | *Delay* | *Event Assignments* | +| _E0 | $geq(time, 0.5)$ | (unset) | true | true | Trigger time | $0$ | $k4 = 0.1$ | +| _E1 | $geq(time, 1)$ | $1$ | true | true | Trigger time | $2$ | $k3 = 4$ | +| _E2 | $geq(time, 1)$ | $2$ | true | true | Assignment time | $2$ | $k4 = k3$ | +| _E3 | $geq(time, 1)$ | $3$ | true | true | Trigger time | $2$ | $k5 = k4$ | +| _E4 | $geq(time, 1)$ | $4$ | true | true | Assignment time | $2$ | $k3 = k5$ | +| _E5 | $leq(comp, 5.1)$ | (unset) | true | false | Trigger time | $1$ | $S3 = 4$ | +| _E6 | $and(geq(time, 1), leq(time, 4))$ | (unset) | true | true | Trigger time | $4.995$ | $k4 = 14.5$ | +| _E7 | $and(geq(time, 1), leq(time, 4))$ | (unset) | false | true | Trigger time | $4.995$ | $k5 = 0$ |] + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | comp | $1$ | +| Assignment | comp2 | $k4$ | +| Rate | k4 | $time$ | +| Assignment | S2ref | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S4 | $2$ | constant | +| Initial amount of species S1 | $1$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial amount of species S3 | $4$ | variable | +| Initial value of parameter kavo | $avogadro / 6.022000e+023$ | constant | +| Initial value of parameter k1 | $1.1$ | constant | +| Initial value of parameter k2 | $8.12$ | constant | +| Initial value of parameter conversion1 | $10$ | constant | +| Initial value of parameter conversion2 | $100$ | constant | +| Initial value of parameter k3 | $2.5$ | variable | +| Initial value of parameter k4 | $1$ | variable | +| Initial value of parameter k5 | $2.8$ | variable | +| Initial volume of compartment 'comp' | $5$ | variable | +| Initial volume of compartment 'comp2' | $k4$ | variable |] + diff --git a/latest/cases/01001/l2v5/heta-code/output.heta b/latest/cases/01001/l2v5/heta-code/output.heta new file mode 100644 index 000000000..82ca8fa99 --- /dev/null +++ b/latest/cases/01001/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.0015; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/01001/l2v5/index.heta b/latest/cases/01001/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01001/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01001/l2v5/json/output.json b/latest/cases/01001/l2v5/json/output.json new file mode 100644 index 000000000..34c391f79 --- /dev/null +++ b/latest/cases/01001/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01001/l3v2/heta-code/output.heta b/latest/cases/01001/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c26d42429 --- /dev/null +++ b/latest/cases/01001/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/01001/l3v2/index.heta b/latest/cases/01001/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01001/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01001/l3v2/json/output.json b/latest/cases/01001/l3v2/json/output.json new file mode 100644 index 000000000..81ff67105 --- /dev/null +++ b/latest/cases/01001/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/01001/model-sbml-l2v5.xml b/latest/cases/01001/model-sbml-l2v5.xml new file mode 100644 index 000000000..7497aa1bf --- /dev/null +++ b/latest/cases/01001/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01001/model-sbml-l3v2.xml b/latest/cases/01001/model-sbml-l3v2.xml new file mode 100644 index 000000000..e26a0bae2 --- /dev/null +++ b/latest/cases/01001/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01001/output.heta b/latest/cases/01001/output.heta new file mode 100644 index 000000000..619cc7967 --- /dev/null +++ b/latest/cases/01001/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00060, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/01001/synopsis.txt b/latest/cases/01001/synopsis.txt new file mode 100644 index 000000000..396efb6c5 --- /dev/null +++ b/latest/cases/01001/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00060, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01002/l2v5/heta-code/output.heta b/latest/cases/01002/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8aead0de5 --- /dev/null +++ b/latest/cases/01002/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.002; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 17; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/01002/l2v5/index.heta b/latest/cases/01002/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01002/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01002/l2v5/json/output.json b/latest/cases/01002/l2v5/json/output.json new file mode 100644 index 000000000..ecced71ea --- /dev/null +++ b/latest/cases/01002/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "17" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01002/l3v2/heta-code/output.heta b/latest/cases/01002/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8983d3ad0 --- /dev/null +++ b/latest/cases/01002/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 17; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/01002/l3v2/index.heta b/latest/cases/01002/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01002/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01002/l3v2/json/output.json b/latest/cases/01002/l3v2/json/output.json new file mode 100644 index 000000000..2aa6ff06d --- /dev/null +++ b/latest/cases/01002/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 17 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/01002/model-sbml-l2v5.xml b/latest/cases/01002/model-sbml-l2v5.xml new file mode 100644 index 000000000..5805d848b --- /dev/null +++ b/latest/cases/01002/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01002/model-sbml-l3v2.xml b/latest/cases/01002/model-sbml-l3v2.xml new file mode 100644 index 000000000..4f8c7a3f0 --- /dev/null +++ b/latest/cases/01002/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01002/output.heta b/latest/cases/01002/output.heta new file mode 100644 index 000000000..1dda14fc7 --- /dev/null +++ b/latest/cases/01002/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Basic reaction with two species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00061, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.7 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 17; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/01002/synopsis.txt b/latest/cases/01002/synopsis.txt new file mode 100644 index 000000000..64946c092 --- /dev/null +++ b/latest/cases/01002/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Basic reaction with two species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00061, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.7 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01003/l2v5/heta-code/output.heta b/latest/cases/01003/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ed9fc3325 --- /dev/null +++ b/latest/cases/01003/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 1.3e+6; +k2 @Record 'k2' { } .= 3e+5; + diff --git a/latest/cases/01003/l2v5/index.heta b/latest/cases/01003/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01003/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01003/l2v5/json/output.json b/latest/cases/01003/l2v5/json/output.json new file mode 100644 index 000000000..f147bab45 --- /dev/null +++ b/latest/cases/01003/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.3e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "3e+5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01003/l3v2/heta-code/output.heta b/latest/cases/01003/l3v2/heta-code/output.heta new file mode 100644 index 000000000..708f2ec35 --- /dev/null +++ b/latest/cases/01003/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 300000; + diff --git a/latest/cases/01003/l3v2/index.heta b/latest/cases/01003/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01003/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01003/l3v2/json/output.json b/latest/cases/01003/l3v2/json/output.json new file mode 100644 index 000000000..c4e84d20c --- /dev/null +++ b/latest/cases/01003/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1300000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 300000 + } +] \ No newline at end of file diff --git a/latest/cases/01003/model-sbml-l2v5.xml b/latest/cases/01003/model-sbml-l2v5.xml new file mode 100644 index 000000000..c147346d7 --- /dev/null +++ b/latest/cases/01003/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/01003/model-sbml-l3v2.xml b/latest/cases/01003/model-sbml-l3v2.xml new file mode 100644 index 000000000..0464b02f7 --- /dev/null +++ b/latest/cases/01003/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/01003/output.heta b/latest/cases/01003/output.heta new file mode 100644 index 000000000..2691b6134 --- /dev/null +++ b/latest/cases/01003/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00062, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 300000; + diff --git a/latest/cases/01003/synopsis.txt b/latest/cases/01003/synopsis.txt new file mode 100644 index 000000000..7685f3e8c --- /dev/null +++ b/latest/cases/01003/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic two reactions with four species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00062, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |litre mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01004/l2v5/heta-code/output.heta b/latest/cases/01004/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8b0401114 --- /dev/null +++ b/latest/cases/01004/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := multiply(k1, S1); + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/01004/l2v5/index.heta b/latest/cases/01004/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01004/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01004/l2v5/json/output.json b/latest/cases/01004/l2v5/json/output.json new file mode 100644 index 000000000..0ad8570ba --- /dev/null +++ b/latest/cases/01004/l2v5/json/output.json @@ -0,0 +1,98 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01004/l3v2/heta-code/output.heta b/latest/cases/01004/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1aba737b6 --- /dev/null +++ b/latest/cases/01004/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := multiply(k1, S1); + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/01004/l3v2/index.heta b/latest/cases/01004/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01004/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01004/l3v2/json/output.json b/latest/cases/01004/l3v2/json/output.json new file mode 100644 index 000000000..8a7b67aa8 --- /dev/null +++ b/latest/cases/01004/l3v2/json/output.json @@ -0,0 +1,72 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "multiply(k1, S1)" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01004/model-sbml-l2v5.xml b/latest/cases/01004/model-sbml-l2v5.xml new file mode 100644 index 000000000..8e510ebb8 --- /dev/null +++ b/latest/cases/01004/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S1 + + + + + + + diff --git a/latest/cases/01004/model-sbml-l3v2.xml b/latest/cases/01004/model-sbml-l3v2.xml new file mode 100644 index 000000000..6c2085b6d --- /dev/null +++ b/latest/cases/01004/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + k1 + S1 + + + + + + + diff --git a/latest/cases/01004/output.heta b/latest/cases/01004/output.heta new file mode 100644 index 000000000..83e393a2c --- /dev/null +++ b/latest/cases/01004/output.heta @@ -0,0 +1,57 @@ +/* +category: Test +synopsis: Basic single forward reaction using functionDefinitions with two +species in a size-10 compartment where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00113, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := multiply(k1, S1); + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/01004/synopsis.txt b/latest/cases/01004/synopsis.txt new file mode 100644 index 000000000..8a2557320 --- /dev/null +++ b/latest/cases/01004/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic single forward reaction using functionDefinitions with two +species in a size-10 compartment where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00113, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. The model contains one +reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $multiply(k1,S1)$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/01005/l2v5/heta-code/output.heta b/latest/cases/01005/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e112ea335 --- /dev/null +++ b/latest/cases/01005/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 1.7; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/01005/l2v5/index.heta b/latest/cases/01005/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01005/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01005/l2v5/json/output.json b/latest/cases/01005/l2v5/json/output.json new file mode 100644 index 000000000..bce8f4eb8 --- /dev/null +++ b/latest/cases/01005/l2v5/json/output.json @@ -0,0 +1,144 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.7" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01005/l3v2/heta-code/output.heta b/latest/cases/01005/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e4b0d2364 --- /dev/null +++ b/latest/cases/01005/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 1.7; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/01005/l3v2/index.heta b/latest/cases/01005/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01005/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01005/l3v2/json/output.json b/latest/cases/01005/l3v2/json/output.json new file mode 100644 index 000000000..eb30903fa --- /dev/null +++ b/latest/cases/01005/l3v2/json/output.json @@ -0,0 +1,116 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.7 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01005/model-sbml-l2v5.xml b/latest/cases/01005/model-sbml-l2v5.xml new file mode 100644 index 000000000..5241fa7f9 --- /dev/null +++ b/latest/cases/01005/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01005/model-sbml-l3v2.xml b/latest/cases/01005/model-sbml-l3v2.xml new file mode 100644 index 000000000..b1b6f6a68 --- /dev/null +++ b/latest/cases/01005/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01005/output.heta b/latest/cases/01005/output.heta new file mode 100644 index 000000000..65872b01d --- /dev/null +++ b/latest/cases/01005/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Basic reactions using functionDefinitions with three species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00114, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * multiply(S1,S2)$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.7 $ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 1.7; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/01005/synopsis.txt b/latest/cases/01005/synopsis.txt new file mode 100644 index 000000000..6b326d1a4 --- /dev/null +++ b/latest/cases/01005/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic reactions using functionDefinitions with three species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00114, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * multiply(S1,S2)$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.7 $ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01006/l2v5/heta-code/output.heta b/latest/cases/01006/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7cdb59e18 --- /dev/null +++ b/latest/cases/01006/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 1.3e+6; +k2 @Record 'k2' { } .= 3e+5; + diff --git a/latest/cases/01006/l2v5/index.heta b/latest/cases/01006/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01006/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01006/l2v5/json/output.json b/latest/cases/01006/l2v5/json/output.json new file mode 100644 index 000000000..8350ad0d2 --- /dev/null +++ b/latest/cases/01006/l2v5/json/output.json @@ -0,0 +1,163 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.3e+6" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "3e+5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01006/l3v2/heta-code/output.heta b/latest/cases/01006/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6716c1a70 --- /dev/null +++ b/latest/cases/01006/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 300000; + diff --git a/latest/cases/01006/l3v2/index.heta b/latest/cases/01006/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01006/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01006/l3v2/json/output.json b/latest/cases/01006/l3v2/json/output.json new file mode 100644 index 000000000..63dfd14a7 --- /dev/null +++ b/latest/cases/01006/l3v2/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "5e-7" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * multiply(S1, S2)" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1300000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 300000 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01006/model-sbml-l2v5.xml b/latest/cases/01006/model-sbml-l2v5.xml new file mode 100644 index 000000000..831e5b873 --- /dev/null +++ b/latest/cases/01006/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/01006/model-sbml-l3v2.xml b/latest/cases/01006/model-sbml-l3v2.xml new file mode 100644 index 000000000..5d8a99a41 --- /dev/null +++ b/latest/cases/01006/model-sbml-l3v2.xml @@ -0,0 +1,99 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + multiply + S1 + S2 + + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/01006/output.heta b/latest/cases/01006/output.heta new file mode 100644 index 000000000..1ad253218 --- /dev/null +++ b/latest/cases/01006/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Basic two reactions using functiondefinitions with four species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00115, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * multiply(S1,S2)$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * multiply(S1, S2); +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 1300000; +k2 @Const 'k2' { } = 300000; + diff --git a/latest/cases/01006/synopsis.txt b/latest/cases/01006/synopsis.txt new file mode 100644 index 000000000..a6decc54a --- /dev/null +++ b/latest/cases/01006/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions using functiondefinitions with four species in a size-10 compartment + where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00115, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * multiply(S1,S2)$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S3 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S4 |$ 0.5 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.3 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3 \x 10^6$ |mole^-1^ second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01007/l2v5/heta-code/output.heta b/latest/cases/01007/l2v5/heta-code/output.heta new file mode 100644 index 000000000..098f8b8c6 --- /dev/null +++ b/latest/cases/01007/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-4; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Record 'k1' { } .= 1; + diff --git a/latest/cases/01007/l2v5/index.heta b/latest/cases/01007/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01007/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01007/l2v5/json/output.json b/latest/cases/01007/l2v5/json/output.json new file mode 100644 index 000000000..e3fa799af --- /dev/null +++ b/latest/cases/01007/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01007/l3v2/heta-code/output.heta b/latest/cases/01007/l3v2/heta-code/output.heta new file mode 100644 index 000000000..eebe21939 --- /dev/null +++ b/latest/cases/01007/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-4; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/01007/l3v2/index.heta b/latest/cases/01007/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01007/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01007/l3v2/json/output.json b/latest/cases/01007/l3v2/json/output.json new file mode 100644 index 000000000..6f6b1e065 --- /dev/null +++ b/latest/cases/01007/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1e-4" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/01007/model-sbml-l2v5.xml b/latest/cases/01007/model-sbml-l2v5.xml new file mode 100644 index 000000000..83c7c9f9e --- /dev/null +++ b/latest/cases/01007/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01007/model-sbml-l3v2.xml b/latest/cases/01007/model-sbml-l3v2.xml new file mode 100644 index 000000000..ad55c5447 --- /dev/null +++ b/latest/cases/01007/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01007/output.heta b/latest/cases/01007/output.heta new file mode 100644 index 000000000..092642284 --- /dev/null +++ b/latest/cases/01007/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00208, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Species S1 and S2 are declared to have +only substance units. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$ 1 \x 10^-4$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 10$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-4; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1; + diff --git a/latest/cases/01007/synopsis.txt b/latest/cases/01007/synopsis.txt new file mode 100644 index 000000000..20867a01c --- /dev/null +++ b/latest/cases/01007/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 2-dimensional +size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00208, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is two-dimensional. Species S1 and S2 are declared to have +only substance units. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$ 1 \x 10^-4$ |mole | +|Value of parameter k1 |$ 1$ |second^-1^ | +|Area of compartment "compartment" |$ 10$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01008/l2v5/heta-code/output.heta b/latest/cases/01008/l2v5/heta-code/output.heta new file mode 100644 index 000000000..debb5846c --- /dev/null +++ b/latest/cases/01008/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.0015; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.002; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.0015; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.004; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Record 'k1' { } .= 0.693; +k2 @Record 'k2' { } .= 0.25; + diff --git a/latest/cases/01008/l2v5/index.heta b/latest/cases/01008/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01008/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01008/l2v5/json/output.json b/latest/cases/01008/l2v5/json/output.json new file mode 100644 index 000000000..2291d33a8 --- /dev/null +++ b/latest/cases/01008/l2v5/json/output.json @@ -0,0 +1,151 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.004" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.693" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.25" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01008/l3v2/heta-code/output.heta b/latest/cases/01008/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1500e016e --- /dev/null +++ b/latest/cases/01008/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.004; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/01008/l3v2/index.heta b/latest/cases/01008/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01008/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01008/l3v2/json/output.json b/latest/cases/01008/l3v2/json/output.json new file mode 100644 index 000000000..3d64d8de5 --- /dev/null +++ b/latest/cases/01008/l3v2/json/output.json @@ -0,0 +1,123 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.004" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.693 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.25 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "5e-4 * k1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule2" + }, + "assignments": { + "ode_": "(-5e-4) * k2" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01008/model-sbml-l2v5.xml b/latest/cases/01008/model-sbml-l2v5.xml new file mode 100644 index 000000000..5447c4103 --- /dev/null +++ b/latest/cases/01008/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01008/model-sbml-l3v2.xml b/latest/cases/01008/model-sbml-l3v2.xml new file mode 100644 index 000000000..e1efb7aa2 --- /dev/null +++ b/latest/cases/01008/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0005 + k1 + + + + + + + + -0.0005 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01008/output.heta b/latest/cases/01008/output.heta new file mode 100644 index 000000000..d4869b986 --- /dev/null +++ b/latest/cases/01008/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: One reactions and two rate rules with four species in a size-10 compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00333, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains one reaction defined as: + +[{width:25em,=}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains two rules: + +[{width:25em,=}| *Type* | *Variable* | *Formula* | +| Rate | S3 | $k1 * 0.5 10^-3$ | +| Rate | S4 | $-k2 * 0.5 10^-3$ |] + +The initial conditions are as follows: + +[{width:35em,=}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only (meaning that +the attribute %hasOnlySubstanceUnits% is set to true). Thus, they must be +treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.004; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := 5e-4 * k1; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule2"}}, }; +S4_proc := (-5e-4) * k2; + +k1 @Const 'k1' { } = 0.693; +k2 @Const 'k2' { } = 0.25; + diff --git a/latest/cases/01008/synopsis.txt b/latest/cases/01008/synopsis.txt new file mode 100644 index 000000000..d1bd1a4bb --- /dev/null +++ b/latest/cases/01008/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a size-10 compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00333, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains one reaction defined as: + +[{width:25em,=}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains two rules: + +[{width:25em,=}| *Type* | *Variable* | *Formula* | +| Rate | S3 | $k1 * 0.5 10^-3$ | +| Rate | S4 | $-k2 * 0.5 10^-3$ |] + +The initial conditions are as follows: + +[{width:35em,=}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-3$ |mole | +|Initial amount of S4 |$ 4 \x 10^-3$ |mole | +|Value of parameter k1 |$ 0.693$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only (meaning that +the attribute %hasOnlySubstanceUnits% is set to true). Thus, they must be +treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/01009/l2v5/heta-code/output.heta b/latest/cases/01009/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f72861e6f --- /dev/null +++ b/latest/cases/01009/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.2; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 75; +k2 @Record 'k2' { } .= 25; + diff --git a/latest/cases/01009/l2v5/index.heta b/latest/cases/01009/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01009/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01009/l2v5/json/output.json b/latest/cases/01009/l2v5/json/output.json new file mode 100644 index 000000000..22d9b541f --- /dev/null +++ b/latest/cases/01009/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "25" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01009/l3v2/heta-code/output.heta b/latest/cases/01009/l3v2/heta-code/output.heta new file mode 100644 index 000000000..439faa864 --- /dev/null +++ b/latest/cases/01009/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/01009/l3v2/index.heta b/latest/cases/01009/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01009/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01009/l3v2/json/output.json b/latest/cases/01009/l3v2/json/output.json new file mode 100644 index 000000000..96b642618 --- /dev/null +++ b/latest/cases/01009/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 25 + } +] \ No newline at end of file diff --git a/latest/cases/01009/model-sbml-l2v5.xml b/latest/cases/01009/model-sbml-l2v5.xml new file mode 100644 index 000000000..f7cab9086 --- /dev/null +++ b/latest/cases/01009/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01009/model-sbml-l3v2.xml b/latest/cases/01009/model-sbml-l3v2.xml new file mode 100644 index 000000000..459c19a5b --- /dev/null +++ b/latest/cases/01009/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01009/output.heta b/latest/cases/01009/output.heta new file mode 100644 index 000000000..57511d6d5 --- /dev/null +++ b/latest/cases/01009/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic reaction with two species in a 2-dimensional +size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00209, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S1, S2 and S3 are +declared to have only substance units. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 25$ |second^-1^ | +|Area of compartment "compartment" |$ 10$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 75; +k2 @Const 'k2' { } = 25; + diff --git a/latest/cases/01009/synopsis.txt b/latest/cases/01009/synopsis.txt new file mode 100644 index 000000000..a23d91faa --- /dev/null +++ b/latest/cases/01009/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reaction with two species in a 2-dimensional +size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00209, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. Species S1, S2 and S3 are +declared to have only substance units. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 75$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 25$ |second^-1^ | +|Area of compartment "compartment" |$ 10$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01010/l2v5/heta-code/output.heta b/latest/cases/01010/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f3468a2f7 --- /dev/null +++ b/latest/cases/01010/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: area, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.002; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 7500; +k2 @Record 'k2' { } .= 250; + diff --git a/latest/cases/01010/l2v5/index.heta b/latest/cases/01010/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01010/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01010/l2v5/json/output.json b/latest/cases/01010/l2v5/json/output.json new file mode 100644 index 000000000..2f9d76dbc --- /dev/null +++ b/latest/cases/01010/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "area", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7500" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "250" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01010/l3v2/heta-code/output.heta b/latest/cases/01010/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4f9d3b493 --- /dev/null +++ b/latest/cases/01010/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/01010/l3v2/index.heta b/latest/cases/01010/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01010/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01010/l3v2/json/output.json b/latest/cases/01010/l3v2/json/output.json new file mode 100644 index 000000000..d7e611ffb --- /dev/null +++ b/latest/cases/01010/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre^2", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.0015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.002" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7500 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 250 + } +] \ No newline at end of file diff --git a/latest/cases/01010/model-sbml-l2v5.xml b/latest/cases/01010/model-sbml-l2v5.xml new file mode 100644 index 000000000..f9e1c34e5 --- /dev/null +++ b/latest/cases/01010/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/01010/model-sbml-l3v2.xml b/latest/cases/01010/model-sbml-l3v2.xml new file mode 100644 index 000000000..f2c8e786a --- /dev/null +++ b/latest/cases/01010/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/01010/output.heta b/latest/cases/01010/output.heta new file mode 100644 index 000000000..8d931f71f --- /dev/null +++ b/latest/cases/01010/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00210, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. All four species are declared +to have only substance units. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 7.5 \x 10^3$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 10$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.002; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 7500; +k2 @Const 'k2' { } = 250; + diff --git a/latest/cases/01010/synopsis.txt b/latest/cases/01010/synopsis.txt new file mode 100644 index 000000000..7353b851c --- /dev/null +++ b/latest/cases/01010/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in a 2-dimensional +compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00210, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 2-dimensional. All four species are declared +to have only substance units. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$1.5 \x 10^-3$ |mole | +|Initial amount of S3 |$2.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 7.5 \x 10^3$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^3$ |mole^-1^ second^-1^ | +|Area of compartment "compartment" |$ 10$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01011/l2v5/heta-code/output.heta b/latest/cases/01011/l2v5/heta-code/output.heta new file mode 100644 index 000000000..97e416b9b --- /dev/null +++ b/latest/cases/01011/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Record 'k1' { } .= 1.5; + diff --git a/latest/cases/01011/l2v5/index.heta b/latest/cases/01011/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01011/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01011/l2v5/json/output.json b/latest/cases/01011/l2v5/json/output.json new file mode 100644 index 000000000..0e449b725 --- /dev/null +++ b/latest/cases/01011/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01011/l3v2/heta-code/output.heta b/latest/cases/01011/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d01d07def --- /dev/null +++ b/latest/cases/01011/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/01011/l3v2/index.heta b/latest/cases/01011/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01011/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01011/l3v2/json/output.json b/latest/cases/01011/l3v2/json/output.json new file mode 100644 index 000000000..5fde27bb8 --- /dev/null +++ b/latest/cases/01011/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/01011/model-sbml-l2v5.xml b/latest/cases/01011/model-sbml-l2v5.xml new file mode 100644 index 000000000..5c05b9d11 --- /dev/null +++ b/latest/cases/01011/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01011/model-sbml-l3v2.xml b/latest/cases/01011/model-sbml-l3v2.xml new file mode 100644 index 000000000..0fa6c997f --- /dev/null +++ b/latest/cases/01011/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01011/output.heta b/latest/cases/01011/output.heta new file mode 100644 index 000000000..a4365c220 --- /dev/null +++ b/latest/cases/01011/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00223, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Species S1 and S2 are declared to have +only substance units. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 10$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; + +k1 @Const 'k1' { } = 1.5; + diff --git a/latest/cases/01011/synopsis.txt b/latest/cases/01011/synopsis.txt new file mode 100644 index 000000000..fc3f0b284 --- /dev/null +++ b/latest/cases/01011/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Basic single forward reaction with two species in a 1-dimensional +size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00223, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and one parameter named k1. Compartment +"compartment" is one-dimensional. Species S1 and S2 are declared to have +only substance units. The model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Area of compartment "compartment" |$ 10$ |metre^2^ |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/01012/l2v5/heta-code/output.heta b/latest/cases/01012/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cd15e56a0 --- /dev/null +++ b/latest/cases/01012/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 2; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 7.5; +k2 @Record 'k2' { } .= 0.3; + diff --git a/latest/cases/01012/l2v5/index.heta b/latest/cases/01012/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01012/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01012/l2v5/json/output.json b/latest/cases/01012/l2v5/json/output.json new file mode 100644 index 000000000..5fa87bacf --- /dev/null +++ b/latest/cases/01012/l2v5/json/output.json @@ -0,0 +1,135 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01012/l3v2/heta-code/output.heta b/latest/cases/01012/l3v2/heta-code/output.heta new file mode 100644 index 000000000..25ce23e69 --- /dev/null +++ b/latest/cases/01012/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/01012/l3v2/index.heta b/latest/cases/01012/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01012/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01012/l3v2/json/output.json b/latest/cases/01012/l3v2/json/output.json new file mode 100644 index 000000000..96e99ee9b --- /dev/null +++ b/latest/cases/01012/l3v2/json/output.json @@ -0,0 +1,107 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1.5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 7.5 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.3 + } +] \ No newline at end of file diff --git a/latest/cases/01012/model-sbml-l2v5.xml b/latest/cases/01012/model-sbml-l2v5.xml new file mode 100644 index 000000000..07af3f409 --- /dev/null +++ b/latest/cases/01012/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01012/model-sbml-l3v2.xml b/latest/cases/01012/model-sbml-l3v2.xml new file mode 100644 index 000000000..825fc214b --- /dev/null +++ b/latest/cases/01012/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01012/output.heta b/latest/cases/01012/output.heta new file mode 100644 index 000000000..22b66b21e --- /dev/null +++ b/latest/cases/01012/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Basic reaction with two species in a 1-dimensional + size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00224, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S1, S2 and S3 are +declared to have only substance units. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 10$ |metre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 7.5; +k2 @Const 'k2' { } = 0.3; + diff --git a/latest/cases/01012/synopsis.txt b/latest/cases/01012/synopsis.txt new file mode 100644 index 000000000..389d4ca32 --- /dev/null +++ b/latest/cases/01012/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic reaction with two species in a 1-dimensional + size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00224, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. Species S1, S2 and S3 are +declared to have only substance units. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.0$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Value of parameter k1 |$ 7.5$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Length of compartment "compartment" |$ 10$ |metre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01013/l2v5/heta-code/output.heta b/latest/cases/01013/l2v5/heta-code/output.heta new file mode 100644 index 000000000..656225e66 --- /dev/null +++ b/latest/cases/01013/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: length, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.015; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.02; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Record 'k1' { } .= 620; +k2 @Record 'k2' { } .= 500; + diff --git a/latest/cases/01013/l2v5/index.heta b/latest/cases/01013/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01013/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01013/l2v5/json/output.json b/latest/cases/01013/l2v5/json/output.json new file mode 100644 index 000000000..8c7b1b260 --- /dev/null +++ b/latest/cases/01013/l2v5/json/output.json @@ -0,0 +1,154 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "length", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "620" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "500" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01013/l3v2/heta-code/output.heta b/latest/cases/01013/l3v2/heta-code/output.heta new file mode 100644 index 000000000..02c517a03 --- /dev/null +++ b/latest/cases/01013/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 620; +k2 @Const 'k2' { } = 500; + diff --git a/latest/cases/01013/l3v2/index.heta b/latest/cases/01013/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01013/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01013/l3v2/json/output.json b/latest/cases/01013/l3v2/json/output.json new file mode 100644 index 000000000..b8f74aff9 --- /dev/null +++ b/latest/cases/01013/l3v2/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "metre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.01" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.015" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.02" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "0.001" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3 * S4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 620 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 500 + } +] \ No newline at end of file diff --git a/latest/cases/01013/model-sbml-l2v5.xml b/latest/cases/01013/model-sbml-l2v5.xml new file mode 100644 index 000000000..665c706de --- /dev/null +++ b/latest/cases/01013/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/01013/model-sbml-l3v2.xml b/latest/cases/01013/model-sbml-l3v2.xml new file mode 100644 index 000000000..cdb0d487a --- /dev/null +++ b/latest/cases/01013/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + k2 + S3 + S4 + + + + + + + diff --git a/latest/cases/01013/output.heta b/latest/cases/01013/output.heta new file mode 100644 index 000000000..9962bb870 --- /dev/null +++ b/latest/cases/01013/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional + size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00225, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. All four species are declared +to have only substance units. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^2$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 10$ |metre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: metre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.015; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.02; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3 * S4; + +k1 @Const 'k1' { } = 620; +k2 @Const 'k2' { } = 500; + diff --git a/latest/cases/01013/synopsis.txt b/latest/cases/01013/synopsis.txt new file mode 100644 index 000000000..fba5dd246 --- /dev/null +++ b/latest/cases/01013/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Basic two reactions with four species in a 1-dimensional + size-10 compartment, where the species have only substance units. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00225, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. +Compartment "compartment" is 1-dimensional. All four species are declared +to have only substance units. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ | +| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$1.5 \x 10^-2$ |mole | +|Initial amount of S3 |$2.0 \x 10^-2$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 6.2 \x 10^2$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5 \x 10^2$ |mole^-1^ second^-1^ | +|Length of compartment "compartment" |$ 10$ |metre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01014/l2v5/heta-code/output.heta b/latest/cases/01014/l2v5/heta-code/output.heta new file mode 100644 index 000000000..679d375b0 --- /dev/null +++ b/latest/cases/01014/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.15; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k2 * S1; + +k1 @Record 'k1' { } .= 1.05; +k2 @Record 'k2' { } .= 1.15; + diff --git a/latest/cases/01014/l2v5/index.heta b/latest/cases/01014/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01014/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01014/l2v5/json/output.json b/latest/cases/01014/l2v5/json/output.json new file mode 100644 index 000000000..2f6ee75e4 --- /dev/null +++ b/latest/cases/01014/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.05" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "1.15" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01014/l3v2/heta-code/output.heta b/latest/cases/01014/l3v2/heta-code/output.heta new file mode 100644 index 000000000..90b03e812 --- /dev/null +++ b/latest/cases/01014/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/01014/l3v2/index.heta b/latest/cases/01014/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01014/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01014/l3v2/json/output.json b/latest/cases/01014/l3v2/json/output.json new file mode 100644 index 000000000..ba0183cab --- /dev/null +++ b/latest/cases/01014/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "ode_": "k1 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k2 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.05 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 1.15 + } +] \ No newline at end of file diff --git a/latest/cases/01014/model-sbml-l2v5.xml b/latest/cases/01014/model-sbml-l2v5.xml new file mode 100644 index 000000000..68134dfc5 --- /dev/null +++ b/latest/cases/01014/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + k2 + S1 + + + + + + + diff --git a/latest/cases/01014/model-sbml-l3v2.xml b/latest/cases/01014/model-sbml-l3v2.xml new file mode 100644 index 000000000..eccf3135b --- /dev/null +++ b/latest/cases/01014/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + k2 + S1 + + + + + + + diff --git a/latest/cases/01014/output.heta b/latest/cases/01014/output.heta new file mode 100644 index 000000000..d1ecebd8c --- /dev/null +++ b/latest/cases/01014/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Basic single forward reaction with three species in one + size-10 compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00295, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, }; +S3 := k1 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k2 * S1; + +k1 @Const 'k1' { } = 1.05; +k2 @Const 'k2' { } = 1.15; + diff --git a/latest/cases/01014/synopsis.txt b/latest/cases/01014/synopsis.txt new file mode 100644 index 000000000..a4c116125 --- /dev/null +++ b/latest/cases/01014/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one + size-10 compartment using an AssignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00295, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $k1 * S2$ |] + +In this case there is no initial value declared for species S3. Thus the +initial value must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.5 \x 10^-1$ |mole | +|Initial amount of S3 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.05$ |dimensionless | +|Value of parameter k2 |$ 1.15$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01015/l2v5/heta-code/output.heta b/latest/cases/01015/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6ba48891d --- /dev/null +++ b/latest/cases/01015/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1e-5; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-5; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 1e-5; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 2.25e-5; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Record 'k1' { } .= 1.5e+5; +k2 @Record 'k2' { } .= 50; +k3 @Record 'k3' { } .= 1.5; + diff --git a/latest/cases/01015/l2v5/index.heta b/latest/cases/01015/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01015/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01015/l2v5/json/output.json b/latest/cases/01015/l2v5/json/output.json new file mode 100644 index 000000000..0e021e655 --- /dev/null +++ b/latest/cases/01015/l2v5/json/output.json @@ -0,0 +1,155 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "2.25e-5", + "ode_": "k3 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "50" + } + }, + { + "class": "Record", + "id": "k3", + "title": "k3", + "assignments": { + "start_": "1.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01015/l3v2/heta-code/output.heta b/latest/cases/01015/l3v2/heta-code/output.heta new file mode 100644 index 000000000..374f6f99c --- /dev/null +++ b/latest/cases/01015/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 2.25e-5; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/01015/l3v2/index.heta b/latest/cases/01015/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01015/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01015/l3v2/json/output.json b/latest/cases/01015/l3v2/json/output.json new file mode 100644 index 000000000..2bea33d29 --- /dev/null +++ b/latest/cases/01015/l3v2/json/output.json @@ -0,0 +1,125 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "1.5e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1e-5" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "2.25e-5", + "ode_": "k3 * S2" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 150000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 50 + }, + { + "class": "Const", + "id": "k3", + "title": "k3", + "num": 1.5 + } +] \ No newline at end of file diff --git a/latest/cases/01015/model-sbml-l2v5.xml b/latest/cases/01015/model-sbml-l2v5.xml new file mode 100644 index 000000000..3f783ddf1 --- /dev/null +++ b/latest/cases/01015/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01015/model-sbml-l3v2.xml b/latest/cases/01015/model-sbml-l3v2.xml new file mode 100644 index 000000000..b3b3c6470 --- /dev/null +++ b/latest/cases/01015/model-sbml-l3v2.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01015/output.heta b/latest/cases/01015/output.heta new file mode 100644 index 000000000..d772647e7 --- /dev/null +++ b/latest/cases/01015/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Two reactions with four species in one + size-10 compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00296, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-5; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 2.25e-5; +S4 := k3 * S2; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; + +k1 @Const 'k1' { } = 150000; +k2 @Const 'k2' { } = 50; +k3 @Const 'k3' { } = 1.5; + diff --git a/latest/cases/01015/synopsis.txt b/latest/cases/01015/synopsis.txt new file mode 100644 index 000000000..8a7212642 --- /dev/null +++ b/latest/cases/01015/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions with four species in one + size-10 compartment using an assignmentRule to vary one species. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00296, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and three parameters named k1, k2 and k3. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$2.25 \x 10^-5$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^5$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01016/l2v5/heta-code/output.heta b/latest/cases/01016/l2v5/heta-code/output.heta new file mode 100644 index 000000000..911e892f6 --- /dev/null +++ b/latest/cases/01016/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Record 'k1' { } .= 1.75; +k2 @Record 'k2' { } .= 0.015; + diff --git a/latest/cases/01016/l2v5/index.heta b/latest/cases/01016/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01016/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01016/l2v5/json/output.json b/latest/cases/01016/l2v5/json/output.json new file mode 100644 index 000000000..649195c12 --- /dev/null +++ b/latest/cases/01016/l2v5/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "1.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.015" + } + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01016/l3v2/heta-code/output.heta b/latest/cases/01016/l3v2/heta-code/output.heta new file mode 100644 index 000000000..63aa18baa --- /dev/null +++ b/latest/cases/01016/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.015; + diff --git a/latest/cases/01016/l3v2/index.heta b/latest/cases/01016/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01016/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01016/l3v2/json/output.json b/latest/cases/01016/l3v2/json/output.json new file mode 100644 index 000000000..7e70eb457 --- /dev/null +++ b/latest/cases/01016/l3v2/json/output.json @@ -0,0 +1,96 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "0.15" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "0.1" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 1.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.015 + }, + { + "class": "Process", + "id": "S3_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "k1 * k2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01016/model-sbml-l2v5.xml b/latest/cases/01016/model-sbml-l2v5.xml new file mode 100644 index 000000000..9dd29849b --- /dev/null +++ b/latest/cases/01016/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01016/model-sbml-l3v2.xml b/latest/cases/01016/model-sbml-l3v2.xml new file mode 100644 index 000000000..1ce06cbfa --- /dev/null +++ b/latest/cases/01016/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + k2 + + + + + + + + + + + + + + + + + k1 + S1 + + + + + + + diff --git a/latest/cases/01016/output.heta b/latest/cases/01016/output.heta new file mode 100644 index 000000000..f34238d10 --- /dev/null +++ b/latest/cases/01016/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Basic reaction and rate rule with three species in a size-10 compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00331, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-2$ |mole | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1; + +reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, }; +reaction1 := k1 * S1; +S3_proc @Process { actors: = S3, aux: {{"metaid":"rule1"}}, }; +S3_proc := k1 * k2; + +k1 @Const 'k1' { } = 1.75; +k2 @Const 'k2' { } = 0.015; + diff --git a/latest/cases/01016/synopsis.txt b/latest/cases/01016/synopsis.txt new file mode 100644 index 000000000..777eacf1b --- /dev/null +++ b/latest/cases/01016/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic reaction and rate rule with three species in a size-10 compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +Note: This test is a direct copy of test 00331, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and two parameters named k1 and k2. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * k2$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1.75$ |second^-1^ | +|Value of parameter k2 |$1.5 \x 10^-2$ |mole | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/01017/l2v5/heta-code/output.heta b/latest/cases/01017/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6346a3868 --- /dev/null +++ b/latest/cases/01017/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 10; + +S1 @Species 'S1' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: substance, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: substance, compartment: compartment, isAmount: true, } .= 1.5e-6; +S4 @Species 'S4' { units: substance, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Record 'k1' { } .= 7.5e+5; +k2 @Record 'k2' { } .= 2.5e-4; + diff --git a/latest/cases/01017/l2v5/index.heta b/latest/cases/01017/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01017/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01017/l2v5/json/output.json b/latest/cases/01017/l2v5/json/output.json new file mode 100644 index 000000000..05108d692 --- /dev/null +++ b/latest/cases/01017/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "volume", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "substance", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "substance", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "substance", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "7.5e+5" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "2.5e-4" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01017/l3v2/heta-code/output.heta b/latest/cases/01017/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0f40c861d --- /dev/null +++ b/latest/cases/01017/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/01017/l3v2/index.heta b/latest/cases/01017/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01017/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01017/l3v2/json/output.json b/latest/cases/01017/l3v2/json/output.json new file mode 100644 index 000000000..5421e99e6 --- /dev/null +++ b/latest/cases/01017/l3v2/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "compartment", + "title": "compartment", + "units": "litre", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole", + "assignments": { + "start_": "2e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole", + "assignments": { + "start_": "1.5e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole", + "assignments": { + "start_": "1e-6" + }, + "compartment": "compartment", + "isAmount": true + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "k1 * S1 * S2" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "k2 * S3" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 750000 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.00025 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(1e-7)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01017/model-sbml-l2v5.xml b/latest/cases/01017/model-sbml-l2v5.xml new file mode 100644 index 000000000..d25ba359d --- /dev/null +++ b/latest/cases/01017/model-sbml-l2v5.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01017/model-sbml-l3v2.xml b/latest/cases/01017/model-sbml-l3v2.xml new file mode 100644 index 000000000..f963c81ed --- /dev/null +++ b/latest/cases/01017/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 -7 + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + + + + + + + + k2 + S3 + + + + + + + diff --git a/latest/cases/01017/output.heta b/latest/cases/01017/output.heta new file mode 100644 index 000000000..97341289b --- /dev/null +++ b/latest/cases/01017/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Two reactions and a rate rule with four species in a size-10 compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00332, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10; + +S1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6; +S3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6; +S4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6; + +reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, }; +reaction1 := k1 * S1 * S2; +reaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, }; +reaction2 := k2 * S3; +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (1e-7); + +k1 @Const 'k1' { } = 750000; +k2 @Const 'k2' { } = 0.00025; + diff --git a/latest/cases/01017/synopsis.txt b/latest/cases/01017/synopsis.txt new file mode 100644 index 000000000..5065a0d90 --- /dev/null +++ b/latest/cases/01017/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a size-10 compartment. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a direct copy of test 00332, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything. + +The model contains one compartment called "compartment". There are four +species named S1, S2, S3 and S4 and two parameters named k1 and k2. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2$ | +| S3 -> S1 + S2 | $k2 * S3$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-7$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-6$ |mole | +|Value of parameter k1 |$0.75 \x 10^6$ |mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-3$ |second^-1^ | +|Volume of compartment "compartment" |$ 10$ |litre |] + +The species have been declared as having substance units only. Thus, they +must be treated as amounts where they appear in expressions. + diff --git a/latest/cases/01018/l2v5/heta-code/output.heta b/latest/cases/01018/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d53a6b2c2 --- /dev/null +++ b/latest/cases/01018/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/01018/l2v5/index.heta b/latest/cases/01018/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01018/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01018/l2v5/json/output.json b/latest/cases/01018/l2v5/json/output.json new file mode 100644 index 000000000..0954e9a85 --- /dev/null +++ b/latest/cases/01018/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01018/l3v2/heta-code/output.heta b/latest/cases/01018/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2f20158d4 --- /dev/null +++ b/latest/cases/01018/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01018/l3v2/index.heta b/latest/cases/01018/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01018/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01018/l3v2/json/output.json b/latest/cases/01018/l3v2/json/output.json new file mode 100644 index 000000000..b71bd3ccf --- /dev/null +++ b/latest/cases/01018/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/01018/model-sbml-l2v5.xml b/latest/cases/01018/model-sbml-l2v5.xml new file mode 100644 index 000000000..861000d07 --- /dev/null +++ b/latest/cases/01018/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01018/model-sbml-l3v2.xml b/latest/cases/01018/model-sbml-l3v2.xml new file mode 100644 index 000000000..593410710 --- /dev/null +++ b/latest/cases/01018/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01018/output.heta b/latest/cases/01018/output.heta new file mode 100644 index 000000000..3e78c2c77 --- /dev/null +++ b/latest/cases/01018/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 818, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. Species S1 is labeled as an +SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01018/synopsis.txt b/latest/cases/01018/synopsis.txt new file mode 100644 index 000000000..3d34f774a --- /dev/null +++ b/latest/cases/01018/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 818, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. Species S1 is labeled as an +SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01019/l2v5/heta-code/output.heta b/latest/cases/01019/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6a30d2486 --- /dev/null +++ b/latest/cases/01019/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/01019/l2v5/index.heta b/latest/cases/01019/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01019/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01019/l2v5/json/output.json b/latest/cases/01019/l2v5/json/output.json new file mode 100644 index 000000000..3c39488a3 --- /dev/null +++ b/latest/cases/01019/l2v5/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01019/l3v2/heta-code/output.heta b/latest/cases/01019/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8a225b2ac --- /dev/null +++ b/latest/cases/01019/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01019/l3v2/index.heta b/latest/cases/01019/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01019/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01019/l3v2/json/output.json b/latest/cases/01019/l3v2/json/output.json new file mode 100644 index 000000000..2cd1337e4 --- /dev/null +++ b/latest/cases/01019/l3v2/json/output.json @@ -0,0 +1,81 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/01019/model-sbml-l2v5.xml b/latest/cases/01019/model-sbml-l2v5.xml new file mode 100644 index 000000000..b6500b564 --- /dev/null +++ b/latest/cases/01019/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01019/model-sbml-l3v2.xml b/latest/cases/01019/model-sbml-l3v2.xml new file mode 100644 index 000000000..e87a26801 --- /dev/null +++ b/latest/cases/01019/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01019/output.heta b/latest/cases/01019/output.heta new file mode 100644 index 000000000..34508359e --- /dev/null +++ b/latest/cases/01019/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 819, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01019/synopsis.txt b/latest/cases/01019/synopsis.txt new file mode 100644 index 000000000..d18bec414 --- /dev/null +++ b/latest/cases/01019/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 819, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01020/l2v5/heta-code/output.heta b/latest/cases/01020/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b9a816c49 --- /dev/null +++ b/latest/cases/01020/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01020/l2v5/index.heta b/latest/cases/01020/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01020/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01020/l2v5/json/output.json b/latest/cases/01020/l2v5/json/output.json new file mode 100644 index 000000000..17681f1c3 --- /dev/null +++ b/latest/cases/01020/l2v5/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01020/l3v2/heta-code/output.heta b/latest/cases/01020/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1274541d8 --- /dev/null +++ b/latest/cases/01020/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01020/l3v2/index.heta b/latest/cases/01020/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01020/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01020/l3v2/json/output.json b/latest/cases/01020/l3v2/json/output.json new file mode 100644 index 000000000..a4f812a00 --- /dev/null +++ b/latest/cases/01020/l3v2/json/output.json @@ -0,0 +1,81 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01020/model-sbml-l2v5.xml b/latest/cases/01020/model-sbml-l2v5.xml new file mode 100644 index 000000000..ca10a8392 --- /dev/null +++ b/latest/cases/01020/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01020/model-sbml-l3v2.xml b/latest/cases/01020/model-sbml-l3v2.xml new file mode 100644 index 000000000..79885a443 --- /dev/null +++ b/latest/cases/01020/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01020/output.heta b/latest/cases/01020/output.heta new file mode 100644 index 000000000..abac01d6c --- /dev/null +++ b/latest/cases/01020/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 820, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01020/synopsis.txt b/latest/cases/01020/synopsis.txt new file mode 100644 index 000000000..9871fd23f --- /dev/null +++ b/latest/cases/01020/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 820, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01021/l2v5/heta-code/output.heta b/latest/cases/01021/l2v5/heta-code/output.heta new file mode 100644 index 000000000..642244ec8 --- /dev/null +++ b/latest/cases/01021/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/01021/l2v5/index.heta b/latest/cases/01021/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01021/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01021/l2v5/json/output.json b/latest/cases/01021/l2v5/json/output.json new file mode 100644 index 000000000..6d4408da3 --- /dev/null +++ b/latest/cases/01021/l2v5/json/output.json @@ -0,0 +1,95 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01021/l3v2/heta-code/output.heta b/latest/cases/01021/l3v2/heta-code/output.heta new file mode 100644 index 000000000..90aeccce0 --- /dev/null +++ b/latest/cases/01021/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01021/l3v2/index.heta b/latest/cases/01021/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01021/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01021/l3v2/json/output.json b/latest/cases/01021/l3v2/json/output.json new file mode 100644 index 000000000..ea1485807 --- /dev/null +++ b/latest/cases/01021/l3v2/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/01021/model-sbml-l2v5.xml b/latest/cases/01021/model-sbml-l2v5.xml new file mode 100644 index 000000000..be2de36dd --- /dev/null +++ b/latest/cases/01021/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01021/model-sbml-l3v2.xml b/latest/cases/01021/model-sbml-l3v2.xml new file mode 100644 index 000000000..2c0961ddf --- /dev/null +++ b/latest/cases/01021/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01021/output.heta b/latest/cases/01021/output.heta new file mode 100644 index 000000000..cbd26374e --- /dev/null +++ b/latest/cases/01021/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 821, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. Species S2 is labeled as an +SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01021/synopsis.txt b/latest/cases/01021/synopsis.txt new file mode 100644 index 000000000..77183ef5a --- /dev/null +++ b/latest/cases/01021/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 821, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. Species S2 is labeled as an +SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01022/l2v5/heta-code/output.heta b/latest/cases/01022/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4a48b378b --- /dev/null +++ b/latest/cases/01022/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0.4 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/01022/l2v5/index.heta b/latest/cases/01022/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01022/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01022/l2v5/json/output.json b/latest/cases/01022/l2v5/json/output.json new file mode 100644 index 000000000..216a54c25 --- /dev/null +++ b/latest/cases/01022/l2v5/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.4 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01022/l3v2/heta-code/output.heta b/latest/cases/01022/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a1c29521f --- /dev/null +++ b/latest/cases/01022/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0.4 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01022/l3v2/index.heta b/latest/cases/01022/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01022/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01022/l3v2/json/output.json b/latest/cases/01022/l3v2/json/output.json new file mode 100644 index 000000000..8be173343 --- /dev/null +++ b/latest/cases/01022/l3v2/json/output.json @@ -0,0 +1,81 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0.4 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/01022/model-sbml-l2v5.xml b/latest/cases/01022/model-sbml-l2v5.xml new file mode 100644 index 000000000..447eb7377 --- /dev/null +++ b/latest/cases/01022/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01022/model-sbml-l3v2.xml b/latest/cases/01022/model-sbml-l3v2.xml new file mode 100644 index 000000000..b39a20314 --- /dev/null +++ b/latest/cases/01022/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01022/output.heta b/latest/cases/01022/output.heta new file mode 100644 index 000000000..e7cc1faf8 --- /dev/null +++ b/latest/cases/01022/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 822, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S3 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0.4$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0.4 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01022/synopsis.txt b/latest/cases/01022/synopsis.txt new file mode 100644 index 000000000..b0c898525 --- /dev/null +++ b/latest/cases/01022/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 822, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S3 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0.4$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01023/l2v5/heta-code/output.heta b/latest/cases/01023/l2v5/heta-code/output.heta new file mode 100644 index 000000000..863fc4d51 --- /dev/null +++ b/latest/cases/01023/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01023/l2v5/index.heta b/latest/cases/01023/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01023/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01023/l2v5/json/output.json b/latest/cases/01023/l2v5/json/output.json new file mode 100644 index 000000000..13ecb7aaf --- /dev/null +++ b/latest/cases/01023/l2v5/json/output.json @@ -0,0 +1,109 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01023/l3v2/heta-code/output.heta b/latest/cases/01023/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c11d8bce7 --- /dev/null +++ b/latest/cases/01023/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01023/l3v2/index.heta b/latest/cases/01023/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01023/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01023/l3v2/json/output.json b/latest/cases/01023/l3v2/json/output.json new file mode 100644 index 000000000..1d9604844 --- /dev/null +++ b/latest/cases/01023/l3v2/json/output.json @@ -0,0 +1,81 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01023/model-sbml-l2v5.xml b/latest/cases/01023/model-sbml-l2v5.xml new file mode 100644 index 000000000..c87ca7aeb --- /dev/null +++ b/latest/cases/01023/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01023/model-sbml-l3v2.xml b/latest/cases/01023/model-sbml-l3v2.xml new file mode 100644 index 000000000..346165445 --- /dev/null +++ b/latest/cases/01023/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01023/output.heta b/latest/cases/01023/output.heta new file mode 100644 index 000000000..0513628ab --- /dev/null +++ b/latest/cases/01023/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 823, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S2 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01023/synopsis.txt b/latest/cases/01023/synopsis.txt new file mode 100644 index 000000000..2b02f90c2 --- /dev/null +++ b/latest/cases/01023/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 823, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. Species S2 is labeled as +an SBML boundary species. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01024/l2v5/heta-code/output.heta b/latest/cases/01024/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cfc2f9391 --- /dev/null +++ b/latest/cases/01024/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: 2*S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/01024/l2v5/index.heta b/latest/cases/01024/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01024/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01024/l2v5/json/output.json b/latest/cases/01024/l2v5/json/output.json new file mode 100644 index 000000000..aee636ebd --- /dev/null +++ b/latest/cases/01024/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01024/l3v2/heta-code/output.heta b/latest/cases/01024/l3v2/heta-code/output.heta new file mode 100644 index 000000000..938deb770 --- /dev/null +++ b/latest/cases/01024/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: 2*S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01024/l3v2/index.heta b/latest/cases/01024/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01024/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01024/l3v2/json/output.json b/latest/cases/01024/l3v2/json/output.json new file mode 100644 index 000000000..7de3511e8 --- /dev/null +++ b/latest/cases/01024/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -2 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/01024/model-sbml-l2v5.xml b/latest/cases/01024/model-sbml-l2v5.xml new file mode 100644 index 000000000..b8a86edbb --- /dev/null +++ b/latest/cases/01024/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01024/model-sbml-l3v2.xml b/latest/cases/01024/model-sbml-l3v2.xml new file mode 100644 index 000000000..d356ccf9e --- /dev/null +++ b/latest/cases/01024/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01024/output.heta b/latest/cases/01024/output.heta new file mode 100644 index 000000000..46f7ba570 --- /dev/null +++ b/latest/cases/01024/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 824, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> 2S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: 2*S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01024/synopsis.txt b/latest/cases/01024/synopsis.txt new file mode 100644 index 000000000..e2edda2cd --- /dev/null +++ b/latest/cases/01024/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 824, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> 2S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01025/l2v5/heta-code/output.heta b/latest/cases/01025/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2fb257263 --- /dev/null +++ b/latest/cases/01025/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + 2*S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/01025/l2v5/index.heta b/latest/cases/01025/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01025/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01025/l2v5/json/output.json b/latest/cases/01025/l2v5/json/output.json new file mode 100644 index 000000000..017b08c52 --- /dev/null +++ b/latest/cases/01025/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01025/l3v2/heta-code/output.heta b/latest/cases/01025/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a1a7e3eb1 --- /dev/null +++ b/latest/cases/01025/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + 2*S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01025/l3v2/index.heta b/latest/cases/01025/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01025/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01025/l3v2/json/output.json b/latest/cases/01025/l3v2/json/output.json new file mode 100644 index 000000000..19c41898e --- /dev/null +++ b/latest/cases/01025/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/01025/model-sbml-l2v5.xml b/latest/cases/01025/model-sbml-l2v5.xml new file mode 100644 index 000000000..28b5a9a91 --- /dev/null +++ b/latest/cases/01025/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01025/model-sbml-l3v2.xml b/latest/cases/01025/model-sbml-l3v2.xml new file mode 100644 index 000000000..a3feff606 --- /dev/null +++ b/latest/cases/01025/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01025/output.heta b/latest/cases/01025/output.heta new file mode 100644 index 000000000..bb1ca3037 --- /dev/null +++ b/latest/cases/01025/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 825, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + 2*S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01025/synopsis.txt b/latest/cases/01025/synopsis.txt new file mode 100644 index 000000000..5d8c9fc55 --- /dev/null +++ b/latest/cases/01025/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 825, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + 2S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01026/l2v5/heta-code/output.heta b/latest/cases/01026/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8c3ea03d0 --- /dev/null +++ b/latest/cases/01026/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + 2*S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01026/l2v5/index.heta b/latest/cases/01026/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01026/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01026/l2v5/json/output.json b/latest/cases/01026/l2v5/json/output.json new file mode 100644 index 000000000..da66301bf --- /dev/null +++ b/latest/cases/01026/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -2 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01026/l3v2/heta-code/output.heta b/latest/cases/01026/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e8ba74973 --- /dev/null +++ b/latest/cases/01026/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + 2*S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01026/l3v2/index.heta b/latest/cases/01026/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01026/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01026/l3v2/json/output.json b/latest/cases/01026/l3v2/json/output.json new file mode 100644 index 000000000..e3c579af4 --- /dev/null +++ b/latest/cases/01026/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -2 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01026/model-sbml-l2v5.xml b/latest/cases/01026/model-sbml-l2v5.xml new file mode 100644 index 000000000..83fb37cce --- /dev/null +++ b/latest/cases/01026/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01026/model-sbml-l3v2.xml b/latest/cases/01026/model-sbml-l3v2.xml new file mode 100644 index 000000000..bc85e6f5d --- /dev/null +++ b/latest/cases/01026/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01026/output.heta b/latest/cases/01026/output.heta new file mode 100644 index 000000000..11e5237e6 --- /dev/null +++ b/latest/cases/01026/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 826, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + 2S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + 2*S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01026/synopsis.txt b/latest/cases/01026/synopsis.txt new file mode 100644 index 000000000..0270c604d --- /dev/null +++ b/latest/cases/01026/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 826, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + 2S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01027/l2v5/build.log b/latest/cases/01027/l2v5/build.log new file mode 100644 index 000000000..7c67c305e --- /dev/null +++ b/latest/cases/01027/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01027/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01027/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01027/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01027/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01027/l2v5/index.heta b/latest/cases/01027/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01027/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01027/l3v2/index.heta b/latest/cases/01027/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01027/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01027/model-sbml-l2v5.xml b/latest/cases/01027/model-sbml-l2v5.xml new file mode 100644 index 000000000..a743a032f --- /dev/null +++ b/latest/cases/01027/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01027/synopsis.txt b/latest/cases/01027/synopsis.txt new file mode 100644 index 000000000..d40a319ed --- /dev/null +++ b/latest/cases/01027/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter +testTags: Amount, DefaultValue, ReversibleReaction, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: This test is a copy of model 827, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The version of this model using Level 3 constructs is present +as test 1110. + +The model contains one compartment called C. There are two species called +S1 and S2 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> (4 * p1)S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01028/l2v5/build.log b/latest/cases/01028/l2v5/build.log new file mode 100644 index 000000000..a917cde27 --- /dev/null +++ b/latest/cases/01028/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01028/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01028/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01028/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01028/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01028/l2v5/index.heta b/latest/cases/01028/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01028/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01028/l3v2/index.heta b/latest/cases/01028/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01028/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01028/model-sbml-l2v5.xml b/latest/cases/01028/model-sbml-l2v5.xml new file mode 100644 index 000000000..efcf8e7ba --- /dev/null +++ b/latest/cases/01028/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01028/synopsis.txt b/latest/cases/01028/synopsis.txt new file mode 100644 index 000000000..16ca78447 --- /dev/null +++ b/latest/cases/01028/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter +testTags: Amount, DefaultValue, ReversibleReaction, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: This test is a copy of model 828, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The version of this model using Level 3 constructs is present +as test 1111. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01029/l2v5/build.log b/latest/cases/01029/l2v5/build.log new file mode 100644 index 000000000..6aace2941 --- /dev/null +++ b/latest/cases/01029/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01029/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01029/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01029/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01029/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01029/l2v5/index.heta b/latest/cases/01029/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01029/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01029/l3v2/index.heta b/latest/cases/01029/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01029/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01029/model-sbml-l2v5.xml b/latest/cases/01029/model-sbml-l2v5.xml new file mode 100644 index 000000000..fefd09ade --- /dev/null +++ b/latest/cases/01029/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01029/synopsis.txt b/latest/cases/01029/synopsis.txt new file mode 100644 index 000000000..525a38504 --- /dev/null +++ b/latest/cases/01029/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter +testTags: Amount, DefaultValue, ReversibleReaction, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric + +Note: This test is a copy of model 829, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The version of this model using Level 3 constructs is present +as test 1064. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + (4 * p1)S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01030/l2v5/heta-code/output.heta b/latest/cases/01030/l2v5/heta-code/output.heta new file mode 100644 index 000000000..58a10b2a9 --- /dev/null +++ b/latest/cases/01030/l2v5/heta-code/output.heta @@ -0,0 +1,27 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (kf * S3 + (-1) * kr * S4))); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; + diff --git a/latest/cases/01030/l2v5/index.heta b/latest/cases/01030/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01030/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01030/l2v5/json/output.json b/latest/cases/01030/l2v5/json/output.json new file mode 100644 index 000000000..821fa9dae --- /dev/null +++ b/latest/cases/01030/l2v5/json/output.json @@ -0,0 +1,142 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "kf__reaction1_local", + "num": 0.8 + }, + { + "class": "Const", + "id": "kr__reaction1_local", + "num": 0.06 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "(-(C * (kf * S3 + (-1) * kr * S4)))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01030/l3v2/heta-code/output.heta b/latest/cases/01030/l3v2/heta-code/output.heta new file mode 100644 index 000000000..aa07650af --- /dev/null +++ b/latest/cases/01030/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (kf * S3 + (-1) * kr * S4))); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01030/l3v2/index.heta b/latest/cases/01030/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01030/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01030/l3v2/json/output.json b/latest/cases/01030/l3v2/json/output.json new file mode 100644 index 000000000..64afc91bb --- /dev/null +++ b/latest/cases/01030/l3v2/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "kf__reaction1_local", + "num": 0.8 + }, + { + "class": "Const", + "id": "kr__reaction1_local", + "num": 0.06 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "(-(C * (kf * S3 + (-1) * kr * S4)))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/01030/model-sbml-l2v5.xml b/latest/cases/01030/model-sbml-l2v5.xml new file mode 100644 index 000000000..c7d401249 --- /dev/null +++ b/latest/cases/01030/model-sbml-l2v5.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S3 + + + + -1 + kr + S4 + + + + + + + + + + diff --git a/latest/cases/01030/model-sbml-l3v2.xml b/latest/cases/01030/model-sbml-l3v2.xml new file mode 100644 index 000000000..b323ca78f --- /dev/null +++ b/latest/cases/01030/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S3 + + + + -1 + kr + S4 + + + + + + + + + + diff --git a/latest/cases/01030/output.heta b/latest/cases/01030/output.heta new file mode 100644 index 000000000..e76343d81 --- /dev/null +++ b/latest/cases/01030/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Two reversible reactions with global and local parameters. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 830, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |] + +Reaction S1 <-> S2 defines two local parameters kf and kr which have a +scope local to the defining reaction and are different from the global parameters kf +and kr used in the Reaction S3 <-> S4. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Value of local parameter kf |$0.8$ |second^-1^ | +|Value of local parameter kr |$0.06$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (kf * S3 + (-1) * kr * S4))); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01030/synopsis.txt b/latest/cases/01030/synopsis.txt new file mode 100644 index 000000000..5965772d2 --- /dev/null +++ b/latest/cases/01030/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reversible reactions with global and local parameters. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 830, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains two reactions +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |] + +Reaction S1 <-> S2 defines two local parameters kf and kr which have a +scope local to the defining reaction and are different from the global parameters kf +and kr used in the Reaction S3 <-> S4. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Value of local parameter kf |$0.8$ |second^-1^ | +|Value of local parameter kr |$0.06$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01031/l2v5/heta-code/output.heta b/latest/cases/01031/l2v5/heta-code/output.heta new file mode 100644 index 000000000..361743259 --- /dev/null +++ b/latest/cases/01031/l2v5/heta-code/output.heta @@ -0,0 +1,26 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4))); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf__reaction2_local @Const { } = 0.9; +kr__reaction2_local @Const { } = 0.075; + diff --git a/latest/cases/01031/l2v5/index.heta b/latest/cases/01031/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01031/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01031/l2v5/json/output.json b/latest/cases/01031/l2v5/json/output.json new file mode 100644 index 000000000..7760f598b --- /dev/null +++ b/latest/cases/01031/l2v5/json/output.json @@ -0,0 +1,136 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "kf__reaction1_local", + "num": 0.8 + }, + { + "class": "Const", + "id": "kr__reaction1_local", + "num": 0.06 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf__reaction2_local", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr__reaction2_local", + "num": 0.075 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "(-(C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4)))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01031/l3v2/heta-code/output.heta b/latest/cases/01031/l3v2/heta-code/output.heta new file mode 100644 index 000000000..777843ca5 --- /dev/null +++ b/latest/cases/01031/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4))); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf__reaction2_local @Const { } = 0.9; +kr__reaction2_local @Const { } = 0.075; + diff --git a/latest/cases/01031/l3v2/index.heta b/latest/cases/01031/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01031/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01031/l3v2/json/output.json b/latest/cases/01031/l3v2/json/output.json new file mode 100644 index 000000000..310b1823b --- /dev/null +++ b/latest/cases/01031/l3v2/json/output.json @@ -0,0 +1,112 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "kf__reaction1_local", + "num": 0.8 + }, + { + "class": "Const", + "id": "kr__reaction1_local", + "num": 0.06 + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf__reaction2_local", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr__reaction2_local", + "num": 0.075 + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "(-(C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4)))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01031/model-sbml-l2v5.xml b/latest/cases/01031/model-sbml-l2v5.xml new file mode 100644 index 000000000..b97f8ac51 --- /dev/null +++ b/latest/cases/01031/model-sbml-l2v5.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S3 + + + + -1 + kr + S4 + + + + + + + + + + + + + + diff --git a/latest/cases/01031/model-sbml-l3v2.xml b/latest/cases/01031/model-sbml-l3v2.xml new file mode 100644 index 000000000..7fc7c5fb7 --- /dev/null +++ b/latest/cases/01031/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S3 + + + + -1 + kr + S4 + + + + + + + + + + + + + + diff --git a/latest/cases/01031/output.heta b/latest/cases/01031/output.heta new file mode 100644 index 000000000..7d7420cb1 --- /dev/null +++ b/latest/cases/01031/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two reversible reactions with local parameters. +componentTags: Compartment, Species, Reaction +testTags: Amount, ReversibleReaction, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 831, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |] + +Both reactions define two local parameters kf and kr which have a +scope local to the defining reaction. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of local parameter kf (R1) |$0.8$ |second^-1^ | +|Value of local parameter kr (R1) |$0.06$ |second^-1^ | +|Value of local parameter kf (R1) |$0.9$ |second^-1^ | +|Value of local parameter kr (R2) |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4))); + +kf__reaction1_local @Const { } = 0.8; +kr__reaction1_local @Const { } = 0.06; +kf__reaction2_local @Const { } = 0.9; +kr__reaction2_local @Const { } = 0.075; + diff --git a/latest/cases/01031/synopsis.txt b/latest/cases/01031/synopsis.txt new file mode 100644 index 000000000..5139a83ad --- /dev/null +++ b/latest/cases/01031/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Two reversible reactions with local parameters. +componentTags: Compartment, Species, Reaction +testTags: Amount, ReversibleReaction, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 831, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |] + +Both reactions define two local parameters kf and kr which have a +scope local to the defining reaction. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of local parameter kf (R1) |$0.8$ |second^-1^ | +|Value of local parameter kr (R1) |$0.06$ |second^-1^ | +|Value of local parameter kf (R1) |$0.9$ |second^-1^ | +|Value of local parameter kr (R2) |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01032/l2v5/heta-code/output.heta b/latest/cases/01032/l2v5/heta-code/output.heta new file mode 100644 index 000000000..999e01de9 --- /dev/null +++ b/latest/cases/01032/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (multiply(kf, S1) + (-1) * kr * S2))); + +kf @Record 'kf' { } .= 0.59; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/01032/l2v5/index.heta b/latest/cases/01032/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01032/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01032/l2v5/json/output.json b/latest/cases/01032/l2v5/json/output.json new file mode 100644 index 000000000..31d79cef6 --- /dev/null +++ b/latest/cases/01032/l2v5/json/output.json @@ -0,0 +1,103 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (multiply(kf, S1) + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.59" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01032/l3v2/heta-code/output.heta b/latest/cases/01032/l3v2/heta-code/output.heta new file mode 100644 index 000000000..72f128638 --- /dev/null +++ b/latest/cases/01032/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (multiply(kf, S1) + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.59; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01032/l3v2/index.heta b/latest/cases/01032/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01032/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01032/l3v2/json/output.json b/latest/cases/01032/l3v2/json/output.json new file mode 100644 index 000000000..d8e11f5eb --- /dev/null +++ b/latest/cases/01032/l3v2/json/output.json @@ -0,0 +1,75 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (multiply(kf, S1) + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.59 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01032/model-sbml-l2v5.xml b/latest/cases/01032/model-sbml-l2v5.xml new file mode 100644 index 000000000..eddaeab00 --- /dev/null +++ b/latest/cases/01032/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + multiply + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01032/model-sbml-l3v2.xml b/latest/cases/01032/model-sbml-l3v2.xml new file mode 100644 index 000000000..8febc8f10 --- /dev/null +++ b/latest/cases/01032/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + multiply + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01032/output.heta b/latest/cases/01032/output.heta new file mode 100644 index 000000000..c8d878c70 --- /dev/null +++ b/latest/cases/01032/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 832, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(multiply(kf, S1) - kr * S2) * C$ |] + +The reaction applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.59$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (multiply(kf, S1) + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.59; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01032/synopsis.txt b/latest/cases/01032/synopsis.txt new file mode 100644 index 000000000..ae00115a7 --- /dev/null +++ b/latest/cases/01032/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 832, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(multiply(kf, S1) - kr * S2) * C$ |] + +The reaction applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.59$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01033/l2v5/heta-code/output.heta b/latest/cases/01033/l2v5/heta-code/output.heta new file mode 100644 index 000000000..44a4d599a --- /dev/null +++ b/latest/cases/01033/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.11; + diff --git a/latest/cases/01033/l2v5/index.heta b/latest/cases/01033/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01033/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01033/l2v5/json/output.json b/latest/cases/01033/l2v5/json/output.json new file mode 100644 index 000000000..b374f8b10 --- /dev/null +++ b/latest/cases/01033/l2v5/json/output.json @@ -0,0 +1,117 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.11" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01033/l3v2/heta-code/output.heta b/latest/cases/01033/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5d403efa7 --- /dev/null +++ b/latest/cases/01033/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.11; + diff --git a/latest/cases/01033/l3v2/index.heta b/latest/cases/01033/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01033/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01033/l3v2/json/output.json b/latest/cases/01033/l3v2/json/output.json new file mode 100644 index 000000000..97ef72283 --- /dev/null +++ b/latest/cases/01033/l3v2/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.11 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01033/model-sbml-l2v5.xml b/latest/cases/01033/model-sbml-l2v5.xml new file mode 100644 index 000000000..d40a191f2 --- /dev/null +++ b/latest/cases/01033/model-sbml-l2v5.xml @@ -0,0 +1,93 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + multiply + + multiply + kf + S1 + + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01033/model-sbml-l3v2.xml b/latest/cases/01033/model-sbml-l3v2.xml new file mode 100644 index 000000000..77e466cb9 --- /dev/null +++ b/latest/cases/01033/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + multiply + + multiply + kf + S1 + + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01033/output.heta b/latest/cases/01033/output.heta new file mode 100644 index 000000000..89695f73a --- /dev/null +++ b/latest/cases/01033/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 833, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(multiply(multiply(kf, S1), S2) - kr * S3) * C$ |] + +The reaction applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.11$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.11; + diff --git a/latest/cases/01033/synopsis.txt b/latest/cases/01033/synopsis.txt new file mode 100644 index 000000000..cf0ca3653 --- /dev/null +++ b/latest/cases/01033/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 833, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(multiply(multiply(kf, S1), S2) - kr * S3) * C$ |] + +The reaction applies the functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.11$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01034/l2v5/heta-code/output.heta b/latest/cases/01034/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5f37c56f6 --- /dev/null +++ b/latest/cases/01034/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +multiply #defineFunction { arguments: [x, y], math: x * y, }; +minus #defineFunction { arguments: [x, y], math: x + (-1) * y, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * minus(multiply(kf, S1), kr * S2 * S3))); + +kf @Record 'kf' { } .= 1.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01034/l2v5/index.heta b/latest/cases/01034/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01034/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01034/l2v5/json/output.json b/latest/cases/01034/l2v5/json/output.json new file mode 100644 index 000000000..8f2dfb5b0 --- /dev/null +++ b/latest/cases/01034/l2v5/json/output.json @@ -0,0 +1,126 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * minus(multiply(kf, S1), kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + }, + { + "id": "minus", + "arguments": [ + "x", + "y" + ], + "math": "x + (-1) * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01034/l3v2/heta-code/output.heta b/latest/cases/01034/l3v2/heta-code/output.heta new file mode 100644 index 000000000..150f87602 --- /dev/null +++ b/latest/cases/01034/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + +multiply #defineFunction { arguments: [x, y], math: x * y, }; +minus #defineFunction { arguments: [x, y], math: x + (-1) * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * minus(multiply(kf, S1), kr * S2 * S3))); + +kf @Const 'kf' { } = 1.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01034/l3v2/index.heta b/latest/cases/01034/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01034/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01034/l3v2/json/output.json b/latest/cases/01034/l3v2/json/output.json new file mode 100644 index 000000000..c772fad00 --- /dev/null +++ b/latest/cases/01034/l3v2/json/output.json @@ -0,0 +1,98 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * minus(multiply(kf, S1), kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + }, + { + "id": "multiply", + "arguments": [ + "x", + "y" + ], + "math": "x * y", + "action": "defineFunction" + }, + { + "id": "minus", + "arguments": [ + "x", + "y" + ], + "math": "x + (-1) * y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01034/model-sbml-l2v5.xml b/latest/cases/01034/model-sbml-l2v5.xml new file mode 100644 index 000000000..b325c5061 --- /dev/null +++ b/latest/cases/01034/model-sbml-l2v5.xml @@ -0,0 +1,110 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + minus + + multiply + kf + S1 + + + + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01034/model-sbml-l3v2.xml b/latest/cases/01034/model-sbml-l3v2.xml new file mode 100644 index 000000000..6eadc5b60 --- /dev/null +++ b/latest/cases/01034/model-sbml-l3v2.xml @@ -0,0 +1,110 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + + + -1 + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + minus + + multiply + kf + S1 + + + + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01034/output.heta b/latest/cases/01034/output.heta new file mode 100644 index 000000000..2a94229a5 --- /dev/null +++ b/latest/cases/01034/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 834, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(minus(multiply(kf, S1), kr * S2 * S3)) * C$ |] + +The reaction applies two functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | minus | x, y | $x - y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + +multiply #defineFunction { arguments: [x, y], math: x * y, }; +minus #defineFunction { arguments: [x, y], math: x + (-1) * y, }; + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * minus(multiply(kf, S1), kr * S2 * S3))); + +kf @Const 'kf' { } = 1.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01034/synopsis.txt b/latest/cases/01034/synopsis.txt new file mode 100644 index 000000000..ec4ae1cf2 --- /dev/null +++ b/latest/cases/01034/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 834, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(minus(multiply(kf, S1), kr * S2 * S3)) * C$ |] + +The reaction applies two functionDefinitions defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ | + | minus | x, y | $x - y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01035/l2v5/heta-code/output.heta b/latest/cases/01035/l2v5/heta-code/output.heta new file mode 100644 index 000000000..294c2a813 --- /dev/null +++ b/latest/cases/01035/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/01035/l2v5/index.heta b/latest/cases/01035/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01035/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01035/l2v5/json/output.json b/latest/cases/01035/l2v5/json/output.json new file mode 100644 index 000000000..8b6efc775 --- /dev/null +++ b/latest/cases/01035/l2v5/json/output.json @@ -0,0 +1,116 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01035/l3v2/heta-code/output.heta b/latest/cases/01035/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d32937e3f --- /dev/null +++ b/latest/cases/01035/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/01035/l3v2/index.heta b/latest/cases/01035/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01035/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01035/l3v2/json/output.json b/latest/cases/01035/l3v2/json/output.json new file mode 100644 index 000000000..9a4480149 --- /dev/null +++ b/latest/cases/01035/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/01035/model-sbml-l2v5.xml b/latest/cases/01035/model-sbml-l2v5.xml new file mode 100644 index 000000000..4d12ea534 --- /dev/null +++ b/latest/cases/01035/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01035/model-sbml-l3v2.xml b/latest/cases/01035/model-sbml-l3v2.xml new file mode 100644 index 000000000..82008a146 --- /dev/null +++ b/latest/cases/01035/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01035/output.heta b/latest/cases/01035/output.heta new file mode 100644 index 000000000..1988e76b9 --- /dev/null +++ b/latest/cases/01035/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 835, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/01035/synopsis.txt b/latest/cases/01035/synopsis.txt new file mode 100644 index 000000000..19b650606 --- /dev/null +++ b/latest/cases/01035/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 835, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01036/l2v5/heta-code/output.heta b/latest/cases/01036/l2v5/heta-code/output.heta new file mode 100644 index 000000000..294c2a813 --- /dev/null +++ b/latest/cases/01036/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/01036/l2v5/index.heta b/latest/cases/01036/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01036/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01036/l2v5/json/output.json b/latest/cases/01036/l2v5/json/output.json new file mode 100644 index 000000000..8b6efc775 --- /dev/null +++ b/latest/cases/01036/l2v5/json/output.json @@ -0,0 +1,116 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01036/l3v2/heta-code/output.heta b/latest/cases/01036/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d32937e3f --- /dev/null +++ b/latest/cases/01036/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/01036/l3v2/index.heta b/latest/cases/01036/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01036/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01036/l3v2/json/output.json b/latest/cases/01036/l3v2/json/output.json new file mode 100644 index 000000000..9a4480149 --- /dev/null +++ b/latest/cases/01036/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/01036/model-sbml-l2v5.xml b/latest/cases/01036/model-sbml-l2v5.xml new file mode 100644 index 000000000..905efbc1b --- /dev/null +++ b/latest/cases/01036/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01036/model-sbml-l3v2.xml b/latest/cases/01036/model-sbml-l3v2.xml new file mode 100644 index 000000000..11324564e --- /dev/null +++ b/latest/cases/01036/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01036/output.heta b/latest/cases/01036/output.heta new file mode 100644 index 000000000..08ca8f616 --- /dev/null +++ b/latest/cases/01036/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 836, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/01036/synopsis.txt b/latest/cases/01036/synopsis.txt new file mode 100644 index 000000000..066234154 --- /dev/null +++ b/latest/cases/01036/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 836, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. The +calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01037/l2v5/heta-code/output.heta b/latest/cases/01037/l2v5/heta-code/output.heta new file mode 100644 index 000000000..294c2a813 --- /dev/null +++ b/latest/cases/01037/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; +p1 @Record 'p1' { } .= 0.5; + diff --git a/latest/cases/01037/l2v5/index.heta b/latest/cases/01037/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01037/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01037/l2v5/json/output.json b/latest/cases/01037/l2v5/json/output.json new file mode 100644 index 000000000..8b6efc775 --- /dev/null +++ b/latest/cases/01037/l2v5/json/output.json @@ -0,0 +1,116 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "class": "Record", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "0.5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01037/l3v2/heta-code/output.heta b/latest/cases/01037/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d32937e3f --- /dev/null +++ b/latest/cases/01037/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/01037/l3v2/index.heta b/latest/cases/01037/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01037/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01037/l3v2/json/output.json b/latest/cases/01037/l3v2/json/output.json new file mode 100644 index 000000000..9a4480149 --- /dev/null +++ b/latest/cases/01037/l3v2/json/output.json @@ -0,0 +1,86 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "2 * p1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + }, + { + "class": "Const", + "id": "p1", + "title": "p1", + "num": 0.5 + } +] \ No newline at end of file diff --git a/latest/cases/01037/model-sbml-l2v5.xml b/latest/cases/01037/model-sbml-l2v5.xml new file mode 100644 index 000000000..1cd9c0e60 --- /dev/null +++ b/latest/cases/01037/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01037/model-sbml-l3v2.xml b/latest/cases/01037/model-sbml-l3v2.xml new file mode 100644 index 000000000..7d4dbe5e9 --- /dev/null +++ b/latest/cases/01037/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01037/output.heta b/latest/cases/01037/output.heta new file mode 100644 index 000000000..7f96b3e60 --- /dev/null +++ b/latest/cases/01037/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 837, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; +p1 @Const 'p1' { } = 0.5; + diff --git a/latest/cases/01037/synopsis.txt b/latest/cases/01037/synopsis.txt new file mode 100644 index 000000000..36260bf9b --- /dev/null +++ b/latest/cases/01037/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Single reversible reaction with an initial assignment. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 837, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |mole | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01038/l2v5/heta-code/output.heta b/latest/cases/01038/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1d576bc03 --- /dev/null +++ b/latest/cases/01038/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { }; +kf := 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01038/l2v5/index.heta b/latest/cases/01038/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01038/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01038/l2v5/json/output.json b/latest/cases/01038/l2v5/json/output.json new file mode 100644 index 000000000..ac1fd006e --- /dev/null +++ b/latest/cases/01038/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "ode_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01038/l3v2/heta-code/output.heta b/latest/cases/01038/l3v2/heta-code/output.heta new file mode 100644 index 000000000..601c1b0cb --- /dev/null +++ b/latest/cases/01038/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { }; +kf := 2.5; + +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01038/l3v2/index.heta b/latest/cases/01038/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01038/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01038/l3v2/json/output.json b/latest/cases/01038/l3v2/json/output.json new file mode 100644 index 000000000..b5b8daae9 --- /dev/null +++ b/latest/cases/01038/l3v2/json/output.json @@ -0,0 +1,82 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "ode_": "2.5" + } + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01038/model-sbml-l2v5.xml b/latest/cases/01038/model-sbml-l2v5.xml new file mode 100644 index 000000000..a39c0ca60 --- /dev/null +++ b/latest/cases/01038/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2.5 + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01038/model-sbml-l3v2.xml b/latest/cases/01038/model-sbml-l3v2.xml new file mode 100644 index 000000000..7e6d4ab91 --- /dev/null +++ b/latest/cases/01038/model-sbml-l3v2.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2.5 + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01038/output.heta b/latest/cases/01038/output.heta new file mode 100644 index 000000000..c718fb62c --- /dev/null +++ b/latest/cases/01038/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 838, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to parameter kf: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | kf | $2.5$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$undeclared$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { }; +kf := 2.5; + +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01038/synopsis.txt b/latest/cases/01038/synopsis.txt new file mode 100644 index 000000000..ba74ec08d --- /dev/null +++ b/latest/cases/01038/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 838, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to parameter kf: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | kf | $2.5$ |] + +In this case there is no initial value declared for parameter k1. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$undeclared$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01039/l2v5/heta-code/output.heta b/latest/cases/01039/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1f8f17d12 --- /dev/null +++ b/latest/cases/01039/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01039/l2v5/index.heta b/latest/cases/01039/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01039/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01039/l2v5/json/output.json b/latest/cases/01039/l2v5/json/output.json new file mode 100644 index 000000000..5b8da73d5 --- /dev/null +++ b/latest/cases/01039/l2v5/json/output.json @@ -0,0 +1,118 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "0.5 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01039/l3v2/heta-code/output.heta b/latest/cases/01039/l3v2/heta-code/output.heta new file mode 100644 index 000000000..21f1b5783 --- /dev/null +++ b/latest/cases/01039/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01039/l3v2/index.heta b/latest/cases/01039/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01039/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01039/l3v2/json/output.json b/latest/cases/01039/l3v2/json/output.json new file mode 100644 index 000000000..b3fab32aa --- /dev/null +++ b/latest/cases/01039/l3v2/json/output.json @@ -0,0 +1,90 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "ode_": "0.5 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01039/model-sbml-l2v5.xml b/latest/cases/01039/model-sbml-l2v5.xml new file mode 100644 index 000000000..1fe08e7c9 --- /dev/null +++ b/latest/cases/01039/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + S1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01039/model-sbml-l3v2.xml b/latest/cases/01039/model-sbml-l3v2.xml new file mode 100644 index 000000000..001599fd5 --- /dev/null +++ b/latest/cases/01039/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + S1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01039/output.heta b/latest/cases/01039/output.heta new file mode 100644 index 000000000..07b9e32c5 --- /dev/null +++ b/latest/cases/01039/output.heta @@ -0,0 +1,65 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 839, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $0.5 * S1$ |] + +In this case there is no initial value declared for species S4. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$undeclared$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, }; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01039/synopsis.txt b/latest/cases/01039/synopsis.txt new file mode 100644 index 000000000..a0db8c38f --- /dev/null +++ b/latest/cases/01039/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 839, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $0.5 * S1$ |] + +In this case there is no initial value declared for species S4. Thus the +value must be calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$undeclared$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01040/l2v5/heta-code/output.heta b/latest/cases/01040/l2v5/heta-code/output.heta new file mode 100644 index 000000000..535417089 --- /dev/null +++ b/latest/cases/01040/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01040/l2v5/index.heta b/latest/cases/01040/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01040/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01040/l2v5/json/output.json b/latest/cases/01040/l2v5/json/output.json new file mode 100644 index 000000000..e3fdf7008 --- /dev/null +++ b/latest/cases/01040/l2v5/json/output.json @@ -0,0 +1,119 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5 / C", + "ode_": "0.5 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01040/l3v2/heta-code/output.heta b/latest/cases/01040/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cf2489943 --- /dev/null +++ b/latest/cases/01040/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01040/l3v2/index.heta b/latest/cases/01040/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01040/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01040/l3v2/json/output.json b/latest/cases/01040/l3v2/json/output.json new file mode 100644 index 000000000..8c7721984 --- /dev/null +++ b/latest/cases/01040/l3v2/json/output.json @@ -0,0 +1,91 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "5 / C", + "ode_": "0.5 * S1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01040/model-sbml-l2v5.xml b/latest/cases/01040/model-sbml-l2v5.xml new file mode 100644 index 000000000..565920f6a --- /dev/null +++ b/latest/cases/01040/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + S1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01040/model-sbml-l3v2.xml b/latest/cases/01040/model-sbml-l3v2.xml new file mode 100644 index 000000000..342bbcb7a --- /dev/null +++ b/latest/cases/01040/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + S1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01040/output.heta b/latest/cases/01040/output.heta new file mode 100644 index 000000000..a4791f63b --- /dev/null +++ b/latest/cases/01040/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 840, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $0.5 * S1$ |] + +In this case the initial value declared for species S4 is inconsistent +with the value calculated using the assignmentRule. The calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C; +S4 := 0.5 * S1; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01040/synopsis.txt b/latest/cases/01040/synopsis.txt new file mode 100644 index 000000000..ef8c93c36 --- /dev/null +++ b/latest/cases/01040/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: Amount, ReversibleReaction, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 840, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which assigns value to species S4: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $0.5 * S1$ |] + +In this case the initial value declared for species S4 is inconsistent +with the value calculated using the assignmentRule. The calculated value +should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01041/l2v5/heta-code/output.heta b/latest/cases/01041/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2c7513240 --- /dev/null +++ b/latest/cases/01041/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01041/l2v5/index.heta b/latest/cases/01041/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01041/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01041/l2v5/json/output.json b/latest/cases/01041/l2v5/json/output.json new file mode 100644 index 000000000..984132798 --- /dev/null +++ b/latest/cases/01041/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-0.5) * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01041/l3v2/heta-code/output.heta b/latest/cases/01041/l3v2/heta-code/output.heta new file mode 100644 index 000000000..21db95615 --- /dev/null +++ b/latest/cases/01041/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01041/l3v2/index.heta b/latest/cases/01041/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01041/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01041/l3v2/json/output.json b/latest/cases/01041/l3v2/json/output.json new file mode 100644 index 000000000..5bd643bac --- /dev/null +++ b/latest/cases/01041/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-0.5) * (kf * S1 + (-1) * kr * S2 * S3)" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01041/model-sbml-l2v5.xml b/latest/cases/01041/model-sbml-l2v5.xml new file mode 100644 index 000000000..dd55649b9 --- /dev/null +++ b/latest/cases/01041/model-sbml-l2v5.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -0.5 + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01041/model-sbml-l3v2.xml b/latest/cases/01041/model-sbml-l3v2.xml new file mode 100644 index 000000000..201929012 --- /dev/null +++ b/latest/cases/01041/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -0.5 + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01041/output.heta b/latest/cases/01041/output.heta new file mode 100644 index 000000000..ad1cc5b21 --- /dev/null +++ b/latest/cases/01041/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 841, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $-0.5 * (kf * S1 - kr * S2 * S3)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * (kf * S1 + (-1) * kr * S2 * S3); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01041/synopsis.txt b/latest/cases/01041/synopsis.txt new file mode 100644 index 000000000..415fc8b42 --- /dev/null +++ b/latest/cases/01041/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 841, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $-0.5 * (kf * S1 - kr * S2 * S3)$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01042/l2v5/heta-code/output.heta b/latest/cases/01042/l2v5/heta-code/output.heta new file mode 100644 index 000000000..390c193dd --- /dev/null +++ b/latest/cases/01042/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * S1; + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01042/l2v5/index.heta b/latest/cases/01042/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01042/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01042/l2v5/json/output.json b/latest/cases/01042/l2v5/json/output.json new file mode 100644 index 000000000..ba7ea4e2b --- /dev/null +++ b/latest/cases/01042/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-0.5) * S1" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01042/l3v2/heta-code/output.heta b/latest/cases/01042/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b6583f340 --- /dev/null +++ b/latest/cases/01042/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * S1; + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01042/l3v2/index.heta b/latest/cases/01042/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01042/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01042/l3v2/json/output.json b/latest/cases/01042/l3v2/json/output.json new file mode 100644 index 000000000..221c90f2d --- /dev/null +++ b/latest/cases/01042/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "(-0.5) * S1" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01042/model-sbml-l2v5.xml b/latest/cases/01042/model-sbml-l2v5.xml new file mode 100644 index 000000000..975e87133 --- /dev/null +++ b/latest/cases/01042/model-sbml-l2v5.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -0.5 + S1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01042/model-sbml-l3v2.xml b/latest/cases/01042/model-sbml-l3v2.xml new file mode 100644 index 000000000..3e7ffe8b6 --- /dev/null +++ b/latest/cases/01042/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -0.5 + S1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01042/output.heta b/latest/cases/01042/output.heta new file mode 100644 index 000000000..fd60aff51 --- /dev/null +++ b/latest/cases/01042/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 842, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $-0.5 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := (-0.5) * S1; + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01042/synopsis.txt b/latest/cases/01042/synopsis.txt new file mode 100644 index 000000000..f81d5ceda --- /dev/null +++ b/latest/cases/01042/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 842, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $-0.5 * S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01043/l2v5/heta-code/output.heta b/latest/cases/01043/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e14c35372 --- /dev/null +++ b/latest/cases/01043/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 0.15; + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01043/l2v5/index.heta b/latest/cases/01043/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01043/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01043/l2v5/json/output.json b/latest/cases/01043/l2v5/json/output.json new file mode 100644 index 000000000..fffe013f4 --- /dev/null +++ b/latest/cases/01043/l2v5/json/output.json @@ -0,0 +1,134 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01043/l3v2/heta-code/output.heta b/latest/cases/01043/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1997e516f --- /dev/null +++ b/latest/cases/01043/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 0.15; + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01043/l3v2/index.heta b/latest/cases/01043/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01043/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01043/l3v2/json/output.json b/latest/cases/01043/l3v2/json/output.json new file mode 100644 index 000000000..9fce87fc2 --- /dev/null +++ b/latest/cases/01043/l3v2/json/output.json @@ -0,0 +1,106 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + }, + { + "class": "Process", + "id": "S4_proc", + "aux": { + "metaid": "rule1" + }, + "assignments": { + "ode_": "0.15" + }, + "actors": [ + { + "target": "S4", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01043/model-sbml-l2v5.xml b/latest/cases/01043/model-sbml-l2v5.xml new file mode 100644 index 000000000..db9f5ec31 --- /dev/null +++ b/latest/cases/01043/model-sbml-l2v5.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01043/model-sbml-l3v2.xml b/latest/cases/01043/model-sbml-l3v2.xml new file mode 100644 index 000000000..d1233208b --- /dev/null +++ b/latest/cases/01043/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.15 + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01043/output.heta b/latest/cases/01043/output.heta new file mode 100644 index 000000000..3a3aad014 --- /dev/null +++ b/latest/cases/01043/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 843, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $0.15$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); +S4_proc @Process { actors: = S4, aux: {{"metaid":"rule1"}}, }; +S4_proc := 0.15; + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01043/synopsis.txt b/latest/cases/01043/synopsis.txt new file mode 100644 index 000000000..1e9336bba --- /dev/null +++ b/latest/cases/01043/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, RateRule +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 843, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The model contains one rule which specifies the rate at which species +S4 is varying: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $0.15$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0.5$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01044/l2v5/build.log b/latest/cases/01044/l2v5/build.log new file mode 100644 index 000000000..99d39a8ef --- /dev/null +++ b/latest/cases/01044/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01044/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01044/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01044/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01044/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01044/l2v5/index.heta b/latest/cases/01044/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01044/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01044/l3v2/build.log b/latest/cases/01044/l3v2/build.log new file mode 100644 index 000000000..a6877122c --- /dev/null +++ b/latest/cases/01044/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01044/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01044/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01044/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01044/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01044/l3v2/index.heta b/latest/cases/01044/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01044/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01044/model-sbml-l2v5.xml b/latest/cases/01044/model-sbml-l2v5.xml new file mode 100644 index 000000000..f06135e6c --- /dev/null +++ b/latest/cases/01044/model-sbml-l2v5.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + kf + -0.75 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01044/model-sbml-l3v2.xml b/latest/cases/01044/model-sbml-l3v2.xml new file mode 100644 index 000000000..92c5f6543 --- /dev/null +++ b/latest/cases/01044/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + kf + -0.75 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01044/synopsis.txt b/latest/cases/01044/synopsis.txt new file mode 100644 index 000000000..e44e349fd --- /dev/null +++ b/latest/cases/01044/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: One reversible reaction with three species in one compartment with +an algebraic rule used to determine value of a parameter. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 844, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law fails to go negative (a requirement for the ReversibeReaction tag). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and two parameters called kf and kr. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $kf - 0.75$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter kf |$undeclared$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01045/l2v5/heta-code/output.heta b/latest/cases/01045/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9bd97dad6 --- /dev/null +++ b/latest/cases/01045/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/01045/l2v5/index.heta b/latest/cases/01045/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01045/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01045/l2v5/json/output.json b/latest/cases/01045/l2v5/json/output.json new file mode 100644 index 000000000..e01926c95 --- /dev/null +++ b/latest/cases/01045/l2v5/json/output.json @@ -0,0 +1,101 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01045/l3v2/heta-code/output.heta b/latest/cases/01045/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4e62c6284 --- /dev/null +++ b/latest/cases/01045/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/01045/l3v2/index.heta b/latest/cases/01045/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01045/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01045/l3v2/json/output.json b/latest/cases/01045/l3v2/json/output.json new file mode 100644 index 000000000..80b421647 --- /dev/null +++ b/latest/cases/01045/l3v2/json/output.json @@ -0,0 +1,73 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/01045/model-sbml-l2v5.xml b/latest/cases/01045/model-sbml-l2v5.xml new file mode 100644 index 000000000..c5c528477 --- /dev/null +++ b/latest/cases/01045/model-sbml-l2v5.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/01045/model-sbml-l3v2.xml b/latest/cases/01045/model-sbml-l3v2.xml new file mode 100644 index 000000000..8eedee3bc --- /dev/null +++ b/latest/cases/01045/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/01045/output.heta b/latest/cases/01045/output.heta new file mode 100644 index 000000000..987f2c5de --- /dev/null +++ b/latest/cases/01045/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: One reversible reactions with two species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 845, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The model contains one event that assigns values to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.75, }; + diff --git a/latest/cases/01045/synopsis.txt b/latest/cases/01045/synopsis.txt new file mode 100644 index 000000000..83013fc80 --- /dev/null +++ b/latest/cases/01045/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: One reversible reactions with two species in one compartment + and one event that assigns value to a species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 845, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The model contains one event that assigns values to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01046/l2v5/heta-code/output.heta b/latest/cases/01046/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6636fbac2 --- /dev/null +++ b/latest/cases/01046/l2v5/heta-code/output.heta @@ -0,0 +1,30 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event1]= S2; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (k1 * S3 + (-1) * k2 * S4))); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.15; +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/01046/l2v5/index.heta b/latest/cases/01046/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01046/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01046/l2v5/json/output.json b/latest/cases/01046/l2v5/json/output.json new file mode 100644 index 000000000..c1a2f78c7 --- /dev/null +++ b/latest/cases/01046/l2v5/json/output.json @@ -0,0 +1,156 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "(-(C * (k1 * S3 + (-1) * k2 * S4)))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01046/l3v2/heta-code/output.heta b/latest/cases/01046/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a8f501e9e --- /dev/null +++ b/latest/cases/01046/l3v2/heta-code/output.heta @@ -0,0 +1,25 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event1]= S2; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (k1 * S3 + (-1) * k2 * S4))); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.15; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/01046/l3v2/index.heta b/latest/cases/01046/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01046/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01046/l3v2/json/output.json b/latest/cases/01046/l3v2/json/output.json new file mode 100644 index 000000000..d360f7e74 --- /dev/null +++ b/latest/cases/01046/l3v2/json/output.json @@ -0,0 +1,124 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C", + "event1": "S2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "(-(C * (k1 * S3 + (-1) * k2 * S4)))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.15 + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + } +] \ No newline at end of file diff --git a/latest/cases/01046/model-sbml-l2v5.xml b/latest/cases/01046/model-sbml-l2v5.xml new file mode 100644 index 000000000..ab924c420 --- /dev/null +++ b/latest/cases/01046/model-sbml-l2v5.xml @@ -0,0 +1,130 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/01046/model-sbml-l3v2.xml b/latest/cases/01046/model-sbml-l3v2.xml new file mode 100644 index 000000000..5a592868f --- /dev/null +++ b/latest/cases/01046/model-sbml-l3v2.xml @@ -0,0 +1,130 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/01046/output.heta b/latest/cases/01046/output.heta new file mode 100644 index 000000000..4d354f09b --- /dev/null +++ b/latest/cases/01046/output.heta @@ -0,0 +1,78 @@ +/* +category: Test +synopsis: Two reversible reactions with four species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 846, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains one event that assigns values to both species S2 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | | | | $S4 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S4 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event1]= S2; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (k1 * S3 + (-1) * k2 * S4))); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.15; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; + diff --git a/latest/cases/01046/synopsis.txt b/latest/cases/01046/synopsis.txt new file mode 100644 index 000000000..e714e6436 --- /dev/null +++ b/latest/cases/01046/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Two reversible reactions with four species in one compartment + and one event that assigns value to two species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 846, with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains one event that assigns values to both species S2 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | | | | $S4 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S4 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01047/l2v5/heta-code/output.heta b/latest/cases/01047/l2v5/heta-code/output.heta new file mode 100644 index 000000000..10d13d3d7 --- /dev/null +++ b/latest/cases/01047/l2v5/heta-code/output.heta @@ -0,0 +1,31 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event2]= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (k1 * S3 + (-1) * k2 * S4))); + +k1 @Record 'k1' { } .= 0.75; +k2 @Record 'k2' { } .= 0.15; +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; +event2 @DSwitcher 'event2' { trigger: S3 < 0.75, }; + diff --git a/latest/cases/01047/l2v5/index.heta b/latest/cases/01047/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01047/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01047/l2v5/json/output.json b/latest/cases/01047/l2v5/json/output.json new file mode 100644 index 000000000..990979dd9 --- /dev/null +++ b/latest/cases/01047/l2v5/json/output.json @@ -0,0 +1,162 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C", + "event2": "0.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "(-(C * (k1 * S3 + (-1) * k2 * S4)))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "title": "k1", + "assignments": { + "start_": "0.75" + } + }, + { + "class": "Record", + "id": "k2", + "title": "k2", + "assignments": { + "start_": "0.15" + } + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 < 0.75" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01047/l3v2/heta-code/output.heta b/latest/cases/01047/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bd01e8d41 --- /dev/null +++ b/latest/cases/01047/l3v2/heta-code/output.heta @@ -0,0 +1,26 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event2]= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (k1 * S3 + (-1) * k2 * S4))); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.15; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; +event2 @DSwitcher 'event2' { trigger: S3 < 0.75, }; + diff --git a/latest/cases/01047/l3v2/index.heta b/latest/cases/01047/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01047/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01047/l3v2/json/output.json b/latest/cases/01047/l3v2/json/output.json new file mode 100644 index 000000000..1e11dd89e --- /dev/null +++ b/latest/cases/01047/l3v2/json/output.json @@ -0,0 +1,130 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "2 / C", + "event1": "1.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "title": "S4", + "units": "mole/litre", + "assignments": { + "start_": "1.5 / C", + "event2": "0.5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Reaction", + "id": "reaction2", + "title": "reaction2", + "assignments": { + "ode_": "(-(C * (k1 * S3 + (-1) * k2 * S4)))" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "title": "k1", + "num": 0.75 + }, + { + "class": "Const", + "id": "k2", + "title": "k2", + "num": 0.15 + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + }, + { + "class": "DSwitcher", + "id": "event1", + "title": "event1", + "trigger": "S1 < 0.5" + }, + { + "class": "DSwitcher", + "id": "event2", + "title": "event2", + "trigger": "S3 < 0.75" + } +] \ No newline at end of file diff --git a/latest/cases/01047/model-sbml-l2v5.xml b/latest/cases/01047/model-sbml-l2v5.xml new file mode 100644 index 000000000..77c9b5312 --- /dev/null +++ b/latest/cases/01047/model-sbml-l2v5.xml @@ -0,0 +1,143 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.5 + + + + + + + + + + S3 + 0.75 + + + + + + + 0.5 + + + + + + + diff --git a/latest/cases/01047/model-sbml-l3v2.xml b/latest/cases/01047/model-sbml-l3v2.xml new file mode 100644 index 000000000..251879047 --- /dev/null +++ b/latest/cases/01047/model-sbml-l3v2.xml @@ -0,0 +1,143 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + + 1.5 + + + + + + + + + + S3 + 0.75 + + + + + + + 0.5 + + + + + + + diff --git a/latest/cases/01047/output.heta b/latest/cases/01047/output.heta new file mode 100644 index 000000000..d8224abf6 --- /dev/null +++ b/latest/cases/01047/output.heta @@ -0,0 +1,72 @@ +/* +category: Test +synopsis: Two reversible reactions with four species in one compartment + and two events that assigns value to species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 847, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains two event that assigns values to species S2 and S4 respectively: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | Event2 | $S3 < 0.75$ | $-$ | $S4 = 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C; +S2 [event1]= 1.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C; +S4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C; +S4 [event2]= 0.5; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); +reaction2 @Reaction 'reaction2' { actors: S4 = S3, }; +reaction2 := (-(C * (k1 * S3 + (-1) * k2 * S4))); + +k1 @Const 'k1' { } = 0.75; +k2 @Const 'k2' { } = 0.15; +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + +event1 @DSwitcher 'event1' { trigger: S1 < 0.5, }; +event2 @DSwitcher 'event2' { trigger: S3 < 0.75, }; + diff --git a/latest/cases/01047/synopsis.txt b/latest/cases/01047/synopsis.txt new file mode 100644 index 000000000..21e06bd42 --- /dev/null +++ b/latest/cases/01047/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Two reversible reactions with four species in one compartment + and two events that assigns value to species. +componentTags: Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 847, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains two event that assigns values to species S2 and S4 respectively: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | Event2 | $S3 < 0.75$ | $-$ | $S4 = 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01048/l2v5/build.log b/latest/cases/01048/l2v5/build.log new file mode 100644 index 000000000..d69c77566 --- /dev/null +++ b/latest/cases/01048/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01048/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01048/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01048/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01048/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01048/l2v5/index.heta b/latest/cases/01048/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01048/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01048/l3v2/build.log b/latest/cases/01048/l3v2/build.log new file mode 100644 index 000000000..834ff0944 --- /dev/null +++ b/latest/cases/01048/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01048/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01048/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01048/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01048/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01048/l3v2/index.heta b/latest/cases/01048/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01048/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01048/model-sbml-l2v5.xml b/latest/cases/01048/model-sbml-l2v5.xml new file mode 100644 index 000000000..8c87987cc --- /dev/null +++ b/latest/cases/01048/model-sbml-l2v5.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/01048/model-sbml-l3v2.xml b/latest/cases/01048/model-sbml-l3v2.xml new file mode 100644 index 000000000..09b6c72a7 --- /dev/null +++ b/latest/cases/01048/model-sbml-l3v2.xml @@ -0,0 +1,93 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + S1 + 0.75 + + + + + + 1 + + + + + + 1.5 + + + + + + + diff --git a/latest/cases/01048/synopsis.txt b/latest/cases/01048/synopsis.txt new file mode 100644 index 000000000..9a808e8f0 --- /dev/null +++ b/latest/cases/01048/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: One reversible reactions with two species in one compartment + and one event that assigns value to a species following a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 848, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains one reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The model contains one event that assigns values to species S1: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $1$ | $S2 = 1.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01049/l2v5/build.log b/latest/cases/01049/l2v5/build.log new file mode 100644 index 000000000..194b543c0 --- /dev/null +++ b/latest/cases/01049/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01049/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01049/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01049/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01049/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01049/l2v5/index.heta b/latest/cases/01049/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01049/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01049/l3v2/build.log b/latest/cases/01049/l3v2/build.log new file mode 100644 index 000000000..be814d019 --- /dev/null +++ b/latest/cases/01049/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01049/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01049/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01049/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01049/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01049/l3v2/index.heta b/latest/cases/01049/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01049/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01049/model-sbml-l2v5.xml b/latest/cases/01049/model-sbml-l2v5.xml new file mode 100644 index 000000000..ea1592d8d --- /dev/null +++ b/latest/cases/01049/model-sbml-l2v5.xml @@ -0,0 +1,135 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 1.89 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/01049/model-sbml-l3v2.xml b/latest/cases/01049/model-sbml-l3v2.xml new file mode 100644 index 000000000..fb7b3a8a8 --- /dev/null +++ b/latest/cases/01049/model-sbml-l3v2.xml @@ -0,0 +1,135 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 1.89 + + + + + + 1.5 + + + + + S2 + + + + + + + diff --git a/latest/cases/01049/synopsis.txt b/latest/cases/01049/synopsis.txt new file mode 100644 index 000000000..52024bcf0 --- /dev/null +++ b/latest/cases/01049/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Two reversible reactions with four species in one compartment + and one event that assigns value to two species subject to a delay. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, ReversibleReaction, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 849, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains one event that assigns values to both species S2 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $1.89$ | $S2 = 1.5$ | + | | | | $S4 = S2$ |] + +Note that the event assignments should happen simultaneously, not +sequentially; i.e., the value of S2 assigned to S4 is the value at the +point at which the event was triggered. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01050/l2v5/build.log b/latest/cases/01050/l2v5/build.log new file mode 100644 index 000000000..c3d2d011a --- /dev/null +++ b/latest/cases/01050/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01050/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01050/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01050/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01050/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01050/l2v5/index.heta b/latest/cases/01050/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01050/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01050/l3v2/build.log b/latest/cases/01050/l3v2/build.log new file mode 100644 index 000000000..c4862abe5 --- /dev/null +++ b/latest/cases/01050/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01050/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01050/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01050/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01050/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01050/l3v2/index.heta b/latest/cases/01050/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01050/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01050/model-sbml-l2v5.xml b/latest/cases/01050/model-sbml-l2v5.xml new file mode 100644 index 000000000..f896a468e --- /dev/null +++ b/latest/cases/01050/model-sbml-l2v5.xml @@ -0,0 +1,153 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 2 + + + + + + 1.5 + + + + + + + + + + S3 + 0.75 + + + + + + 2.5 + + + + + + 0.5 + + + + + + + diff --git a/latest/cases/01050/model-sbml-l3v2.xml b/latest/cases/01050/model-sbml-l3v2.xml new file mode 100644 index 000000000..9f33a553d --- /dev/null +++ b/latest/cases/01050/model-sbml-l3v2.xml @@ -0,0 +1,153 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + + + + + + + + + + + + C + + + + + k1 + S3 + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + S1 + 0.5 + + + + + + 2 + + + + + + 1.5 + + + + + + + + + + S3 + 0.75 + + + + + + 2.5 + + + + + + 0.5 + + + + + + + diff --git a/latest/cases/01050/synopsis.txt b/latest/cases/01050/synopsis.txt new file mode 100644 index 000000000..156b04dcc --- /dev/null +++ b/latest/cases/01050/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Two reversible reactions with four species in one compartment + and two events that assigns value to species subject to delays. +componentTags: Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: Amount, ReversibleReaction, EventIsPersistent +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 850, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four species +called S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ | +| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |] + +The model contains two event that assigns values to species S2 and S4 respectively: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ | + | Event2 | $S3 < 0.75$ | $-$ | $S4 = 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Initial amount of S4 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |second^-1^ | +|Value of parameter k2 |$0.15$ |second^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01051/l2v5/build.log b/latest/cases/01051/l2v5/build.log new file mode 100644 index 000000000..09ebd6570 --- /dev/null +++ b/latest/cases/01051/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01051/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01051/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01051/model-sbml-l2v5.xml"... +[error] "fast" reactions "fasterReaction" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01051/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01051/l2v5/index.heta b/latest/cases/01051/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01051/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01051/l3v2/index.heta b/latest/cases/01051/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01051/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01051/model-sbml-l2v5.xml b/latest/cases/01051/model-sbml-l2v5.xml new file mode 100644 index 000000000..615b65d67 --- /dev/null +++ b/latest/cases/01051/model-sbml-l2v5.xml @@ -0,0 +1,111 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Kf1 + A4 + + + + + + Kr1 + A2 + + + + C + + + + + + + + + + + + + + + + + + + + + + + + Kf + A1 + A2 + + + + + + Kr + A3 + + + + C + + + + + + + + diff --git a/latest/cases/01051/synopsis.txt b/latest/cases/01051/synopsis.txt new file mode 100644 index 000000000..55192adad --- /dev/null +++ b/latest/cases/01051/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Two reversible reactions in one compartment +with one reaction marked as fast. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, FastReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +Note: This test is a copy of model 870, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law fails to go negative (a requirement for the ReversibeReaction tag). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four +species called A1, A2, A3 and A4 and four parameters called Kf1, Kr1, Kf +and Kr. The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A4 <-> A2 | $(Kf1 * A4 - Kr1 * A2) * C$ | +| A1 + A2 <-> A3 | $(Kf * A1 * A2 - Kr * A3) * C$ |] +where the first reaction is marked as 'fast' and therefore should be assumed +to be operating on a time scale significantly faster than the second reaction. +Fast reactions are considered to be instantaneous relative to slow +reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of A1 |$2$ |mole | +|Initial amount of A2 |$3$ |mole | +|Initial amount of A3 |$4$ |mole | +|Initial amount of A4 |$1$ |mole | +|Value of parameter Kf1 |$1$ |second^-1^ | +|Value of parameter Kr1 |$2$ |second^-1^ | +|Value of parameter Kf |$1$ |litre mole^-1^ second^-1^ | +|Value of parameter Kr |$2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01052/l2v5/build.log b/latest/cases/01052/l2v5/build.log new file mode 100644 index 000000000..ced3c3e8e --- /dev/null +++ b/latest/cases/01052/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01052/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01052/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01052/model-sbml-l2v5.xml"... +[error] "fast" reactions "reaction1" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01052/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01052/l2v5/index.heta b/latest/cases/01052/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01052/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01052/l3v2/index.heta b/latest/cases/01052/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01052/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01052/model-sbml-l2v5.xml b/latest/cases/01052/model-sbml-l2v5.xml new file mode 100644 index 000000000..5ad1e2778 --- /dev/null +++ b/latest/cases/01052/model-sbml-l2v5.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + A4 + Kf1 + + + + -1 + A2 + Kr1 + + + + + + + + + + + + + + + + + + + + + + C + + + + + A1 + A2 + Kf + + + + -1 + A3 + Kr + + + + + + + + + + diff --git a/latest/cases/01052/synopsis.txt b/latest/cases/01052/synopsis.txt new file mode 100644 index 000000000..36cb435dc --- /dev/null +++ b/latest/cases/01052/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reversible reactions in one compartment +with one reaction marked as fast and one species a boundary. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, FastReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +Note: This test is a copy of model 872, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law fails to go negative (a requirement for the ReversibeReaction tag). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four +species called A1, A2, A3 and A4 and four parameters called Kf1, Kr1, Kf +and Kr. Species A1 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A4 <-> A2 | $(Kf1 * A4 - Kr1 * A2) * C$ | +| A1 + A2 <-> A3 | $(Kf * A1 * A2 - Kr * A3) * C$ |] +where the first reaction is marked as 'fast' and therefore should be assumed +to be operating on a time scale significantly faster than the second reaction. +Fast reactions are considered to be instantaneous relative to slow +reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of A1 |$2$ |mole | +|Initial amount of A2 |$3$ |mole | +|Initial amount of A3 |$4$ |mole | +|Initial amount of A4 |$1$ |mole | +|Value of parameter Kf1 |$1$ |second^-1^ | +|Value of parameter Kr1 |$2$ |second^-1^ | +|Value of parameter Kf |$1$ |litre mole^-1^ second^-1^ | +|Value of parameter Kr |$2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01053/l2v5/build.log b/latest/cases/01053/l2v5/build.log new file mode 100644 index 000000000..593aab88e --- /dev/null +++ b/latest/cases/01053/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01053/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01053/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01053/model-sbml-l2v5.xml"... +[error] "fast" reactions "reaction1" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01053/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01053/l2v5/index.heta b/latest/cases/01053/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01053/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01053/l3v2/index.heta b/latest/cases/01053/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01053/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01053/model-sbml-l2v5.xml b/latest/cases/01053/model-sbml-l2v5.xml new file mode 100644 index 000000000..1ba297d02 --- /dev/null +++ b/latest/cases/01053/model-sbml-l2v5.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + A4 + Kf1 + + + + -1 + A2 + Kr1 + + + + + + + + + + + + + + + + + + + + + + C + + + + + A1 + A2 + Kf + + + + -1 + A3 + Kr + + + + + + + + + + diff --git a/latest/cases/01053/synopsis.txt b/latest/cases/01053/synopsis.txt new file mode 100644 index 000000000..e5c537d2a --- /dev/null +++ b/latest/cases/01053/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Two reversible reactions in one compartment +with one reaction marked as fast and one species a boundary. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, FastReaction, BoundaryCondition +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Numeric + +Note: This test is a copy of model 873, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law fails to go negative (a requirement for the ReversibeReaction tag). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four +species called A1, A2, A3 and A4 and four parameters called Kf1, Kr1, Kf +and Kr. Species A2 is labeled as an SBML boundary species. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A4 <-> A2 | $(Kf1 * A4 - Kr1 * A2) * C$ | +| A1 + A2 <-> A3 | $(Kf * A1 * A2 - Kr * A3) * C$ |] +where the first reaction is marked as 'fast' and therefore should be assumed +to be operating on a time scale significantly faster than the second reaction. +Fast reactions are considered to be instantaneous relative to slow +reactions. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of A1 |$2$ |mole | +|Initial amount of A2 |$3$ |mole | +|Initial amount of A3 |$4$ |mole | +|Initial amount of A4 |$1$ |mole | +|Value of parameter Kf1 |$1$ |second^-1^ | +|Value of parameter Kr1 |$2$ |second^-1^ | +|Value of parameter Kf |$1$ |litre mole^-1^ second^-1^ | +|Value of parameter Kr |$2$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01054/l2v5/build.log b/latest/cases/01054/l2v5/build.log new file mode 100644 index 000000000..1ad6ef8fa --- /dev/null +++ b/latest/cases/01054/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01054/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01054/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01054/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01054/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01054/l2v5/index.heta b/latest/cases/01054/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01054/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01054/l3v2/build.log b/latest/cases/01054/l3v2/build.log new file mode 100644 index 000000000..5ee2709ed --- /dev/null +++ b/latest/cases/01054/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01054/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01054/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01054/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01054/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01054/l3v2/index.heta b/latest/cases/01054/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01054/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01054/model-sbml-l2v5.xml b/latest/cases/01054/model-sbml-l2v5.xml new file mode 100644 index 000000000..21e653380 --- /dev/null +++ b/latest/cases/01054/model-sbml-l2v5.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01054/model-sbml-l3v2.xml b/latest/cases/01054/model-sbml-l3v2.xml new file mode 100644 index 000000000..c1ce84ce2 --- /dev/null +++ b/latest/cases/01054/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01054/synopsis.txt b/latest/cases/01054/synopsis.txt new file mode 100644 index 000000000..7c6e765cc --- /dev/null +++ b/latest/cases/01054/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: One reversible reaction with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 876, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law fails to go negative (a requirement for the ReversibeReaction tag). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called kf and kr. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01055/l2v5/heta-code/output.heta b/latest/cases/01055/l2v5/heta-code/output.heta new file mode 100644 index 000000000..31ad01509 --- /dev/null +++ b/latest/cases/01055/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/01055/l2v5/index.heta b/latest/cases/01055/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01055/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01055/l2v5/json/output.json b/latest/cases/01055/l2v5/json/output.json new file mode 100644 index 000000000..9052156ec --- /dev/null +++ b/latest/cases/01055/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01055/l3v2/heta-code/output.heta b/latest/cases/01055/l3v2/heta-code/output.heta new file mode 100644 index 000000000..27d5f2f7e --- /dev/null +++ b/latest/cases/01055/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01055/l3v2/index.heta b/latest/cases/01055/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01055/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01055/l3v2/json/output.json b/latest/cases/01055/l3v2/json/output.json new file mode 100644 index 000000000..b0710415a --- /dev/null +++ b/latest/cases/01055/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/01055/model-sbml-l2v5.xml b/latest/cases/01055/model-sbml-l2v5.xml new file mode 100644 index 000000000..078e6192c --- /dev/null +++ b/latest/cases/01055/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01055/model-sbml-l3v2.xml b/latest/cases/01055/model-sbml-l3v2.xml new file mode 100644 index 000000000..6103a9ab0 --- /dev/null +++ b/latest/cases/01055/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01055/output.heta b/latest/cases/01055/output.heta new file mode 100644 index 000000000..a556b5715 --- /dev/null +++ b/latest/cases/01055/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 809, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01055/synopsis.txt b/latest/cases/01055/synopsis.txt new file mode 100644 index 000000000..5312badcd --- /dev/null +++ b/latest/cases/01055/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 809, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01056/l2v5/heta-code/output.heta b/latest/cases/01056/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0841b7293 --- /dev/null +++ b/latest/cases/01056/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/01056/l2v5/index.heta b/latest/cases/01056/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01056/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01056/l2v5/json/output.json b/latest/cases/01056/l2v5/json/output.json new file mode 100644 index 000000000..2790d6264 --- /dev/null +++ b/latest/cases/01056/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01056/l3v2/heta-code/output.heta b/latest/cases/01056/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6eb005564 --- /dev/null +++ b/latest/cases/01056/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01056/l3v2/index.heta b/latest/cases/01056/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01056/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01056/l3v2/json/output.json b/latest/cases/01056/l3v2/json/output.json new file mode 100644 index 000000000..7f864df4f --- /dev/null +++ b/latest/cases/01056/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/01056/model-sbml-l2v5.xml b/latest/cases/01056/model-sbml-l2v5.xml new file mode 100644 index 000000000..c47b17845 --- /dev/null +++ b/latest/cases/01056/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01056/model-sbml-l3v2.xml b/latest/cases/01056/model-sbml-l3v2.xml new file mode 100644 index 000000000..e256a2e83 --- /dev/null +++ b/latest/cases/01056/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01056/output.heta b/latest/cases/01056/output.heta new file mode 100644 index 000000000..75bda7080 --- /dev/null +++ b/latest/cases/01056/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 810, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01056/synopsis.txt b/latest/cases/01056/synopsis.txt new file mode 100644 index 000000000..4cc974d4b --- /dev/null +++ b/latest/cases/01056/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 810, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01057/l2v5/heta-code/output.heta b/latest/cases/01057/l2v5/heta-code/output.heta new file mode 100644 index 000000000..26177c729 --- /dev/null +++ b/latest/cases/01057/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01057/l2v5/index.heta b/latest/cases/01057/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01057/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01057/l2v5/json/output.json b/latest/cases/01057/l2v5/json/output.json new file mode 100644 index 000000000..78afdbae4 --- /dev/null +++ b/latest/cases/01057/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01057/l3v2/heta-code/output.heta b/latest/cases/01057/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f810f5ace --- /dev/null +++ b/latest/cases/01057/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01057/l3v2/index.heta b/latest/cases/01057/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01057/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01057/l3v2/json/output.json b/latest/cases/01057/l3v2/json/output.json new file mode 100644 index 000000000..24b0a1e6e --- /dev/null +++ b/latest/cases/01057/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01057/model-sbml-l2v5.xml b/latest/cases/01057/model-sbml-l2v5.xml new file mode 100644 index 000000000..6a45010b2 --- /dev/null +++ b/latest/cases/01057/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01057/model-sbml-l3v2.xml b/latest/cases/01057/model-sbml-l3v2.xml new file mode 100644 index 000000000..8e28f60e2 --- /dev/null +++ b/latest/cases/01057/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01057/output.heta b/latest/cases/01057/output.heta new file mode 100644 index 000000000..71286cf5c --- /dev/null +++ b/latest/cases/01057/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 811, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 1; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01057/synopsis.txt b/latest/cases/01057/synopsis.txt new file mode 100644 index 000000000..059f49396 --- /dev/null +++ b/latest/cases/01057/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + +Note: This test is a copy of model 811, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01058/l2v5/heta-code/output.heta b/latest/cases/01058/l2v5/heta-code/output.heta new file mode 100644 index 000000000..daaf3ce62 --- /dev/null +++ b/latest/cases/01058/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/01058/l2v5/index.heta b/latest/cases/01058/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01058/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01058/l2v5/json/output.json b/latest/cases/01058/l2v5/json/output.json new file mode 100644 index 000000000..d66c94e9f --- /dev/null +++ b/latest/cases/01058/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01058/l3v2/heta-code/output.heta b/latest/cases/01058/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ca8fae236 --- /dev/null +++ b/latest/cases/01058/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01058/l3v2/index.heta b/latest/cases/01058/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01058/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01058/l3v2/json/output.json b/latest/cases/01058/l3v2/json/output.json new file mode 100644 index 000000000..551e87166 --- /dev/null +++ b/latest/cases/01058/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/01058/model-sbml-l2v5.xml b/latest/cases/01058/model-sbml-l2v5.xml new file mode 100644 index 000000000..4435bb93f --- /dev/null +++ b/latest/cases/01058/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01058/model-sbml-l3v2.xml b/latest/cases/01058/model-sbml-l3v2.xml new file mode 100644 index 000000000..4334c855f --- /dev/null +++ b/latest/cases/01058/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01058/output.heta b/latest/cases/01058/output.heta new file mode 100644 index 000000000..77d3ef8b3 --- /dev/null +++ b/latest/cases/01058/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 812, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$0.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01058/synopsis.txt b/latest/cases/01058/synopsis.txt new file mode 100644 index 000000000..cdefe2cf8 --- /dev/null +++ b/latest/cases/01058/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 812, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$0.5$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01059/l2v5/heta-code/output.heta b/latest/cases/01059/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7046b9f74 --- /dev/null +++ b/latest/cases/01059/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/01059/l2v5/index.heta b/latest/cases/01059/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01059/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01059/l2v5/json/output.json b/latest/cases/01059/l2v5/json/output.json new file mode 100644 index 000000000..1a7caf114 --- /dev/null +++ b/latest/cases/01059/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01059/l3v2/heta-code/output.heta b/latest/cases/01059/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3c85b5062 --- /dev/null +++ b/latest/cases/01059/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01059/l3v2/index.heta b/latest/cases/01059/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01059/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01059/l3v2/json/output.json b/latest/cases/01059/l3v2/json/output.json new file mode 100644 index 000000000..cb15b6b5d --- /dev/null +++ b/latest/cases/01059/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/01059/model-sbml-l2v5.xml b/latest/cases/01059/model-sbml-l2v5.xml new file mode 100644 index 000000000..7f5517666 --- /dev/null +++ b/latest/cases/01059/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01059/model-sbml-l3v2.xml b/latest/cases/01059/model-sbml-l3v2.xml new file mode 100644 index 000000000..a6ca8055e --- /dev/null +++ b/latest/cases/01059/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01059/output.heta b/latest/cases/01059/output.heta new file mode 100644 index 000000000..40fca9ec1 --- /dev/null +++ b/latest/cases/01059/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 813, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$2.3$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01059/synopsis.txt b/latest/cases/01059/synopsis.txt new file mode 100644 index 000000000..b16cac558 --- /dev/null +++ b/latest/cases/01059/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 813, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$2.3$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01060/l2v5/heta-code/output.heta b/latest/cases/01060/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7c5bec06a --- /dev/null +++ b/latest/cases/01060/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01060/l2v5/index.heta b/latest/cases/01060/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01060/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01060/l2v5/json/output.json b/latest/cases/01060/l2v5/json/output.json new file mode 100644 index 000000000..c84577da9 --- /dev/null +++ b/latest/cases/01060/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.95" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01060/l3v2/heta-code/output.heta b/latest/cases/01060/l3v2/heta-code/output.heta new file mode 100644 index 000000000..39ad6511c --- /dev/null +++ b/latest/cases/01060/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01060/l3v2/index.heta b/latest/cases/01060/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01060/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01060/l3v2/json/output.json b/latest/cases/01060/l3v2/json/output.json new file mode 100644 index 000000000..e344aa9ef --- /dev/null +++ b/latest/cases/01060/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.95" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01060/model-sbml-l2v5.xml b/latest/cases/01060/model-sbml-l2v5.xml new file mode 100644 index 000000000..a9fe3bdd2 --- /dev/null +++ b/latest/cases/01060/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01060/model-sbml-l3v2.xml b/latest/cases/01060/model-sbml-l3v2.xml new file mode 100644 index 000000000..121af96a1 --- /dev/null +++ b/latest/cases/01060/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01060/output.heta b/latest/cases/01060/output.heta new file mode 100644 index 000000000..6ab5c1d6f --- /dev/null +++ b/latest/cases/01060/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 814, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.95$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01060/synopsis.txt b/latest/cases/01060/synopsis.txt new file mode 100644 index 000000000..97c5b73d5 --- /dev/null +++ b/latest/cases/01060/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Amount, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 814, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.95$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01061/l2v5/heta-code/output.heta b/latest/cases/01061/l2v5/heta-code/output.heta new file mode 100644 index 000000000..395bdb7c0 --- /dev/null +++ b/latest/cases/01061/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Record 'kf' { } .= 0.9; +kr @Record 'kr' { } .= 0.075; + diff --git a/latest/cases/01061/l2v5/index.heta b/latest/cases/01061/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01061/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01061/l2v5/json/output.json b/latest/cases/01061/l2v5/json/output.json new file mode 100644 index 000000000..161237fad --- /dev/null +++ b/latest/cases/01061/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "0.9" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.075" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01061/l3v2/heta-code/output.heta b/latest/cases/01061/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bb5bb4cb8 --- /dev/null +++ b/latest/cases/01061/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01061/l3v2/index.heta b/latest/cases/01061/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01061/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01061/l3v2/json/output.json b/latest/cases/01061/l3v2/json/output.json new file mode 100644 index 000000000..3791ed506 --- /dev/null +++ b/latest/cases/01061/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 0.9 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.075 + } +] \ No newline at end of file diff --git a/latest/cases/01061/model-sbml-l2v5.xml b/latest/cases/01061/model-sbml-l2v5.xml new file mode 100644 index 000000000..dfacf49a8 --- /dev/null +++ b/latest/cases/01061/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01061/model-sbml-l3v2.xml b/latest/cases/01061/model-sbml-l3v2.xml new file mode 100644 index 000000000..77126e525 --- /dev/null +++ b/latest/cases/01061/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01061/output.heta b/latest/cases/01061/output.heta new file mode 100644 index 000000000..9de3fef00 --- /dev/null +++ b/latest/cases/01061/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 815, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$0.5$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.5; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S2 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2))); + +kf @Const 'kf' { } = 0.9; +kr @Const 'kr' { } = 0.075; + diff --git a/latest/cases/01061/synopsis.txt b/latest/cases/01061/synopsis.txt new file mode 100644 index 000000000..d770e52fc --- /dev/null +++ b/latest/cases/01061/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 815, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0$ |mole litre^-1^ | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Volume of compartment C |$0.5$ |litre |] + diff --git a/latest/cases/01062/l2v5/heta-code/output.heta b/latest/cases/01062/l2v5/heta-code/output.heta new file mode 100644 index 000000000..85e767a0d --- /dev/null +++ b/latest/cases/01062/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Record 'kf' { } .= 1.1; +kr @Record 'kr' { } .= 0.09; + diff --git a/latest/cases/01062/l2v5/index.heta b/latest/cases/01062/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01062/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01062/l2v5/json/output.json b/latest/cases/01062/l2v5/json/output.json new file mode 100644 index 000000000..d850f55b0 --- /dev/null +++ b/latest/cases/01062/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "1.1" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.09" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01062/l3v2/heta-code/output.heta b/latest/cases/01062/l3v2/heta-code/output.heta new file mode 100644 index 000000000..393571d83 --- /dev/null +++ b/latest/cases/01062/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01062/l3v2/index.heta b/latest/cases/01062/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01062/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01062/l3v2/json/output.json b/latest/cases/01062/l3v2/json/output.json new file mode 100644 index 000000000..8fb56cc70 --- /dev/null +++ b/latest/cases/01062/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "2.3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 * S2 + (-1) * kr * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 1.1 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.09 + } +] \ No newline at end of file diff --git a/latest/cases/01062/model-sbml-l2v5.xml b/latest/cases/01062/model-sbml-l2v5.xml new file mode 100644 index 000000000..ecdb8e49d --- /dev/null +++ b/latest/cases/01062/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01062/model-sbml-l3v2.xml b/latest/cases/01062/model-sbml-l3v2.xml new file mode 100644 index 000000000..37d5ae0d4 --- /dev/null +++ b/latest/cases/01062/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01062/output.heta b/latest/cases/01062/output.heta new file mode 100644 index 000000000..91ee4e0b3 --- /dev/null +++ b/latest/cases/01062/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 816, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$2.3$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 2.3; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, }; +reaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3))); + +kf @Const 'kf' { } = 1.1; +kr @Const 'kr' { } = 0.09; + diff --git a/latest/cases/01062/synopsis.txt b/latest/cases/01062/synopsis.txt new file mode 100644 index 000000000..3abe5ea26 --- /dev/null +++ b/latest/cases/01062/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 816, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Volume of compartment C |$2.3$ |litre |] + diff --git a/latest/cases/01063/l2v5/heta-code/output.heta b/latest/cases/01063/l2v5/heta-code/output.heta new file mode 100644 index 000000000..941861c2b --- /dev/null +++ b/latest/cases/01063/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Record 'kf' { } .= 2.5; +kr @Record 'kr' { } .= 0.2; + diff --git a/latest/cases/01063/l2v5/index.heta b/latest/cases/01063/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01063/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01063/l2v5/json/output.json b/latest/cases/01063/l2v5/json/output.json new file mode 100644 index 000000000..bcd500204 --- /dev/null +++ b/latest/cases/01063/l2v5/json/output.json @@ -0,0 +1,108 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.95" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Record", + "id": "kf", + "title": "kf", + "assignments": { + "start_": "2.5" + } + }, + { + "class": "Record", + "id": "kr", + "title": "kr", + "assignments": { + "start_": "0.2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01063/l3v2/heta-code/output.heta b/latest/cases/01063/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1404b3325 --- /dev/null +++ b/latest/cases/01063/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01063/l3v2/index.heta b/latest/cases/01063/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01063/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01063/l3v2/json/output.json b/latest/cases/01063/l3v2/json/output.json new file mode 100644 index 000000000..8fc0da485 --- /dev/null +++ b/latest/cases/01063/l3v2/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t", + "units": "second" + }, + { + "class": "Compartment", + "id": "C", + "title": "C", + "units": "litre", + "assignments": { + "start_": "0.95" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "title": "S1", + "units": "mole/litre", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "title": "S2", + "units": "mole/litre", + "assignments": { + "start_": "0.5" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "title": "S3", + "units": "mole/litre", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "reaction1", + "title": "reaction1", + "assignments": { + "ode_": "(-(C * (kf * S1 + (-1) * kr * S2 * S3)))" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + }, + { + "target": "S2", + "stoichiometry": -1 + }, + { + "target": "S3", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "kf", + "title": "kf", + "num": 2.5 + }, + { + "class": "Const", + "id": "kr", + "title": "kr", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01063/model-sbml-l2v5.xml b/latest/cases/01063/model-sbml-l2v5.xml new file mode 100644 index 000000000..1d8c22f0b --- /dev/null +++ b/latest/cases/01063/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01063/model-sbml-l3v2.xml b/latest/cases/01063/model-sbml-l3v2.xml new file mode 100644 index 000000000..e6469b3e3 --- /dev/null +++ b/latest/cases/01063/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01063/output.heta b/latest/cases/01063/output.heta new file mode 100644 index 000000000..310c31e2a --- /dev/null +++ b/latest/cases/01063/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 817, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.95$ |litre |] + +*/ + + + +t @TimeScale { units: second, }; + +C @Compartment 'C' { units: litre, boundary: true, } .= 0.95; + +S1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1; +S2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5; +S3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0; + +reaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, }; +reaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3))); + +kf @Const 'kf' { } = 2.5; +kr @Const 'kr' { } = 0.2; + diff --git a/latest/cases/01063/synopsis.txt b/latest/cases/01063/synopsis.txt new file mode 100644 index 000000000..ae56df40f --- /dev/null +++ b/latest/cases/01063/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter +testTags: Concentration, ReversibleReaction, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric + + Note: This test is a copy of model 817, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and two parameters called kf and kr. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial concentration of S1 |$1.0$ |mole litre^-1^ | +|Initial concentration of S2 |$0.5$ |mole litre^-1^ | +|Initial concentration of S3 |$0$ |mole litre^-1^ | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Volume of compartment C |$0.95$ |litre |] + diff --git a/latest/cases/01064/l2v5/index.heta b/latest/cases/01064/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01064/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01064/l3v2/build.log b/latest/cases/01064/l3v2/build.log new file mode 100644 index 000000000..bc4575714 --- /dev/null +++ b/latest/cases/01064/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01064/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01064/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01064/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 87 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01064/l3v2/index.heta b/latest/cases/01064/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01064/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01064/model-sbml-l3v2.xml b/latest/cases/01064/model-sbml-l3v2.xml new file mode 100644 index 000000000..5fce3b700 --- /dev/null +++ b/latest/cases/01064/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + + diff --git a/latest/cases/01064/synopsis.txt b/latest/cases/01064/synopsis.txt new file mode 100644 index 000000000..c72aeacbe --- /dev/null +++ b/latest/cases/01064/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, ReversibleReaction, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 1029, itself a copy of 829 with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + (4 * p1)S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01065/l2v5/index.heta b/latest/cases/01065/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01065/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01065/l3v2/build.log b/latest/cases/01065/l3v2/build.log new file mode 100644 index 000000000..e7f2c54dd --- /dev/null +++ b/latest/cases/01065/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01065/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01065/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01065/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01065/l3v2/index.heta b/latest/cases/01065/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01065/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01065/model-sbml-l3v2.xml b/latest/cases/01065/model-sbml-l3v2.xml new file mode 100644 index 000000000..47ef54d0a --- /dev/null +++ b/latest/cases/01065/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/01065/synopsis.txt b/latest/cases/01065/synopsis.txt new file mode 100644 index 000000000..676d58da1 --- /dev/null +++ b/latest/cases/01065/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic single forward reaction involving two species and a + stoichiometryMath element. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +Note: This test is the L3 version of model 68. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and p1. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (2 * p1)S2 | $k1 * S1 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Value of parameter p1 |$ 1$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/01066/l2v5/index.heta b/latest/cases/01066/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01066/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01066/l3v2/build.log b/latest/cases/01066/l3v2/build.log new file mode 100644 index 000000000..20cc4675a --- /dev/null +++ b/latest/cases/01066/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01066/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01066/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01066/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01066/l3v2/index.heta b/latest/cases/01066/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01066/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01066/model-sbml-l3v2.xml b/latest/cases/01066/model-sbml-l3v2.xml new file mode 100644 index 000000000..f3237172c --- /dev/null +++ b/latest/cases/01066/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/01066/synopsis.txt b/latest/cases/01066/synopsis.txt new file mode 100644 index 000000000..2bb1d5140 --- /dev/null +++ b/latest/cases/01066/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic reactions with three species in a compartment + involving a stoichiometryMath element. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 69. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and three parameters named k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| (2 * p1)S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$ 1.7 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter p1 |$ 1$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01067/l2v5/index.heta b/latest/cases/01067/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01067/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01067/l3v2/build.log b/latest/cases/01067/l3v2/build.log new file mode 100644 index 000000000..84523b555 --- /dev/null +++ b/latest/cases/01067/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01067/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01067/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01067/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[error] generatedId_1 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01067/l3v2/index.heta b/latest/cases/01067/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01067/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01067/model-sbml-l3v2.xml b/latest/cases/01067/model-sbml-l3v2.xml new file mode 100644 index 000000000..ee4e7c824 --- /dev/null +++ b/latest/cases/01067/model-sbml-l3v2.xml @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/01067/synopsis.txt b/latest/cases/01067/synopsis.txt new file mode 100644 index 000000000..d2ee2c5fa --- /dev/null +++ b/latest/cases/01067/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Basic reactions with three species in a compartment + involving a stoichiometryMath element. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 70. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and three parameters named k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> (2 * p1)S1 + (p1 / 0.5)S2 | $k2 * S3 * compartment$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter p1 |$ 1$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |rlitre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01068/l2v5/index.heta b/latest/cases/01068/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01068/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01068/l3v2/build.log b/latest/cases/01068/l3v2/build.log new file mode 100644 index 000000000..3defc965b --- /dev/null +++ b/latest/cases/01068/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01068/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01068/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01068/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01068/l3v2/index.heta b/latest/cases/01068/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01068/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01068/model-sbml-l3v2.xml b/latest/cases/01068/model-sbml-l3v2.xml new file mode 100644 index 000000000..e1b12ebbf --- /dev/null +++ b/latest/cases/01068/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + 2 + p1 + + + + + + + + + + + + + + + + + compartment + k1 + S1 + + + + + + + diff --git a/latest/cases/01068/synopsis.txt b/latest/cases/01068/synopsis.txt new file mode 100644 index 000000000..082779514 --- /dev/null +++ b/latest/cases/01068/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic single forward reaction involving two species and a + stoichiometryMath element that uses a functionDefinition. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 129. + +The model contains one compartment called "compartment". There are two +species named S1 and S2 and two parameters named k1 and p1. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> multiply(2, p1)S2 | $k1 * S1 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 0$ |mole | +|Value of parameter k1 |$ 1.5$ |second^-1^ | +|Value of parameter p1 |$ 1$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01069/l2v5/index.heta b/latest/cases/01069/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01069/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01069/l3v2/build.log b/latest/cases/01069/l3v2/build.log new file mode 100644 index 000000000..2900a2c07 --- /dev/null +++ b/latest/cases/01069/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01069/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01069/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01069/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01069/l3v2/index.heta b/latest/cases/01069/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01069/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01069/model-sbml-l3v2.xml b/latest/cases/01069/model-sbml-l3v2.xml new file mode 100644 index 000000000..0fc5eb999 --- /dev/null +++ b/latest/cases/01069/model-sbml-l3v2.xml @@ -0,0 +1,106 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + multiply + 2 + p1 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/01069/synopsis.txt b/latest/cases/01069/synopsis.txt new file mode 100644 index 000000000..109b9c684 --- /dev/null +++ b/latest/cases/01069/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic reactions with three species in a compartment + involving a stoichiometryMath element that uses a functionDefinition. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 130. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and three parameters named k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| multiply(2, p1)S3 -> S1 + S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$ 1.7 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter p1 |$ 1$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01070/l2v5/index.heta b/latest/cases/01070/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01070/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01070/l3v2/build.log b/latest/cases/01070/l3v2/build.log new file mode 100644 index 000000000..4d1b37cff --- /dev/null +++ b/latest/cases/01070/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01070/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01070/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01070/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[error] generatedId_1 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01070/l3v2/index.heta b/latest/cases/01070/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01070/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01070/model-sbml-l3v2.xml b/latest/cases/01070/model-sbml-l3v2.xml new file mode 100644 index 000000000..9f15ed129 --- /dev/null +++ b/latest/cases/01070/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + multiply + p1 + 2 + + + + + + + + + + + + + + + + + + compartment + k1 + S1 + S2 + + + + + + + + + + + + + + + + + compartment + k2 + S3 + + + + + + + diff --git a/latest/cases/01070/synopsis.txt b/latest/cases/01070/synopsis.txt new file mode 100644 index 000000000..9248bed5f --- /dev/null +++ b/latest/cases/01070/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic reactions with three species in a compartment + involving a stoichiometryMath element that uses a functionDefinition. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, FunctionDefinition +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 131. + +The model contains one compartment called "compartment". There are three +species named S1, S2 and S3 and three parameters named k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ | +| S3 -> (2 * p1)S1 + multiply(p1, 1 / 0.5)S2 | $k2 * S3 * compartment$ |] + + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$ 1.7 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.3$ |second^-1^ | +|Value of parameter p1 |$ 1$ |dimensionless | +|Volume of compartment "compartment" |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01071/l2v5/index.heta b/latest/cases/01071/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01071/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01071/l3v2/build.log b/latest/cases/01071/l3v2/build.log new file mode 100644 index 000000000..58562cd44 --- /dev/null +++ b/latest/cases/01071/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01071/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01071/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01071/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 89 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01071/l3v2/index.heta b/latest/cases/01071/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01071/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01071/model-sbml-l3v2.xml b/latest/cases/01071/model-sbml-l3v2.xml new file mode 100644 index 000000000..c97ff4449 --- /dev/null +++ b/latest/cases/01071/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01071/synopsis.txt b/latest/cases/01071/synopsis.txt new file mode 100644 index 000000000..a8373fc94 --- /dev/null +++ b/latest/cases/01071/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 388. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (2 * p1) S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01072/l2v5/index.heta b/latest/cases/01072/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01072/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01072/l3v2/build.log b/latest/cases/01072/l3v2/build.log new file mode 100644 index 000000000..996365323 --- /dev/null +++ b/latest/cases/01072/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01072/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01072/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01072/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 91 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01072/l3v2/index.heta b/latest/cases/01072/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01072/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01072/model-sbml-l3v2.xml b/latest/cases/01072/model-sbml-l3v2.xml new file mode 100644 index 000000000..200932ba9 --- /dev/null +++ b/latest/cases/01072/model-sbml-l3v2.xml @@ -0,0 +1,129 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + + 1 5000 + + + + + + + + + + S3 + 1 4000 + + + + + + + 1 10000 + + + + + + + diff --git a/latest/cases/01072/synopsis.txt b/latest/cases/01072/synopsis.txt new file mode 100644 index 000000000..0927a7962 --- /dev/null +++ b/latest/cases/01072/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 391. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p1)S3 + S4 | $k1 * S1 * S2 * C$ | +| 2S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign values to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \x 10^-4$ |] + | Event2 | $S3 > 2.5 \x 10^-4$ | $-$ | $S4 -> 1 \x 10^-4$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-4$ |mole | +|Initial amount of S2 |$1.0 \x 10^-4$ |mole | +|Initial amount of S3 |$2.0 \x 10^-4$ |mole | +|Initial amount of S4 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$ 0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01073/l2v5/index.heta b/latest/cases/01073/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01073/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01073/l3v2/build.log b/latest/cases/01073/l3v2/build.log new file mode 100644 index 000000000..f94a75672 --- /dev/null +++ b/latest/cases/01073/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01073/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01073/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01073/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 89 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01073/l3v2/index.heta b/latest/cases/01073/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01073/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01073/model-sbml-l3v2.xml b/latest/cases/01073/model-sbml-l3v2.xml new file mode 100644 index 000000000..4be6d34c3 --- /dev/null +++ b/latest/cases/01073/model-sbml-l3v2.xml @@ -0,0 +1,112 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + + 1.75 + + + + + 1 + + + + + + + diff --git a/latest/cases/01073/synopsis.txt b/latest/cases/01073/synopsis.txt new file mode 100644 index 000000000..a56eb5321 --- /dev/null +++ b/latest/cases/01073/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, EventNoDelay +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 394. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.75$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$ 0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01074/l2v5/index.heta b/latest/cases/01074/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01074/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01074/l3v2/build.log b/latest/cases/01074/l3v2/build.log new file mode 100644 index 000000000..c80262dfb --- /dev/null +++ b/latest/cases/01074/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01074/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01074/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01074/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01074/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01074/l3v2/index.heta b/latest/cases/01074/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01074/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01074/model-sbml-l3v2.xml b/latest/cases/01074/model-sbml-l3v2.xml new file mode 100644 index 000000000..08542842f --- /dev/null +++ b/latest/cases/01074/model-sbml-l3v2.xml @@ -0,0 +1,112 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 0.95 + + + + + + 1 + + + + + + + diff --git a/latest/cases/01074/synopsis.txt b/latest/cases/01074/synopsis.txt new file mode 100644 index 000000000..858e288cc --- /dev/null +++ b/latest/cases/01074/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to a species, subject to a delay. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 445. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (2 * p1) S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $0.95$ | $S2 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01075/l2v5/index.heta b/latest/cases/01075/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01075/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01075/l3v2/build.log b/latest/cases/01075/l3v2/build.log new file mode 100644 index 000000000..145488bab --- /dev/null +++ b/latest/cases/01075/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01075/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01075/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01075/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01075/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01075/l3v2/index.heta b/latest/cases/01075/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01075/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01075/model-sbml-l3v2.xml b/latest/cases/01075/model-sbml-l3v2.xml new file mode 100644 index 000000000..3a4bae248 --- /dev/null +++ b/latest/cases/01075/model-sbml-l3v2.xml @@ -0,0 +1,139 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + + C + k2 + S3 + S4 + + + + + + + + + + + + S4 + S2 + + + + + + 0.5 + + + + + + 1 5 + + + + + + + + + + S3 + 1 4 + + + + + + 1.5 + + + + + + 1 10 + + + + + + + diff --git a/latest/cases/01075/synopsis.txt b/latest/cases/01075/synopsis.txt new file mode 100644 index 000000000..b999be0a5 --- /dev/null +++ b/latest/cases/01075/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment + and two events that assign value to a species, subject to a delay. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 448. + +The model contains one compartment called C. There are four species called +S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p1)S3 + S4 | $k1 * S1 * S2 * C$ | +| 2S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |] + +The model contains two events that assign value to species S1 and S4: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S4 > S2$ | $0.5$ | $S1 -> 2 \x 10^-1$ |] + | Event2 | $S3 > 2.5 \x 10^-1$ | $1.5$ | $S4 -> 1 \x 10^-1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$1.0 \x 10^-1$ |mole | +|Initial amount of S3 |$2.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^1$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01076/l2v5/index.heta b/latest/cases/01076/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01076/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01076/l3v2/build.log b/latest/cases/01076/l3v2/build.log new file mode 100644 index 000000000..7b775832e --- /dev/null +++ b/latest/cases/01076/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01076/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01076/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01076/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01076/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01076/l3v2/index.heta b/latest/cases/01076/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01076/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01076/model-sbml-l3v2.xml b/latest/cases/01076/model-sbml-l3v2.xml new file mode 100644 index 000000000..03ec3a874 --- /dev/null +++ b/latest/cases/01076/model-sbml-l3v2.xml @@ -0,0 +1,117 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.75 + + + + + + 2.2 + + + + + + 1.75 + + + + + 1 + + + + + + + diff --git a/latest/cases/01076/synopsis.txt b/latest/cases/01076/synopsis.txt new file mode 100644 index 000000000..ac2010104 --- /dev/null +++ b/latest/cases/01076/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Basic two reactions with three species in one compartment + and one event that assigns value to two species, subject to a delay. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, EventWithDelay +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 451. + +The model contains one compartment called C. There are three species +called S1, S2 and S3 and two parameters called k1 and k2. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one event that assigns values to both species S1 and S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.75$ | $2.2$ | $S2 = 1.75$ | + | | | | $S1 = 1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.0$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01077/l2v5/index.heta b/latest/cases/01077/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01077/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01077/l3v2/build.log b/latest/cases/01077/l3v2/build.log new file mode 100644 index 000000000..48e2d3057 --- /dev/null +++ b/latest/cases/01077/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01077/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01077/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01077/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01077/l3v2/index.heta b/latest/cases/01077/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01077/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01077/model-sbml-l3v2.xml b/latest/cases/01077/model-sbml-l3v2.xml new file mode 100644 index 000000000..7ff591cfa --- /dev/null +++ b/latest/cases/01077/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/01077/synopsis.txt b/latest/cases/01077/synopsis.txt new file mode 100644 index 000000000..56a06b427 --- /dev/null +++ b/latest/cases/01077/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +Note: This test is the L3 version of model 516. + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, k2 and p1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/01078/l2v5/index.heta b/latest/cases/01078/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01078/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01078/l3v2/build.log b/latest/cases/01078/l3v2/build.log new file mode 100644 index 000000000..082658ae9 --- /dev/null +++ b/latest/cases/01078/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01078/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01078/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01078/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01078/l3v2/index.heta b/latest/cases/01078/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01078/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01078/model-sbml-l3v2.xml b/latest/cases/01078/model-sbml-l3v2.xml new file mode 100644 index 000000000..fd76c6b8f --- /dev/null +++ b/latest/cases/01078/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/01078/synopsis.txt b/latest/cases/01078/synopsis.txt new file mode 100644 index 000000000..53f65f478 --- /dev/null +++ b/latest/cases/01078/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +Note: This test is the L3 version of model 517. + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, k2 and p1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$5$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/01079/l2v5/index.heta b/latest/cases/01079/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01079/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01079/l3v2/build.log b/latest/cases/01079/l3v2/build.log new file mode 100644 index 000000000..b4b10cd4c --- /dev/null +++ b/latest/cases/01079/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01079/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01079/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01079/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01079/l3v2/index.heta b/latest/cases/01079/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01079/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01079/model-sbml-l3v2.xml b/latest/cases/01079/model-sbml-l3v2.xml new file mode 100644 index 000000000..df03d6544 --- /dev/null +++ b/latest/cases/01079/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + S2 + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/01079/synopsis.txt b/latest/cases/01079/synopsis.txt new file mode 100644 index 000000000..0439bed10 --- /dev/null +++ b/latest/cases/01079/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one +compartment using initialAssignment to set the initial value of one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +Note: This test is the L3 version of model 518. + +The model contains one compartment called C. There are two +species called S1 and S2 and three parameters called k1, k2 and p1. The model contains +one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $C * k2 * S$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $k1 * S2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.125$ |mole | +|Initial amount of S2 |$1.5$ |mole | +|Value of parameter k1 |$0.75$ |dimensionless | +|Value of parameter k2 |$5$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/01080/l2v5/index.heta b/latest/cases/01080/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01080/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01080/l3v2/build.log b/latest/cases/01080/l3v2/build.log new file mode 100644 index 000000000..f41e540ce --- /dev/null +++ b/latest/cases/01080/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01080/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01080/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01080/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 89 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01080/l3v2/index.heta b/latest/cases/01080/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01080/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01080/model-sbml-l3v2.xml b/latest/cases/01080/model-sbml-l3v2.xml new file mode 100644 index 000000000..a00643e60 --- /dev/null +++ b/latest/cases/01080/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/01080/synopsis.txt b/latest/cases/01080/synopsis.txt new file mode 100644 index 000000000..bc254fc43 --- /dev/null +++ b/latest/cases/01080/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 519. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p2)S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +inconsistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.0 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-3$ |mole | +|Value of parameter p2 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/01081/l2v5/index.heta b/latest/cases/01081/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01081/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01081/l3v2/build.log b/latest/cases/01081/l3v2/build.log new file mode 100644 index 000000000..382608e0a --- /dev/null +++ b/latest/cases/01081/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01081/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01081/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01081/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 89 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01081/l3v2/index.heta b/latest/cases/01081/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01081/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01081/model-sbml-l3v2.xml b/latest/cases/01081/model-sbml-l3v2.xml new file mode 100644 index 000000000..6b1363b9a --- /dev/null +++ b/latest/cases/01081/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/01081/synopsis.txt b/latest/cases/01081/synopsis.txt new file mode 100644 index 000000000..3082e1f0c --- /dev/null +++ b/latest/cases/01081/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 520. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p2)S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this case the initial value declared for species S1 is +consistent with the value returned by the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$0.25 \x 10^-4$ |mole | +|Initial amount of S2 |$2.0 \x 10^-4$ |mole | +|Initial amount of S3 |$1.0 \x 10^-4$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-5$ |mole | +|Value of parameter p2 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/01082/l2v5/index.heta b/latest/cases/01082/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01082/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01082/l3v2/build.log b/latest/cases/01082/l3v2/build.log new file mode 100644 index 000000000..ee14e65a9 --- /dev/null +++ b/latest/cases/01082/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01082/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01082/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01082/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 89 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01082/l3v2/index.heta b/latest/cases/01082/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01082/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01082/model-sbml-l3v2.xml b/latest/cases/01082/model-sbml-l3v2.xml new file mode 100644 index 000000000..a10baea26 --- /dev/null +++ b/latest/cases/01082/model-sbml-l3v2.xml @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/01082/synopsis.txt b/latest/cases/01082/synopsis.txt new file mode 100644 index 000000000..a07213650 --- /dev/null +++ b/latest/cases/01082/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Basic two reactions with three species in a compartment using +initialAssignment to set the initial value of one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 521. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The model contains +two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> (4 * p2)S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 * 2$ |] + +Note: SBML's InitialAssignment construct override any declared initial +values. In this model, the initial value for the species S1 has not been +explicitly declared and must be calculated using the InitialAssignment. + +The initial conditions are as follows: + +[{width 30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$undeclared$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$1.25 \x 10^-2$ |mole | +|Value of parameter p2 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) they must be treated as concentrations where they appear in +expressions. + diff --git a/latest/cases/01083/l2v5/index.heta b/latest/cases/01083/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01083/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01083/l3v2/build.log b/latest/cases/01083/l3v2/build.log new file mode 100644 index 000000000..04687967e --- /dev/null +++ b/latest/cases/01083/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01083/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01083/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01083/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01083/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01083/l3v2/index.heta b/latest/cases/01083/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01083/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01083/model-sbml-l3v2.xml b/latest/cases/01083/model-sbml-l3v2.xml new file mode 100644 index 000000000..c4e6eae35 --- /dev/null +++ b/latest/cases/01083/model-sbml-l3v2.xml @@ -0,0 +1,112 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/01083/synopsis.txt b/latest/cases/01083/synopsis.txt new file mode 100644 index 000000000..81d96c1ca --- /dev/null +++ b/latest/cases/01083/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 561. + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and four parameters called k1, k2, k3 and p1. +Species X0 is labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| X0 -> (4 * p1)T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$1$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01084/l2v5/index.heta b/latest/cases/01084/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01084/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01084/l3v2/build.log b/latest/cases/01084/l3v2/build.log new file mode 100644 index 000000000..f325650d4 --- /dev/null +++ b/latest/cases/01084/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01084/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01084/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01084/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01084/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01084/l3v2/index.heta b/latest/cases/01084/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01084/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01084/model-sbml-l3v2.xml b/latest/cases/01084/model-sbml-l3v2.xml new file mode 100644 index 000000000..7f3be8411 --- /dev/null +++ b/latest/cases/01084/model-sbml-l3v2.xml @@ -0,0 +1,112 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + k3 + 1 + + S1 + + + + -1 + T + + + + + + + + + + + + + + + + + + C + k1 + X0 + + + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/01084/synopsis.txt b/latest/cases/01084/synopsis.txt new file mode 100644 index 000000000..1a3f035d6 --- /dev/null +++ b/latest/cases/01084/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Algebraic rule used to determine rate of species change. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 562. + +The model contains one compartment called C. There are four +species called X0, X1, T and S1 and four parameters called k1, k2, k3 and p1. +Species X0 is labeled as an SBML boundary species. The model +contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| (4 * p1)X0 -> T | $C * k1 * X0$ | +| T -> X1 | $C * k2 * S1$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $(1 + k3) * S1 - T$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of X0 |$0.5$ |mole | +|Initial amount of X1 |$0$ |mole | +|Initial amount of T |$0$ |mole | +|Initial amount of S1 |$0$ |mole | +|Value of parameter k1 |$0.1$ |second^-1^ | +|Value of parameter k2 |$0.375$ |second^-1^ | +|Value of parameter k3 |$2.5$ |dimensionless | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01085/l2v5/index.heta b/latest/cases/01085/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01085/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01085/l3v2/build.log b/latest/cases/01085/l3v2/build.log new file mode 100644 index 000000000..2f85f3e46 --- /dev/null +++ b/latest/cases/01085/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01085/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01085/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01085/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01085/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01085/l3v2/index.heta b/latest/cases/01085/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01085/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01085/model-sbml-l3v2.xml b/latest/cases/01085/model-sbml-l3v2.xml new file mode 100644 index 000000000..98fd1bfe7 --- /dev/null +++ b/latest/cases/01085/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/01085/synopsis.txt b/latest/cases/01085/synopsis.txt new file mode 100644 index 000000000..bd5fec999 --- /dev/null +++ b/latest/cases/01085/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 563. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +Species S3 is labeled as an SBML boundary species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-3$ |mole | +|Initial amount of S2 |$2.0 \x 10^-3$ |mole | +|Initial amount of S3 |$1.0 \x 10^-3$ |mole | +|Initial amount of S4 |$1.0 \x 10^-3$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01086/l2v5/index.heta b/latest/cases/01086/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01086/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01086/l3v2/build.log b/latest/cases/01086/l3v2/build.log new file mode 100644 index 000000000..a52ae457c --- /dev/null +++ b/latest/cases/01086/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01086/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01086/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01086/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01086/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01086/l3v2/index.heta b/latest/cases/01086/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01086/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01086/model-sbml-l3v2.xml b/latest/cases/01086/model-sbml-l3v2.xml new file mode 100644 index 000000000..dc6eb38ef --- /dev/null +++ b/latest/cases/01086/model-sbml-l3v2.xml @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + S4 + + + -1 + S1 + + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/01086/synopsis.txt b/latest/cases/01086/synopsis.txt new file mode 100644 index 000000000..b83edf788 --- /dev/null +++ b/latest/cases/01086/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Basic two reactions with four species in one compartment with +an algebraic rule used to determine rate of change of one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, AlgebraicRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 564. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. +Species S3 is labeled as an SBML boundary species. The model +contains two reactions defined as: + + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| (4 * p1)S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Algebraic | n/a | $S4 - S1$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$2.0 \x 10^-1$ |mole | +|Initial amount of S3 |$1.0 \x 10^-1$ |mole | +|Initial amount of S4 |$1.0 \x 10^-1$ |mole | +|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01087/l2v5/index.heta b/latest/cases/01087/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01087/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01087/l3v2/build.log b/latest/cases/01087/l3v2/build.log new file mode 100644 index 000000000..ee2955764 --- /dev/null +++ b/latest/cases/01087/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01087/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01087/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01087/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 87 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01087/l3v2/index.heta b/latest/cases/01087/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01087/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01087/model-sbml-l3v2.xml b/latest/cases/01087/model-sbml-l3v2.xml new file mode 100644 index 000000000..bef79c61d --- /dev/null +++ b/latest/cases/01087/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + k1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S1 + + + + + + + diff --git a/latest/cases/01087/synopsis.txt b/latest/cases/01087/synopsis.txt new file mode 100644 index 000000000..0cbf2be0c --- /dev/null +++ b/latest/cases/01087/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Basic single forward reaction with three species in one +compartment using an assignmentRule to vary one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 609. + +The model contains one compartment called C. There are three +species called S1, S2 and S3 and three parameters called k1, k2 and p1. The model +contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $C * k2 * S$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S3 | $1 * S2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-4$ |mole | +|Initial amount of S2 |$1.5 \x 10^-4$ |mole | +|Initial amount of S3 |$ 1$ |mole | +|Value of parameter k1 |$ 0.75$ |dimensionless | +|Value of parameter k2 |$ 50$ |second^-1^ | +|Value of parameter p1 |$ 0.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01088/l2v5/index.heta b/latest/cases/01088/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01088/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01088/l3v2/build.log b/latest/cases/01088/l3v2/build.log new file mode 100644 index 000000000..0bb3ddd7d --- /dev/null +++ b/latest/cases/01088/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01088/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01088/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01088/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 90 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01088/l3v2/index.heta b/latest/cases/01088/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01088/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01088/model-sbml-l3v2.xml b/latest/cases/01088/model-sbml-l3v2.xml new file mode 100644 index 000000000..54333a5e9 --- /dev/null +++ b/latest/cases/01088/model-sbml-l3v2.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + k3 + S2 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/01088/synopsis.txt b/latest/cases/01088/synopsis.txt new file mode 100644 index 000000000..7cff89231 --- /dev/null +++ b/latest/cases/01088/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule to vary one species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, AssignmentRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 610. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $3 * S2$ |] + +Note that in this case the initial value of species S4 has not been declared and must be +calculated using the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5 |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 1.5 \x 10^4$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$ 0.5$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01089/l2v5/index.heta b/latest/cases/01089/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01089/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01089/l3v2/build.log b/latest/cases/01089/l3v2/build.log new file mode 100644 index 000000000..44d4c32d6 --- /dev/null +++ b/latest/cases/01089/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01089/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01089/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01089/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 90 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01089/l3v2/index.heta b/latest/cases/01089/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01089/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01089/model-sbml-l3v2.xml b/latest/cases/01089/model-sbml-l3v2.xml new file mode 100644 index 000000000..97b0a8856 --- /dev/null +++ b/latest/cases/01089/model-sbml-l3v2.xml @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + 1 100 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/01089/synopsis.txt b/latest/cases/01089/synopsis.txt new file mode 100644 index 000000000..ccdffc82e --- /dev/null +++ b/latest/cases/01089/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, RateRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 725. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| (4 * p1) S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1 10^-2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-2$ |mole | +|Initial amount of S2 |$2.0 \x 10^-2$ |mole | +|Initial amount of S3 |$1.5 \x 10^-2$ |mole | +|Initial amount of S4 |$ 1 \x 10^-2$ |mole | +|Value of parameter k1 |$0.75 \x 10^2$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.25 \x 10^-1$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01090/l2v5/index.heta b/latest/cases/01090/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01090/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01090/l3v2/build.log b/latest/cases/01090/l3v2/build.log new file mode 100644 index 000000000..2e613e8be --- /dev/null +++ b/latest/cases/01090/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01090/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01090/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01090/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 90 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01090/l3v2/index.heta b/latest/cases/01090/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01090/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01090/model-sbml-l3v2.xml b/latest/cases/01090/model-sbml-l3v2.xml new file mode 100644 index 000000000..ba5a96840 --- /dev/null +++ b/latest/cases/01090/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/01090/synopsis.txt b/latest/cases/01090/synopsis.txt new file mode 100644 index 000000000..bd91db173 --- /dev/null +++ b/latest/cases/01090/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, RateRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 726. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01091/l2v5/index.heta b/latest/cases/01091/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01091/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01091/l3v2/build.log b/latest/cases/01091/l3v2/build.log new file mode 100644 index 000000000..008df3fa5 --- /dev/null +++ b/latest/cases/01091/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01091/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01091/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01091/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 90 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01091/l3v2/index.heta b/latest/cases/01091/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01091/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01091/model-sbml-l3v2.xml b/latest/cases/01091/model-sbml-l3v2.xml new file mode 100644 index 000000000..8de5e36a9 --- /dev/null +++ b/latest/cases/01091/model-sbml-l3v2.xml @@ -0,0 +1,118 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + multiply + k2 + 1 250000 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/01091/synopsis.txt b/latest/cases/01091/synopsis.txt new file mode 100644 index 000000000..a73aef7c0 --- /dev/null +++ b/latest/cases/01091/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Two reactions and a rate rule that applies a functionDefinition + with four species in a compartment. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 727. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $multiply(k2, 4 \x 10^-6$ |] + +The model contains one functionDefinition defined as: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | multiply | x, y | $x * y$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S2 |$ 2.0 \x 10^-6$ |mole | +|Initial amount of S3 |$ 1.5 \x 10^-6$ |mole | +|Initial amount of S4 |$ 1 \x 10^-7$ |mole | +|Value of parameter k1 |$ 0.75 \x 10^6$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01092/l2v5/index.heta b/latest/cases/01092/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01092/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01092/l3v2/build.log b/latest/cases/01092/l3v2/build.log new file mode 100644 index 000000000..abddd0aa4 --- /dev/null +++ b/latest/cases/01092/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01092/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01092/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01092/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 91 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01092/l3v2/index.heta b/latest/cases/01092/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01092/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01092/model-sbml-l3v2.xml b/latest/cases/01092/model-sbml-l3v2.xml new file mode 100644 index 000000000..b80020dc4 --- /dev/null +++ b/latest/cases/01092/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + k3 + S1 + + + + + + + + + + k2 + S3 + + + + -1 + k1 + S1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + diff --git a/latest/cases/01092/synopsis.txt b/latest/cases/01092/synopsis.txt new file mode 100644 index 000000000..b712d32ce --- /dev/null +++ b/latest/cases/01092/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Two reactions with four species in one +compartment using an assignmentRule and a rateRule to vary species. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 728. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S and four parameters called k1, k2, k3 and p1. +The model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| (4 * p1)S1 -> S3 | $k1 * S1 * C$ | +| S3 -> S1 | $k2 * S3 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Assignment | S4 | $k3 * S1$ | + | Rate | S2 | $k2 * S3-k1 * S1$ |] + +Note that in this case the initial value of species S4 is not explicitly +declared and must be calculated by the assignmentRule. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1 \x 10^-5$ |mole | +|Initial amount of S2 |$ 1.5 \x 10^-5$ |mole | +|Initial amount of S3 |$ 1 \x 10^-5$ |mole | +|Initial amount of S4 |$ undeclared$ |mole | +|Value of parameter k1 |$ 0.015$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter k3 |$ 1.5$ |dimensionless | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01093/l2v5/index.heta b/latest/cases/01093/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01093/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01093/l3v2/build.log b/latest/cases/01093/l3v2/build.log new file mode 100644 index 000000000..ca1f658e3 --- /dev/null +++ b/latest/cases/01093/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01093/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01093/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01093/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 91 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01093/l3v2/index.heta b/latest/cases/01093/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01093/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01093/model-sbml-l3v2.xml b/latest/cases/01093/model-sbml-l3v2.xml new file mode 100644 index 000000000..71a93ae63 --- /dev/null +++ b/latest/cases/01093/model-sbml-l3v2.xml @@ -0,0 +1,98 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + 4 + p2 + + + + + + + + + + k2 + S4 + + + + + + + + -1 + k2 + S4 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + diff --git a/latest/cases/01093/synopsis.txt b/latest/cases/01093/synopsis.txt new file mode 100644 index 000000000..dbe6563a9 --- /dev/null +++ b/latest/cases/01093/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, RateRule +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 729. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and four parameters called k1, k2, p1 and p2. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p2)S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k2 * S4$ | + | Rate | S4 | $-k2 * S4$ |] + +The model contains one initialAssignment: + +[{width:30em,margin: 1em auto}| Variable | Formula | + | S1 | $p1 / 0.5$ |] + +Note: InitialAssignments override any declared initial values. In this case the +value of species S1 is not declared by the model definition. The calculated value should be used. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ undeclared$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.5$ |second^-1^ | +|Value of parameter p1 |$ 0.75$ |mole litre^-1^ | +|Value of parameter p2 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01094/l2v5/index.heta b/latest/cases/01094/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01094/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01094/l3v2/build.log b/latest/cases/01094/l3v2/build.log new file mode 100644 index 000000000..ada4dd136 --- /dev/null +++ b/latest/cases/01094/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01094/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01094/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01094/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 91 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01094/l3v2/index.heta b/latest/cases/01094/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01094/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01094/model-sbml-l3v2.xml b/latest/cases/01094/model-sbml-l3v2.xml new file mode 100644 index 000000000..45ed8b189 --- /dev/null +++ b/latest/cases/01094/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + 0.5 + k1 + + + + + + + + -0.5 + k2 + + + + + + + + + + + + + + + + + C + k1 + S1 + + + + + + + + + + + + S1 + 0.5 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01094/synopsis.txt b/latest/cases/01094/synopsis.txt new file mode 100644 index 000000000..63398b8de --- /dev/null +++ b/latest/cases/01094/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: One reactions and two rate rules with four species in a compartment. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 730. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains one reaction defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (4 * p1)S2 | $k1 * S1 * C$ |] + +The model contains two rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S3 | $k1 * 0.5$ | + | Rate | S4 | $-k2 * 0.5$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$ 1.5$ |mole | +|Initial amount of S2 |$ 2.0$ |mole | +|Initial amount of S3 |$ 1.5$ |mole | +|Initial amount of S4 |$ 4$ |mole | +|Value of parameter k1 |$ 0.75$ |second^-1^ | +|Value of parameter k2 |$ 0.25$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01095/l2v5/index.heta b/latest/cases/01095/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01095/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01095/l3v2/build.log b/latest/cases/01095/l3v2/build.log new file mode 100644 index 000000000..17e49ab57 --- /dev/null +++ b/latest/cases/01095/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01095/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01095/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01095/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01095/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01095/l3v2/index.heta b/latest/cases/01095/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01095/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01095/model-sbml-l3v2.xml b/latest/cases/01095/model-sbml-l3v2.xml new file mode 100644 index 000000000..c2edd7ce1 --- /dev/null +++ b/latest/cases/01095/model-sbml-l3v2.xml @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + 1 + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + + + + + + + + + + + + + + + + + C + k2 + S3 + + + + + + + + + + + + S1 + 0.5 + + + + + + 2.5 + + + + + + 2 + + + + + + + diff --git a/latest/cases/01095/synopsis.txt b/latest/cases/01095/synopsis.txt new file mode 100644 index 000000000..765e48ff0 --- /dev/null +++ b/latest/cases/01095/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Two reactions and a rate rule with four species in a compartment. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, RateRule, EventWithDelay +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 731. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The +model contains two reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ | +| S3 -> S1 + (4 * p1)S2 | $k2 * S3 * C$ |] + +The model contains one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | + | Rate | S4 | $1$ |] + +The model contains one event that assigns a value to species S2: + +[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* | + | Event1 | $S1 < 0.5$ | $2.5$ | $S2 = 2$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$1.5$ |mole | +|Initial amount of S4 |$ 1$ |mole | +|Value of parameter k1 |$0.$ |litre mole^-1^ second^-1^ | +|Value of parameter k2 |$0.00025$ |second^-1^ | +|Value of parameter p1 |$0.25$ |dimensionless | +|Volume of compartment C |$ 1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01096/l2v5/index.heta b/latest/cases/01096/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01096/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01096/l3v2/build.log b/latest/cases/01096/l3v2/build.log new file mode 100644 index 000000000..49c36d7c2 --- /dev/null +++ b/latest/cases/01096/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01096/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01096/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01096/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01096/l3v2/index.heta b/latest/cases/01096/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01096/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01096/model-sbml-l3v2.xml b/latest/cases/01096/model-sbml-l3v2.xml new file mode 100644 index 000000000..ee3a65ce5 --- /dev/null +++ b/latest/cases/01096/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + diff --git a/latest/cases/01096/synopsis.txt b/latest/cases/01096/synopsis.txt new file mode 100644 index 000000000..867312457 --- /dev/null +++ b/latest/cases/01096/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 827. + +The model contains one compartment called C. There are two species called +S1 and S2 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> (4 * p1)S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01097/l2v5/index.heta b/latest/cases/01097/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01097/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01097/l3v2/build.log b/latest/cases/01097/l3v2/build.log new file mode 100644 index 000000000..68615e5e3 --- /dev/null +++ b/latest/cases/01097/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01097/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01097/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01097/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 87 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01097/l3v2/index.heta b/latest/cases/01097/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01097/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01097/model-sbml-l3v2.xml b/latest/cases/01097/model-sbml-l3v2.xml new file mode 100644 index 000000000..66b8707d2 --- /dev/null +++ b/latest/cases/01097/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + diff --git a/latest/cases/01097/synopsis.txt b/latest/cases/01097/synopsis.txt new file mode 100644 index 000000000..a10edad1e --- /dev/null +++ b/latest/cases/01097/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 828. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01098/l2v5/index.heta b/latest/cases/01098/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01098/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01098/l3v2/build.log b/latest/cases/01098/l3v2/build.log new file mode 100644 index 000000000..be414ca35 --- /dev/null +++ b/latest/cases/01098/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01098/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01098/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01098/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 87 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01098/l3v2/index.heta b/latest/cases/01098/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01098/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01098/model-sbml-l3v2.xml b/latest/cases/01098/model-sbml-l3v2.xml new file mode 100644 index 000000000..aac0dab28 --- /dev/null +++ b/latest/cases/01098/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + S3 + + + + + + + + + diff --git a/latest/cases/01098/synopsis.txt b/latest/cases/01098/synopsis.txt new file mode 100644 index 000000000..a06a48982 --- /dev/null +++ b/latest/cases/01098/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 829. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> S2 + (4 * p1)S3 | $(kf * S1 - kr * S2 * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$2.5$ |second^-1^ | +|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01099/l2v5/index.heta b/latest/cases/01099/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01099/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01099/l3v2/build.log b/latest/cases/01099/l3v2/build.log new file mode 100644 index 000000000..00b3f092b --- /dev/null +++ b/latest/cases/01099/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01099/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01099/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01099/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01099/l3v2/index.heta b/latest/cases/01099/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01099/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01099/model-sbml-l3v2.xml b/latest/cases/01099/model-sbml-l3v2.xml new file mode 100644 index 000000000..a565a0d96 --- /dev/null +++ b/latest/cases/01099/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + C + k1 + S1 + t + + + + + + + diff --git a/latest/cases/01099/synopsis.txt b/latest/cases/01099/synopsis.txt new file mode 100644 index 000000000..68112154b --- /dev/null +++ b/latest/cases/01099/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Basic single forward reaction with two species in one compartment +using csymbol time within a math expression. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter, CSymbolTime +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +Note: This test is the L3 version of model 898. + +The model contains one compartment called C. There are two +species called S1 and S2 and two parameters called k1 and p1. The model contains +one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> (2 * p1) S2 | $k1 * S1 * C * t$ |] +where the symbol 't' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.5 \x 10^-3$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter k1 |$1$ |second^-2^ | +|Value of parameter p1 |$1$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but (as +per usual SBML principles) their symbols represent their values in +concentration units where they appear in expressions. + +Note: The test data for this model was generated from an analytical solution +of the system of equations. + diff --git a/latest/cases/01100/l2v5/index.heta b/latest/cases/01100/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01100/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01100/l3v2/build.log b/latest/cases/01100/l3v2/build.log new file mode 100644 index 000000000..25a885b1a --- /dev/null +++ b/latest/cases/01100/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01100/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01100/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01100/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 91 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01100/l3v2/index.heta b/latest/cases/01100/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01100/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01100/model-sbml-l3v2.xml b/latest/cases/01100/model-sbml-l3v2.xml new file mode 100644 index 000000000..26846fd2c --- /dev/null +++ b/latest/cases/01100/model-sbml-l3v2.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + C + k1 + S1 + time + + + + + + + + + + + + + + + + C + k2 + S2 + time + + + + + + + + + + + + + + + + C + k3 + S3 + time + + + + + + + diff --git a/latest/cases/01100/synopsis.txt b/latest/cases/01100/synopsis.txt new file mode 100644 index 000000000..b94002b1e --- /dev/null +++ b/latest/cases/01100/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Linear chain of reactions in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, InitialAssignment +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 899. + +The model contains one compartment called C. There are four +species named S1, S2, S3 and S4 and four parameters named k1, k2, k3 and p1. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 -> S2 | $k1 * S1 * C * time$ | +| (2 * p1)S2 -> S3 | $k2 * S2 * C * time$ | +| S3 -> S4 | $k3 * S3 * C * time$ |] +where the symbol 'time' denotes the current simulation time. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0 \x 10^-1$ |mole | +|Initial amount of S2 |$0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$0.7$ |second^-2^ | +|Value of parameter k2 |$0.5$ |second^-2^ | +|Value of parameter k3 |$1$ |second^-2^ | +|Value of parameter p1 |$1$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01101/l2v5/index.heta b/latest/cases/01101/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01101/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01101/l3v2/build.log b/latest/cases/01101/l3v2/build.log new file mode 100644 index 000000000..53be7e90f --- /dev/null +++ b/latest/cases/01101/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01101/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01101/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01101/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 91 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01101/l3v2/index.heta b/latest/cases/01101/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01101/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01101/model-sbml-l3v2.xml b/latest/cases/01101/model-sbml-l3v2.xml new file mode 100644 index 000000000..e63a3e50b --- /dev/null +++ b/latest/cases/01101/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + p1 + + + + + + + + + + + + + + + + + + C + k1 + S1 + S2 + s + + + + + + + + + + + + + + + + + C + k1 + S3 + s + + + + + + + + + + + + + + + + + + + + C + k1 + S3 + s + + + + + + + + + + diff --git a/latest/cases/01101/synopsis.txt b/latest/cases/01101/synopsis.txt new file mode 100644 index 000000000..6343ccbcc --- /dev/null +++ b/latest/cases/01101/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Three reactions with four species in one compartment +using csymbol time within a math expression. +componentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, InitialAssignment +testTags: InitialValueReassigned, Amount, LocalParameters, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 900. + +The model contains one compartment called C. There are four +species called S1, S2, S3 and S4 and two parameters called k1 and p1. +The model contains three reactions defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| (2 * p1)S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ | +| S3 -> S1 + S2 | $k1 * S3 * C * s$ | +| S3 -> S1 + S4 | $k1 * S3 * C * s$ |] +where the symbol 's' denotes the current simulation time. + +Both reactions S3 -> S1 + S2 and S3 -> S1 + S4 define a local parameters k1 which has a +scope local to the defining reaction and are different from each other and the global parameter k1 +used in the reaction S1 + S2 -> S3. + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$2.0$ |mole | +|Initial amount of S2 |$2.0$ |mole | +|Initial amount of S3 |$0$ |mole | +|Initial amount of S4 |$0$ |mole | +|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ | +|Value of parameter p1 |$1.0$ |dimensionless | +|Value of local parameter k1 (R2) |$0.9$ |second^-2^ | +|Value of local parameter k1 (R3) |$0.7$ |second^-2^ | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01102/l2v5/index.heta b/latest/cases/01102/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01102/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01102/l3v2/build.log b/latest/cases/01102/l3v2/build.log new file mode 100644 index 000000000..0ac944bc5 --- /dev/null +++ b/latest/cases/01102/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01102/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01102/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01102/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01102/l3v2/index.heta b/latest/cases/01102/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01102/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01102/model-sbml-l3v2.xml b/latest/cases/01102/model-sbml-l3v2.xml new file mode 100644 index 000000000..fc361510f --- /dev/null +++ b/latest/cases/01102/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + 3 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01102/synopsis.txt b/latest/cases/01102/synopsis.txt new file mode 100644 index 000000000..f31d6df98 --- /dev/null +++ b/latest/cases/01102/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A very simple reaction with stoichiometry set by an initialAssignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: InitialValueReassigned, Amount, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +Note: This test is the L3 version of model 968. + +The speciesReference ('Xref') is set with an initialAssignment of 3 for the L3 model, and with stoichiometryMath in the L2 models. No 'stoichiometry' value is provided in the speciesReference in the reaction itself. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species X | $0$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01103/l2v5/index.heta b/latest/cases/01103/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01103/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01103/l3v2/build.log b/latest/cases/01103/l3v2/build.log new file mode 100644 index 000000000..4427654f2 --- /dev/null +++ b/latest/cases/01103/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01103/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01103/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01103/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] Xref_proc Property "actors[0].target" has lost reference "Xref". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01103/l3v2/index.heta b/latest/cases/01103/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01103/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01103/model-sbml-l3v2.xml b/latest/cases/01103/model-sbml-l3v2.xml new file mode 100644 index 000000000..65d63999e --- /dev/null +++ b/latest/cases/01103/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01103/synopsis.txt b/latest/cases/01103/synopsis.txt new file mode 100644 index 000000000..14c801f01 --- /dev/null +++ b/latest/cases/01103/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A very simple reaction with stoichiometry changed by a rate rule. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + +Note: This test is the L3 version of model 973. + +Over the course of the simulation, the stoichiometry 'Xref' changes at a rate of 0.01/time, so the effective rate of synthesis increases as well, identically to the same model with k1 changing instead of Xref. The Level 2 versions of this test create a new parameter 'parameterId_0' which functions identically to 'Xref' in the Level 3 version of the model. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | Xref | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01104/l2v5/index.heta b/latest/cases/01104/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01104/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01104/l3v2/build.log b/latest/cases/01104/l3v2/build.log new file mode 100644 index 000000000..58babc439 --- /dev/null +++ b/latest/cases/01104/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01104/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01104/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01104/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01104/l3v2/index.heta b/latest/cases/01104/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01104/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01104/model-sbml-l3v2.xml b/latest/cases/01104/model-sbml-l3v2.xml new file mode 100644 index 000000000..a4899d1fc --- /dev/null +++ b/latest/cases/01104/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + X + + + + + + + + + + + k1 + + + + + + + + + + + + k1 + Y + + + + + + + diff --git a/latest/cases/01104/synopsis.txt b/latest/cases/01104/synopsis.txt new file mode 100644 index 000000000..0eb21d0fe --- /dev/null +++ b/latest/cases/01104/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A simple reaction with stoichiometry the same as its species. For convenience, another reaction is present with the same kinetics, as the species is used in the kinetic law instead. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry, HasOnlySubstanceUnits +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 989. + +This model contains two reactions that do the same thing, one by having a kinetic law that varies with the produced species, and the other by having a variable stoichiometry set to equal the produced species, for a sort of auto-catalytic reaction. + + +The model contains: +* 2 species (X, Y) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ | +| -> Y | $k1 * Y$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $X$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species X | $1$ | variable | +| Initial amount of species Y | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/01105/l2v5/index.heta b/latest/cases/01105/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01105/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01105/l3v2/build.log b/latest/cases/01105/l3v2/build.log new file mode 100644 index 000000000..d500f9d7d --- /dev/null +++ b/latest/cases/01105/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01105/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01105/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01105/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01105/l3v2/index.heta b/latest/cases/01105/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01105/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01105/model-sbml-l3v2.xml b/latest/cases/01105/model-sbml-l3v2.xml new file mode 100644 index 000000000..64d4e39fa --- /dev/null +++ b/latest/cases/01105/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + p1 + + + + + 1 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01105/synopsis.txt b/latest/cases/01105/synopsis.txt new file mode 100644 index 000000000..b624ff314 --- /dev/null +++ b/latest/cases/01105/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to a parameter that varies due to a rate law. +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NonUnityStoichiometry, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 990. + +The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that starts at 1 and increases at a rate of 1. + +The model contains: +* 1 species (X) +* 2 parameters (p1, k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $p1$ | +| Rate | p1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter p1 | $1$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/01106/l2v5/index.heta b/latest/cases/01106/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01106/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01106/l3v2/build.log b/latest/cases/01106/l3v2/build.log new file mode 100644 index 000000000..c6631caec --- /dev/null +++ b/latest/cases/01106/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01106/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01106/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01106/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01106/l3v2/index.heta b/latest/cases/01106/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01106/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01106/model-sbml-l3v2.xml b/latest/cases/01106/model-sbml-l3v2.xml new file mode 100644 index 000000000..8bf72d5fb --- /dev/null +++ b/latest/cases/01106/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + p1 + + + + + + + + + + + k1 + + + + + + + + + + + X + 2 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01106/synopsis.txt b/latest/cases/01106/synopsis.txt new file mode 100644 index 000000000..993c9b72f --- /dev/null +++ b/latest/cases/01106/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to a parameter that varies from an Event. +componentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NonUnityStoichiometry, NonConstantParameter, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 991. + +The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that starts at 1 and switches to 2 due to an event. + +The model contains: +* 1 species (X) +* 2 parameters (p1, k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $X ≥ 2$ | $p1 = 2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter p1 | $1$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/01107/l2v5/index.heta b/latest/cases/01107/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01107/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01107/l3v2/build.log b/latest/cases/01107/l3v2/build.log new file mode 100644 index 000000000..034fd9ffc --- /dev/null +++ b/latest/cases/01107/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01107/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01107/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01107/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01107/l3v2/index.heta b/latest/cases/01107/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01107/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01107/model-sbml-l3v2.xml b/latest/cases/01107/model-sbml-l3v2.xml new file mode 100644 index 000000000..7ca5ca53a --- /dev/null +++ b/latest/cases/01107/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + p1 + + + + + X + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01107/synopsis.txt b/latest/cases/01107/synopsis.txt new file mode 100644 index 000000000..f5fcfb854 --- /dev/null +++ b/latest/cases/01107/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to a parameter, which in turn is set to be the same as its species. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: InitialValueReassigned, Amount, AssignedVariableStoichiometry, NonUnityStoichiometry, NonConstantParameter, HasOnlySubstanceUnits +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 992. + +The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that is set by an assignment rule to be equal to X. + +The model contains: +* 1 species (X) +* 2 parameters (p1, k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $p1$ | +| Assignment | p1 | $X$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter p1 | $X$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/01108/l2v5/index.heta b/latest/cases/01108/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01108/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01108/l3v2/build.log b/latest/cases/01108/l3v2/build.log new file mode 100644 index 000000000..d8e2a2383 --- /dev/null +++ b/latest/cases/01108/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01108/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01108/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01108/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01108/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01108/l3v2/index.heta b/latest/cases/01108/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01108/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01108/model-sbml-l3v2.xml b/latest/cases/01108/model-sbml-l3v2.xml new file mode 100644 index 000000000..f82701ba5 --- /dev/null +++ b/latest/cases/01108/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + + X + p1 + + + + + + p1 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01108/synopsis.txt b/latest/cases/01108/synopsis.txt new file mode 100644 index 000000000..bd2bb5cda --- /dev/null +++ b/latest/cases/01108/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to a parameter, which in turn is set to be the same as its species via an algebraic rule. +componentTags: AlgebraicRule, AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: InitialValueReassigned, Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 993. + +The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that is set by an algebraic rule to be equal to X. + +The model contains: +* 1 species (X) +* 2 parameters (p1, k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $X - p1$ | +| Assignment | Xref | $p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial value of parameter p1 | $unknown$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/01109/l2v5/index.heta b/latest/cases/01109/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01109/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01109/l3v2/build.log b/latest/cases/01109/l3v2/build.log new file mode 100644 index 000000000..3647e752e --- /dev/null +++ b/latest/cases/01109/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01109/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01109/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01109/model-sbml-l3v2.xml"... +[error] Xref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01109/l3v2/index.heta b/latest/cases/01109/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01109/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01109/model-sbml-l3v2.xml b/latest/cases/01109/model-sbml-l3v2.xml new file mode 100644 index 000000000..2d045981b --- /dev/null +++ b/latest/cases/01109/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + time + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01109/synopsis.txt b/latest/cases/01109/synopsis.txt new file mode 100644 index 000000000..8da0319b7 --- /dev/null +++ b/latest/cases/01109/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A simple reaction with stoichiometry set to be equal to 'time'. +componentTags: AssignmentRule, CSymbolTime, Compartment, Parameter, Reaction, Species +testTags: InitialValueReassigned, Amount, AssignedVariableStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 994. + +Variable stoichiometry: the stoichiometry is literally 'time'. + +The model contains: +* 1 species (X) +* 1 parameter (k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> Xref X | $k1$ |] +Note: the following stoichiometries are set separately: Xref + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Xref | $time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species X | $1$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + diff --git a/latest/cases/01110/l2v5/index.heta b/latest/cases/01110/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01110/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01110/l3v2/build.log b/latest/cases/01110/l3v2/build.log new file mode 100644 index 000000000..b3fcf4bd1 --- /dev/null +++ b/latest/cases/01110/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01110/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01110/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01110/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01110/l3v2/index.heta b/latest/cases/01110/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01110/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01110/model-sbml-l3v2.xml b/latest/cases/01110/model-sbml-l3v2.xml new file mode 100644 index 000000000..155e41911 --- /dev/null +++ b/latest/cases/01110/model-sbml-l3v2.xml @@ -0,0 +1,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + + + + -1 + kr + S2 + + + + + + + + + + diff --git a/latest/cases/01110/synopsis.txt b/latest/cases/01110/synopsis.txt new file mode 100644 index 000000000..6ab4464fa --- /dev/null +++ b/latest/cases/01110/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: Compartment, Species, Reaction, Parameter, InitialAssignment +testTags: InitialValueReassigned, Amount, ReversibleReaction, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test the L3 version of model 1027, itself a copy of 827 with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are two species called +S1 and S2 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 <-> (4 * p1)S2 | $(kf * S1 - kr * S2) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0$ |mole | +|Value of parameter kf |$0.9$ |second^-1^ | +|Value of parameter kr |$0.075$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01111/l2v5/index.heta b/latest/cases/01111/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01111/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01111/l3v2/build.log b/latest/cases/01111/l3v2/build.log new file mode 100644 index 000000000..46e36788c --- /dev/null +++ b/latest/cases/01111/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01111/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01111/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01111/model-sbml-l3v2.xml"... +[error] generatedId_0 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 87 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01111/l3v2/index.heta b/latest/cases/01111/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01111/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01111/model-sbml-l3v2.xml b/latest/cases/01111/model-sbml-l3v2.xml new file mode 100644 index 000000000..c89baaa84 --- /dev/null +++ b/latest/cases/01111/model-sbml-l3v2.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p1 + + + + + + + + + + + + + + + + + + + + C + + + + + kf + S1 + S2 + + + + -1 + kr + S3 + + + + + + + + + + diff --git a/latest/cases/01111/synopsis.txt b/latest/cases/01111/synopsis.txt new file mode 100644 index 000000000..e65ae5222 --- /dev/null +++ b/latest/cases/01111/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Single reversible reaction. +componentTags: InitialAssignment, Compartment, Species, Reaction, Parameter +testTags: InitialValueReassigned, Amount, ReversibleReaction, AssignedConstantStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + +Note: This test is the L3 version of model 1028, itself a copy of 828 with the products and reactants reversed, +and a negative kinetic law. This gives the same results, but during the simulation, +the kinetic law actually goes negative (a requirement for reversibe reactions). +The reaction listed below is therfore equivalent to the one in the file, but reversed from it. + +The model contains one compartment called C. There are three species called +S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction +defined as: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S1 + (4 * p1)S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |] + +The initial conditions are as follows: + +[{width:30em,margin: 1em auto}| |*Value* |*Units* | +|Initial amount of S1 |$1.0$ |mole | +|Initial amount of S2 |$0.5$ |mole | +|Initial amount of S3 |$0$ |mole | +|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ | +|Value of parameter kr |$0.09$ |second^-1^ | +|Value of parameter p1 |$0.5$ |dimensionless | +|Volume of compartment C |$1$ |litre |] + +The species values are given as amounts of substance to make it easier to +use the model in a discrete stochastic simulator, but (as per usual SBML +principles) their symbols represent their values in concentration units +where they appear in expressions. + diff --git a/latest/cases/01112/l2v5/build.log b/latest/cases/01112/l2v5/build.log new file mode 100644 index 000000000..cc7912e1b --- /dev/null +++ b/latest/cases/01112/l2v5/build.log @@ -0,0 +1,27 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01112/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01112/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01112/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] a Some of properties do not satisfy requirements for class "Record" + 1. /assignments/start_ should NOT be shorter than 1 characters + 2. /assignments/start_ should be number + 3. /assignments/start_ should match exactly one schema in oneOf +[warn] Some of component properties will not be updated. +[error] b Some of properties do not satisfy requirements for class "Record" + 1. /assignments/start_ should NOT be shorter than 1 characters + 2. /assignments/start_ should be number + 3. /assignments/start_ should match exactly one schema in oneOf +[warn] Some of component properties will not be updated. +[error] c: Cannot parse MathExpr properly. Value expected (char 3) in "( ? 1 : 0 )" +[error] d: Cannot parse MathExpr properly. Value expected (char 3) in "( ? 1 : 0 )" +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[error] Record "a" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "b" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "c" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "d" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01112/l2v5/index.heta b/latest/cases/01112/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01112/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01112/l3v2/build.log b/latest/cases/01112/l3v2/build.log new file mode 100644 index 000000000..204616b50 --- /dev/null +++ b/latest/cases/01112/l3v2/build.log @@ -0,0 +1,15 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01112/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01112/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01112/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01112/l3v2/index.heta b/latest/cases/01112/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01112/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01112/model-sbml-l2v5.xml b/latest/cases/01112/model-sbml-l2v5.xml new file mode 100644 index 000000000..0ffb49a25 --- /dev/null +++ b/latest/cases/01112/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + 0 + + + + + + + + + 1 + + + + + + 0 + + + + + + + + + 1 + + + + + + 0 + + + + + + + diff --git a/latest/cases/01112/model-sbml-l3v2.xml b/latest/cases/01112/model-sbml-l3v2.xml new file mode 100644 index 000000000..c213b4231 --- /dev/null +++ b/latest/cases/01112/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + 0 + + + + + + + + + 1 + + + + + + 0 + + + + + + + + + 1 + + + + + + 0 + + + + + + + diff --git a/latest/cases/01112/synopsis.txt b/latest/cases/01112/synopsis.txt new file mode 100644 index 000000000..faa6c4d92 --- /dev/null +++ b/latest/cases/01112/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Test of 0-child MathML constructs plus, times, and, or, and xor. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +In the official MathML spec, plus, times, and, or, and xor may all have 0 arguments. When they do, they are supposed return identity for that construct, namely: +*plus: 0 +*times: 1 +*and: true +*or: false +*xor: false + +The model contains: +* 5 parameters (a, b, c, d, e) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $plus()$ | constant | +| Initial value of parameter b | $times()$ | constant | +| Initial value of parameter c | $piecewise(and(), 1, 0)$ | constant | +| Initial value of parameter d | $piecewise(or(), 1, 0)$ | constant | +| Initial value of parameter e | $piecewise(xor(), 1, 0)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01113/l2v5/build.log b/latest/cases/01113/l2v5/build.log new file mode 100644 index 000000000..6abe080b8 --- /dev/null +++ b/latest/cases/01113/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01113/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01113/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01113/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01113/l2v5/index.heta b/latest/cases/01113/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01113/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01113/l3v2/build.log b/latest/cases/01113/l3v2/build.log new file mode 100644 index 000000000..f9eefd240 --- /dev/null +++ b/latest/cases/01113/l3v2/build.log @@ -0,0 +1,15 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01113/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01113/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01113/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01113/l3v2/index.heta b/latest/cases/01113/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01113/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01113/model-sbml-l2v5.xml b/latest/cases/01113/model-sbml-l2v5.xml new file mode 100644 index 000000000..f93b09048 --- /dev/null +++ b/latest/cases/01113/model-sbml-l2v5.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + 2 + + + + + + + + 1 + + + + + + + 0 + + + + + + + + + 1 + + + + + + + 0 + + + + + + + + + 1 + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01113/model-sbml-l3v2.xml b/latest/cases/01113/model-sbml-l3v2.xml new file mode 100644 index 000000000..2fe182b01 --- /dev/null +++ b/latest/cases/01113/model-sbml-l3v2.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + 2 + + + + + + + + 1 + + + + + + + 0 + + + + + + + + + 1 + + + + + + + 0 + + + + + + + + + 1 + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01113/synopsis.txt b/latest/cases/01113/synopsis.txt new file mode 100644 index 000000000..8d721d953 --- /dev/null +++ b/latest/cases/01113/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Test of 1-child MathML constructs plus, times, and, or, and xor. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +In the official MathML spec, plus, times, and, or, and xor may all have 1 arguments. When they do, they are supposed return that argument. + +The model contains: +* 5 parameters (a, b, c, d, e) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $plus(1)$ | constant | +| Initial value of parameter b | $times(2) $ | constant | +| Initial value of parameter c | $piecewise(and(true), 1, 0)$ | constant | +| Initial value of parameter d | $piecewise(or(true), 1, 0)$ | constant | +| Initial value of parameter e | $piecewise(xor(true)), 1, 0)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01114/l2v5/build.log b/latest/cases/01114/l2v5/build.log new file mode 100644 index 000000000..91c40e922 --- /dev/null +++ b/latest/cases/01114/l2v5/build.log @@ -0,0 +1,15 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01114/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01114/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01114/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01114/l2v5/index.heta b/latest/cases/01114/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01114/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01114/l3v2/build.log b/latest/cases/01114/l3v2/build.log new file mode 100644 index 000000000..088e054ce --- /dev/null +++ b/latest/cases/01114/l3v2/build.log @@ -0,0 +1,15 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01114/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01114/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01114/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01114/l3v2/index.heta b/latest/cases/01114/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01114/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01114/model-sbml-l2v5.xml b/latest/cases/01114/model-sbml-l2v5.xml new file mode 100644 index 000000000..590b3fb5f --- /dev/null +++ b/latest/cases/01114/model-sbml-l2v5.xml @@ -0,0 +1,114 @@ + + + + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + 2 + + + 2 + + + + + + + + + + + + 1 + + + + + + + + + + + + + + 0 + + + + + + + + + 1 + + + + + + + + + + + + + + 0 + + + + + + + + + 1 + + + + + + + + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01114/model-sbml-l3v2.xml b/latest/cases/01114/model-sbml-l3v2.xml new file mode 100644 index 000000000..5ca722cb1 --- /dev/null +++ b/latest/cases/01114/model-sbml-l3v2.xml @@ -0,0 +1,114 @@ + + + + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + 2 + + + 2 + + + + + + + + + + + + 1 + + + + + + + + + + + + + + 0 + + + + + + + + + 1 + + + + + + + + + + + + + + 0 + + + + + + + + + 1 + + + + + + + + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01114/synopsis.txt b/latest/cases/01114/synopsis.txt new file mode 100644 index 000000000..1531e2814 --- /dev/null +++ b/latest/cases/01114/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Test of nested 0-child MathML constructs plus, times, and, or, and xor. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +In the official MathML spec, plus, times, and, or, and xor may all have 0 arguments. When they do, they are supposed return identity for that construct, namely: +*plus: 0 +*times: 1 +*and: true +*or: false +*xor: false + +The model contains: +* 5 parameters (a, b, c, d, e) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $plus(1, plus(1, plus()))$ | constant | +| Initial value of parameter b | $times(2, times(2, times())) $ | constant | +| Initial value of parameter c | $piecewise(and(and(and(), true), true), 1, 0)$ | constant | +| Initial value of parameter d | $piecewise(or(or(or(), true), true), 1, 0)$ | constant | +| Initial value of parameter e | $piecewise(xor(xor(xor(), true), true), 1, 0)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01115/l2v5/build.log b/latest/cases/01115/l2v5/build.log new file mode 100644 index 000000000..79052ad25 --- /dev/null +++ b/latest/cases/01115/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01115/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01115/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01115/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01115/l2v5/index.heta b/latest/cases/01115/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01115/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01115/l3v2/build.log b/latest/cases/01115/l3v2/build.log new file mode 100644 index 000000000..b32b6b0ff --- /dev/null +++ b/latest/cases/01115/l3v2/build.log @@ -0,0 +1,15 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01115/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01115/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01115/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01115/l3v2/index.heta b/latest/cases/01115/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01115/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01115/model-sbml-l2v5.xml b/latest/cases/01115/model-sbml-l2v5.xml new file mode 100644 index 000000000..9b85ae81b --- /dev/null +++ b/latest/cases/01115/model-sbml-l2v5.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + 1 + 1 + 1 + + + + + + + + 2 + 2 + 2 + + + + + + + + 1 + + + + + + + + + + + + + + + 0 + + + + + + + + + 1 + + + + + + + + + + + + + + + 0 + + + + + + + + + 1 + + + + + + + + + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01115/model-sbml-l3v2.xml b/latest/cases/01115/model-sbml-l3v2.xml new file mode 100644 index 000000000..874d20226 --- /dev/null +++ b/latest/cases/01115/model-sbml-l3v2.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + 1 + 1 + 1 + + + + + + + + 2 + 2 + 2 + + + + + + + + 1 + + + + + + + + + + + + + + + 0 + + + + + + + + + 1 + + + + + + + + + + + + + + + 0 + + + + + + + + + 1 + + + + + + + + + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01115/synopsis.txt b/latest/cases/01115/synopsis.txt new file mode 100644 index 000000000..f976a0cf7 --- /dev/null +++ b/latest/cases/01115/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Test of nested 1-child MathML constructs plus, times, and, or, and xor. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + +In the official MathML spec, plus, times, and, or, and xor may all have 1 arguments. When they do, they are supposed return that argument. + +The model contains: +* 5 parameters (a, b, c, d, e) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $plus(1, plus(1, plus(1)))$ | constant | +| Initial value of parameter b | $times(2, times(2, times(2))) $ | constant | +| Initial value of parameter c | $piecewise(and(and(and(true), true), true), 1, 0)$ | constant | +| Initial value of parameter d | $piecewise(or(or(or(true), true), true), 1, 0)$ | constant | +| Initial value of parameter e | $piecewise(xor(xor(xor(true), true), true), 1, 0)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01116/l2v5/heta-code/output.heta b/latest/cases/01116/l2v5/heta-code/output.heta new file mode 100644 index 000000000..5bbffb0c9 --- /dev/null +++ b/latest/cases/01116/l2v5/heta-code/output.heta @@ -0,0 +1,12 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +a @Record { } .= piecewise(1, true); +b @Record { } .= piecewise(1, a > 0, 2, a <= 0); + diff --git a/latest/cases/01116/l2v5/index.heta b/latest/cases/01116/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01116/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01116/l2v5/json/output.json b/latest/cases/01116/l2v5/json/output.json new file mode 100644 index 000000000..e11c45cd7 --- /dev/null +++ b/latest/cases/01116/l2v5/json/output.json @@ -0,0 +1,44 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "a", + "assignments": { + "start_": "piecewise(1, true)" + } + }, + { + "class": "Record", + "id": "b", + "assignments": { + "start_": "piecewise(1, a > 0, 2, a <= 0)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01116/l3v2/build.log b/latest/cases/01116/l3v2/build.log new file mode 100644 index 000000000..df3ec6e4f --- /dev/null +++ b/latest/cases/01116/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01116/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01116/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01116/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01116/l3v2/index.heta b/latest/cases/01116/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01116/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01116/model-sbml-l2v5.xml b/latest/cases/01116/model-sbml-l2v5.xml new file mode 100644 index 000000000..76facd028 --- /dev/null +++ b/latest/cases/01116/model-sbml-l2v5.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + 1 + + + + + + + + + + 1 + + + a + 0 + + + + 2 + + + a + 0 + + + + + + + + diff --git a/latest/cases/01116/model-sbml-l3v2.xml b/latest/cases/01116/model-sbml-l3v2.xml new file mode 100644 index 000000000..494f1466a --- /dev/null +++ b/latest/cases/01116/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + 1 + + + + + + + + + + 1 + + + a + 0 + + + + 2 + + + a + 0 + + + + + + + + diff --git a/latest/cases/01116/output.heta b/latest/cases/01116/output.heta new file mode 100644 index 000000000..93528c8d5 --- /dev/null +++ b/latest/cases/01116/output.heta @@ -0,0 +1,36 @@ +/* +category: Test +synopsis: Testing 'piecewise' without 'otherwise'. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + MathML allows the construction of 'piecwise' functions without 'otherwise'. When all cases are accounted for, this shouldn't make a difference in the output of the model. + +The model contains: +* 2 parameters (a, b) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $piecewise(1, true)$ | constant | +| Initial value of parameter b | $piecewise(1, gt(a, 0), 2, leq(a, 0))$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +a @Record { } .= piecewise(1, true); +b @Record { } .= piecewise(1, a > 0, 2, a <= 0); + diff --git a/latest/cases/01116/synopsis.txt b/latest/cases/01116/synopsis.txt new file mode 100644 index 000000000..2f3229ce9 --- /dev/null +++ b/latest/cases/01116/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: Testing 'piecewise' without 'otherwise'. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + MathML allows the construction of 'piecwise' functions without 'otherwise'. When all cases are accounted for, this shouldn't make a difference in the output of the model. + +The model contains: +* 2 parameters (a, b) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $piecewise(1, true)$ | constant | +| Initial value of parameter b | $piecewise(1, gt(a, 0), 2, leq(a, 0))$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01117/l2v5/heta-code/output.heta b/latest/cases/01117/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8e2bf0c2d --- /dev/null +++ b/latest/cases/01117/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 1; + +C_proc @Process { actors: = C, }; +C_proc := 1; + diff --git a/latest/cases/01117/l2v5/index.heta b/latest/cases/01117/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01117/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01117/l2v5/json/output.json b/latest/cases/01117/l2v5/json/output.json new file mode 100644 index 000000000..9d6f93e5a --- /dev/null +++ b/latest/cases/01117/l2v5/json/output.json @@ -0,0 +1,59 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Process", + "id": "C_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01117/l3v2/heta-code/output.heta b/latest/cases/01117/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e2c04c1e5 --- /dev/null +++ b/latest/cases/01117/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 1; + +C_proc @Process { actors: = C, }; +C_proc := 1; + diff --git a/latest/cases/01117/l3v2/index.heta b/latest/cases/01117/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01117/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01117/l3v2/json/output.json b/latest/cases/01117/l3v2/json/output.json new file mode 100644 index 000000000..7b545f2e6 --- /dev/null +++ b/latest/cases/01117/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Process", + "id": "C_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01117/model-sbml-l2v5.xml b/latest/cases/01117/model-sbml-l2v5.xml new file mode 100644 index 000000000..322ea4d55 --- /dev/null +++ b/latest/cases/01117/model-sbml-l2v5.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01117/model-sbml-l3v2.xml b/latest/cases/01117/model-sbml-l3v2.xml new file mode 100644 index 000000000..0d504c684 --- /dev/null +++ b/latest/cases/01117/model-sbml-l3v2.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01117/output.heta b/latest/cases/01117/output.heta new file mode 100644 index 000000000..16f5a50ef --- /dev/null +++ b/latest/cases/01117/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Testing that the species amount does not change, even in a changing compartment. +componentTags: Compartment, RateRule, Species +testTags: Amount, ConstantSpecies, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model tests that the simulator should, by default, assume that a species set boundaryCondition=false and hasOnlySubstanceUnits=false, residing in a compartment that changes over time, should keep its *amount* constant, not its concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 1; + +C_proc @Process { actors: = C, }; +C_proc := 1; + diff --git a/latest/cases/01117/synopsis.txt b/latest/cases/01117/synopsis.txt new file mode 100644 index 000000000..a086cb340 --- /dev/null +++ b/latest/cases/01117/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Testing that the species amount does not change, even in a changing compartment. +componentTags: Compartment, RateRule, Species +testTags: Amount, ConstantSpecies, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model tests that the simulator should, by default, assume that a species set boundaryCondition=false and hasOnlySubstanceUnits=false, residing in a compartment that changes over time, should keep its *amount* constant, not its concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01118/l2v5/heta-code/output.heta b/latest/cases/01118/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8e2bf0c2d --- /dev/null +++ b/latest/cases/01118/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 1; + +C_proc @Process { actors: = C, }; +C_proc := 1; + diff --git a/latest/cases/01118/l2v5/index.heta b/latest/cases/01118/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01118/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01118/l2v5/json/output.json b/latest/cases/01118/l2v5/json/output.json new file mode 100644 index 000000000..9d6f93e5a --- /dev/null +++ b/latest/cases/01118/l2v5/json/output.json @@ -0,0 +1,59 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Process", + "id": "C_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01118/l3v2/heta-code/output.heta b/latest/cases/01118/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e2c04c1e5 --- /dev/null +++ b/latest/cases/01118/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 1; + +C_proc @Process { actors: = C, }; +C_proc := 1; + diff --git a/latest/cases/01118/l3v2/index.heta b/latest/cases/01118/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01118/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01118/l3v2/json/output.json b/latest/cases/01118/l3v2/json/output.json new file mode 100644 index 000000000..7b545f2e6 --- /dev/null +++ b/latest/cases/01118/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Process", + "id": "C_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01118/model-sbml-l2v5.xml b/latest/cases/01118/model-sbml-l2v5.xml new file mode 100644 index 000000000..0ee61ffb3 --- /dev/null +++ b/latest/cases/01118/model-sbml-l2v5.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01118/model-sbml-l3v2.xml b/latest/cases/01118/model-sbml-l3v2.xml new file mode 100644 index 000000000..5d2f4a1fd --- /dev/null +++ b/latest/cases/01118/model-sbml-l3v2.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01118/output.heta b/latest/cases/01118/output.heta new file mode 100644 index 000000000..789cbd100 --- /dev/null +++ b/latest/cases/01118/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: A model that tests how not to vary a species. +componentTags: Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, ConstantSpecies, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model tests that the simulator should, by default, assume that a species set boundaryCondition=true and hasOnlySubstanceUnits=false, residing in a compartment that changes over time, should keep its *amount* constant, not its concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 1; + +C_proc @Process { actors: = C, }; +C_proc := 1; + diff --git a/latest/cases/01118/synopsis.txt b/latest/cases/01118/synopsis.txt new file mode 100644 index 000000000..f3af245d2 --- /dev/null +++ b/latest/cases/01118/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A model that tests how not to vary a species. +componentTags: Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, ConstantSpecies, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic + + This model tests that the simulator should, by default, assume that a species set boundaryCondition=true and hasOnlySubstanceUnits=false, residing in a compartment that changes over time, should keep its *amount* constant, not its concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01119/l2v5/index.heta b/latest/cases/01119/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01119/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01119/l3v2/build.log b/latest/cases/01119/l3v2/build.log new file mode 100644 index 000000000..2c6bb1b23 --- /dev/null +++ b/latest/cases/01119/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01119/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01119/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01119/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01119/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01119/l3v2/index.heta b/latest/cases/01119/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01119/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01119/model-sbml-l3v2.xml b/latest/cases/01119/model-sbml-l3v2.xml new file mode 100644 index 000000000..00fbd84d2 --- /dev/null +++ b/latest/cases/01119/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + time + 3 + + + + + + 1.5 + + + + + 10 + + + + + + 3 + + + + + + + + + + time + 3 + + + + + + 1.5 + + + + + 5 + + + + + + 2 + + + + + + + + + + time + 3 + + + + + + 1.5 + + + + + 4 + + + + + + 3 + + + + + + + + + + time + 3 + + + + + + 1.5 + + + + + 9 + + + + + + 2 + + + + + + + diff --git a/latest/cases/01119/synopsis.txt b/latest/cases/01119/synopsis.txt new file mode 100644 index 000000000..8cfdd8683 --- /dev/null +++ b/latest/cases/01119/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Competing events with the same trigger and delay, but different priorities +componentTags: CSymbolTime, EventPriority, EventWithDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric + + This test ensures that when two events have the same trigger and same delay, they will still execute in the correct order (by priority). + + There are four models that test basically the same thing twice (for e1 and then e2) to ensure that the order in which the events are discovered within the model will not affect the outcome. + +The model contains: +* 2 parameters (e1, e2) + +There are 4 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Delay* | *Event Assignments* | +| E1 | $time ≥ 3$ | $10$ | $1.5$ | $e1 = 3$ | +| E2 | $time ≥ 3$ | $5$ | $1.5$ | $e1 = 2$ | +| E3 | $time ≥ 3$ | $4$ | $1.5$ | $e2 = 3$ | +| E4 | $time ≥ 3$ | $9$ | $1.5$ | $e2 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter e1 | $0$ | variable | +| Initial value of parameter e2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01120/l2v5/index.heta b/latest/cases/01120/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01120/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01120/l3v2/build.log b/latest/cases/01120/l3v2/build.log new file mode 100644 index 000000000..ed5d8fa85 --- /dev/null +++ b/latest/cases/01120/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01120/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01120/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01120/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01120/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01120/l3v2/index.heta b/latest/cases/01120/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01120/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01120/model-sbml-l3v2.xml b/latest/cases/01120/model-sbml-l3v2.xml new file mode 100644 index 000000000..6f84a04a5 --- /dev/null +++ b/latest/cases/01120/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + 1 + + + + + + + + + + comp + 5.1 + + + + + + 1.05 + + + + + + 4 + + + + + + + diff --git a/latest/cases/01120/synopsis.txt b/latest/cases/01120/synopsis.txt new file mode 100644 index 000000000..810652f2f --- /dev/null +++ b/latest/cases/01120/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Test a delayed event trigger that transitions from false to true at t0. +componentTags: Compartment, EventWithDelay, RateRule, Species +testTags: Amount, EventT0Firing, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic + + This model has a delayed event which fires at t0 due to it being set 'initialValue=false'. + +The model contains: +* 1 species (S3) +* 1 compartment (comp) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Delay* | *Event Assignments* | +| E1 | $comp ≤ 5.1$ | false | $1.05$ | $S3 = 4$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | comp | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S3 | $2$ | variable | +| Initial volume of compartment 'comp' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01121/l2v5/index.heta b/latest/cases/01121/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01121/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01121/l3v2/build.log b/latest/cases/01121/l3v2/build.log new file mode 100644 index 000000000..cd037abb0 --- /dev/null +++ b/latest/cases/01121/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01121/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01121/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01121/model-sbml-l3v2.xml"... +[error] S1ref component does not exist which is not allowed for the "update" action. +[error] S2ref component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 98 +[error] Component "S1ref" is not found in space "nameless" as expected in expression: _J0 [ode_]= kinetics(k1___J0_local, k2, k3, k4, k5, S1, S1ref, S3, S4, S2); +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01121/l3v2/index.heta b/latest/cases/01121/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01121/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01121/model-sbml-l3v2.xml b/latest/cases/01121/model-sbml-l3v2.xml new file mode 100644 index 000000000..24c2f69eb --- /dev/null +++ b/latest/cases/01121/model-sbml-l3v2.xml @@ -0,0 +1,159 @@ + + + + + + + + + a + + + b + + + c + + + d + + + e + + + f + + + g + + + h + + + i + + + j + + + + + + + + a + + b + c + d + e + f + g + h + i + j + + 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + avogadro + 6.022 23 + + + + + + k1 + + + + + + + 1 + + + + + k4 + + + + + time + + + + + + + k1 + S1 + + + + + + + + + + + + + + + + + + + + kinetics + k1 + k2 + k3 + k4 + k5 + S1 + S1ref + S3 + S4 + S2 + + + + + + + + + + diff --git a/latest/cases/01121/synopsis.txt b/latest/cases/01121/synopsis.txt new file mode 100644 index 000000000..fc7275730 --- /dev/null +++ b/latest/cases/01121/synopsis.txt @@ -0,0 +1,53 @@ + +category: Test +synopsis: A combination test of almost everything but events. +componentTags: AssignmentRule, CSymbolAvogadro, CSymbolTime, Compartment, FunctionDefinition, InitialAssignment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, AssignedVariableStoichiometry, BoundaryCondition, ConstantSpecies, ConversionFactors, HasOnlySubstanceUnits, InitialValueReassigned, LocalParameters, MultiCompartment, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A stripped-down version of model 1000, without events. Designed to test a lot of thing in concert. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 8 parameters (kavo, k1, k3, k4, k5, k2, conversion1, conversion2) +* 2 compartments (comp, comp2) + +It also contains 1 function definition(s): +; kinetics: $(-a + b + c + d + e + f + g + h + i + j) / 10$ + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: S3 + S1ref S1 -> S2ref S2 | $kinetics(k1, k2, k3, k4, k5, S1, S1ref, S3, S4, S2)$ |] +Note: the following stoichiometries are set separately: S1ref, S2ref + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | comp | $1$ | +| Assignment | comp2 | $k4$ | +| Rate | k4 | $time$ | +| Assignment | S2ref | $k1 * S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S4 | $2$ | constant | +| Initial amount of species S1 | $1$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial amount of species S3 | $4$ | variable | +| Initial value of parameter kavo | $avogadro / 6.022000e+023$ | constant | +| Initial value of parameter k1 | $1.1$ | constant | +| Initial value of parameter k2 | $8.12$ | constant | +| Initial value of parameter conversion1 | $10$ | constant | +| Initial value of parameter conversion2 | $100$ | constant | +| Initial value of parameter k3 | $2.5$ | variable | +| Initial value of parameter k4 | $1$ | variable | +| Initial value of parameter k5 | $2.8$ | variable | +| Initial volume of compartment 'comp' | $5$ | variable | +| Initial volume of compartment 'comp2' | $k4$ | variable |] + diff --git a/latest/cases/01122/l2v5/heta-code/output.heta b/latest/cases/01122/l2v5/heta-code/output.heta new file mode 100644 index 000000000..844803946 --- /dev/null +++ b/latest/cases/01122/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +comp @Compartment { } .= 5; + +S1 @Species { compartment: comp, } .= 1 / comp; +S3 @Species { boundary: true, compartment: comp, } .= 4 / comp; + +_J0 @Reaction { actors: S1 = , modifiers: [S3], }; +_J0 := S3 / 10; +comp_proc @Process { actors: = comp, }; +comp_proc := 1; + diff --git a/latest/cases/01122/l2v5/index.heta b/latest/cases/01122/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01122/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01122/l2v5/json/output.json b/latest/cases/01122/l2v5/json/output.json new file mode 100644 index 000000000..50945583f --- /dev/null +++ b/latest/cases/01122/l2v5/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / comp" + }, + "compartment": "comp" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "4 / comp" + }, + "boundary": true, + "compartment": "comp" + }, + { + "class": "Reaction", + "id": "_J0", + "assignments": { + "ode_": "S3 / 10" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": -1 + } + ], + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Process", + "id": "comp_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "comp", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01122/l3v2/heta-code/output.heta b/latest/cases/01122/l3v2/heta-code/output.heta new file mode 100644 index 000000000..496b550e4 --- /dev/null +++ b/latest/cases/01122/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +comp @Compartment { } .= 5; + +S1 @Species { compartment: comp, } .= 1 / comp; +S3 @Species { boundary: true, compartment: comp, } .= 4 / comp; + +_J0 @Reaction { actors: S1 = , modifiers: [S3], }; +_J0 := S3 / 10; +comp_proc @Process { actors: = comp, }; +comp_proc := 1; + diff --git a/latest/cases/01122/l3v2/index.heta b/latest/cases/01122/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01122/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01122/l3v2/json/output.json b/latest/cases/01122/l3v2/json/output.json new file mode 100644 index 000000000..ceef7887f --- /dev/null +++ b/latest/cases/01122/l3v2/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / comp" + }, + "compartment": "comp" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "4 / comp" + }, + "boundary": true, + "compartment": "comp" + }, + { + "class": "Reaction", + "id": "_J0", + "assignments": { + "ode_": "S3 / 10" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": -1 + } + ], + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Process", + "id": "comp_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "comp", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01122/model-sbml-l2v5.xml b/latest/cases/01122/model-sbml-l2v5.xml new file mode 100644 index 000000000..f17cf8f85 --- /dev/null +++ b/latest/cases/01122/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + S3 + 10 + + + + + + + diff --git a/latest/cases/01122/model-sbml-l3v2.xml b/latest/cases/01122/model-sbml-l3v2.xml new file mode 100644 index 000000000..a73a50439 --- /dev/null +++ b/latest/cases/01122/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + S3 + 10 + + + + + + + diff --git a/latest/cases/01122/output.heta b/latest/cases/01122/output.heta new file mode 100644 index 000000000..3b9b843bc --- /dev/null +++ b/latest/cases/01122/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Test of proper interpretation of a boundary species set hasOnlySubstanceUnits=false in a reaction rate. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, BoundaryCondition, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + This model is a further simplification of test 1000/1121 that only test the use of a boundary species, used in the model in terms of concentrations, from a compartment that varies in time, used in a reaction rate, with hasOnlySubstanceUnits = false. + +The model contains: +* 2 species (S1, S3) +* 1 compartment (comp) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: S1 -> | $S3 / 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | comp | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $4$ | variable | +| Initial volume of compartment 'comp' | $5$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +comp @Compartment { } .= 5; + +S1 @Species { compartment: comp, } .= 1 / comp; +S3 @Species { boundary: true, compartment: comp, } .= 4 / comp; + +_J0 @Reaction { actors: S1 = , modifiers: [S3], }; +_J0 := S3 / 10; +comp_proc @Process { actors: = comp, }; +comp_proc := 1; + diff --git a/latest/cases/01122/synopsis.txt b/latest/cases/01122/synopsis.txt new file mode 100644 index 000000000..ddcaf7211 --- /dev/null +++ b/latest/cases/01122/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Test of proper interpretation of a boundary species set hasOnlySubstanceUnits=false in a reaction rate. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, BoundaryCondition, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + This model is a further simplification of test 1000/1121 that only test the use of a boundary species, used in the model in terms of concentrations, from a compartment that varies in time, used in a reaction rate, with hasOnlySubstanceUnits = false. + +The model contains: +* 2 species (S1, S3) +* 1 compartment (comp) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: S1 -> | $S3 / 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | comp | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $4$ | variable | +| Initial volume of compartment 'comp' | $5$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01123/l2v5/index.heta b/latest/cases/01123/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01123/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01123/l3v2/heta-code/output.heta b/latest/cases/01123/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6c6d695ae --- /dev/null +++ b/latest/cases/01123/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +comp @Compartment { } .= 5; + +S1 @Species { compartment: comp, } .= 1 / comp; +S3 @Species { boundary: true, compartment: comp, isAmount: true, } .= 4; + +_J0 @Reaction { actors: S1 = , modifiers: [S3], }; +_J0 := S3 / 10; +comp_proc @Process { actors: = comp, }; +comp_proc := 1; + diff --git a/latest/cases/01123/l3v2/index.heta b/latest/cases/01123/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01123/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01123/l3v2/json/output.json b/latest/cases/01123/l3v2/json/output.json new file mode 100644 index 000000000..711ac4fbd --- /dev/null +++ b/latest/cases/01123/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / comp" + }, + "compartment": "comp" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "4" + }, + "boundary": true, + "compartment": "comp", + "isAmount": true + }, + { + "class": "Reaction", + "id": "_J0", + "assignments": { + "ode_": "S3 / 10" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": -1 + } + ], + "modifiers": [ + { + "target": "S3" + } + ] + }, + { + "class": "Process", + "id": "comp_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "comp", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01123/model-sbml-l3v2.xml b/latest/cases/01123/model-sbml-l3v2.xml new file mode 100644 index 000000000..ddc8dd220 --- /dev/null +++ b/latest/cases/01123/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + S3 + 10 + + + + + + + diff --git a/latest/cases/01123/output.heta b/latest/cases/01123/output.heta new file mode 100644 index 000000000..06d292e9e --- /dev/null +++ b/latest/cases/01123/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: Test of proper interpretation of a boundary species set hasOnlySubstanceUnits=true in a reaction rate. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + This model is a further simplification of test 1000/1121 that only test the use of a boundary species, used in the model in terms of concentrations, from a compartment that varies in time, used in a reaction rate, with hasOnlySubstanceUnits = true. + +The model contains: +* 2 species (S1, S3) +* 1 compartment (comp) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: S1 -> | $S3 / 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | comp | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $4$ | variable | +| Initial volume of compartment 'comp' | $5$ | variable |] + +*/ + + + +t @TimeScale { }; + +comp @Compartment { } .= 5; + +S1 @Species { compartment: comp, } .= 1 / comp; +S3 @Species { boundary: true, compartment: comp, isAmount: true, } .= 4; + +_J0 @Reaction { actors: S1 = , modifiers: [S3], }; +_J0 := S3 / 10; +comp_proc @Process { actors: = comp, }; +comp_proc := 1; + diff --git a/latest/cases/01123/synopsis.txt b/latest/cases/01123/synopsis.txt new file mode 100644 index 000000000..3edf3af90 --- /dev/null +++ b/latest/cases/01123/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Test of proper interpretation of a boundary species set hasOnlySubstanceUnits=true in a reaction rate. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + This model is a further simplification of test 1000/1121 that only test the use of a boundary species, used in the model in terms of concentrations, from a compartment that varies in time, used in a reaction rate, with hasOnlySubstanceUnits = true. + +The model contains: +* 2 species (S1, S3) +* 1 compartment (comp) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: S1 -> | $S3 / 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | comp | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S3 | $4$ | variable | +| Initial volume of compartment 'comp' | $5$ | variable |] + diff --git a/latest/cases/01124/l2v5/index.heta b/latest/cases/01124/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01124/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01124/l3v2/heta-code/output.heta b/latest/cases/01124/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1784d13d7 --- /dev/null +++ b/latest/cases/01124/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +param1 @Const { } = 10.42; + diff --git a/latest/cases/01124/l3v2/index.heta b/latest/cases/01124/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01124/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01124/l3v2/json/output.json b/latest/cases/01124/l3v2/json/output.json new file mode 100644 index 000000000..5f2685e84 --- /dev/null +++ b/latest/cases/01124/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "param1", + "num": 10.42 + } +] \ No newline at end of file diff --git a/latest/cases/01124/model-sbml-l3v2.xml b/latest/cases/01124/model-sbml-l3v2.xml new file mode 100644 index 000000000..f28c569a4 --- /dev/null +++ b/latest/cases/01124/model-sbml-l3v2.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01124/output.heta b/latest/cases/01124/output.heta new file mode 100644 index 000000000..702fd28c2 --- /dev/null +++ b/latest/cases/01124/output.heta @@ -0,0 +1,30 @@ +/* +category: Test +synopsis: Simple non-required comp model. +componentTags: Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This hierarchical model replaces the single parameter in the submodel, and therefore behaves as if the submodel did not exist. The comp package 'required' attribute is therefore 'false', meaning that the mathematical meaning of the model is not changed by the presence of 'comp' elements. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (param1) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter param1 | $10.42$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +param1 @Const { } = 10.42; + diff --git a/latest/cases/01124/synopsis.txt b/latest/cases/01124/synopsis.txt new file mode 100644 index 000000000..2fb432097 --- /dev/null +++ b/latest/cases/01124/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: Simple non-required comp model. +componentTags: Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This hierarchical model replaces the single parameter in the submodel, and therefore behaves as if the submodel did not exist. The comp package 'required' attribute is therefore 'false', meaning that the mathematical meaning of the model is not changed by the presence of 'comp' elements. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (param1) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter param1 | $10.42$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01125/l2v5/index.heta b/latest/cases/01125/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01125/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01125/l3v2/heta-code/output.heta b/latest/cases/01125/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1784d13d7 --- /dev/null +++ b/latest/cases/01125/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +param1 @Const { } = 10.42; + diff --git a/latest/cases/01125/l3v2/index.heta b/latest/cases/01125/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01125/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01125/l3v2/json/output.json b/latest/cases/01125/l3v2/json/output.json new file mode 100644 index 000000000..5f2685e84 --- /dev/null +++ b/latest/cases/01125/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "param1", + "num": 10.42 + } +] \ No newline at end of file diff --git a/latest/cases/01125/model-sbml-l3v2.xml b/latest/cases/01125/model-sbml-l3v2.xml new file mode 100644 index 000000000..8a27754f1 --- /dev/null +++ b/latest/cases/01125/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01125/output.heta b/latest/cases/01125/output.heta new file mode 100644 index 000000000..e3c6356ea --- /dev/null +++ b/latest/cases/01125/output.heta @@ -0,0 +1,30 @@ +/* +category: Test +synopsis: Simple non-required comp model +componentTags: Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This hierarchical model replaces the single parameter in the submodel, and therefore behaves as if the submodel did not exist. The comp package 'required' attribute is therefore 'false', meaning that the mathematical meaning of the model is not changed by the presence of 'comp' elements. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (param1) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter param1 | $10.42$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +param1 @Const { } = 10.42; + diff --git a/latest/cases/01125/synopsis.txt b/latest/cases/01125/synopsis.txt new file mode 100644 index 000000000..9d26c8854 --- /dev/null +++ b/latest/cases/01125/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: Simple non-required comp model +componentTags: Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This hierarchical model replaces the single parameter in the submodel, and therefore behaves as if the submodel did not exist. The comp package 'required' attribute is therefore 'false', meaning that the mathematical meaning of the model is not changed by the presence of 'comp' elements. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (param1) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter param1 | $10.42$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01126/l2v5/index.heta b/latest/cases/01126/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01126/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01126/l3v2/heta-code/output.heta b/latest/cases/01126/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1784d13d7 --- /dev/null +++ b/latest/cases/01126/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +param1 @Const { } = 10.42; + diff --git a/latest/cases/01126/l3v2/index.heta b/latest/cases/01126/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01126/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01126/l3v2/json/output.json b/latest/cases/01126/l3v2/json/output.json new file mode 100644 index 000000000..5f2685e84 --- /dev/null +++ b/latest/cases/01126/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "param1", + "num": 10.42 + } +] \ No newline at end of file diff --git a/latest/cases/01126/model-sbml-l3v2.xml b/latest/cases/01126/model-sbml-l3v2.xml new file mode 100644 index 000000000..59e38e196 --- /dev/null +++ b/latest/cases/01126/model-sbml-l3v2.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01126/output.heta b/latest/cases/01126/output.heta new file mode 100644 index 000000000..bde53da8b --- /dev/null +++ b/latest/cases/01126/output.heta @@ -0,0 +1,31 @@ +/* +category: Test +synopsis: A simple hierarchical model with a submodel parameter +componentTags: Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +There are two parameters in this model, one in the parent model which replaces a paramter in the submodel, and a second parameter from the submodel that remains unreplaced. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (param1, submod1__subparam2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter param1 | $10.42$ | constant | +| Initial value of parameter submod1__subparam2 | $6$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +param1 @Const { } = 10.42; + diff --git a/latest/cases/01126/synopsis.txt b/latest/cases/01126/synopsis.txt new file mode 100644 index 000000000..0615d0357 --- /dev/null +++ b/latest/cases/01126/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: A simple hierarchical model with a submodel parameter +componentTags: Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +There are two parameters in this model, one in the parent model which replaces a paramter in the submodel, and a second parameter from the submodel that remains unreplaced. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (param1, submod1__subparam2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter param1 | $10.42$ | constant | +| Initial value of parameter submod1__subparam2 | $6$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01127/l2v5/index.heta b/latest/cases/01127/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01127/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01127/l3v2/heta-code/output.heta b/latest/cases/01127/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a8ab0bb7b --- /dev/null +++ b/latest/cases/01127/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +param1 @Record { } .= 10.42; + diff --git a/latest/cases/01127/l3v2/index.heta b/latest/cases/01127/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01127/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01127/l3v2/json/output.json b/latest/cases/01127/l3v2/json/output.json new file mode 100644 index 000000000..46351fc08 --- /dev/null +++ b/latest/cases/01127/l3v2/json/output.json @@ -0,0 +1,12 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "param1", + "assignments": { + "start_": "10.42" + } + } +] \ No newline at end of file diff --git a/latest/cases/01127/model-sbml-l3v2.xml b/latest/cases/01127/model-sbml-l3v2.xml new file mode 100644 index 000000000..fd7590ff4 --- /dev/null +++ b/latest/cases/01127/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + subparam2 + 6 + + + + + + + + + + + + 8 + subparam2 + + subparam1 + + + + + + + + + + diff --git a/latest/cases/01127/output.heta b/latest/cases/01127/output.heta new file mode 100644 index 000000000..0f56317e3 --- /dev/null +++ b/latest/cases/01127/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A hierarchical model with a submodel initial assignment and rate rule. +componentTags: InitialAssignment, Parameter, RateRule, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The parent model contains a parameter that replaces a paramter of the submodel. That submodel has an initial assignment and a rate rule that both affect that replaced parameter, and should continue to affect the replacement parameter. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (param1, submod1__subparam2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | param1 | $8 * submod1__subparam2 + param1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter submod1__subparam2 | $6$ | constant | +| Initial value of parameter param1 | $submod1__subparam2 + 6$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +param1 @Record { } .= 10.42; + diff --git a/latest/cases/01127/synopsis.txt b/latest/cases/01127/synopsis.txt new file mode 100644 index 000000000..7c3a762e0 --- /dev/null +++ b/latest/cases/01127/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a submodel initial assignment and rate rule. +componentTags: InitialAssignment, Parameter, RateRule, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The parent model contains a parameter that replaces a paramter of the submodel. That submodel has an initial assignment and a rate rule that both affect that replaced parameter, and should continue to affect the replacement parameter. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (param1, submod1__subparam2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | param1 | $8 * submod1__subparam2 + param1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter submod1__subparam2 | $6$ | constant | +| Initial value of parameter param1 | $submod1__subparam2 + 6$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01128/l2v5/index.heta b/latest/cases/01128/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01128/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01128/l3v2/build.log b/latest/cases/01128/l3v2/build.log new file mode 100644 index 000000000..bac926bdd --- /dev/null +++ b/latest/cases/01128/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01128/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01128/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01128/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 80 +[error] Record "param2" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01128/l3v2/index.heta b/latest/cases/01128/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01128/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01128/model-sbml-l3v2.xml b/latest/cases/01128/model-sbml-l3v2.xml new file mode 100644 index 000000000..ddfb1e754 --- /dev/null +++ b/latest/cases/01128/model-sbml-l3v2.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01128/synopsis.txt b/latest/cases/01128/synopsis.txt new file mode 100644 index 000000000..3f8410174 --- /dev/null +++ b/latest/cases/01128/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: A hierarchical model testing ReplacedBy +componentTags: Parameter, comp:ModelDefinition, comp:ReplacedBy, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model has a parameter in the parent model replaced by a parameter in the submodel. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (param2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter param2 | $6$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01129/l2v5/index.heta b/latest/cases/01129/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01129/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01129/l3v2/heta-code/output.heta b/latest/cases/01129/l3v2/heta-code/output.heta new file mode 100644 index 000000000..81c95b953 --- /dev/null +++ b/latest/cases/01129/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01129/l3v2/index.heta b/latest/cases/01129/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01129/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01129/l3v2/json/output.json b/latest/cases/01129/l3v2/json/output.json new file mode 100644 index 000000000..9b8c24daf --- /dev/null +++ b/latest/cases/01129/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "5 / C" + }, + "boundary": true, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01129/model-sbml-l3v2.xml b/latest/cases/01129/model-sbml-l3v2.xml new file mode 100644 index 000000000..8f66000aa --- /dev/null +++ b/latest/cases/01129/model-sbml-l3v2.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01129/output.heta b/latest/cases/01129/output.heta new file mode 100644 index 000000000..3b62e202b --- /dev/null +++ b/latest/cases/01129/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: An aggregate model with species. +componentTags: Compartment, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, ConstantSpecies, MultiCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +A simple multi-level aggregate model with species and compartments. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1) +* 4 compartments (C, sub1__C, sub2__C, sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | constant | +| Initial amount of species sub1__S1 | $7$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial amount of species sub2__sub1__S1 | $7$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub2__sub1__C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01129/synopsis.txt b/latest/cases/01129/synopsis.txt new file mode 100644 index 000000000..8c5022c7a --- /dev/null +++ b/latest/cases/01129/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An aggregate model with species. +componentTags: Compartment, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, ConstantSpecies, MultiCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +A simple multi-level aggregate model with species and compartments. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1) +* 4 compartments (C, sub1__C, sub2__C, sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | constant | +| Initial amount of species sub1__S1 | $7$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial amount of species sub2__sub1__S1 | $7$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub2__sub1__C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01130/l2v5/index.heta b/latest/cases/01130/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01130/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01130/l3v2/heta-code/output.heta b/latest/cases/01130/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bc9f44110 --- /dev/null +++ b/latest/cases/01130/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 10; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01130/l3v2/index.heta b/latest/cases/01130/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01130/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01130/l3v2/json/output.json b/latest/cases/01130/l3v2/json/output.json new file mode 100644 index 000000000..623e42343 --- /dev/null +++ b/latest/cases/01130/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "5 / C" + }, + "boundary": true, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01130/model-sbml-l3v2.xml b/latest/cases/01130/model-sbml-l3v2.xml new file mode 100644 index 000000000..ca31c0056 --- /dev/null +++ b/latest/cases/01130/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01130/output.heta b/latest/cases/01130/output.heta new file mode 100644 index 000000000..99f3a7fb6 --- /dev/null +++ b/latest/cases/01130/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: A hierarchical model with a sub-submodel compartment replacement. +componentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, ConstantSpecies, NonUnityCompartment, MultiCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model tests replacing a compartment in a sub-submodel with a comparment from the parent model, changing the concentration of the species in that submodel. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1) +* 3 compartments (C, sub1__C, sub2__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | constant | +| Initial amount of species sub1__S1 | $7$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial amount of species sub2__sub1__S1 | $7$ | constant | +| Initial volume of compartment 'C' | $10$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 10; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01130/synopsis.txt b/latest/cases/01130/synopsis.txt new file mode 100644 index 000000000..577c22890 --- /dev/null +++ b/latest/cases/01130/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A hierarchical model with a sub-submodel compartment replacement. +componentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, ConstantSpecies, NonUnityCompartment, MultiCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model tests replacing a compartment in a sub-submodel with a comparment from the parent model, changing the concentration of the species in that submodel. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1) +* 3 compartments (C, sub1__C, sub2__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | constant | +| Initial amount of species sub1__S1 | $7$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial amount of species sub2__sub1__S1 | $7$ | constant | +| Initial volume of compartment 'C' | $10$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01131/l2v5/index.heta b/latest/cases/01131/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01131/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01131/l3v2/heta-code/output.heta b/latest/cases/01131/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bc9f44110 --- /dev/null +++ b/latest/cases/01131/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 10; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01131/l3v2/index.heta b/latest/cases/01131/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01131/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01131/l3v2/json/output.json b/latest/cases/01131/l3v2/json/output.json new file mode 100644 index 000000000..623e42343 --- /dev/null +++ b/latest/cases/01131/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "5 / C" + }, + "boundary": true, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01131/model-sbml-l3v2.xml b/latest/cases/01131/model-sbml-l3v2.xml new file mode 100644 index 000000000..59c113033 --- /dev/null +++ b/latest/cases/01131/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01131/output.heta b/latest/cases/01131/output.heta new file mode 100644 index 000000000..0e02fe6d6 --- /dev/null +++ b/latest/cases/01131/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A three-level-deep hierarchical model. +componentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, ConstantSpecies, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model contains submodels three levels deep. A compartment replacement changes the concentration of a species. + +The 'flattened' version of this hierarchical model contains: +* 8 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1, sub3__sub2__sub1__S1) +* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | constant | +| Initial amount of species sub1__S1 | $7$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial amount of species sub2__sub1__S1 | $7$ | constant | +| Initial amount of species sub3__S1 | $11$ | constant | +| Initial amount of species sub3__sub1__S1 | $7$ | constant | +| Initial amount of species sub3__sub2__S1 | $9$ | constant | +| Initial amount of species sub3__sub2__sub1__S1 | $7$ | constant | +| Initial volume of compartment 'C' | $10$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 10; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01131/synopsis.txt b/latest/cases/01131/synopsis.txt new file mode 100644 index 000000000..dc755fe8f --- /dev/null +++ b/latest/cases/01131/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: A three-level-deep hierarchical model. +componentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, ConstantSpecies, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model contains submodels three levels deep. A compartment replacement changes the concentration of a species. + +The 'flattened' version of this hierarchical model contains: +* 8 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1, sub3__sub2__sub1__S1) +* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | constant | +| Initial amount of species sub1__S1 | $7$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial amount of species sub2__sub1__S1 | $7$ | constant | +| Initial amount of species sub3__S1 | $11$ | constant | +| Initial amount of species sub3__sub1__S1 | $7$ | constant | +| Initial amount of species sub3__sub2__S1 | $9$ | constant | +| Initial amount of species sub3__sub2__sub1__S1 | $7$ | constant | +| Initial volume of compartment 'C' | $10$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01132/l2v5/index.heta b/latest/cases/01132/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01132/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01132/l3v2/heta-code/output.heta b/latest/cases/01132/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bc9f44110 --- /dev/null +++ b/latest/cases/01132/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 10; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01132/l3v2/index.heta b/latest/cases/01132/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01132/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01132/l3v2/json/output.json b/latest/cases/01132/l3v2/json/output.json new file mode 100644 index 000000000..623e42343 --- /dev/null +++ b/latest/cases/01132/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "5 / C" + }, + "boundary": true, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01132/model-sbml-l3v2.xml b/latest/cases/01132/model-sbml-l3v2.xml new file mode 100644 index 000000000..87573f244 --- /dev/null +++ b/latest/cases/01132/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01132/output.heta b/latest/cases/01132/output.heta new file mode 100644 index 000000000..233f6e9cc --- /dev/null +++ b/latest/cases/01132/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A hierarchical model with a three-level-deep replacement. +componentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, ConstantSpecies, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model contains submodels three levels deep, with the top model replacing the species at the deepest level, and the compartment at a level two down. + +The 'flattened' version of this hierarchical model contains: +* 7 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1) +* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | constant | +| Initial amount of species sub1__S1 | $7$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial amount of species sub2__sub1__S1 | $7$ | constant | +| Initial amount of species sub3__S1 | $11$ | constant | +| Initial amount of species sub3__sub1__S1 | $7$ | constant | +| Initial amount of species sub3__sub2__S1 | $9$ | constant | +| Initial volume of compartment 'C' | $10$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 10; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01132/synopsis.txt b/latest/cases/01132/synopsis.txt new file mode 100644 index 000000000..a115a8a0b --- /dev/null +++ b/latest/cases/01132/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A hierarchical model with a three-level-deep replacement. +componentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, ConstantSpecies, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model contains submodels three levels deep, with the top model replacing the species at the deepest level, and the compartment at a level two down. + +The 'flattened' version of this hierarchical model contains: +* 7 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1) +* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $5$ | constant | +| Initial amount of species sub1__S1 | $7$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial amount of species sub2__sub1__S1 | $7$ | constant | +| Initial amount of species sub3__S1 | $11$ | constant | +| Initial amount of species sub3__sub1__S1 | $7$ | constant | +| Initial amount of species sub3__sub2__S1 | $9$ | constant | +| Initial volume of compartment 'C' | $10$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01133/l2v5/index.heta b/latest/cases/01133/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01133/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01133/l3v2/heta-code/output.heta b/latest/cases/01133/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bc9f44110 --- /dev/null +++ b/latest/cases/01133/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 10; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01133/l3v2/index.heta b/latest/cases/01133/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01133/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01133/l3v2/json/output.json b/latest/cases/01133/l3v2/json/output.json new file mode 100644 index 000000000..623e42343 --- /dev/null +++ b/latest/cases/01133/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "10" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "5 / C" + }, + "boundary": true, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01133/model-sbml-l3v2.xml b/latest/cases/01133/model-sbml-l3v2.xml new file mode 100644 index 000000000..ea8ce3519 --- /dev/null +++ b/latest/cases/01133/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01133/output.heta b/latest/cases/01133/output.heta new file mode 100644 index 000000000..2f49edf90 --- /dev/null +++ b/latest/cases/01133/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: A species replacing one thing and replaced by something else. +componentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, ConstantSpecies, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + A three-level deep hierarchical model with a replaced compartment, and a top-level species that replaces a three-deep speces, and is replaced in turn by a two-deep species. + +The 'flattened' version of this hierarchical model contains: +* 6 species (sub1__S1, sub2__S1, S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1) +* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species sub1__S1 | $2.5$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial concentration of species S1 | $2.5$ | constant | +| Initial amount of species sub3__S1 | $11$ | constant | +| Initial concentration of species sub3__sub1__S1 | $2.5$ | constant | +| Initial amount of species sub3__sub2__S1 | $9$ | constant | +| Initial volume of compartment 'C' | $10$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 10; + +S1 @Species { boundary: true, compartment: C, } .= 5 / C; + diff --git a/latest/cases/01133/synopsis.txt b/latest/cases/01133/synopsis.txt new file mode 100644 index 000000000..7e2d09f01 --- /dev/null +++ b/latest/cases/01133/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A species replacing one thing and replaced by something else. +componentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, ConstantSpecies, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + A three-level deep hierarchical model with a replaced compartment, and a top-level species that replaces a three-deep speces, and is replaced in turn by a two-deep species. + +The 'flattened' version of this hierarchical model contains: +* 6 species (sub1__S1, sub2__S1, S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1) +* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species sub1__S1 | $2.5$ | constant | +| Initial amount of species sub2__S1 | $9$ | constant | +| Initial concentration of species S1 | $2.5$ | constant | +| Initial amount of species sub3__S1 | $11$ | constant | +| Initial concentration of species sub3__sub1__S1 | $2.5$ | constant | +| Initial amount of species sub3__sub2__S1 | $9$ | constant | +| Initial volume of compartment 'C' | $10$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub1__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__C' | $1$ | constant | +| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01134/l2v5/index.heta b/latest/cases/01134/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01134/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01134/l3v2/heta-code/output.heta b/latest/cases/01134/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ce14aa543 --- /dev/null +++ b/latest/cases/01134/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +C @Compartment { } .= 10; + +S1 @Species { compartment: C, } .= 5 / C; + diff --git a/latest/cases/01134/l3v2/index.heta b/latest/cases/01134/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01134/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01134/l3v2/json/output.json b/latest/cases/01134/l3v2/json/output.json new file mode 100644 index 000000000..5e2c66500 --- /dev/null +++ b/latest/cases/01134/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "10" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "5 / C" + }, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01134/model-sbml-l3v2.xml b/latest/cases/01134/model-sbml-l3v2.xml new file mode 100644 index 000000000..e008deabe --- /dev/null +++ b/latest/cases/01134/model-sbml-l3v2.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01134/output.heta b/latest/cases/01134/output.heta new file mode 100644 index 000000000..742b3797e --- /dev/null +++ b/latest/cases/01134/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: A species replacing one thing and replaced by something else, with ports. +componentTags: Compartment, Species, comp:ModelDefinition, comp:Port, comp:ReplacedBy, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model is exactly the same as model 01133, but additionally contains ports in the parent model. They are (obviously) unused, so this is simply a test to ensure that their presence doesn't confuse the simulator. + +The 'flattened' version of this hierarchical model contains: +* 6 species (sub1__S1, sub2__S1, S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1) +* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species sub1__S1 | $2.5$ | variable | +| Initial amount of species sub2__S1 | $9$ | variable | +| Initial concentration of species S1 | $2.5$ | variable | +| Initial amount of species sub3__S1 | $11$ | variable | +| Initial concentration of species sub3__sub1__S1 | $2.5$ | variable | +| Initial amount of species sub3__sub2__S1 | $9$ | variable | +| Initial volume of compartment 'C' | $10$ | variable | +| Initial volume of compartment 'sub1__C' | $1$ | variable | +| Initial volume of compartment 'sub2__C' | $1$ | variable | +| Initial volume of compartment 'sub3__C' | $1$ | variable | +| Initial volume of compartment 'sub3__sub1__C' | $1$ | variable | +| Initial volume of compartment 'sub3__sub2__C' | $1$ | variable | +| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { } .= 10; + +S1 @Species { compartment: C, } .= 5 / C; + diff --git a/latest/cases/01134/synopsis.txt b/latest/cases/01134/synopsis.txt new file mode 100644 index 000000000..c76d345ba --- /dev/null +++ b/latest/cases/01134/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A species replacing one thing and replaced by something else, with ports. +componentTags: Compartment, Species, comp:ModelDefinition, comp:Port, comp:ReplacedBy, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Concentration, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model is exactly the same as model 01133, but additionally contains ports in the parent model. They are (obviously) unused, so this is simply a test to ensure that their presence doesn't confuse the simulator. + +The 'flattened' version of this hierarchical model contains: +* 6 species (sub1__S1, sub2__S1, S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1) +* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species sub1__S1 | $2.5$ | variable | +| Initial amount of species sub2__S1 | $9$ | variable | +| Initial concentration of species S1 | $2.5$ | variable | +| Initial amount of species sub3__S1 | $11$ | variable | +| Initial concentration of species sub3__sub1__S1 | $2.5$ | variable | +| Initial amount of species sub3__sub2__S1 | $9$ | variable | +| Initial volume of compartment 'C' | $10$ | variable | +| Initial volume of compartment 'sub1__C' | $1$ | variable | +| Initial volume of compartment 'sub2__C' | $1$ | variable | +| Initial volume of compartment 'sub3__C' | $1$ | variable | +| Initial volume of compartment 'sub3__sub1__C' | $1$ | variable | +| Initial volume of compartment 'sub3__sub2__C' | $1$ | variable | +| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01135/l2v5/index.heta b/latest/cases/01135/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01135/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01135/l3v2/heta-code/output.heta b/latest/cases/01135/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ca5ee7cf1 --- /dev/null +++ b/latest/cases/01135/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +p2 @Record { } .= 2; + diff --git a/latest/cases/01135/l3v2/index.heta b/latest/cases/01135/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01135/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01135/l3v2/json/output.json b/latest/cases/01135/l3v2/json/output.json new file mode 100644 index 000000000..3520fd97d --- /dev/null +++ b/latest/cases/01135/l3v2/json/output.json @@ -0,0 +1,12 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "start_": "2" + } + } +] \ No newline at end of file diff --git a/latest/cases/01135/model-sbml-l3v2.xml b/latest/cases/01135/model-sbml-l3v2.xml new file mode 100644 index 000000000..d104598d8 --- /dev/null +++ b/latest/cases/01135/model-sbml-l3v2.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01135/output.heta b/latest/cases/01135/output.heta new file mode 100644 index 000000000..56b9b32f6 --- /dev/null +++ b/latest/cases/01135/output.heta @@ -0,0 +1,30 @@ +/* +category: Test +synopsis: Hierarchical model with chained replacedBys. +componentTags: Parameter, comp:ModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The parameter in the parent model is replaced by a parameter in the submodel, which in turn is replaced by a parameter in *its* submodel. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p2 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p2 @Record { } .= 2; + diff --git a/latest/cases/01135/synopsis.txt b/latest/cases/01135/synopsis.txt new file mode 100644 index 000000000..4522179e2 --- /dev/null +++ b/latest/cases/01135/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: Hierarchical model with chained replacedBys. +componentTags: Parameter, comp:ModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The parameter in the parent model is replaced by a parameter in the submodel, which in turn is replaced by a parameter in *its* submodel. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p2 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01136/l2v5/index.heta b/latest/cases/01136/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01136/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01136/l3v2/heta-code/output.heta b/latest/cases/01136/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ca5ee7cf1 --- /dev/null +++ b/latest/cases/01136/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +p2 @Record { } .= 2; + diff --git a/latest/cases/01136/l3v2/index.heta b/latest/cases/01136/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01136/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01136/l3v2/json/output.json b/latest/cases/01136/l3v2/json/output.json new file mode 100644 index 000000000..3520fd97d --- /dev/null +++ b/latest/cases/01136/l3v2/json/output.json @@ -0,0 +1,12 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "start_": "2" + } + } +] \ No newline at end of file diff --git a/latest/cases/01136/model-sbml-l3v2.xml b/latest/cases/01136/model-sbml-l3v2.xml new file mode 100644 index 000000000..316404e85 --- /dev/null +++ b/latest/cases/01136/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01136/output.heta b/latest/cases/01136/output.heta new file mode 100644 index 000000000..9b639b207 --- /dev/null +++ b/latest/cases/01136/output.heta @@ -0,0 +1,30 @@ +/* +category: Test +synopsis: Chained replaced/replacedBy elements. +componentTags: Parameter, comp:ModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + Despite starting off with five parameters at three levels, all aggregate parameters collapse down to a single parameter, as one set is replaced by parameters in models above them, and the other is replaced by parameters below them. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p2 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p2 @Record { } .= 2; + diff --git a/latest/cases/01136/synopsis.txt b/latest/cases/01136/synopsis.txt new file mode 100644 index 000000000..965983f93 --- /dev/null +++ b/latest/cases/01136/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: Chained replaced/replacedBy elements. +componentTags: Parameter, comp:ModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + Despite starting off with five parameters at three levels, all aggregate parameters collapse down to a single parameter, as one set is replaced by parameters in models above them, and the other is replaced by parameters below them. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p2 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01137/l2v5/index.heta b/latest/cases/01137/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01137/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01137/l3v2/build.log b/latest/cases/01137/l3v2/build.log new file mode 100644 index 000000000..dd28aa7b5 --- /dev/null +++ b/latest/cases/01137/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01137/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01137/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01137/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] Record "p8" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01137/l3v2/index.heta b/latest/cases/01137/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01137/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01137/model-sbml-l3v2.xml b/latest/cases/01137/model-sbml-l3v2.xml new file mode 100644 index 000000000..15e450266 --- /dev/null +++ b/latest/cases/01137/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + 80 + + + + + + diff --git a/latest/cases/01137/synopsis.txt b/latest/cases/01137/synopsis.txt new file mode 100644 index 000000000..b26e38f5b --- /dev/null +++ b/latest/cases/01137/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Hierarchical model with conversion factor test. +componentTags: AssignmentRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model is a simple test of a replacement with a conversion factor that affects the assignment rule of the replaced parameter. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (p8, conv) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p8 | $80 * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial value of parameter p8 | $80 * conv$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01138/l2v5/index.heta b/latest/cases/01138/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01138/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01138/l3v2/heta-code/output.heta b/latest/cases/01138/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7c3633600 --- /dev/null +++ b/latest/cases/01138/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +p8 @Record { } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01138/l3v2/index.heta b/latest/cases/01138/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01138/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01138/l3v2/json/output.json b/latest/cases/01138/l3v2/json/output.json new file mode 100644 index 000000000..9cb8d6976 --- /dev/null +++ b/latest/cases/01138/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "start_": "8" + } + }, + { + "class": "Const", + "id": "conv", + "num": 0.1 + } +] \ No newline at end of file diff --git a/latest/cases/01138/model-sbml-l3v2.xml b/latest/cases/01138/model-sbml-l3v2.xml new file mode 100644 index 000000000..bf71c4f60 --- /dev/null +++ b/latest/cases/01138/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + p80 + 8 + + + + + + + diff --git a/latest/cases/01138/output.heta b/latest/cases/01138/output.heta new file mode 100644 index 000000000..172afd8bd --- /dev/null +++ b/latest/cases/01138/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: A hierarchical model with a conversion factor +componentTags: AssignmentRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:ConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model is a simple test of a replacement with a conversion factor that affects the assignment rule of another parameter. + +The 'flattened' version of this hierarchical model contains: +* 3 parameters (p8, conv, sub1__prel) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__prel | $p8 / conv / 8$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial value of parameter p8 | $8$ | variable | +| Initial value of parameter sub1__prel | $p8 / conv / 8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p8 @Record { } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01138/synopsis.txt b/latest/cases/01138/synopsis.txt new file mode 100644 index 000000000..7264df6c1 --- /dev/null +++ b/latest/cases/01138/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A hierarchical model with a conversion factor +componentTags: AssignmentRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:ConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model is a simple test of a replacement with a conversion factor that affects the assignment rule of another parameter. + +The 'flattened' version of this hierarchical model contains: +* 3 parameters (p8, conv, sub1__prel) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__prel | $p8 / conv / 8$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial value of parameter p8 | $8$ | variable | +| Initial value of parameter sub1__prel | $p8 / conv / 8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01139/l2v5/index.heta b/latest/cases/01139/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01139/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01139/l3v2/heta-code/output.heta b/latest/cases/01139/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7c3633600 --- /dev/null +++ b/latest/cases/01139/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +p8 @Record { } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01139/l3v2/index.heta b/latest/cases/01139/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01139/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01139/l3v2/json/output.json b/latest/cases/01139/l3v2/json/output.json new file mode 100644 index 000000000..9cb8d6976 --- /dev/null +++ b/latest/cases/01139/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "start_": "8" + } + }, + { + "class": "Const", + "id": "conv", + "num": 0.1 + } +] \ No newline at end of file diff --git a/latest/cases/01139/model-sbml-l3v2.xml b/latest/cases/01139/model-sbml-l3v2.xml new file mode 100644 index 000000000..24e54f44d --- /dev/null +++ b/latest/cases/01139/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p80 + + 3 + + + + + + + diff --git a/latest/cases/01139/output.heta b/latest/cases/01139/output.heta new file mode 100644 index 000000000..719519f45 --- /dev/null +++ b/latest/cases/01139/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A hierarchical model with a conversion factor. +componentTags: Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model is a simple test of a replacement with a conversion factor that affects the rate rule of the replaced parameter. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (p8, conv) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p8 | $(4 * (p8 / conv) + 3) * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p8 @Record { } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01139/synopsis.txt b/latest/cases/01139/synopsis.txt new file mode 100644 index 000000000..777771b96 --- /dev/null +++ b/latest/cases/01139/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a conversion factor. +componentTags: Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model is a simple test of a replacement with a conversion factor that affects the rate rule of the replaced parameter. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (p8, conv) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p8 | $(4 * (p8 / conv) + 3) * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01140/l2v5/index.heta b/latest/cases/01140/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01140/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01140/l3v2/heta-code/output.heta b/latest/cases/01140/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2bcdb6e2d --- /dev/null +++ b/latest/cases/01140/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s8 @Species { compartment: C, isAmount: true, } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01140/l3v2/index.heta b/latest/cases/01140/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01140/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01140/l3v2/json/output.json b/latest/cases/01140/l3v2/json/output.json new file mode 100644 index 000000000..3997960f5 --- /dev/null +++ b/latest/cases/01140/l3v2/json/output.json @@ -0,0 +1,27 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s8", + "assignments": { + "start_": "8" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "conv", + "num": 0.1 + } +] \ No newline at end of file diff --git a/latest/cases/01140/model-sbml-l3v2.xml b/latest/cases/01140/model-sbml-l3v2.xml new file mode 100644 index 000000000..1cd026375 --- /dev/null +++ b/latest/cases/01140/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + s80 + + 3 + + + + + + + diff --git a/latest/cases/01140/output.heta b/latest/cases/01140/output.heta new file mode 100644 index 000000000..19644ce65 --- /dev/null +++ b/latest/cases/01140/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: A hierarchical model with a conversion factor on a species. +componentTags: Compartment, Parameter, RateRule, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, MultiCompartment, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model is a simple test of a replacement with a conversion factor that affects the rate rule of the replaced species. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s8) +* 1 parameter (conv) +* 2 compartments (C, sub1__C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | s8 | $(4 * (s8 / conv) + 3) * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s8 | $8$ | variable | +| Initial value of parameter conv | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s8 @Species { compartment: C, isAmount: true, } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01140/synopsis.txt b/latest/cases/01140/synopsis.txt new file mode 100644 index 000000000..7d5fe5871 --- /dev/null +++ b/latest/cases/01140/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A hierarchical model with a conversion factor on a species. +componentTags: Compartment, Parameter, RateRule, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, MultiCompartment, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model is a simple test of a replacement with a conversion factor that affects the rate rule of the replaced species. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s8) +* 1 parameter (conv) +* 2 compartments (C, sub1__C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | s8 | $(4 * (s8 / conv) + 3) * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s8 | $8$ | variable | +| Initial value of parameter conv | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01141/l2v5/index.heta b/latest/cases/01141/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01141/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01141/l3v2/heta-code/output.heta b/latest/cases/01141/l3v2/heta-code/output.heta new file mode 100644 index 000000000..fd164e1ae --- /dev/null +++ b/latest/cases/01141/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +C8 @Compartment { } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01141/l3v2/index.heta b/latest/cases/01141/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01141/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01141/l3v2/json/output.json b/latest/cases/01141/l3v2/json/output.json new file mode 100644 index 000000000..26794da6f --- /dev/null +++ b/latest/cases/01141/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C8", + "assignments": { + "start_": "8" + } + }, + { + "class": "Const", + "id": "conv", + "num": 0.1 + } +] \ No newline at end of file diff --git a/latest/cases/01141/model-sbml-l3v2.xml b/latest/cases/01141/model-sbml-l3v2.xml new file mode 100644 index 000000000..e28d29e11 --- /dev/null +++ b/latest/cases/01141/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + C80 + + 3 + + + + + + + diff --git a/latest/cases/01141/output.heta b/latest/cases/01141/output.heta new file mode 100644 index 000000000..ebcb4f701 --- /dev/null +++ b/latest/cases/01141/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: A hierarchical model with a conversion factor on a compartment. +componentTags: Compartment, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantCompartment, NonUnityCompartment, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model is a simple test of a replacement with a conversion factor that affects the rate rule of the replaced compartment. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (conv) +* 1 compartment (C8) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C8 | $(4 * (C8 / conv) + 3) * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial volume of compartment 'C8' | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C8 @Compartment { } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01141/synopsis.txt b/latest/cases/01141/synopsis.txt new file mode 100644 index 000000000..a6e469a46 --- /dev/null +++ b/latest/cases/01141/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A hierarchical model with a conversion factor on a compartment. +componentTags: Compartment, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantCompartment, NonUnityCompartment, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model is a simple test of a replacement with a conversion factor that affects the rate rule of the replaced compartment. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (conv) +* 1 compartment (C8) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C8 | $(4 * (C8 / conv) + 3) * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial volume of compartment 'C8' | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01142/l2v5/index.heta b/latest/cases/01142/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01142/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01142/l3v2/heta-code/output.heta b/latest/cases/01142/l3v2/heta-code/output.heta new file mode 100644 index 000000000..93e2545f0 --- /dev/null +++ b/latest/cases/01142/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 0.001; + +t1 @Record { } .= 1; +t2 @Record { } .= 1; +t3 @Record { } .= 1; +t4 @Record { } .= 1; +t5 @Record { } .= 1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01142/l3v2/index.heta b/latest/cases/01142/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01142/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01142/l3v2/json/output.json b/latest/cases/01142/l3v2/json/output.json new file mode 100644 index 000000000..f3bf8a619 --- /dev/null +++ b/latest/cases/01142/l3v2/json/output.json @@ -0,0 +1,62 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "0.001" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Record", + "id": "t1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "t2", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "t3", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "t4", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "t5", + "assignments": { + "start_": "1" + } + } +] \ No newline at end of file diff --git a/latest/cases/01142/model-sbml-l3v2.xml b/latest/cases/01142/model-sbml-l3v2.xml new file mode 100644 index 000000000..8d212de47 --- /dev/null +++ b/latest/cases/01142/model-sbml-l3v2.xml @@ -0,0 +1,172 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 3 + + + + + + + + + + + + time + t1 + + 3 + + + + + + + delay + t1 + 3 + + + + + + + + t4 + + delay + t3 + + + time + 2 + + + + + + + + + + + + + + + + + + t3 + time + + + + s1 + + delay + t5 + 2 -1 + + + + + + + + + + + + + + time + 3 + + + + + + + + 1 + time + + + + + + + time + + + + + + + + diff --git a/latest/cases/01142/output.heta b/latest/cases/01142/output.heta new file mode 100644 index 000000000..5b6f4d8f0 --- /dev/null +++ b/latest/cases/01142/output.heta @@ -0,0 +1,66 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion factor affecting many components. +componentTags: AlgebraicRule, AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, EventWithDelay, InitialAssignment, Parameter, RateRule, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + This model contains a submodel with various time-based constructs in it, contained in a model with a time conversion factor. For broken-down versions of this model that test only one construct at a time, see tests 01170-01177. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 6 parameters (timeconv, t1, t2, t3, t4, t5) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub1__J0: -> s1 | $1 / timeconv * (t3 * (time / timeconv) / (s1 * delay(t5, timeconv * 2.000000e-001)))$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| event_0 | $gt(time / timeconv, 3)$ | $timeconv * (1 / (time / timeconv))$ | $t5 = time / timeconv$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | t1 | $(time / timeconv / t1 + 3) / timeconv$ | +| Assignment | t3 | $delay(t1, timeconv * 3)$ | +| Algebraic | $0$ | $t4 - delay(t3, timeconv * (time / timeconv / 2))$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t1 | $1$ | variable | +| Initial value of parameter t2 | $time / timeconv + 3$ | variable | +| Initial value of parameter t3 | $delay(t1, timeconv * 3)$ | variable | +| Initial value of parameter t4 | $1$ | variable | +| Initial value of parameter t5 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 0.001; + +t1 @Record { } .= 1; +t2 @Record { } .= 1; +t3 @Record { } .= 1; +t4 @Record { } .= 1; +t5 @Record { } .= 1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01142/synopsis.txt b/latest/cases/01142/synopsis.txt new file mode 100644 index 000000000..d4e5ecb8c --- /dev/null +++ b/latest/cases/01142/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor affecting many components. +componentTags: AlgebraicRule, AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, EventWithDelay, InitialAssignment, Parameter, RateRule, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + This model contains a submodel with various time-based constructs in it, contained in a model with a time conversion factor. For broken-down versions of this model that test only one construct at a time, see tests 01170-01177. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 6 parameters (timeconv, t1, t2, t3, t4, t5) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub1__J0: -> s1 | $1 / timeconv * (t3 * (time / timeconv) / (s1 * delay(t5, timeconv * 2.000000e-001)))$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| event_0 | $gt(time / timeconv, 3)$ | $timeconv * (1 / (time / timeconv))$ | $t5 = time / timeconv$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | t1 | $(time / timeconv / t1 + 3) / timeconv$ | +| Assignment | t3 | $delay(t1, timeconv * 3)$ | +| Algebraic | $0$ | $t4 - delay(t3, timeconv * (time / timeconv / 2))$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t1 | $1$ | variable | +| Initial value of parameter t2 | $time / timeconv + 3$ | variable | +| Initial value of parameter t3 | $delay(t1, timeconv * 3)$ | variable | +| Initial value of parameter t4 | $1$ | variable | +| Initial value of parameter t5 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01143/l2v5/index.heta b/latest/cases/01143/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01143/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01143/l3v2/heta-code/output.heta b/latest/cases/01143/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2a4369a14 --- /dev/null +++ b/latest/cases/01143/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01143/l3v2/index.heta b/latest/cases/01143/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01143/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01143/l3v2/json/output.json b/latest/cases/01143/l3v2/json/output.json new file mode 100644 index 000000000..679092c23 --- /dev/null +++ b/latest/cases/01143/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + } +] \ No newline at end of file diff --git a/latest/cases/01143/model-sbml-l3v2.xml b/latest/cases/01143/model-sbml-l3v2.xml new file mode 100644 index 000000000..c12dc96e1 --- /dev/null +++ b/latest/cases/01143/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + 10 + + + + + + + diff --git a/latest/cases/01143/output.heta b/latest/cases/01143/output.heta new file mode 100644 index 000000000..139739e90 --- /dev/null +++ b/latest/cases/01143/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + +The reaction in the submodel must be converted by the extent conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 1 parameter (extentconv) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'sub1__C' | $0$ | constant |] + +*/ + + + +t @TimeScale { }; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01143/synopsis.txt b/latest/cases/01143/synopsis.txt new file mode 100644 index 000000000..5acfab230 --- /dev/null +++ b/latest/cases/01143/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + +The reaction in the submodel must be converted by the extent conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 1 parameter (extentconv) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'sub1__C' | $0$ | constant |] + diff --git a/latest/cases/01144/l2v5/index.heta b/latest/cases/01144/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01144/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01144/l3v2/heta-code/output.heta b/latest/cases/01144/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9d695a097 --- /dev/null +++ b/latest/cases/01144/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +timeconv @Const { } = 60; +extentconv @Const { } = 1000; +t3 @Const { } = 0.2; + diff --git a/latest/cases/01144/l3v2/index.heta b/latest/cases/01144/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01144/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01144/l3v2/json/output.json b/latest/cases/01144/l3v2/json/output.json new file mode 100644 index 000000000..d175f33ab --- /dev/null +++ b/latest/cases/01144/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + }, + { + "class": "Const", + "id": "t3", + "num": 0.2 + } +] \ No newline at end of file diff --git a/latest/cases/01144/model-sbml-l3v2.xml b/latest/cases/01144/model-sbml-l3v2.xml new file mode 100644 index 000000000..e3476527c --- /dev/null +++ b/latest/cases/01144/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + s1 + t3 + time + + + + + + + + diff --git a/latest/cases/01144/output.heta b/latest/cases/01144/output.heta new file mode 100644 index 000000000..b7274e4d6 --- /dev/null +++ b/latest/cases/01144/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: A hierarchical model with a submodel reaction modified by time and extent conversion factors. +componentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +The kinetic law of the reaction in the submodel in this model must be modified by both the time conversion factor and the extent conversion factor of the parent model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 3 parameters (timeconv, extentconv, t3) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $extentconv / timeconv * sub1__s1 * t3 * (time / timeconv)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter t3 | $0.2$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +timeconv @Const { } = 60; +extentconv @Const { } = 1000; +t3 @Const { } = 0.2; + diff --git a/latest/cases/01144/synopsis.txt b/latest/cases/01144/synopsis.txt new file mode 100644 index 000000000..66f9aed51 --- /dev/null +++ b/latest/cases/01144/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A hierarchical model with a submodel reaction modified by time and extent conversion factors. +componentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +The kinetic law of the reaction in the submodel in this model must be modified by both the time conversion factor and the extent conversion factor of the parent model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 3 parameters (timeconv, extentconv, t3) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $extentconv / timeconv * sub1__s1 * t3 * (time / timeconv)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter t3 | $0.2$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01145/l2v5/index.heta b/latest/cases/01145/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01145/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01145/l3v2/heta-code/output.heta b/latest/cases/01145/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b7ec692e1 --- /dev/null +++ b/latest/cases/01145/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +extentconv @Const { } = 10; + diff --git a/latest/cases/01145/l3v2/index.heta b/latest/cases/01145/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01145/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01145/l3v2/json/output.json b/latest/cases/01145/l3v2/json/output.json new file mode 100644 index 000000000..483c5911c --- /dev/null +++ b/latest/cases/01145/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "extentconv", + "num": 10 + } +] \ No newline at end of file diff --git a/latest/cases/01145/model-sbml-l3v2.xml b/latest/cases/01145/model-sbml-l3v2.xml new file mode 100644 index 000000000..6fac6841d --- /dev/null +++ b/latest/cases/01145/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + s1 + + + + + + + diff --git a/latest/cases/01145/output.heta b/latest/cases/01145/output.heta new file mode 100644 index 000000000..1f84a2f69 --- /dev/null +++ b/latest/cases/01145/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: A hierarchical model with an extent conversion factor affecting a sub-submodel. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The extent conversion factor in the parent model must affect the reaction in the sub-submodel. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__sub1__s1) +* 1 parameter (extentconv) +* 1 compartment (sub1__sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__sub1__s1 | $extentconv * sub1__sub1__s1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__sub1__s1 | $0.01$ | variable | +| Initial value of parameter extentconv | $10$ | constant | +| Initial volume of compartment 'sub1__sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +extentconv @Const { } = 10; + diff --git a/latest/cases/01145/synopsis.txt b/latest/cases/01145/synopsis.txt new file mode 100644 index 000000000..a179db990 --- /dev/null +++ b/latest/cases/01145/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A hierarchical model with an extent conversion factor affecting a sub-submodel. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The extent conversion factor in the parent model must affect the reaction in the sub-submodel. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__sub1__s1) +* 1 parameter (extentconv) +* 1 compartment (sub1__sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__sub1__s1 | $extentconv * sub1__sub1__s1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__sub1__s1 | $0.01$ | variable | +| Initial value of parameter extentconv | $10$ | constant | +| Initial volume of compartment 'sub1__sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01146/l2v5/index.heta b/latest/cases/01146/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01146/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01146/l3v2/heta-code/output.heta b/latest/cases/01146/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2eacd7a46 --- /dev/null +++ b/latest/cases/01146/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01146/l3v2/index.heta b/latest/cases/01146/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01146/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01146/l3v2/json/output.json b/latest/cases/01146/l3v2/json/output.json new file mode 100644 index 000000000..acd7113da --- /dev/null +++ b/latest/cases/01146/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + } +] \ No newline at end of file diff --git a/latest/cases/01146/model-sbml-l3v2.xml b/latest/cases/01146/model-sbml-l3v2.xml new file mode 100644 index 000000000..f2a7515a8 --- /dev/null +++ b/latest/cases/01146/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + time + 3 + + + + + + + diff --git a/latest/cases/01146/output.heta b/latest/cases/01146/output.heta new file mode 100644 index 000000000..a3f015065 --- /dev/null +++ b/latest/cases/01146/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion factor affecting an assignment rule in a sub-submodel. +componentTags: AssignmentRule, CSymbolTime, Parameter, comp:ModelDefinition, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The assignment rule in the sub-submodel has 'time' in it, which must be converted by the time conversion factor of the original submodel. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (timeconv, sub1__sub1__t1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__sub1__t1 | $time / timeconv + 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__sub1__t1 | $time / timeconv + 3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01146/synopsis.txt b/latest/cases/01146/synopsis.txt new file mode 100644 index 000000000..68e9a9f7d --- /dev/null +++ b/latest/cases/01146/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor affecting an assignment rule in a sub-submodel. +componentTags: AssignmentRule, CSymbolTime, Parameter, comp:ModelDefinition, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The assignment rule in the sub-submodel has 'time' in it, which must be converted by the time conversion factor of the original submodel. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (timeconv, sub1__sub1__t1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__sub1__t1 | $time / timeconv + 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__sub1__t1 | $time / timeconv + 3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01147/l2v5/index.heta b/latest/cases/01147/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01147/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01147/l3v2/heta-code/output.heta b/latest/cases/01147/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2eacd7a46 --- /dev/null +++ b/latest/cases/01147/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01147/l3v2/index.heta b/latest/cases/01147/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01147/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01147/l3v2/json/output.json b/latest/cases/01147/l3v2/json/output.json new file mode 100644 index 000000000..acd7113da --- /dev/null +++ b/latest/cases/01147/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + } +] \ No newline at end of file diff --git a/latest/cases/01147/model-sbml-l3v2.xml b/latest/cases/01147/model-sbml-l3v2.xml new file mode 100644 index 000000000..85e78647f --- /dev/null +++ b/latest/cases/01147/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 3 + + + + + + + diff --git a/latest/cases/01147/output.heta b/latest/cases/01147/output.heta new file mode 100644 index 000000000..a59099dd3 --- /dev/null +++ b/latest/cases/01147/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A hierarchical model with two levels of time conversion factors. +componentTags: AssignmentRule, CSymbolTime, InitialAssignment, Parameter, comp:ModelDefinition, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The assignment rule in the sub-submodel must be converted by time conversion factors at both levels of submodel creation. + +The 'flattened' version of this hierarchical model contains: +* 4 parameters (timeconv, sub1__timeconv, sub1__timeconv_times_timeconv, sub1__sub1__t1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__sub1__t1 | $time / sub1__timeconv_times_timeconv + 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__timeconv | $60$ | constant | +| Initial value of parameter sub1__timeconv_times_timeconv | $sub1__timeconv * timeconv$ | constant | +| Initial value of parameter sub1__sub1__t1 | $time / sub1__timeconv_times_timeconv + 3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01147/synopsis.txt b/latest/cases/01147/synopsis.txt new file mode 100644 index 000000000..4ce308542 --- /dev/null +++ b/latest/cases/01147/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A hierarchical model with two levels of time conversion factors. +componentTags: AssignmentRule, CSymbolTime, InitialAssignment, Parameter, comp:ModelDefinition, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The assignment rule in the sub-submodel must be converted by time conversion factors at both levels of submodel creation. + +The 'flattened' version of this hierarchical model contains: +* 4 parameters (timeconv, sub1__timeconv, sub1__timeconv_times_timeconv, sub1__sub1__t1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__sub1__t1 | $time / sub1__timeconv_times_timeconv + 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__timeconv | $60$ | constant | +| Initial value of parameter sub1__timeconv_times_timeconv | $sub1__timeconv * timeconv$ | constant | +| Initial value of parameter sub1__sub1__t1 | $time / sub1__timeconv_times_timeconv + 3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01148/l2v5/index.heta b/latest/cases/01148/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01148/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01148/l3v2/heta-code/output.heta b/latest/cases/01148/l3v2/heta-code/output.heta new file mode 100644 index 000000000..44e8904f9 --- /dev/null +++ b/latest/cases/01148/l3v2/heta-code/output.heta @@ -0,0 +1,7 @@ + + +t @TimeScale { }; + +timeconv @Const { } = 60; +extentconv @Const { } = 10; + diff --git a/latest/cases/01148/l3v2/index.heta b/latest/cases/01148/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01148/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01148/l3v2/json/output.json b/latest/cases/01148/l3v2/json/output.json new file mode 100644 index 000000000..23e995a91 --- /dev/null +++ b/latest/cases/01148/l3v2/json/output.json @@ -0,0 +1,15 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Const", + "id": "extentconv", + "num": 10 + } +] \ No newline at end of file diff --git a/latest/cases/01148/model-sbml-l3v2.xml b/latest/cases/01148/model-sbml-l3v2.xml new file mode 100644 index 000000000..6428865b8 --- /dev/null +++ b/latest/cases/01148/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1000000000 + s1 + time + + + + + + + + diff --git a/latest/cases/01148/output.heta b/latest/cases/01148/output.heta new file mode 100644 index 000000000..7a64d80dc --- /dev/null +++ b/latest/cases/01148/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: A hierarchical model with three levels of time and extent conversion factors. +componentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The reaction in the sub-submodel is affected by time and extent conversion factors three levels deep. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__sub1__sub1__s1) +* 10 parameters (timeconv, extentconv, sub1__timeconv, sub1__extentconv, sub1__timeconv_times_timeconv, sub1__extentconv_times_extentconv, sub1__sub1__timeconv, sub1__sub1__extentconv, sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv, sub1__sub1__extentconv_times_sub1__extentconv_times_extentconv) +* 1 compartment (sub1__sub1__sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__sub1__sub1__s1 | $sub1__sub1__extentconv_times_sub1__extentconv_times_extentconv / sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv * 1000000000 * sub1__sub1__sub1__s1 * (time / sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__sub1__sub1__s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter extentconv | $10$ | constant | +| Initial value of parameter sub1__timeconv | $60$ | constant | +| Initial value of parameter sub1__extentconv | $10$ | constant | +| Initial value of parameter sub1__timeconv_times_timeconv | $sub1__timeconv * timeconv$ | constant | +| Initial value of parameter sub1__extentconv_times_extentconv | $sub1__extentconv * extentconv$ | constant | +| Initial value of parameter sub1__sub1__timeconv | $60$ | constant | +| Initial value of parameter sub1__sub1__extentconv | $10$ | constant | +| Initial value of parameter sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv | $sub1__sub1__timeconv * sub1__timeconv_times_timeconv$ | constant | +| Initial value of parameter sub1__sub1__extentconv_times_sub1__extentconv_times_extentconv | $sub1__sub1__extentconv * sub1__extentconv_times_extentconv$ | constant | +| Initial volume of compartment 'sub1__sub1__sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +timeconv @Const { } = 60; +extentconv @Const { } = 10; + diff --git a/latest/cases/01148/synopsis.txt b/latest/cases/01148/synopsis.txt new file mode 100644 index 000000000..704ad4ff3 --- /dev/null +++ b/latest/cases/01148/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A hierarchical model with three levels of time and extent conversion factors. +componentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The reaction in the sub-submodel is affected by time and extent conversion factors three levels deep. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__sub1__sub1__s1) +* 10 parameters (timeconv, extentconv, sub1__timeconv, sub1__extentconv, sub1__timeconv_times_timeconv, sub1__extentconv_times_extentconv, sub1__sub1__timeconv, sub1__sub1__extentconv, sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv, sub1__sub1__extentconv_times_sub1__extentconv_times_extentconv) +* 1 compartment (sub1__sub1__sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__sub1__sub1__s1 | $sub1__sub1__extentconv_times_sub1__extentconv_times_extentconv / sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv * 1000000000 * sub1__sub1__sub1__s1 * (time / sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__sub1__sub1__s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter extentconv | $10$ | constant | +| Initial value of parameter sub1__timeconv | $60$ | constant | +| Initial value of parameter sub1__extentconv | $10$ | constant | +| Initial value of parameter sub1__timeconv_times_timeconv | $sub1__timeconv * timeconv$ | constant | +| Initial value of parameter sub1__extentconv_times_extentconv | $sub1__extentconv * extentconv$ | constant | +| Initial value of parameter sub1__sub1__timeconv | $60$ | constant | +| Initial value of parameter sub1__sub1__extentconv | $10$ | constant | +| Initial value of parameter sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv | $sub1__sub1__timeconv * sub1__timeconv_times_timeconv$ | constant | +| Initial value of parameter sub1__sub1__extentconv_times_sub1__extentconv_times_extentconv | $sub1__sub1__extentconv * sub1__extentconv_times_extentconv$ | constant | +| Initial volume of compartment 'sub1__sub1__sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01149/l2v5/index.heta b/latest/cases/01149/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01149/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01149/l3v2/heta-code/output.heta b/latest/cases/01149/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a64b0bf39 --- /dev/null +++ b/latest/cases/01149/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01149/l3v2/index.heta b/latest/cases/01149/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01149/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01149/l3v2/json/output.json b/latest/cases/01149/l3v2/json/output.json new file mode 100644 index 000000000..ea3d4a5c5 --- /dev/null +++ b/latest/cases/01149/l3v2/json/output.json @@ -0,0 +1,12 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "start_": "8" + } + } +] \ No newline at end of file diff --git a/latest/cases/01149/model-sbml-l3v2.xml b/latest/cases/01149/model-sbml-l3v2.xml new file mode 100644 index 000000000..e155717de --- /dev/null +++ b/latest/cases/01149/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p80 + + 3 + + + + + + + diff --git a/latest/cases/01149/output.heta b/latest/cases/01149/output.heta new file mode 100644 index 000000000..00b392d80 --- /dev/null +++ b/latest/cases/01149/output.heta @@ -0,0 +1,30 @@ +/* +category: Test +synopsis: A hierarchical model with a deleted rate rule. +componentTags: Parameter, comp:Deletion, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The rate rule in the submodel is deleted, and should not affect the parameter. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01149/synopsis.txt b/latest/cases/01149/synopsis.txt new file mode 100644 index 000000000..0eccee84d --- /dev/null +++ b/latest/cases/01149/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: A hierarchical model with a deleted rate rule. +componentTags: Parameter, comp:Deletion, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The rate rule in the submodel is deleted, and should not affect the parameter. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01150/l2v5/index.heta b/latest/cases/01150/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01150/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01150/l3v2/heta-code/output.heta b/latest/cases/01150/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bf7ae751f --- /dev/null +++ b/latest/cases/01150/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +p8_proc @Process { actors: = p8, aux: {{"metaid":"p8_raterule"}}, }; +p8_proc := 3; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01150/l3v2/index.heta b/latest/cases/01150/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01150/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01150/l3v2/json/output.json b/latest/cases/01150/l3v2/json/output.json new file mode 100644 index 000000000..02a13dd92 --- /dev/null +++ b/latest/cases/01150/l3v2/json/output.json @@ -0,0 +1,28 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "start_": "8" + } + }, + { + "class": "Process", + "id": "p8_proc", + "aux": { + "metaid": "p8_raterule" + }, + "assignments": { + "ode_": "3" + }, + "actors": [ + { + "target": "p8", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01150/model-sbml-l3v2.xml b/latest/cases/01150/model-sbml-l3v2.xml new file mode 100644 index 000000000..d537875ef --- /dev/null +++ b/latest/cases/01150/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + 3 + + + + + + + + + + + + + + + + + + + + + + + 4 + p80 + + 3 + + + + + + + diff --git a/latest/cases/01150/output.heta b/latest/cases/01150/output.heta new file mode 100644 index 000000000..80f320266 --- /dev/null +++ b/latest/cases/01150/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A hierarchical model with a replaced rate rule. +componentTags: Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model contains a rate rule in the parent that replaces a rate rule in the submodel. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p8 | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p8_proc @Process { actors: = p8, aux: {{"metaid":"p8_raterule"}}, }; +p8_proc := 3; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01150/synopsis.txt b/latest/cases/01150/synopsis.txt new file mode 100644 index 000000000..da49ec126 --- /dev/null +++ b/latest/cases/01150/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A hierarchical model with a replaced rate rule. +componentTags: Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model contains a rate rule in the parent that replaces a rate rule in the submodel. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p8 | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01151/l2v5/index.heta b/latest/cases/01151/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01151/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01151/l3v2/heta-code/output.heta b/latest/cases/01151/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bf7ae751f --- /dev/null +++ b/latest/cases/01151/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +p8_proc @Process { actors: = p8, aux: {{"metaid":"p8_raterule"}}, }; +p8_proc := 3; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01151/l3v2/index.heta b/latest/cases/01151/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01151/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01151/l3v2/json/output.json b/latest/cases/01151/l3v2/json/output.json new file mode 100644 index 000000000..02a13dd92 --- /dev/null +++ b/latest/cases/01151/l3v2/json/output.json @@ -0,0 +1,28 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "start_": "8" + } + }, + { + "class": "Process", + "id": "p8_proc", + "aux": { + "metaid": "p8_raterule" + }, + "assignments": { + "ode_": "3" + }, + "actors": [ + { + "target": "p8", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01151/model-sbml-l3v2.xml b/latest/cases/01151/model-sbml-l3v2.xml new file mode 100644 index 000000000..fe857d242 --- /dev/null +++ b/latest/cases/01151/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + 3 + + + + + + + + + + + + + + + + + + + + + + + + 4 + p80 + + 3 + + + + + + + diff --git a/latest/cases/01151/output.heta b/latest/cases/01151/output.heta new file mode 100644 index 000000000..5a3b705ee --- /dev/null +++ b/latest/cases/01151/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A hierarchical model with a deleted rate rule. +componentTags: Parameter, RateRule, comp:Deletion, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + Flattened, this model is functionally identical to model 01150, but instead of having the parent rate rule replace the submodel rate rule, the submodel rate rule is simply deleted. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p8 | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p8_proc @Process { actors: = p8, aux: {{"metaid":"p8_raterule"}}, }; +p8_proc := 3; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01151/synopsis.txt b/latest/cases/01151/synopsis.txt new file mode 100644 index 000000000..097a282c1 --- /dev/null +++ b/latest/cases/01151/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A hierarchical model with a deleted rate rule. +componentTags: Parameter, RateRule, comp:Deletion, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + Flattened, this model is functionally identical to model 01150, but instead of having the parent rate rule replace the submodel rate rule, the submodel rate rule is simply deleted. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p8 | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01152/l2v5/index.heta b/latest/cases/01152/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01152/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01152/l3v2/heta-code/output.heta b/latest/cases/01152/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7c3633600 --- /dev/null +++ b/latest/cases/01152/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +p8 @Record { } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01152/l3v2/index.heta b/latest/cases/01152/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01152/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01152/l3v2/json/output.json b/latest/cases/01152/l3v2/json/output.json new file mode 100644 index 000000000..791b5a409 --- /dev/null +++ b/latest/cases/01152/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "conv", + "num": 0.1 + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "start_": "8" + } + } +] \ No newline at end of file diff --git a/latest/cases/01152/model-sbml-l3v2.xml b/latest/cases/01152/model-sbml-l3v2.xml new file mode 100644 index 000000000..4cc14c444 --- /dev/null +++ b/latest/cases/01152/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 0.31 + + + + + + + + + 800 + p80 + + + + + + + + + diff --git a/latest/cases/01152/output.heta b/latest/cases/01152/output.heta new file mode 100644 index 000000000..a0a881f03 --- /dev/null +++ b/latest/cases/01152/output.heta @@ -0,0 +1,36 @@ +/* +category: Test +synopsis: A hierarchical model with a conversion factor affecting an event assignment. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The replaced parameter in the submodel is assigned a value by an event. The replacement contains a conversion factor, affecting the value given by the event. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (conv, p8) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| sub1__E1 | $gt(time, 0.31)$ | $p8 = (800 + p8 / conv) * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial value of parameter p8 | $8$ | variable |] + +*/ + + + +t @TimeScale { }; + +p8 @Record { } .= 8; + +conv @Const { } = 0.1; + diff --git a/latest/cases/01152/synopsis.txt b/latest/cases/01152/synopsis.txt new file mode 100644 index 000000000..9b78006e8 --- /dev/null +++ b/latest/cases/01152/synopsis.txt @@ -0,0 +1,26 @@ + +category: Test +synopsis: A hierarchical model with a conversion factor affecting an event assignment. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The replaced parameter in the submodel is assigned a value by an event. The replacement contains a conversion factor, affecting the value given by the event. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (conv, p8) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| sub1__E1 | $gt(time, 0.31)$ | $p8 = (800 + p8 / conv) * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial value of parameter p8 | $8$ | variable |] + diff --git a/latest/cases/01153/l2v5/index.heta b/latest/cases/01153/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01153/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01153/l3v2/heta-code/output.heta b/latest/cases/01153/l3v2/heta-code/output.heta new file mode 100644 index 000000000..400da9923 --- /dev/null +++ b/latest/cases/01153/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +z @Record { } .= 34 * i; + +i @Const { } = 2; + diff --git a/latest/cases/01153/l3v2/index.heta b/latest/cases/01153/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01153/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01153/l3v2/json/output.json b/latest/cases/01153/l3v2/json/output.json new file mode 100644 index 000000000..289b65ef0 --- /dev/null +++ b/latest/cases/01153/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "start_": "34 * i" + } + }, + { + "class": "Const", + "id": "i", + "num": 2 + } +] \ No newline at end of file diff --git a/latest/cases/01153/model-sbml-l3v2.xml b/latest/cases/01153/model-sbml-l3v2.xml new file mode 100644 index 000000000..a9673f665 --- /dev/null +++ b/latest/cases/01153/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + + + + + + + + 34 + i + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 50 + Q + + + + + + + + + + 37 + y + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01153/output.heta b/latest/cases/01153/output.heta new file mode 100644 index 000000000..e19af4ffe --- /dev/null +++ b/latest/cases/01153/output.heta @@ -0,0 +1,35 @@ +/* +category: Test +synopsis: A hierarchical model with a deleted rate rule and initial assignment +componentTags: InitialAssignment, Parameter, comp:Deletion, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The parent model in this document contains deletions that remove an initial assignment and a rate rule two levels down. The parent model contains only an initial assignment for that parameter, leaving it constant. + +The 'flattened' version of this hierarchical model contains: +* 4 parameters (z, i, A__A__y, A__A__Q) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter i | $2$ | constant | +| Initial value of parameter A__A__y | $7$ | constant | +| Initial value of parameter A__A__Q | $2$ | constant | +| Initial value of parameter z | $34 * i$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +z @Record { } .= 34 * i; + +i @Const { } = 2; + diff --git a/latest/cases/01153/synopsis.txt b/latest/cases/01153/synopsis.txt new file mode 100644 index 000000000..4ae714977 --- /dev/null +++ b/latest/cases/01153/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: A hierarchical model with a deleted rate rule and initial assignment +componentTags: InitialAssignment, Parameter, comp:Deletion, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The parent model in this document contains deletions that remove an initial assignment and a rate rule two levels down. The parent model contains only an initial assignment for that parameter, leaving it constant. + +The 'flattened' version of this hierarchical model contains: +* 4 parameters (z, i, A__A__y, A__A__Q) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter i | $2$ | constant | +| Initial value of parameter A__A__y | $7$ | constant | +| Initial value of parameter A__A__Q | $2$ | constant | +| Initial value of parameter z | $34 * i$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01154/l2v5/index.heta b/latest/cases/01154/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01154/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01154/l3v2/heta-code/output.heta b/latest/cases/01154/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01154/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01154/l3v2/index.heta b/latest/cases/01154/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01154/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01154/l3v2/json/output.json b/latest/cases/01154/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01154/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01154/model-sbml-l3v2.xml b/latest/cases/01154/model-sbml-l3v2.xml new file mode 100644 index 000000000..35d3cad5d --- /dev/null +++ b/latest/cases/01154/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + + + + + + + + time + 0.31 + + + + + + + 3.3 + + + + + 5.5 + + + + + + + + diff --git a/latest/cases/01154/output.heta b/latest/cases/01154/output.heta new file mode 100644 index 000000000..46c217464 --- /dev/null +++ b/latest/cases/01154/output.heta @@ -0,0 +1,26 @@ +/* +category: Test +synopsis: This hierarchical model contains a deleted event. +componentTags: Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The event that would change the values of the two parameters in this model is deleted, causing the parameters to remain unchanged. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01154/synopsis.txt b/latest/cases/01154/synopsis.txt new file mode 100644 index 000000000..d8c30be3b --- /dev/null +++ b/latest/cases/01154/synopsis.txt @@ -0,0 +1,20 @@ + +category: Test +synopsis: This hierarchical model contains a deleted event. +componentTags: Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The event that would change the values of the two parameters in this model is deleted, causing the parameters to remain unchanged. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + diff --git a/latest/cases/01155/l2v5/index.heta b/latest/cases/01155/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01155/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01155/l3v2/heta-code/output.heta b/latest/cases/01155/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01155/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01155/l3v2/index.heta b/latest/cases/01155/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01155/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01155/l3v2/json/output.json b/latest/cases/01155/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01155/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01155/model-sbml-l3v2.xml b/latest/cases/01155/model-sbml-l3v2.xml new file mode 100644 index 000000000..a55955540 --- /dev/null +++ b/latest/cases/01155/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + time + 0.31 + + + + + + + + 0.1 + time + + + + + + + 3.3 + + + + + 5.5 + + + + + + + + diff --git a/latest/cases/01155/output.heta b/latest/cases/01155/output.heta new file mode 100644 index 000000000..a7952007c --- /dev/null +++ b/latest/cases/01155/output.heta @@ -0,0 +1,33 @@ +/* +category: Test +synopsis: This hierarchical model deletes the delay of an event. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The event in the submodel contains a delay, but this delay is deleted when the submodel is imported into the parent model, causing the event to fire instantly. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| sub1__E0 | $gt(time, 3)$ | $sub1__t1 = 3.3$ | +| | | | $sub1__t2 = 5.5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01155/synopsis.txt b/latest/cases/01155/synopsis.txt new file mode 100644 index 000000000..8eaaf508f --- /dev/null +++ b/latest/cases/01155/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: This hierarchical model deletes the delay of an event. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The event in the submodel contains a delay, but this delay is deleted when the submodel is imported into the parent model, causing the event to fire instantly. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| sub1__E0 | $gt(time, 3)$ | $sub1__t1 = 3.3$ | +| | | | $sub1__t2 = 5.5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + diff --git a/latest/cases/01156/l2v5/index.heta b/latest/cases/01156/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01156/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01156/l3v2/heta-code/output.heta b/latest/cases/01156/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01156/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01156/l3v2/index.heta b/latest/cases/01156/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01156/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01156/l3v2/json/output.json b/latest/cases/01156/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01156/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01156/model-sbml-l3v2.xml b/latest/cases/01156/model-sbml-l3v2.xml new file mode 100644 index 000000000..ed89212a5 --- /dev/null +++ b/latest/cases/01156/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + time + 0.31 + + + + + + 0.1 + + + + + 10 + + + + + + 3.3 + + + + + 5.5 + + + + + + + + diff --git a/latest/cases/01156/output.heta b/latest/cases/01156/output.heta new file mode 100644 index 000000000..8f4c5da5f --- /dev/null +++ b/latest/cases/01156/output.heta @@ -0,0 +1,33 @@ +/* +category: Test +synopsis: A hierarchical model with a deleted event priority. +componentTags: CSymbolTime, EventWithDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + This model contains an event with a priority which is deleted when imported as part of a submodel. It is actually impossible to test the behavior of a model that deletes a priority, because the behavior of an event without a priority has fewer restrictions on its behavior in a simulator than that same event with a priority, and allowing the event to behave as if it had any arbitrary priority (including the one deleted) is actually perfectly legal. As a result, this test merely checks to ensure that the simulation occurred at all, despite containing that deletion construct. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| sub1__E0 | $gt(time, 3)$ | $1 / time$ | $sub1__t1 = 3.3$ | +| | | | $sub1__t2 = 5.5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01156/synopsis.txt b/latest/cases/01156/synopsis.txt new file mode 100644 index 000000000..ada3b431e --- /dev/null +++ b/latest/cases/01156/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: A hierarchical model with a deleted event priority. +componentTags: CSymbolTime, EventWithDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + This model contains an event with a priority which is deleted when imported as part of a submodel. It is actually impossible to test the behavior of a model that deletes a priority, because the behavior of an event without a priority has fewer restrictions on its behavior in a simulator than that same event with a priority, and allowing the event to behave as if it had any arbitrary priority (including the one deleted) is actually perfectly legal. As a result, this test merely checks to ensure that the simulation occurred at all, despite containing that deletion construct. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| sub1__E0 | $gt(time, 3)$ | $1 / time$ | $sub1__t1 = 3.3$ | +| | | | $sub1__t2 = 5.5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + diff --git a/latest/cases/01157/l2v5/index.heta b/latest/cases/01157/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01157/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01157/l3v2/heta-code/output.heta b/latest/cases/01157/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01157/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01157/l3v2/index.heta b/latest/cases/01157/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01157/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01157/l3v2/json/output.json b/latest/cases/01157/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01157/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01157/model-sbml-l3v2.xml b/latest/cases/01157/model-sbml-l3v2.xml new file mode 100644 index 000000000..b6e40b3c8 --- /dev/null +++ b/latest/cases/01157/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + + + + + + + + time + 0.31 + + + + + + + 3.3 + + + + + 5.5 + + + + + + + + diff --git a/latest/cases/01157/output.heta b/latest/cases/01157/output.heta new file mode 100644 index 000000000..842bd7398 --- /dev/null +++ b/latest/cases/01157/output.heta @@ -0,0 +1,32 @@ +/* +category: Test +synopsis: A hierarchical model that deletes an event assignment. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The original event in the submodel contains two event assignments, one of which is deleted when the event's submodel is imported into the parent model. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Delay* | *Event Assignments* | +| sub1__E0 | $gt(time, 3)$ | $10$ | $1 / time$ | $sub1__t2 = 5.5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01157/synopsis.txt b/latest/cases/01157/synopsis.txt new file mode 100644 index 000000000..55edcc7d3 --- /dev/null +++ b/latest/cases/01157/synopsis.txt @@ -0,0 +1,26 @@ + +category: Test +synopsis: A hierarchical model that deletes an event assignment. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The original event in the submodel contains two event assignments, one of which is deleted when the event's submodel is imported into the parent model. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Delay* | *Event Assignments* | +| sub1__E0 | $gt(time, 3)$ | $10$ | $1 / time$ | $sub1__t2 = 5.5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + diff --git a/latest/cases/01158/l2v5/index.heta b/latest/cases/01158/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01158/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01158/l3v2/heta-code/output.heta b/latest/cases/01158/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01158/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01158/l3v2/index.heta b/latest/cases/01158/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01158/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01158/l3v2/json/output.json b/latest/cases/01158/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01158/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01158/model-sbml-l3v2.xml b/latest/cases/01158/model-sbml-l3v2.xml new file mode 100644 index 000000000..1250643cd --- /dev/null +++ b/latest/cases/01158/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + time + 0.31 + + + + + + 0.1 + + + + + 10 + + + + + + 3.3 + + + + + 5.5 + + + + + + + + diff --git a/latest/cases/01158/output.heta b/latest/cases/01158/output.heta new file mode 100644 index 000000000..8bb640bda --- /dev/null +++ b/latest/cases/01158/output.heta @@ -0,0 +1,32 @@ +/* +category: Test + synopsis: A hierarchical model that deletes a priority, delay, and event assignment +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In this model, a submodel event is greatly changed through deletions: its delay, priority, and one of its event assignements are all deleted. As in model 01156, the fact that the priority has been deleted cannot be tested numerically, but the other deletions all directly affect the expected output of the model. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| sub1__E0 | $gt(time, 3)$ | $sub1__t1 = 3.3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01158/synopsis.txt b/latest/cases/01158/synopsis.txt new file mode 100644 index 000000000..051c5c8f5 --- /dev/null +++ b/latest/cases/01158/synopsis.txt @@ -0,0 +1,26 @@ + +category: Test + synopsis: A hierarchical model that deletes a priority, delay, and event assignment +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In this model, a submodel event is greatly changed through deletions: its delay, priority, and one of its event assignements are all deleted. As in model 01156, the fact that the priority has been deleted cannot be tested numerically, but the other deletions all directly affect the expected output of the model. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (sub1__t1, sub1__t2) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| sub1__E0 | $gt(time, 3)$ | $sub1__t1 = 3.3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter sub1__t1 | $1$ | variable | +| Initial value of parameter sub1__t2 | $1$ | variable |] + diff --git a/latest/cases/01159/l2v5/index.heta b/latest/cases/01159/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01159/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01159/l3v2/heta-code/output.heta b/latest/cases/01159/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01159/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01159/l3v2/index.heta b/latest/cases/01159/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01159/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01159/l3v2/json/output.json b/latest/cases/01159/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01159/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01159/model-sbml-l3v2.xml b/latest/cases/01159/model-sbml-l3v2.xml new file mode 100644 index 000000000..f690da646 --- /dev/null +++ b/latest/cases/01159/model-sbml-l3v2.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + s1 + + + + + + + + + + + diff --git a/latest/cases/01159/output.heta b/latest/cases/01159/output.heta new file mode 100644 index 000000000..509754310 --- /dev/null +++ b/latest/cases/01159/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: This hieararchical model deletes a local parameter +componentTags: Compartment, Parameter, Reaction, Species, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In the original submodel, there is a local parameter whose value is used in the kinetic law of a reaction. When it is imported as a submodel, the local parameter is deleted, causing the kinetic law to instead reference a global parameter with the same ID, but a different value. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 1 parameter (sub1__p1) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $sub1__p1 * sub1__s1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $0.001$ | variable | +| Initial value of parameter sub1__p1 | $100$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01159/synopsis.txt b/latest/cases/01159/synopsis.txt new file mode 100644 index 000000000..b44e6c2ca --- /dev/null +++ b/latest/cases/01159/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: This hieararchical model deletes a local parameter +componentTags: Compartment, Parameter, Reaction, Species, comp:Deletion, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In the original submodel, there is a local parameter whose value is used in the kinetic law of a reaction. When it is imported as a submodel, the local parameter is deleted, causing the kinetic law to instead reference a global parameter with the same ID, but a different value. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 1 parameter (sub1__p1) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $sub1__p1 * sub1__s1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $0.001$ | variable | +| Initial value of parameter sub1__p1 | $100$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01160/l2v5/index.heta b/latest/cases/01160/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01160/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01160/l3v2/heta-code/output.heta b/latest/cases/01160/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9419c93e1 --- /dev/null +++ b/latest/cases/01160/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +new_p1 @Const { aux: {{"metaid":"new_p1_metaid"}}, } = 10; + diff --git a/latest/cases/01160/l3v2/index.heta b/latest/cases/01160/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01160/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01160/l3v2/json/output.json b/latest/cases/01160/l3v2/json/output.json new file mode 100644 index 000000000..487daae4a --- /dev/null +++ b/latest/cases/01160/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "new_p1", + "aux": { + "metaid": "new_p1_metaid" + }, + "num": 10 + } +] \ No newline at end of file diff --git a/latest/cases/01160/model-sbml-l3v2.xml b/latest/cases/01160/model-sbml-l3v2.xml new file mode 100644 index 000000000..19645e082 --- /dev/null +++ b/latest/cases/01160/model-sbml-l3v2.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + s1 + + + + + + + + + + + diff --git a/latest/cases/01160/output.heta b/latest/cases/01160/output.heta new file mode 100644 index 000000000..0cdad6f85 --- /dev/null +++ b/latest/cases/01160/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: A hierarchical model with a replacement of a local parameter. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +A local parameter in the submodel is replaced here by a global parameter. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 1 parameter (new_p1) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $new_p1 * sub1__s1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $0.001$ | variable | +| Initial value of parameter new_p1 | $100$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +new_p1 @Const { aux: {{"metaid":"new_p1_metaid"}}, } = 10; + diff --git a/latest/cases/01160/synopsis.txt b/latest/cases/01160/synopsis.txt new file mode 100644 index 000000000..4e3015444 --- /dev/null +++ b/latest/cases/01160/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A hierarchical model with a replacement of a local parameter. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +A local parameter in the submodel is replaced here by a global parameter. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 1 parameter (new_p1) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $new_p1 * sub1__s1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $0.001$ | variable | +| Initial value of parameter new_p1 | $100$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01161/l2v5/index.heta b/latest/cases/01161/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01161/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01161/l3v2/heta-code/output.heta b/latest/cases/01161/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01161/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01161/l3v2/index.heta b/latest/cases/01161/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01161/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01161/l3v2/json/output.json b/latest/cases/01161/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01161/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01161/model-sbml-l3v2.xml b/latest/cases/01161/model-sbml-l3v2.xml new file mode 100644 index 000000000..bef1c7bc1 --- /dev/null +++ b/latest/cases/01161/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + p1 + s1 + + + + + + + + + + + diff --git a/latest/cases/01161/output.heta b/latest/cases/01161/output.heta new file mode 100644 index 000000000..41671c835 --- /dev/null +++ b/latest/cases/01161/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: A hierarchical model whose submodel has a local parameter. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + A quick test to make sure a submodel local parameter is left alone and not renamed without a commensurate renaming of its reference in the kinetic law as part of any flattening routine a simulator might use, especially when there is a 'shadow' parameter of the same name. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 1 parameter (sub1__p1) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $p1 * sub1__s1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $0.001$ | variable | +| Initial value of parameter sub1__p1 | $100$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01161/synopsis.txt b/latest/cases/01161/synopsis.txt new file mode 100644 index 000000000..522097d54 --- /dev/null +++ b/latest/cases/01161/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A hierarchical model whose submodel has a local parameter. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + A quick test to make sure a submodel local parameter is left alone and not renamed without a commensurate renaming of its reference in the kinetic law as part of any flattening routine a simulator might use, especially when there is a 'shadow' parameter of the same name. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 1 parameter (sub1__p1) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $p1 * sub1__s1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $0.001$ | variable | +| Initial value of parameter sub1__p1 | $100$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01162/l2v5/index.heta b/latest/cases/01162/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01162/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01162/l3v2/heta-code/output.heta b/latest/cases/01162/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a64b0bf39 --- /dev/null +++ b/latest/cases/01162/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01162/l3v2/index.heta b/latest/cases/01162/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01162/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01162/l3v2/json/output.json b/latest/cases/01162/l3v2/json/output.json new file mode 100644 index 000000000..ea3d4a5c5 --- /dev/null +++ b/latest/cases/01162/l3v2/json/output.json @@ -0,0 +1,12 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "start_": "8" + } + } +] \ No newline at end of file diff --git a/latest/cases/01162/model-sbml-l3v2.xml b/latest/cases/01162/model-sbml-l3v2.xml new file mode 100644 index 000000000..ff89a9030 --- /dev/null +++ b/latest/cases/01162/model-sbml-l3v2.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4 + p80 + + 3 + + + + + + + + + + diff --git a/latest/cases/01162/output.heta b/latest/cases/01162/output.heta new file mode 100644 index 000000000..77936f358 --- /dev/null +++ b/latest/cases/01162/output.heta @@ -0,0 +1,30 @@ +/* +category: Test +synopsis: A hierarchical model with a rate rule deleted via a port. +componentTags: Parameter, comp:Deletion, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The rate rule for the parameter in the submodel is defined with a port, and the model that imports it sets the port as the target of a 'delete' construct. This should, by proxy, delete the rate rule. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01162/synopsis.txt b/latest/cases/01162/synopsis.txt new file mode 100644 index 000000000..1ac50e24a --- /dev/null +++ b/latest/cases/01162/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: A hierarchical model with a rate rule deleted via a port. +componentTags: Parameter, comp:Deletion, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The rate rule for the parameter in the submodel is defined with a port, and the model that imports it sets the port as the target of a 'delete' construct. This should, by proxy, delete the rate rule. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01163/l2v5/index.heta b/latest/cases/01163/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01163/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01163/l3v2/heta-code/output.heta b/latest/cases/01163/l3v2/heta-code/output.heta new file mode 100644 index 000000000..bf7ae751f --- /dev/null +++ b/latest/cases/01163/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +p8_proc @Process { actors: = p8, aux: {{"metaid":"p8_raterule"}}, }; +p8_proc := 3; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01163/l3v2/index.heta b/latest/cases/01163/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01163/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01163/l3v2/json/output.json b/latest/cases/01163/l3v2/json/output.json new file mode 100644 index 000000000..02a13dd92 --- /dev/null +++ b/latest/cases/01163/l3v2/json/output.json @@ -0,0 +1,28 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p8", + "assignments": { + "start_": "8" + } + }, + { + "class": "Process", + "id": "p8_proc", + "aux": { + "metaid": "p8_raterule" + }, + "assignments": { + "ode_": "3" + }, + "actors": [ + { + "target": "p8", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01163/model-sbml-l3v2.xml b/latest/cases/01163/model-sbml-l3v2.xml new file mode 100644 index 000000000..fa781a470 --- /dev/null +++ b/latest/cases/01163/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + 3 + + + + + + + + + + + + + + + + + + + + + + + 4 + p80 + + 3 + + + + + + + + + + diff --git a/latest/cases/01163/output.heta b/latest/cases/01163/output.heta new file mode 100644 index 000000000..2a62599b4 --- /dev/null +++ b/latest/cases/01163/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A hierarchical model with a replaced rate rule and parameter. +componentTags: Parameter, RateRule, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The submodel contains a parameter and rate rule, both of which are replaced by the parent model. This means that it is not actually necessary to understand the 'comp' package to pass the test; a simulator should be able to note the 'required="false"' line and attempt to simulate anyway. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p8 | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p8_proc @Process { actors: = p8, aux: {{"metaid":"p8_raterule"}}, }; +p8_proc := 3; + +p8 @Record { } .= 8; + diff --git a/latest/cases/01163/synopsis.txt b/latest/cases/01163/synopsis.txt new file mode 100644 index 000000000..1f0f3f82f --- /dev/null +++ b/latest/cases/01163/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A hierarchical model with a replaced rate rule and parameter. +componentTags: Parameter, RateRule, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + The submodel contains a parameter and rate rule, both of which are replaced by the parent model. This means that it is not actually necessary to understand the 'comp' package to pass the test; a simulator should be able to note the 'required="false"' line and attempt to simulate anyway. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (p8) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p8 | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p8 | $8$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01164/l2v5/index.heta b/latest/cases/01164/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01164/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01164/l3v2/heta-code/output.heta b/latest/cases/01164/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01164/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01164/l3v2/index.heta b/latest/cases/01164/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01164/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01164/l3v2/json/output.json b/latest/cases/01164/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01164/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01164/model-sbml-l3v2.xml b/latest/cases/01164/model-sbml-l3v2.xml new file mode 100644 index 000000000..d96713f57 --- /dev/null +++ b/latest/cases/01164/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S + E + + ES + + + + + + + + + + + + + + + + + ES + + + E + D + + + + + + + + + diff --git a/latest/cases/01164/output.heta b/latest/cases/01164/output.heta new file mode 100644 index 000000000..a833e5f60 --- /dev/null +++ b/latest/cases/01164/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: A simple aggregate hieararchical model. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, MultiCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + A submodel with a two-step reaction is imported twice into the parent model, creating parallel sets of species affected by parallel reactions. + +The 'flattened' version of this hierarchical model contains: +* 8 species (submod1__S, submod1__E, submod1__D, submod1__ES, submod2__S, submod2__E, submod2__D, submod2__ES) +* 2 compartments (submod1__comp, submod2__comp) + +There are 4 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| submod1__S + submod1__E -> submod1__ES | $(submod1__S + submod1__E) / submod1__ES$ | +| submod1__ES -> submod1__E + submod1__D | $submod1__ES / (submod1__E + submod1__D)$ | +| submod2__S + submod2__E -> submod2__ES | $(submod2__S + submod2__E) / submod2__ES$ | +| submod2__ES -> submod2__E + submod2__D | $submod2__ES / (submod2__E + submod2__D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species submod1__S | $1$ | variable | +| Initial concentration of species submod1__E | $1$ | variable | +| Initial concentration of species submod1__D | $1$ | variable | +| Initial concentration of species submod1__ES | $1$ | variable | +| Initial concentration of species submod2__S | $1$ | variable | +| Initial concentration of species submod2__E | $1$ | variable | +| Initial concentration of species submod2__D | $1$ | variable | +| Initial concentration of species submod2__ES | $1$ | variable | +| Initial volume of compartment 'submod1__comp' | $1$ | constant | +| Initial volume of compartment 'submod2__comp' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01164/synopsis.txt b/latest/cases/01164/synopsis.txt new file mode 100644 index 000000000..06568024f --- /dev/null +++ b/latest/cases/01164/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A simple aggregate hieararchical model. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, MultiCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + A submodel with a two-step reaction is imported twice into the parent model, creating parallel sets of species affected by parallel reactions. + +The 'flattened' version of this hierarchical model contains: +* 8 species (submod1__S, submod1__E, submod1__D, submod1__ES, submod2__S, submod2__E, submod2__D, submod2__ES) +* 2 compartments (submod1__comp, submod2__comp) + +There are 4 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| submod1__S + submod1__E -> submod1__ES | $(submod1__S + submod1__E) / submod1__ES$ | +| submod1__ES -> submod1__E + submod1__D | $submod1__ES / (submod1__E + submod1__D)$ | +| submod2__S + submod2__E -> submod2__ES | $(submod2__S + submod2__E) / submod2__ES$ | +| submod2__ES -> submod2__E + submod2__D | $submod2__ES / (submod2__E + submod2__D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species submod1__S | $1$ | variable | +| Initial concentration of species submod1__E | $1$ | variable | +| Initial concentration of species submod1__D | $1$ | variable | +| Initial concentration of species submod1__ES | $1$ | variable | +| Initial concentration of species submod2__S | $1$ | variable | +| Initial concentration of species submod2__E | $1$ | variable | +| Initial concentration of species submod2__D | $1$ | variable | +| Initial concentration of species submod2__ES | $1$ | variable | +| Initial volume of compartment 'submod1__comp' | $1$ | constant | +| Initial volume of compartment 'submod2__comp' | $1$ | constant |] + diff --git a/latest/cases/01165/l2v5/index.heta b/latest/cases/01165/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01165/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01165/l3v2/heta-code/output.heta b/latest/cases/01165/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5155a7fc1 --- /dev/null +++ b/latest/cases/01165/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 1; + +S @Species { compartment: comp, } .= 5; +D @Species { compartment: comp, } .= 10; + diff --git a/latest/cases/01165/l3v2/index.heta b/latest/cases/01165/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01165/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01165/l3v2/json/output.json b/latest/cases/01165/l3v2/json/output.json new file mode 100644 index 000000000..506f1f0f2 --- /dev/null +++ b/latest/cases/01165/l3v2/json/output.json @@ -0,0 +1,29 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S", + "assignments": { + "start_": "5" + }, + "compartment": "comp" + }, + { + "class": "Species", + "id": "D", + "assignments": { + "start_": "10" + }, + "compartment": "comp" + } +] \ No newline at end of file diff --git a/latest/cases/01165/model-sbml-l3v2.xml b/latest/cases/01165/model-sbml-l3v2.xml new file mode 100644 index 000000000..eb163b838 --- /dev/null +++ b/latest/cases/01165/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01165/output.heta b/latest/cases/01165/output.heta new file mode 100644 index 000000000..8c2d69eb0 --- /dev/null +++ b/latest/cases/01165/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: A hierarchical model from the specification +componentTags: Compartment, Reaction, Species, comp:Deletion, comp:ExternalModelDefinition, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + An example from the 'comp' specification: two submodels, one simple, and one complex, are synchronized to match the complex version: 'S' converted to 'D' via an intermediate instead of via a single step. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S, D, A__E, A__ES) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S + A__E -> A__ES | $(S + A__E) / A__ES$ | +| A__ES -> A__E + D | $A__ES / (A__E + D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S | $5$ | variable | +| Initial concentration of species D | $10$ | variable | +| Initial concentration of species A__E | $1$ | variable | +| Initial concentration of species A__ES | $1$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 1; + +S @Species { compartment: comp, } .= 5; +D @Species { compartment: comp, } .= 10; + diff --git a/latest/cases/01165/synopsis.txt b/latest/cases/01165/synopsis.txt new file mode 100644 index 000000000..f4519a2a0 --- /dev/null +++ b/latest/cases/01165/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A hierarchical model from the specification +componentTags: Compartment, Reaction, Species, comp:Deletion, comp:ExternalModelDefinition, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + An example from the 'comp' specification: two submodels, one simple, and one complex, are synchronized to match the complex version: 'S' converted to 'D' via an intermediate instead of via a single step. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S, D, A__E, A__ES) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S + A__E -> A__ES | $(S + A__E) / A__ES$ | +| A__ES -> A__E + D | $A__ES / (A__E + D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S | $5$ | variable | +| Initial concentration of species D | $10$ | variable | +| Initial concentration of species A__E | $1$ | variable | +| Initial concentration of species A__ES | $1$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + diff --git a/latest/cases/01166/l2v5/index.heta b/latest/cases/01166/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01166/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01166/l3v2/build.log b/latest/cases/01166/l3v2/build.log new file mode 100644 index 000000000..66135b3f7 --- /dev/null +++ b/latest/cases/01166/l3v2/build.log @@ -0,0 +1,14 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01166/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01166/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01166/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 85 +[error] J0 Property "actors[2].target" has lost reference "E". +[error] Component "E" is not found in space "nameless" as expected in expression: J0 [ode_]= (S + E) / ES; +[error] J1 Property "actors[0].target" has lost reference "E". +[error] Component "E" is not found in space "nameless" as expected in expression: J1 [ode_]= ES / (E + D); +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01166/l3v2/index.heta b/latest/cases/01166/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01166/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01166/model-sbml-l3v2.xml b/latest/cases/01166/model-sbml-l3v2.xml new file mode 100644 index 000000000..00cb61bcf --- /dev/null +++ b/latest/cases/01166/model-sbml-l3v2.xml @@ -0,0 +1,166 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S + E + + ES + + + + + + + + + + + + + + + + + + + + + ES + + + E + D + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01166/synopsis.txt b/latest/cases/01166/synopsis.txt new file mode 100644 index 000000000..20d0dc351 --- /dev/null +++ b/latest/cases/01166/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A hierarchical model from the specification that uses replacements of deletions +componentTags: Compartment, Reaction, Species, comp:Deletion, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: Amount +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + Another model from the specification: this model meticulously recreates the submodel 'enzyme' in the parent model, essentially documenting how it differs from the other submodel 'simple'. Because the process removes or deletes everything from both submodels, it is not necessary to understand the 'comp' package to successfully simulate this model. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S, D, E, ES) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| S + E -> ES | $(S + E) / ES$ | +| ES -> E + D | $ES / (E + D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S | $5$ | variable | +| Initial concentration of species D | $10$ | variable | +| Initial concentration of species E | $7$ | variable | +| Initial concentration of species ES | $0.1$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + diff --git a/latest/cases/01167/l2v5/index.heta b/latest/cases/01167/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01167/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01167/l3v2/heta-code/output.heta b/latest/cases/01167/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01167/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01167/l3v2/index.heta b/latest/cases/01167/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01167/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01167/l3v2/json/output.json b/latest/cases/01167/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01167/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01167/model-sbml-l3v2.xml b/latest/cases/01167/model-sbml-l3v2.xml new file mode 100644 index 000000000..65499b1c5 --- /dev/null +++ b/latest/cases/01167/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01167/output.heta b/latest/cases/01167/output.heta new file mode 100644 index 000000000..b0caeeef0 --- /dev/null +++ b/latest/cases/01167/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A hierarchical model with two levels of external model definitions. +componentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The external model definition in the main model file references another external model definition in a second file, which in turn references an actual model in a third file. + +The 'flattened' version of this hierarchical model contains: +* 4 species (A__S, A__E, A__D, A__ES) +* 1 compartment (A__comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__S + A__E -> A__ES | $(A__S + A__E) / A__ES$ | +| A__ES -> A__E + A__D | $A__ES / (A__E + A__D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A__S | $10$ | variable | +| Initial concentration of species A__E | $5$ | variable | +| Initial concentration of species A__D | $7$ | variable | +| Initial concentration of species A__ES | $0.1$ | variable | +| Initial volume of compartment 'A__comp' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01167/synopsis.txt b/latest/cases/01167/synopsis.txt new file mode 100644 index 000000000..02202d5e2 --- /dev/null +++ b/latest/cases/01167/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A hierarchical model with two levels of external model definitions. +componentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The external model definition in the main model file references another external model definition in a second file, which in turn references an actual model in a third file. + +The 'flattened' version of this hierarchical model contains: +* 4 species (A__S, A__E, A__D, A__ES) +* 1 compartment (A__comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__S + A__E -> A__ES | $(A__S + A__E) / A__ES$ | +| A__ES -> A__E + A__D | $A__ES / (A__E + A__D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A__S | $10$ | variable | +| Initial concentration of species A__E | $5$ | variable | +| Initial concentration of species A__D | $7$ | variable | +| Initial concentration of species A__ES | $0.1$ | variable | +| Initial volume of compartment 'A__comp' | $1$ | constant |] + diff --git a/latest/cases/01168/l2v5/index.heta b/latest/cases/01168/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01168/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01168/l3v2/heta-code/output.heta b/latest/cases/01168/l3v2/heta-code/output.heta new file mode 100644 index 000000000..95ec972a2 --- /dev/null +++ b/latest/cases/01168/l3v2/heta-code/output.heta @@ -0,0 +1,4 @@ + + +t @TimeScale { }; + diff --git a/latest/cases/01168/l3v2/index.heta b/latest/cases/01168/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01168/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01168/l3v2/json/output.json b/latest/cases/01168/l3v2/json/output.json new file mode 100644 index 000000000..918b17eb4 --- /dev/null +++ b/latest/cases/01168/l3v2/json/output.json @@ -0,0 +1,5 @@ +[ + { + "id": "t" + } +] \ No newline at end of file diff --git a/latest/cases/01168/model-sbml-l3v2.xml b/latest/cases/01168/model-sbml-l3v2.xml new file mode 100644 index 000000000..09bfd67ee --- /dev/null +++ b/latest/cases/01168/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01168/output.heta b/latest/cases/01168/output.heta new file mode 100644 index 000000000..87f9ca922 --- /dev/null +++ b/latest/cases/01168/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: This hierarchical model references an external model definition with a submodel with an external model definition. +componentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + +This model tests multiple layers of external model definitions, where the model referenced by an external model definition contains a submodel which is itself defined in a third file via an external model definition in the second file. + +The 'flattened' version of this hierarchical model contains: +* 7 species (A__S, A__A__E, A__A__D, A__A__ES, A__B__E, A__B__D, A__B__ES) +* 1 compartment (A__comp) + +There are 4 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__S + A__A__E -> A__A__ES | $(A__S + A__A__E) / A__A__ES$ | +| A__A__ES -> A__A__E + A__A__D | $A__A__ES / (A__A__E + A__A__D)$ | +| A__S + A__B__E -> A__B__ES | $(A__S + A__B__E) / A__B__ES$ | +| A__B__ES -> A__B__E + A__B__D | $A__B__ES / (A__B__E + A__B__D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A__S | $11$ | variable | +| Initial concentration of species A__A__E | $5$ | variable | +| Initial concentration of species A__A__D | $7$ | variable | +| Initial concentration of species A__A__ES | $0.1$ | variable | +| Initial concentration of species A__B__E | $5$ | variable | +| Initial concentration of species A__B__D | $7$ | variable | +| Initial concentration of species A__B__ES | $0.1$ | variable | +| Initial volume of compartment 'A__comp' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + diff --git a/latest/cases/01168/synopsis.txt b/latest/cases/01168/synopsis.txt new file mode 100644 index 000000000..d62fd5d5e --- /dev/null +++ b/latest/cases/01168/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: This hierarchical model references an external model definition with a submodel with an external model definition. +componentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + +This model tests multiple layers of external model definitions, where the model referenced by an external model definition contains a submodel which is itself defined in a third file via an external model definition in the second file. + +The 'flattened' version of this hierarchical model contains: +* 7 species (A__S, A__A__E, A__A__D, A__A__ES, A__B__E, A__B__D, A__B__ES) +* 1 compartment (A__comp) + +There are 4 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__S + A__A__E -> A__A__ES | $(A__S + A__A__E) / A__A__ES$ | +| A__A__ES -> A__A__E + A__A__D | $A__A__ES / (A__A__E + A__A__D)$ | +| A__S + A__B__E -> A__B__ES | $(A__S + A__B__E) / A__B__ES$ | +| A__B__ES -> A__B__E + A__B__D | $A__B__ES / (A__B__E + A__B__D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A__S | $11$ | variable | +| Initial concentration of species A__A__E | $5$ | variable | +| Initial concentration of species A__A__D | $7$ | variable | +| Initial concentration of species A__A__ES | $0.1$ | variable | +| Initial concentration of species A__B__E | $5$ | variable | +| Initial concentration of species A__B__D | $7$ | variable | +| Initial concentration of species A__B__ES | $0.1$ | variable | +| Initial volume of compartment 'A__comp' | $1$ | constant |] + diff --git a/latest/cases/01169/l2v5/index.heta b/latest/cases/01169/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01169/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01169/l3v2/build.log b/latest/cases/01169/l3v2/build.log new file mode 100644 index 000000000..98d2a3cb8 --- /dev/null +++ b/latest/cases/01169/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01169/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01169/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01169/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 88 +[error] Record "Q" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01169/l3v2/index.heta b/latest/cases/01169/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01169/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01169/model-sbml-l3v2.xml b/latest/cases/01169/model-sbml-l3v2.xml new file mode 100644 index 000000000..fc4152272 --- /dev/null +++ b/latest/cases/01169/model-sbml-l3v2.xml @@ -0,0 +1,173 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + X + 100 + + + + + + 23 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x + 3 + + + + + + 0.2 + + + + + 3 + + + + + 0.3 + + + + + + + + + + + + + k1 + S1 + + + + + + + + + + + + x + 0.1515 + + + + + + q + + + + + + 4 + + + + + + + + + + x + 0.1515 + + + + + + r + + + + + + 5 + + + + + + + + + + + + + diff --git a/latest/cases/01169/synopsis.txt b/latest/cases/01169/synopsis.txt new file mode 100644 index 000000000..d36d67a28 --- /dev/null +++ b/latest/cases/01169/synopsis.txt @@ -0,0 +1,54 @@ + +category: Test +synopsis: A hierarchical model with time, extent, and replacement conversion factors. +componentTags: AssignmentRule, Compartment, EventNoDelay, EventPriority, Parameter, RateRule, Reaction, Species, comp:Deletion, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, NonConstantParameter, comp:ConversionFactor, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + Time, extent, and replacement conversion factors all combine in this model to affect a variety of constructs. + +The 'flattened' version of this hierarchical model contains: +* 1 species (A__S1) +* 10 parameters (extentconv, timeconv, Q, R, cf, X, U1, U2, A__k1, A__y) +* 1 compartment (A__default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A___J0: A__S1 -> | $extentconv / timeconv * A__k1 * A__S1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A___E0 | $gt(X / cf, 0.1515)$ | $Q$ | $A__y = 4$ | +| A___E1 | $gt(X / cf, 0.1515)$ | $R$ | $A__y = 5$ |] + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | U1 | $X / 100$ | +| Assignment | U2 | $23$ | +| Assignment | Q | $X / cf - 3$ | +| Rate | X | $0.2 * cf / timeconv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A__S1 | $7.2$ | variable | +| Initial value of parameter extentconv | $10$ | constant | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter R | $20$ | constant | +| Initial value of parameter cf | $100$ | constant | +| Initial value of parameter A__k1 | $1.06$ | constant | +| Initial value of parameter Q | $X / cf - 3$ | variable | +| Initial value of parameter X | $15$ | variable | +| Initial value of parameter U1 | $1.1$ | variable | +| Initial value of parameter U2 | $23$ | variable | +| Initial value of parameter A__y | $8.8$ | variable | +| Initial volume of compartment 'A__default_compartment' | $1$ | constant |] + diff --git a/latest/cases/01170/l2v5/index.heta b/latest/cases/01170/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01170/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01170/l3v2/heta-code/output.heta b/latest/cases/01170/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ac9246cfd --- /dev/null +++ b/latest/cases/01170/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 0.001; + +t3 @Record { } .= 10; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01170/l3v2/index.heta b/latest/cases/01170/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01170/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01170/l3v2/json/output.json b/latest/cases/01170/l3v2/json/output.json new file mode 100644 index 000000000..1de86b7b8 --- /dev/null +++ b/latest/cases/01170/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "0.001" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Record", + "id": "t3", + "assignments": { + "start_": "10" + } + } +] \ No newline at end of file diff --git a/latest/cases/01170/model-sbml-l3v2.xml b/latest/cases/01170/model-sbml-l3v2.xml new file mode 100644 index 000000000..d8ae2fb66 --- /dev/null +++ b/latest/cases/01170/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + t3 + time + + + + + + + + diff --git a/latest/cases/01170/output.heta b/latest/cases/01170/output.heta new file mode 100644 index 000000000..e3133a798 --- /dev/null +++ b/latest/cases/01170/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion factor. +componentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with a reaction in it, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 2 parameters (timeconv, t3) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $1 / timeconv * t3 * (time / timeconv)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t3 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 0.001; + +t3 @Record { } .= 10; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01170/synopsis.txt b/latest/cases/01170/synopsis.txt new file mode 100644 index 000000000..dfaa2224b --- /dev/null +++ b/latest/cases/01170/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor. +componentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with a reaction in it, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 2 parameters (timeconv, t3) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $1 / timeconv * t3 * (time / timeconv)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t3 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01171/l2v5/index.heta b/latest/cases/01171/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01171/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01171/l3v2/build.log b/latest/cases/01171/l3v2/build.log new file mode 100644 index 000000000..bb2ed1377 --- /dev/null +++ b/latest/cases/01171/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01171/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01171/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01171/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] Record "t2" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01171/l3v2/index.heta b/latest/cases/01171/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01171/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01171/model-sbml-l3v2.xml b/latest/cases/01171/model-sbml-l3v2.xml new file mode 100644 index 000000000..1494df732 --- /dev/null +++ b/latest/cases/01171/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + time + 3 + + + + + + + diff --git a/latest/cases/01171/synopsis.txt b/latest/cases/01171/synopsis.txt new file mode 100644 index 000000000..e2bdd7f98 --- /dev/null +++ b/latest/cases/01171/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor. +componentTags: AssignmentRule, CSymbolTime, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with an initial assignment using the 'time' csymbol, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (timeconv, t2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | t2 | $time / timeconv + 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t2 | $time / timeconv + 3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01172/l2v5/index.heta b/latest/cases/01172/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01172/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01172/l3v2/heta-code/output.heta b/latest/cases/01172/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2498ad2d4 --- /dev/null +++ b/latest/cases/01172/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +t1 @Record { } .= 1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01172/l3v2/index.heta b/latest/cases/01172/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01172/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01172/l3v2/json/output.json b/latest/cases/01172/l3v2/json/output.json new file mode 100644 index 000000000..ddc4a8418 --- /dev/null +++ b/latest/cases/01172/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Record", + "id": "t1", + "assignments": { + "start_": "1" + } + } +] \ No newline at end of file diff --git a/latest/cases/01172/model-sbml-l3v2.xml b/latest/cases/01172/model-sbml-l3v2.xml new file mode 100644 index 000000000..81c3c123d --- /dev/null +++ b/latest/cases/01172/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + t1 + + 3 + + + + + + + diff --git a/latest/cases/01172/output.heta b/latest/cases/01172/output.heta new file mode 100644 index 000000000..ac68ab799 --- /dev/null +++ b/latest/cases/01172/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion factor and a rate rule. +componentTags: CSymbolTime, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with a rate rule in it, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (timeconv, t1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | t1 | $(time / timeconv / t1 + 3) / timeconv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +t1 @Record { } .= 1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01172/synopsis.txt b/latest/cases/01172/synopsis.txt new file mode 100644 index 000000000..e584d8393 --- /dev/null +++ b/latest/cases/01172/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor and a rate rule. +componentTags: CSymbolTime, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with a rate rule in it, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (timeconv, t1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | t1 | $(time / timeconv / t1 + 3) / timeconv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01173/l2v5/index.heta b/latest/cases/01173/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01173/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01173/l3v2/heta-code/output.heta b/latest/cases/01173/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0b65d72f0 --- /dev/null +++ b/latest/cases/01173/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +t1 @Record { } .= 1; +t3 @Record { } .= 1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01173/l3v2/index.heta b/latest/cases/01173/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01173/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01173/l3v2/json/output.json b/latest/cases/01173/l3v2/json/output.json new file mode 100644 index 000000000..2fe0ee498 --- /dev/null +++ b/latest/cases/01173/l3v2/json/output.json @@ -0,0 +1,24 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Record", + "id": "t1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "t3", + "assignments": { + "start_": "1" + } + } +] \ No newline at end of file diff --git a/latest/cases/01173/model-sbml-l3v2.xml b/latest/cases/01173/model-sbml-l3v2.xml new file mode 100644 index 000000000..c43248b0c --- /dev/null +++ b/latest/cases/01173/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + + + + delay + t1 + 3 + + + + + + + diff --git a/latest/cases/01173/output.heta b/latest/cases/01173/output.heta new file mode 100644 index 000000000..c7455d54d --- /dev/null +++ b/latest/cases/01173/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion factor and delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with the csymbol delay, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 3 parameters (timeconv, t1, t3) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | t1 | $time / timeconv$ | +| Assignment | t3 | $delay(t1, timeconv * 3)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t1 | $time / timeconv$ | variable | +| Initial value of parameter t3 | $delay(t1, timeconv * 3)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +t1 @Record { } .= 1; +t3 @Record { } .= 1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01173/synopsis.txt b/latest/cases/01173/synopsis.txt new file mode 100644 index 000000000..221fb035c --- /dev/null +++ b/latest/cases/01173/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor and delay. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with the csymbol delay, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 3 parameters (timeconv, t1, t3) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | t1 | $time / timeconv$ | +| Assignment | t3 | $delay(t1, timeconv * 3)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t1 | $time / timeconv$ | variable | +| Initial value of parameter t3 | $delay(t1, timeconv * 3)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01174/l2v5/index.heta b/latest/cases/01174/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01174/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01174/l3v2/heta-code/output.heta b/latest/cases/01174/l3v2/heta-code/output.heta new file mode 100644 index 000000000..25a381541 --- /dev/null +++ b/latest/cases/01174/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +t4 @Record { } .= 1; + +timeconv @Const { } = 60; +t3 @Const { } = 1; + diff --git a/latest/cases/01174/l3v2/index.heta b/latest/cases/01174/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01174/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01174/l3v2/json/output.json b/latest/cases/01174/l3v2/json/output.json new file mode 100644 index 000000000..0f11913bc --- /dev/null +++ b/latest/cases/01174/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Const", + "id": "t3", + "num": 1 + }, + { + "class": "Record", + "id": "t4", + "assignments": { + "start_": "1" + } + } +] \ No newline at end of file diff --git a/latest/cases/01174/model-sbml-l3v2.xml b/latest/cases/01174/model-sbml-l3v2.xml new file mode 100644 index 000000000..9694bb3c8 --- /dev/null +++ b/latest/cases/01174/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 3 + + + + + + + + + + t4 + + delay + t3 + + + time + 2 + + + + + + + + + diff --git a/latest/cases/01174/output.heta b/latest/cases/01174/output.heta new file mode 100644 index 000000000..21882314a --- /dev/null +++ b/latest/cases/01174/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion factor and an algebraic rule. +componentTags: AlgebraicRule, CSymbolDelay, CSymbolTime, InitialAssignment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model contains a submodel with an algebraic rule containing the csymbols 'time' and 'delay' , contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 3 parameters (timeconv, t3, t4) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $t4 - delay(t3, timeconv * (time / timeconv / 2))$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t3 | $time / timeconv + 3$ | constant | +| Initial value of parameter t4 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +t4 @Record { } .= 1; + +timeconv @Const { } = 60; +t3 @Const { } = 1; + diff --git a/latest/cases/01174/synopsis.txt b/latest/cases/01174/synopsis.txt new file mode 100644 index 000000000..36aa5a98c --- /dev/null +++ b/latest/cases/01174/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor and an algebraic rule. +componentTags: AlgebraicRule, CSymbolDelay, CSymbolTime, InitialAssignment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model contains a submodel with an algebraic rule containing the csymbols 'time' and 'delay' , contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 3 parameters (timeconv, t3, t4) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $t4 - delay(t3, timeconv * (time / timeconv / 2))$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t3 | $time / timeconv + 3$ | constant | +| Initial value of parameter t4 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01175/l2v5/index.heta b/latest/cases/01175/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01175/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01175/l3v2/heta-code/output.heta b/latest/cases/01175/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3a93e243c --- /dev/null +++ b/latest/cases/01175/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 0.001; + +t5 @Record { } .= 3.1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01175/l3v2/index.heta b/latest/cases/01175/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01175/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01175/l3v2/json/output.json b/latest/cases/01175/l3v2/json/output.json new file mode 100644 index 000000000..da60f1d9d --- /dev/null +++ b/latest/cases/01175/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "0.001" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Record", + "id": "t5", + "assignments": { + "start_": "3.1" + } + } +] \ No newline at end of file diff --git a/latest/cases/01175/model-sbml-l3v2.xml b/latest/cases/01175/model-sbml-l3v2.xml new file mode 100644 index 000000000..146321bcd --- /dev/null +++ b/latest/cases/01175/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + t5 + time + + + + s1 + t5 + + + + + + + + + diff --git a/latest/cases/01175/output.heta b/latest/cases/01175/output.heta new file mode 100644 index 000000000..2bbee5bb6 --- /dev/null +++ b/latest/cases/01175/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion factor and reaction. +componentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with a reaction, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 2 parameters (timeconv, t5) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $1 / timeconv * (t5 * (time / timeconv) / (s1 * t5))$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t5 | $3.1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 0.001; + +t5 @Record { } .= 3.1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01175/synopsis.txt b/latest/cases/01175/synopsis.txt new file mode 100644 index 000000000..e7e6cfdb6 --- /dev/null +++ b/latest/cases/01175/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor and reaction. +componentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with a reaction, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 2 parameters (timeconv, t5) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $1 / timeconv * (t5 * (time / timeconv) / (s1 * t5))$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t5 | $3.1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01176/l2v5/index.heta b/latest/cases/01176/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01176/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01176/l3v2/heta-code/output.heta b/latest/cases/01176/l3v2/heta-code/output.heta new file mode 100644 index 000000000..161bf9179 --- /dev/null +++ b/latest/cases/01176/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 0.001; + +t5 @Record { } .= 3.2; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01176/l3v2/index.heta b/latest/cases/01176/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01176/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01176/l3v2/json/output.json b/latest/cases/01176/l3v2/json/output.json new file mode 100644 index 000000000..28f5495ad --- /dev/null +++ b/latest/cases/01176/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "0.001" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Record", + "id": "t5", + "assignments": { + "start_": "3.2" + } + } +] \ No newline at end of file diff --git a/latest/cases/01176/model-sbml-l3v2.xml b/latest/cases/01176/model-sbml-l3v2.xml new file mode 100644 index 000000000..f23c0f68d --- /dev/null +++ b/latest/cases/01176/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + + + + + + + + + + + + delay + t5 + 0.2 + + time + + + + + + + + diff --git a/latest/cases/01176/output.heta b/latest/cases/01176/output.heta new file mode 100644 index 000000000..d437fe352 --- /dev/null +++ b/latest/cases/01176/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion factor and a delay in a kinetic law. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with a reaction whose kinetic law contains a delay, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 2 parameters (timeconv, t5) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $1 / timeconv * delay(t5, timeconv * 0.2) * (time / timeconv)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | t5 | $time / timeconv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t5 | $time / timeconv$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 0.001; + +t5 @Record { } .= 3.2; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01176/synopsis.txt b/latest/cases/01176/synopsis.txt new file mode 100644 index 000000000..ead0c46dd --- /dev/null +++ b/latest/cases/01176/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor and a delay in a kinetic law. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +This model contains a submodel with a reaction whose kinetic law contains a delay, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 2 parameters (timeconv, t5) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $1 / timeconv * delay(t5, timeconv * 0.2) * (time / timeconv)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | t5 | $time / timeconv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0.001$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t5 | $time / timeconv$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01177/l2v5/index.heta b/latest/cases/01177/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01177/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01177/l3v2/heta-code/output.heta b/latest/cases/01177/l3v2/heta-code/output.heta new file mode 100644 index 000000000..aa7302750 --- /dev/null +++ b/latest/cases/01177/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +t5 @Record { } .= 1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01177/l3v2/index.heta b/latest/cases/01177/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01177/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01177/l3v2/json/output.json b/latest/cases/01177/l3v2/json/output.json new file mode 100644 index 000000000..05e7b8612 --- /dev/null +++ b/latest/cases/01177/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Record", + "id": "t5", + "assignments": { + "start_": "1" + } + } +] \ No newline at end of file diff --git a/latest/cases/01177/model-sbml-l3v2.xml b/latest/cases/01177/model-sbml-l3v2.xml new file mode 100644 index 000000000..de5a8dbb2 --- /dev/null +++ b/latest/cases/01177/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 0.005 + + + + + + + + 1 -5 + time + + + + + + + time + + + + + + + + diff --git a/latest/cases/01177/output.heta b/latest/cases/01177/output.heta new file mode 100644 index 000000000..cdfb39736 --- /dev/null +++ b/latest/cases/01177/output.heta @@ -0,0 +1,36 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion factor. +componentTags: CSymbolTime, EventWithDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: EventUsesTriggerTimeValues, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + +This model contains a submodel with an event with various time-based constructs in it, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (timeconv, t5) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| | $gt(time / timeconv, 3)$ | $timeconv * (1 / (time / timeconv))$ | $t5 = time / timeconv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t5 | $1$ | variable |] + +*/ + + + +t @TimeScale { }; + +t5 @Record { } .= 1; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01177/synopsis.txt b/latest/cases/01177/synopsis.txt new file mode 100644 index 000000000..f971182a9 --- /dev/null +++ b/latest/cases/01177/synopsis.txt @@ -0,0 +1,26 @@ + +category: Test +synopsis: A hierarchical model with a time conversion factor. +componentTags: CSymbolTime, EventWithDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: EventUsesTriggerTimeValues, NonConstantParameter, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + +This model contains a submodel with an event with various time-based constructs in it, contained in a model with a time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (timeconv, t5) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| | $gt(time / timeconv, 3)$ | $timeconv * (1 / (time / timeconv))$ | $t5 = time / timeconv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter t5 | $1$ | variable |] + diff --git a/latest/cases/01178/l2v5/index.heta b/latest/cases/01178/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01178/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01178/l3v2/heta-code/output.heta b/latest/cases/01178/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2a4369a14 --- /dev/null +++ b/latest/cases/01178/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01178/l3v2/index.heta b/latest/cases/01178/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01178/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01178/l3v2/json/output.json b/latest/cases/01178/l3v2/json/output.json new file mode 100644 index 000000000..679092c23 --- /dev/null +++ b/latest/cases/01178/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + } +] \ No newline at end of file diff --git a/latest/cases/01178/model-sbml-l3v2.xml b/latest/cases/01178/model-sbml-l3v2.xml new file mode 100644 index 000000000..667639168 --- /dev/null +++ b/latest/cases/01178/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + 6 + + + + + + + + + + + + 10 + + + + + + + diff --git a/latest/cases/01178/output.heta b/latest/cases/01178/output.heta new file mode 100644 index 000000000..121f9195a --- /dev/null +++ b/latest/cases/01178/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: A hierarchical model with extent conversion and a reference to a modified reaction. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, comp:ExtentConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference must be modified by the extent conversion factor just as the kinetic law itself is modified by the extent conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 2 parameters (extentconv, sub1__p80) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $extentconv * 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $sub1__J0 / extentconv + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter sub1__p80 | $sub1__J0 / extentconv + 6$ | variable | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01178/synopsis.txt b/latest/cases/01178/synopsis.txt new file mode 100644 index 000000000..e5f8e0ddd --- /dev/null +++ b/latest/cases/01178/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A hierarchical model with extent conversion and a reference to a modified reaction. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, comp:ExtentConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference must be modified by the extent conversion factor just as the kinetic law itself is modified by the extent conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 2 parameters (extentconv, sub1__p80) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $extentconv * 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $sub1__J0 / extentconv + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter sub1__p80 | $sub1__J0 / extentconv + 6$ | variable | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + diff --git a/latest/cases/01179/l2v5/index.heta b/latest/cases/01179/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01179/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01179/l3v2/heta-code/output.heta b/latest/cases/01179/l3v2/heta-code/output.heta new file mode 100644 index 000000000..493b669cb --- /dev/null +++ b/latest/cases/01179/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +t1 @Record { } .= 1; + +timeconv @Const { } = 60; +paramconv @Const { } = 0.01; + diff --git a/latest/cases/01179/l3v2/index.heta b/latest/cases/01179/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01179/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01179/l3v2/json/output.json b/latest/cases/01179/l3v2/json/output.json new file mode 100644 index 000000000..287d339e7 --- /dev/null +++ b/latest/cases/01179/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Const", + "id": "paramconv", + "num": 0.01 + }, + { + "class": "Record", + "id": "t1", + "assignments": { + "start_": "1" + } + } +] \ No newline at end of file diff --git a/latest/cases/01179/model-sbml-l3v2.xml b/latest/cases/01179/model-sbml-l3v2.xml new file mode 100644 index 000000000..3f9741add --- /dev/null +++ b/latest/cases/01179/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + t1 + + 3 + + + + + + + diff --git a/latest/cases/01179/output.heta b/latest/cases/01179/output.heta new file mode 100644 index 000000000..ae0d94573 --- /dev/null +++ b/latest/cases/01179/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: A hierarchical model with a time conversion and a replacement conversion factor both affecting a rate rule. +componentTags: CSymbolTime, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:ConversionFactor, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The rate rule in the submodel affects a parameter that has been replaced with a conversion factor, necessitating a conversion of the rate rule. In addition, the submodel as a whole has a time conversion factor, so the rate rule must additionally be affected by that. Just to go whole hog, the parameter itself is used in its own rate rule, as is the csymbol 'time'. + +The 'flattened' version of this hierarchical model contains: +* 3 parameters (timeconv, paramconv, t1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | t1 | $(time / timeconv / (t1 / paramconv) + 3) * paramconv / timeconv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter paramconv | $0.01$ | constant | +| Initial value of parameter t1 | $1$ | variable |] + +*/ + + + +t @TimeScale { }; + +t1 @Record { } .= 1; + +timeconv @Const { } = 60; +paramconv @Const { } = 0.01; + diff --git a/latest/cases/01179/synopsis.txt b/latest/cases/01179/synopsis.txt new file mode 100644 index 000000000..823b6befd --- /dev/null +++ b/latest/cases/01179/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: A hierarchical model with a time conversion and a replacement conversion factor both affecting a rate rule. +componentTags: CSymbolTime, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:ConversionFactor, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The rate rule in the submodel affects a parameter that has been replaced with a conversion factor, necessitating a conversion of the rate rule. In addition, the submodel as a whole has a time conversion factor, so the rate rule must additionally be affected by that. Just to go whole hog, the parameter itself is used in its own rate rule, as is the csymbol 'time'. + +The 'flattened' version of this hierarchical model contains: +* 3 parameters (timeconv, paramconv, t1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | t1 | $(time / timeconv / (t1 / paramconv) + 3) * paramconv / timeconv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter paramconv | $0.01$ | constant | +| Initial value of parameter t1 | $1$ | variable |] + diff --git a/latest/cases/01180/l2v5/index.heta b/latest/cases/01180/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01180/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01180/l3v2/heta-code/output.heta b/latest/cases/01180/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2eacd7a46 --- /dev/null +++ b/latest/cases/01180/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01180/l3v2/index.heta b/latest/cases/01180/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01180/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01180/l3v2/json/output.json b/latest/cases/01180/l3v2/json/output.json new file mode 100644 index 000000000..acd7113da --- /dev/null +++ b/latest/cases/01180/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + } +] \ No newline at end of file diff --git a/latest/cases/01180/model-sbml-l3v2.xml b/latest/cases/01180/model-sbml-l3v2.xml new file mode 100644 index 000000000..06583d2f0 --- /dev/null +++ b/latest/cases/01180/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + 6 + + + + + + + + + + + + 10 + + + + + + + diff --git a/latest/cases/01180/output.heta b/latest/cases/01180/output.heta new file mode 100644 index 000000000..235f5c2a5 --- /dev/null +++ b/latest/cases/01180/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: A hierarchical model with time conversion and a reference to a modified reaction. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference must be modified by the time conversion factor just as the kinetic law itself is modified by the time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 2 parameters (timeconv, sub1__p80) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $1 / timeconv * 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $sub1__J0 / (1 / timeconv) + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__p80 | $sub1__J0 / (1 / timeconv) + 6$ | variable | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +timeconv @Const { } = 60; + diff --git a/latest/cases/01180/synopsis.txt b/latest/cases/01180/synopsis.txt new file mode 100644 index 000000000..189b447c8 --- /dev/null +++ b/latest/cases/01180/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A hierarchical model with time conversion and a reference to a modified reaction. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + +In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference must be modified by the time conversion factor just as the kinetic law itself is modified by the time conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 2 parameters (timeconv, sub1__p80) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $1 / timeconv * 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $sub1__J0 / (1 / timeconv) + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__p80 | $sub1__J0 / (1 / timeconv) + 6$ | variable | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01181/l2v5/index.heta b/latest/cases/01181/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01181/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01181/l3v2/heta-code/output.heta b/latest/cases/01181/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a51662e4b --- /dev/null +++ b/latest/cases/01181/l3v2/heta-code/output.heta @@ -0,0 +1,7 @@ + + +t @TimeScale { }; + +extentconv @Const { } = 1000; +timeconv @Const { } = 60; + diff --git a/latest/cases/01181/l3v2/index.heta b/latest/cases/01181/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01181/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01181/l3v2/json/output.json b/latest/cases/01181/l3v2/json/output.json new file mode 100644 index 000000000..feda34cab --- /dev/null +++ b/latest/cases/01181/l3v2/json/output.json @@ -0,0 +1,15 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + } +] \ No newline at end of file diff --git a/latest/cases/01181/model-sbml-l3v2.xml b/latest/cases/01181/model-sbml-l3v2.xml new file mode 100644 index 000000000..30b7a8052 --- /dev/null +++ b/latest/cases/01181/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + 6 + + + + + + + + + + + + 10 + + + + + + + diff --git a/latest/cases/01181/output.heta b/latest/cases/01181/output.heta new file mode 100644 index 000000000..4cdc433b6 --- /dev/null +++ b/latest/cases/01181/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: A hierarchical model with extent and time conversion and a reference to a modified reaction. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference must be modified by the time and extent conversion factor just as the kinetic law itself is modified by the time and extent conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 3 parameters (extentconv, timeconv, sub1__p80) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $extentconv / timeconv * 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $sub1__J0 / (extentconv / timeconv) + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__p80 | $sub1__J0 / (extentconv / timeconv) + 6$ | variable | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +extentconv @Const { } = 1000; +timeconv @Const { } = 60; + diff --git a/latest/cases/01181/synopsis.txt b/latest/cases/01181/synopsis.txt new file mode 100644 index 000000000..8d4ccfddc --- /dev/null +++ b/latest/cases/01181/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A hierarchical model with extent and time conversion and a reference to a modified reaction. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference must be modified by the time and extent conversion factor just as the kinetic law itself is modified by the time and extent conversion factor. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub1__s1) +* 3 parameters (extentconv, timeconv, sub1__p80) +* 1 compartment (sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> sub1__s1 | $extentconv / timeconv * 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $sub1__J0 / (extentconv / timeconv) + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__p80 | $sub1__J0 / (extentconv / timeconv) + 6$ | variable | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01182/l2v5/index.heta b/latest/cases/01182/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01182/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01182/l3v2/heta-code/output.heta b/latest/cases/01182/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4a9e59c4f --- /dev/null +++ b/latest/cases/01182/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 1; + +J0 @Reaction { actors: = s1, }; +J0 := 10; + +extentconv @Const { } = 1000; +timeconv @Const { } = 60; + diff --git a/latest/cases/01182/l3v2/index.heta b/latest/cases/01182/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01182/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01182/l3v2/json/output.json b/latest/cases/01182/l3v2/json/output.json new file mode 100644 index 000000000..6b8580520 --- /dev/null +++ b/latest/cases/01182/l3v2/json/output.json @@ -0,0 +1,45 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "10" + }, + "actors": [ + { + "target": "s1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + } +] \ No newline at end of file diff --git a/latest/cases/01182/model-sbml-l3v2.xml b/latest/cases/01182/model-sbml-l3v2.xml new file mode 100644 index 000000000..493704b6d --- /dev/null +++ b/latest/cases/01182/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + 6 + + + + + + + + + + + + 10 + + + + + + + diff --git a/latest/cases/01182/output.heta b/latest/cases/01182/output.heta new file mode 100644 index 000000000..6b13cf6a8 --- /dev/null +++ b/latest/cases/01182/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: A hierarchical model with time and extent conversion and a reference to a modified replaced reaction. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, MultiCompartment, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference would normally be modified by the time and extent conversion factors, however, the reaction is replaced, meaning that the only conversion factor to be applied is the conversion factor on the replacement. Since there is no such factor, the assignment rule should pass through unmolested, and point to the new reaction. + +The 'flattened' version of this hierarchical model contains: +* 2 species (s1, sub1__s1) +* 3 parameters (extentconv, timeconv, sub1__p80) +* 2 compartments (C, sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $J0 + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $1$ | variable | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__p80 | $J0 + 6$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 1; + +J0 @Reaction { actors: = s1, }; +J0 := 10; + +extentconv @Const { } = 1000; +timeconv @Const { } = 60; + diff --git a/latest/cases/01182/synopsis.txt b/latest/cases/01182/synopsis.txt new file mode 100644 index 000000000..7dcf32c8f --- /dev/null +++ b/latest/cases/01182/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: A hierarchical model with time and extent conversion and a reference to a modified replaced reaction. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, MultiCompartment, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference would normally be modified by the time and extent conversion factors, however, the reaction is replaced, meaning that the only conversion factor to be applied is the conversion factor on the replacement. Since there is no such factor, the assignment rule should pass through unmolested, and point to the new reaction. + +The 'flattened' version of this hierarchical model contains: +* 2 species (s1, sub1__s1) +* 3 parameters (extentconv, timeconv, sub1__p80) +* 2 compartments (C, sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $J0 + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $1$ | variable | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter sub1__p80 | $J0 + 6$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01183/l2v5/index.heta b/latest/cases/01183/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01183/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01183/l3v2/heta-code/output.heta b/latest/cases/01183/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f12da73aa --- /dev/null +++ b/latest/cases/01183/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 1; + +J0 @Reaction { actors: = s1, }; +J0 := 10; + +extentconv @Const { } = 1000; +timeconv @Const { } = 60; +extentpertimeconv @Const { } = 16.6666666666667; + diff --git a/latest/cases/01183/l3v2/index.heta b/latest/cases/01183/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01183/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01183/l3v2/json/output.json b/latest/cases/01183/l3v2/json/output.json new file mode 100644 index 000000000..4bb1097a1 --- /dev/null +++ b/latest/cases/01183/l3v2/json/output.json @@ -0,0 +1,50 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "1" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "10" + }, + "actors": [ + { + "target": "s1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + }, + { + "class": "Const", + "id": "timeconv", + "num": 60 + }, + { + "class": "Const", + "id": "extentpertimeconv", + "num": 16.6666666666667 + } +] \ No newline at end of file diff --git a/latest/cases/01183/model-sbml-l3v2.xml b/latest/cases/01183/model-sbml-l3v2.xml new file mode 100644 index 000000000..46e68451b --- /dev/null +++ b/latest/cases/01183/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + 6 + + + + + + + + + + + + 10 + + + + + + + diff --git a/latest/cases/01183/output.heta b/latest/cases/01183/output.heta new file mode 100644 index 000000000..47193e26f --- /dev/null +++ b/latest/cases/01183/output.heta @@ -0,0 +1,60 @@ +/* +category: Test + synopsis: A hierarchical model with time and extent conversion and a reference to a modified replaced reaction, itself with a conversion factor. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, MultiCompartment, comp:ConversionFactor, comp:ExtentConversionFactor, comp:SubmodelOutput , comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference would normally be modified by the time and extent conversion factors, however, the reaction is replaced, meaning that the only conversion factor to be applied is the conversion factor on the replacement (which, unlike test 1182, exists in this model). + +The 'flattened' version of this hierarchical model contains: +* 2 species (s1, sub1__s1) +* 4 parameters (extentconv, timeconv, extentpertimeconv, sub1__p80) +* 2 compartments (C, sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $J0 / extentpertimeconv + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $1$ | variable | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter extentpertimeconv | $16.6667$ | constant | +| Initial value of parameter sub1__p80 | $J0 / extentpertimeconv + 6$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, isAmount: true, } .= 1; + +J0 @Reaction { actors: = s1, }; +J0 := 10; + +extentconv @Const { } = 1000; +timeconv @Const { } = 60; +extentpertimeconv @Const { } = 16.6666666666667; + diff --git a/latest/cases/01183/synopsis.txt b/latest/cases/01183/synopsis.txt new file mode 100644 index 000000000..d3a4f7b16 --- /dev/null +++ b/latest/cases/01183/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test + synopsis: A hierarchical model with time and extent conversion and a reference to a modified replaced reaction, itself with a conversion factor. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, MultiCompartment, comp:ConversionFactor, comp:ExtentConversionFactor, comp:SubmodelOutput , comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference would normally be modified by the time and extent conversion factors, however, the reaction is replaced, meaning that the only conversion factor to be applied is the conversion factor on the replacement (which, unlike test 1182, exists in this model). + +The 'flattened' version of this hierarchical model contains: +* 2 species (s1, sub1__s1) +* 4 parameters (extentconv, timeconv, extentpertimeconv, sub1__p80) +* 2 compartments (C, sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| -> s1 | $10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | sub1__p80 | $J0 / extentpertimeconv + 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $1$ | variable | +| Initial amount of species sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial value of parameter timeconv | $60$ | constant | +| Initial value of parameter extentpertimeconv | $16.6667$ | constant | +| Initial value of parameter sub1__p80 | $J0 / extentpertimeconv + 6$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'sub1__C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01184/l2v5/heta-code/output.heta b/latest/cases/01184/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7c0cc7a28 --- /dev/null +++ b/latest/cases/01184/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; + +k1 @Record { } .= y; +y @Record { } .= 3; + diff --git a/latest/cases/01184/l2v5/index.heta b/latest/cases/01184/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01184/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01184/l2v5/json/output.json b/latest/cases/01184/l2v5/json/output.json new file mode 100644 index 000000000..1502e2059 --- /dev/null +++ b/latest/cases/01184/l2v5/json/output.json @@ -0,0 +1,73 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "_J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "y" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01184/l3v2/build.log b/latest/cases/01184/l3v2/build.log new file mode 100644 index 000000000..1520f6b77 --- /dev/null +++ b/latest/cases/01184/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01184/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01184/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01184/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 84 +[error] No required "num" property for "k1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01184/l3v2/index.heta b/latest/cases/01184/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01184/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01184/model-sbml-l2v5.xml b/latest/cases/01184/model-sbml-l2v5.xml new file mode 100644 index 000000000..c93780de5 --- /dev/null +++ b/latest/cases/01184/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + y + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01184/model-sbml-l3v2.xml b/latest/cases/01184/model-sbml-l3v2.xml new file mode 100644 index 000000000..e21fb7efc --- /dev/null +++ b/latest/cases/01184/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + y + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01184/output.heta b/latest/cases/01184/output.heta new file mode 100644 index 000000000..731cff764 --- /dev/null +++ b/latest/cases/01184/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: A kinetic law set by a constant with an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In some software packages, constant kinetic laws are pre-processed to a single value. This tests to ensure that if a kinetic law is constant but depends on an initial assignment to a variable, this processing is still accurate. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, y) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: -> S1 | $k1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $y$ | constant | +| Initial value of parameter y | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; + +k1 @Record { } .= y; +y @Record { } .= 3; + diff --git a/latest/cases/01184/synopsis.txt b/latest/cases/01184/synopsis.txt new file mode 100644 index 000000000..31578d72b --- /dev/null +++ b/latest/cases/01184/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A kinetic law set by a constant with an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In some software packages, constant kinetic laws are pre-processed to a single value. This tests to ensure that if a kinetic law is constant but depends on an initial assignment to a variable, this processing is still accurate. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, y) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: -> S1 | $k1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $y$ | constant | +| Initial value of parameter y | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01185/l2v5/heta-code/output.heta b/latest/cases/01185/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7c0cc7a28 --- /dev/null +++ b/latest/cases/01185/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; + +k1 @Record { } .= y; +y @Record { } .= 3; + diff --git a/latest/cases/01185/l2v5/index.heta b/latest/cases/01185/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01185/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01185/l2v5/json/output.json b/latest/cases/01185/l2v5/json/output.json new file mode 100644 index 000000000..1502e2059 --- /dev/null +++ b/latest/cases/01185/l2v5/json/output.json @@ -0,0 +1,73 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "_J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "y" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01185/l3v2/heta-code/output.heta b/latest/cases/01185/l3v2/heta-code/output.heta new file mode 100644 index 000000000..584d92f81 --- /dev/null +++ b/latest/cases/01185/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; + +k1 @Const { } = -2; +y @Const { } = 3; + diff --git a/latest/cases/01185/l3v2/index.heta b/latest/cases/01185/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01185/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01185/l3v2/json/output.json b/latest/cases/01185/l3v2/json/output.json new file mode 100644 index 000000000..8a3a6517a --- /dev/null +++ b/latest/cases/01185/l3v2/json/output.json @@ -0,0 +1,44 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "_J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Const", + "id": "k1", + "num": -2 + }, + { + "class": "Const", + "id": "y", + "num": 3 + } +] \ No newline at end of file diff --git a/latest/cases/01185/model-sbml-l2v5.xml b/latest/cases/01185/model-sbml-l2v5.xml new file mode 100644 index 000000000..03d383fb8 --- /dev/null +++ b/latest/cases/01185/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + y + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01185/model-sbml-l3v2.xml b/latest/cases/01185/model-sbml-l3v2.xml new file mode 100644 index 000000000..b063ccee6 --- /dev/null +++ b/latest/cases/01185/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + y + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01185/output.heta b/latest/cases/01185/output.heta new file mode 100644 index 000000000..c31532499 --- /dev/null +++ b/latest/cases/01185/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A kinetic law set by a constant with an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In some software packages, constant kinetic laws are pre-processed to a single value. This tests to ensure that if a kinetic law is constant but depends on an initial assignment to a variable, this processing is still accurate, even when that value is given an (overridden) 'value' attribute. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, y) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: -> S1 | $k1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $y$ | constant | +| Initial value of parameter y | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; + +_J0 @Reaction { actors: = S1, }; +_J0 := k1; + +k1 @Const { } = -2; +y @Const { } = 3; + diff --git a/latest/cases/01185/synopsis.txt b/latest/cases/01185/synopsis.txt new file mode 100644 index 000000000..3d492b518 --- /dev/null +++ b/latest/cases/01185/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A kinetic law set by a constant with an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In some software packages, constant kinetic laws are pre-processed to a single value. This tests to ensure that if a kinetic law is constant but depends on an initial assignment to a variable, this processing is still accurate, even when that value is given an (overridden) 'value' attribute. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, y) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| _J0: -> S1 | $k1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $y$ | constant | +| Initial value of parameter y | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01186/l2v5/index.heta b/latest/cases/01186/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01186/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01186/l3v2/build.log b/latest/cases/01186/l3v2/build.log new file mode 100644 index 000000000..e278f4c00 --- /dev/null +++ b/latest/cases/01186/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01186/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01186/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01186/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01186/l3v2/index.heta b/latest/cases/01186/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01186/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01186/model-sbml-l3v2.xml b/latest/cases/01186/model-sbml-l3v2.xml new file mode 100644 index 000000000..aae097080 --- /dev/null +++ b/latest/cases/01186/model-sbml-l3v2.xml @@ -0,0 +1,633 @@ + + + + + +

+ Maximize single objective function, hard bounds. +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:21Z + + + 2012-12-21T10:05:21Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01186/synopsis.txt b/latest/cases/01186/synopsis.txt new file mode 100644 index 000000000..e60f657c5 --- /dev/null +++ b/latest/cases/01186/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Maximize single objective function, hard bounds. +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + +Maximize single objective function, hard bounds. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions, and 52 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R02: A -> B | $R02 >= -1000 && R02 <= 1000$ | +| R03: A -> C | $R03 >= -1000 && R03 <= 1000$ | +| R04: C -> B | $R04 >= -1000 && R04 <= 1000$ | +| R05: B -> D | $R05 >= 0 && R05 <= 1000$ | +| R06: D -> E | $R06 >= 0 && R06 <= 1000$ | +| R07: E -> F | $R07 >= 0 && R07 <= 1000$ | +| R08: F -> I | $R08 >= 0 && R08 <= 1000$ | +| R09: D -> G | $R09 >= 0 && R09 <= 1000$ | +| R10: G -> H | $R10 >= 0 && R10 <= 1000$ | +| R11: H -> I | $R11 >= 0 && R11 <= 1000$ | +| R12: I -> J | $R12 >= 0 && R12 <= 1000$ | +| R13: J -> K | $R13 >= 0 && R13 <= 1000$ | +| R14: K -> L | $R14 >= -1000 && R14 <= 1000$ | +| R15: L -> Q | $R15 >= 0 && R15 <= 1000$ | +| R16: J -> M | $R16 >= 0 && R16 <= 1000$ | +| R17: M -> N | $R17 >= 0 && R17 <= 1000$ | +| R18: N -> Q | $R18 >= 0 && R18 <= 1000$ | +| R19: K -> O | $R19 >= -1000 && R19 <= 1000$ | +| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ | +| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ | +| R22: Q -> R | $R22 >= 0 && R22 <= 1000$ | +| R23: R -> S | $R23 >= -1000 && R23 <= 1000$ | +| R24: R -> S | $R24 >= 0 && R24 <= 1000$ | +| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ | +| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |] + + diff --git a/latest/cases/01187/l2v5/index.heta b/latest/cases/01187/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01187/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01187/l3v2/build.log b/latest/cases/01187/l3v2/build.log new file mode 100644 index 000000000..84307b766 --- /dev/null +++ b/latest/cases/01187/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01187/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01187/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01187/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01187/l3v2/index.heta b/latest/cases/01187/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01187/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01187/model-sbml-l3v2.xml b/latest/cases/01187/model-sbml-l3v2.xml new file mode 100644 index 000000000..0e9a560ff --- /dev/null +++ b/latest/cases/01187/model-sbml-l3v2.xml @@ -0,0 +1,633 @@ + + + + + +

+ Minimize single objective function, hard bounds. +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:21Z + + + 2012-12-21T10:05:21Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01187/synopsis.txt b/latest/cases/01187/synopsis.txt new file mode 100644 index 000000000..ea5921d84 --- /dev/null +++ b/latest/cases/01187/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Minimize single objective function, hard bounds. +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MinimizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + + Minimize single objective function, hard bounds. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions, and 52 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R02: A -> B | $R02 >= -1000 && R02 <= 1000$ | +| R03: A -> C | $R03 >= -1000 && R03 <= 1000$ | +| R04: C -> B | $R04 >= -1000 && R04 <= 1000$ | +| R05: B -> D | $R05 >= 0 && R05 <= 1000$ | +| R06: D -> E | $R06 >= 0 && R06 <= 1000$ | +| R07: E -> F | $R07 >= 0 && R07 <= 1000$ | +| R08: F -> I | $R08 >= 0 && R08 <= 1000$ | +| R09: D -> G | $R09 >= 0 && R09 <= 1000$ | +| R10: G -> H | $R10 >= 0 && R10 <= 1000$ | +| R11: H -> I | $R11 >= 0 && R11 <= 1000$ | +| R12: I -> J | $R12 >= 0 && R12 <= 1000$ | +| R13: J -> K | $R13 >= 0 && R13 <= 1000$ | +| R14: K -> L | $R14 >= -1000 && R14 <= 1000$ | +| R15: L -> Q | $R15 >= 0 && R15 <= 1000$ | +| R16: J -> M | $R16 >= 0 && R16 <= 1000$ | +| R17: M -> N | $R17 >= 0 && R17 <= 1000$ | +| R18: N -> Q | $R18 >= 0 && R18 <= 1000$ | +| R19: K -> O | $R19 >= -1000 && R19 <= 1000$ | +| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ | +| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ | +| R22: Q -> R | $R22 >= 0 && R22 <= 1000$ | +| R23: R -> S | $R23 >= -1000 && R23 <= 1000$ | +| R24: R -> S | $R24 >= 0 && R24 <= 1000$ | +| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ | +| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |] + diff --git a/latest/cases/01188/l2v5/index.heta b/latest/cases/01188/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01188/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01188/l3v2/build.log b/latest/cases/01188/l3v2/build.log new file mode 100644 index 000000000..bb2e9ff91 --- /dev/null +++ b/latest/cases/01188/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01188/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01188/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01188/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01188/l3v2/index.heta b/latest/cases/01188/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01188/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01188/model-sbml-l3v2.xml b/latest/cases/01188/model-sbml-l3v2.xml new file mode 100644 index 000000000..c3302f24d --- /dev/null +++ b/latest/cases/01188/model-sbml-l3v2.xml @@ -0,0 +1,633 @@ + + + + + +

+ Maximize single objective function, infinite bounds. +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:21Z + + + 2012-12-21T10:05:21Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01188/synopsis.txt b/latest/cases/01188/synopsis.txt new file mode 100644 index 000000000..681de9d86 --- /dev/null +++ b/latest/cases/01188/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Maximize single objective function, infinite bounds. +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + + Maximize single objective function, infinite bounds. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions, and 52 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R02: A -> B | $R02 >= -INF && R02 <= INF$ | +| R03: A -> C | $R03 >= -INF && R03 <= INF$ | +| R04: C -> B | $R04 >= -INF && R04 <= INF$ | +| R05: B -> D | $R05 >= 0 && R05 <= INF$ | +| R06: D -> E | $R06 >= 0 && R06 <= INF$ | +| R07: E -> F | $R07 >= 0 && R07 <= INF$ | +| R08: F -> I | $R08 >= 0 && R08 <= INF$ | +| R09: D -> G | $R09 >= 0 && R09 <= INF$ | +| R10: G -> H | $R10 >= 0 && R10 <= INF$ | +| R11: H -> I | $R11 >= 0 && R11 <= INF$ | +| R12: I -> J | $R12 >= 0 && R12 <= INF$ | +| R13: J -> K | $R13 >= 0 && R13 <= INF$ | +| R14: K -> L | $R14 >= -INF && R14 <= INF$ | +| R15: L -> Q | $R15 >= 0 && R15 <= INF$ | +| R16: J -> M | $R16 >= 0 && R16 <= INF$ | +| R17: M -> N | $R17 >= 0 && R17 <= INF$ | +| R18: N -> Q | $R18 >= 0 && R18 <= INF$ | +| R19: K -> O | $R19 >= -INF && R19 <= INF$ | +| R20: O -> P | $R20 >= -INF && R20 <= INF$ | +| R21: P -> L | $R21 >= -INF && R21 <= INF$ | +| R22: Q -> R | $R22 >= 0 && R22 <= INF$ | +| R23: R -> S | $R23 >= -INF && R23 <= INF$ | +| R24: R -> S | $R24 >= 0 && R24 <= INF$ | +| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= INF$ | +| R26: S -> Y | $R26 >= 0 && R26 <= INF$ |] + diff --git a/latest/cases/01189/l2v5/index.heta b/latest/cases/01189/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01189/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01189/l3v2/build.log b/latest/cases/01189/l3v2/build.log new file mode 100644 index 000000000..e96214ee1 --- /dev/null +++ b/latest/cases/01189/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01189/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01189/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01189/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01189/l3v2/index.heta b/latest/cases/01189/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01189/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01189/model-sbml-l3v2.xml b/latest/cases/01189/model-sbml-l3v2.xml new file mode 100644 index 000000000..7855cc079 --- /dev/null +++ b/latest/cases/01189/model-sbml-l3v2.xml @@ -0,0 +1,633 @@ + + + + + +

+ Minimize single objective function, infinite bounds. +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:21Z + + + 2012-12-21T10:05:21Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01189/synopsis.txt b/latest/cases/01189/synopsis.txt new file mode 100644 index 000000000..f1dd47b00 --- /dev/null +++ b/latest/cases/01189/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Minimize single objective function, infinite bounds. +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MinimizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + + Minimize single objective function, infinite bounds. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions, and 52 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R02: A -> B | $R02 >= -INF && R02 <= INF$ | +| R03: A -> C | $R03 >= -INF && R03 <= INF$ | +| R04: C -> B | $R04 >= -INF && R04 <= INF$ | +| R05: B -> D | $R05 >= 0 && R05 <= INF$ | +| R06: D -> E | $R06 >= 0 && R06 <= INF$ | +| R07: E -> F | $R07 >= 0 && R07 <= INF$ | +| R08: F -> I | $R08 >= 0 && R08 <= INF$ | +| R09: D -> G | $R09 >= 0 && R09 <= INF$ | +| R10: G -> H | $R10 >= 0 && R10 <= INF$ | +| R11: H -> I | $R11 >= 0 && R11 <= INF$ | +| R12: I -> J | $R12 >= 0 && R12 <= INF$ | +| R13: J -> K | $R13 >= 0 && R13 <= INF$ | +| R14: K -> L | $R14 >= -INF && R14 <= INF$ | +| R15: L -> Q | $R15 >= 0 && R15 <= INF$ | +| R16: J -> M | $R16 >= 0 && R16 <= INF$ | +| R17: M -> N | $R17 >= 0 && R17 <= INF$ | +| R18: N -> Q | $R18 >= 0 && R18 <= INF$ | +| R19: K -> O | $R19 >= -INF && R19 <= INF$ | +| R20: O -> P | $R20 >= -INF && R20 <= INF$ | +| R21: P -> L | $R21 >= -INF && R21 <= INF$ | +| R22: Q -> R | $R22 >= 0 && R22 <= INF$ | +| R23: R -> S | $R23 >= -INF && R23 <= INF$ | +| R24: R -> S | $R24 >= 0 && R24 <= INF$ | +| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= INF$ | +| R26: S -> Y | $R26 >= 0 && R26 <= INF$ |] + diff --git a/latest/cases/01190/l2v5/index.heta b/latest/cases/01190/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01190/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01190/l3v2/build.log b/latest/cases/01190/l3v2/build.log new file mode 100644 index 000000000..03e3503be --- /dev/null +++ b/latest/cases/01190/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01190/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01190/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01190/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01190/l3v2/index.heta b/latest/cases/01190/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01190/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01190/model-sbml-l3v2.xml b/latest/cases/01190/model-sbml-l3v2.xml new file mode 100644 index 000000000..7da3ee1ee --- /dev/null +++ b/latest/cases/01190/model-sbml-l3v2.xml @@ -0,0 +1,633 @@ + + + + + +

+ Maximize single objective function, non-unitary objective flux coefficient +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:21Z + + + 2012-12-21T10:05:21Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01190/synopsis.txt b/latest/cases/01190/synopsis.txt new file mode 100644 index 000000000..4a8e831a1 --- /dev/null +++ b/latest/cases/01190/synopsis.txt @@ -0,0 +1,10 @@ + +category: Test +synopsis: Maximize single objective function, non-unitary objective flux coefficient +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + diff --git a/latest/cases/01191/l2v5/index.heta b/latest/cases/01191/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01191/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01191/l3v2/build.log b/latest/cases/01191/l3v2/build.log new file mode 100644 index 000000000..76e5ee335 --- /dev/null +++ b/latest/cases/01191/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01191/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01191/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01191/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01191/l3v2/index.heta b/latest/cases/01191/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01191/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01191/model-sbml-l3v2.xml b/latest/cases/01191/model-sbml-l3v2.xml new file mode 100644 index 000000000..1b4045d77 --- /dev/null +++ b/latest/cases/01191/model-sbml-l3v2.xml @@ -0,0 +1,638 @@ + + + + + +

+ Multiple objectives defined, optimize active one (maximize) +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:21Z + + + 2012-12-21T10:05:21Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01191/synopsis.txt b/latest/cases/01191/synopsis.txt new file mode 100644 index 000000000..41e9d37fa --- /dev/null +++ b/latest/cases/01191/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Multiple objectives defined, optimize active one (maximize) +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MaximizeObjective, fbc:MinimizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + + Multiple objectives defined, optimize active one (maximize) + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 2 objectives (OBJF, OBJF2) + +The active objective is OBJF2, which is to be maximized: + + 1 R26 + +There are 26 reactions, and 52 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R02: A -> B | $R02 >= -1000 && R02 <= 1000$ | +| R03: A -> C | $R03 >= -1000 && R03 <= 1000$ | +| R04: C -> B | $R04 >= -1000 && R04 <= 1000$ | +| R05: B -> D | $R05 >= 0 && R05 <= 1000$ | +| R06: D -> E | $R06 >= 0 && R06 <= 1000$ | +| R07: E -> F | $R07 >= 0 && R07 <= 1000$ | +| R08: F -> I | $R08 >= 0 && R08 <= 1000$ | +| R09: D -> G | $R09 >= 0 && R09 <= 1000$ | +| R10: G -> H | $R10 >= 0 && R10 <= 1000$ | +| R11: H -> I | $R11 >= 0 && R11 <= 1000$ | +| R12: I -> J | $R12 >= 0 && R12 <= 1000$ | +| R13: J -> K | $R13 >= 0 && R13 <= 1000$ | +| R14: K -> L | $R14 >= -1000 && R14 <= 1000$ | +| R15: L -> Q | $R15 >= 0 && R15 <= 1000$ | +| R16: J -> M | $R16 >= 0 && R16 <= 1000$ | +| R17: M -> N | $R17 >= 0 && R17 <= 1000$ | +| R18: N -> Q | $R18 >= 0 && R18 <= 1000$ | +| R19: K -> O | $R19 >= -1000 && R19 <= 1000$ | +| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ | +| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ | +| R22: Q -> R | $R22 >= 0 && R22 <= 1000$ | +| R23: R -> S | $R23 >= -1000 && R23 <= 1000$ | +| R24: R -> S | $R24 >= 0 && R24 <= 1000$ | +| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ | +| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |] + diff --git a/latest/cases/01192/l2v5/index.heta b/latest/cases/01192/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01192/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01192/l3v2/build.log b/latest/cases/01192/l3v2/build.log new file mode 100644 index 000000000..c773f78d7 --- /dev/null +++ b/latest/cases/01192/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01192/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01192/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01192/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01192/l3v2/index.heta b/latest/cases/01192/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01192/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01192/model-sbml-l3v2.xml b/latest/cases/01192/model-sbml-l3v2.xml new file mode 100644 index 000000000..b51e12e58 --- /dev/null +++ b/latest/cases/01192/model-sbml-l3v2.xml @@ -0,0 +1,634 @@ + + + + + +

+ Single objective, multiple flux objectives +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:21Z + + + 2012-12-21T10:05:21Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01192/synopsis.txt b/latest/cases/01192/synopsis.txt new file mode 100644 index 000000000..4eba500c9 --- /dev/null +++ b/latest/cases/01192/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Single objective, multiple flux objectives +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + + Single objective, multiple flux objectives + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + + 1 R10 + +There are 26 reactions, and 52 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R02: A -> B | $R02 >= -1000 && R02 <= 1000$ | +| R03: A -> C | $R03 >= -1000 && R03 <= 1000$ | +| R04: C -> B | $R04 >= -1000 && R04 <= 1000$ | +| R05: B -> D | $R05 >= 0 && R05 <= 1000$ | +| R06: D -> E | $R06 >= 0 && R06 <= 1000$ | +| R07: E -> F | $R07 >= 0 && R07 <= 1000$ | +| R08: F -> I | $R08 >= 0 && R08 <= 1000$ | +| R09: D -> G | $R09 >= 0 && R09 <= 1000$ | +| R10: G -> H | $R10 >= 0 && R10 <= 1000$ | +| R11: H -> I | $R11 >= 0 && R11 <= 1000$ | +| R12: I -> J | $R12 >= 0 && R12 <= 1000$ | +| R13: J -> K | $R13 >= 0 && R13 <= 1000$ | +| R14: K -> L | $R14 >= -1000 && R14 <= 1000$ | +| R15: L -> Q | $R15 >= 0 && R15 <= 1000$ | +| R16: J -> M | $R16 >= 0 && R16 <= 1000$ | +| R17: M -> N | $R17 >= 0 && R17 <= 1000$ | +| R18: N -> Q | $R18 >= 0 && R18 <= 1000$ | +| R19: K -> O | $R19 >= -1000 && R19 <= 1000$ | +| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ | +| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ | +| R22: Q -> R | $R22 >= 0 && R22 <= 1000$ | +| R23: R -> S | $R23 >= -1000 && R23 <= 1000$ | +| R24: R -> S | $R24 >= 0 && R24 <= 1000$ | +| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ | +| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |] + diff --git a/latest/cases/01193/l2v5/index.heta b/latest/cases/01193/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01193/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01193/l3v2/build.log b/latest/cases/01193/l3v2/build.log new file mode 100644 index 000000000..72dd29cea --- /dev/null +++ b/latest/cases/01193/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01193/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01193/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01193/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01193/l3v2/index.heta b/latest/cases/01193/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01193/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01193/model-sbml-l3v2.xml b/latest/cases/01193/model-sbml-l3v2.xml new file mode 100644 index 000000000..ce2788f6d --- /dev/null +++ b/latest/cases/01193/model-sbml-l3v2.xml @@ -0,0 +1,633 @@ + + + + + +

+ Single objective, test R07 GE 0.5, R10 GE 0.5 +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:21Z + + + 2012-12-21T10:05:21Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01193/synopsis.txt b/latest/cases/01193/synopsis.txt new file mode 100644 index 000000000..9c8d4870a --- /dev/null +++ b/latest/cases/01193/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Single objective, test R07 GE 0.5, R10 GE 0.5 +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + + Single objective, test R07 GE 0.5, R10 GE 0.5 + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions, and 52 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R02: A -> B | $R02 >= -1000 && R02 <= 1000$ | +| R03: A -> C | $R03 >= -1000 && R03 <= 1000$ | +| R04: C -> B | $R04 >= -1000 && R04 <= 1000$ | +| R05: B -> D | $R05 >= 0 && R05 <= 1000$ | +| R06: D -> E | $R06 >= 0 && R06 <= 1000$ | +| R07: E -> F | $R07 >= 0.5 && R07 <= 1000$ | +| R08: F -> I | $R08 >= 0 && R08 <= 1000$ | +| R09: D -> G | $R09 >= 0 && R09 <= 1000$ | +| R10: G -> H | $R10 >= 0.5 && R10 <= 1000$ | +| R11: H -> I | $R11 >= 0 && R11 <= 1000$ | +| R12: I -> J | $R12 >= 0 && R12 <= 1000$ | +| R13: J -> K | $R13 >= 0 && R13 <= 1000$ | +| R14: K -> L | $R14 >= -1000 && R14 <= 1000$ | +| R15: L -> Q | $R15 >= 0 && R15 <= 1000$ | +| R16: J -> M | $R16 >= 0 && R16 <= 1000$ | +| R17: M -> N | $R17 >= 0 && R17 <= 1000$ | +| R18: N -> Q | $R18 >= 0 && R18 <= 1000$ | +| R19: K -> O | $R19 >= -1000 && R19 <= 1000$ | +| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ | +| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ | +| R22: Q -> R | $R22 >= 0 && R22 <= 1000$ | +| R23: R -> S | $R23 >= -1000 && R23 <= 1000$ | +| R24: R -> S | $R24 >= 0 && R24 <= 1000$ | +| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ | +| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |] + diff --git a/latest/cases/01194/l2v5/index.heta b/latest/cases/01194/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01194/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01194/l3v2/build.log b/latest/cases/01194/l3v2/build.log new file mode 100644 index 000000000..2c64f2825 --- /dev/null +++ b/latest/cases/01194/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01194/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01194/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01194/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01194/l3v2/index.heta b/latest/cases/01194/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01194/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01194/model-sbml-l3v2.xml b/latest/cases/01194/model-sbml-l3v2.xml new file mode 100644 index 000000000..690566721 --- /dev/null +++ b/latest/cases/01194/model-sbml-l3v2.xml @@ -0,0 +1,633 @@ + + + + + +

+ Single objective, test R07 LE 0.2, R10 LE 0.3 +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:22Z + + + 2012-12-21T10:05:22Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

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subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: L

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subsystem: C4

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subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01194/synopsis.txt b/latest/cases/01194/synopsis.txt new file mode 100644 index 000000000..0d5b32bd8 --- /dev/null +++ b/latest/cases/01194/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Single objective, test R07 LE 0.2, R10 LE 0.3 +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + + Single objective, test R07 LE 0.2, R10 LE 0.3 + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions, and 52 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R02: A -> B | $R02 >= -1000 && R02 <= 1000$ | +| R03: A -> C | $R03 >= -1000 && R03 <= 1000$ | +| R04: C -> B | $R04 >= -1000 && R04 <= 1000$ | +| R05: B -> D | $R05 >= 0 && R05 <= 1000$ | +| R06: D -> E | $R06 >= 0 && R06 <= 1000$ | +| R07: E -> F | $R07 >= 0 && R07 <= 0.2$ | +| R08: F -> I | $R08 >= 0 && R08 <= 1000$ | +| R09: D -> G | $R09 >= 0 && R09 <= 1000$ | +| R10: G -> H | $R10 >= 0 && R10 <= 0.3$ | +| R11: H -> I | $R11 >= 0 && R11 <= 1000$ | +| R12: I -> J | $R12 >= 0 && R12 <= 1000$ | +| R13: J -> K | $R13 >= 0 && R13 <= 1000$ | +| R14: K -> L | $R14 >= -1000 && R14 <= 1000$ | +| R15: L -> Q | $R15 >= 0 && R15 <= 1000$ | +| R16: J -> M | $R16 >= 0 && R16 <= 1000$ | +| R17: M -> N | $R17 >= 0 && R17 <= 1000$ | +| R18: N -> Q | $R18 >= 0 && R18 <= 1000$ | +| R19: K -> O | $R19 >= -1000 && R19 <= 1000$ | +| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ | +| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ | +| R22: Q -> R | $R22 >= 0 && R22 <= 1000$ | +| R23: R -> S | $R23 >= -1000 && R23 <= 1000$ | +| R24: R -> S | $R24 >= 0 && R24 <= 1000$ | +| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ | +| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |] + diff --git a/latest/cases/01195/l2v5/index.heta b/latest/cases/01195/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01195/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01195/l3v2/build.log b/latest/cases/01195/l3v2/build.log new file mode 100644 index 000000000..e2a19be88 --- /dev/null +++ b/latest/cases/01195/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01195/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01195/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01195/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01195/l3v2/index.heta b/latest/cases/01195/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01195/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01195/model-sbml-l3v2.xml b/latest/cases/01195/model-sbml-l3v2.xml new file mode 100644 index 000000000..577961bbe --- /dev/null +++ b/latest/cases/01195/model-sbml-l3v2.xml @@ -0,0 +1,630 @@ + + + + + +

+ Single objective, test: R07 EQ 0.2, R10 EQ 0.2, R25 EQ 0.6 +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:22Z + + + 2012-12-21T10:05:22Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01195/synopsis.txt b/latest/cases/01195/synopsis.txt new file mode 100644 index 000000000..d5955b359 --- /dev/null +++ b/latest/cases/01195/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Single objective, test: R07 EQ 0.2, R10 EQ 0.2, R25 EQ 0.6 +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundEqual, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + + Single objective, test: R07 EQ 0.2, R10 EQ 0.2, R25 EQ 0.6 + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions, and 49 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R02: A -> B | $R02 >= -1000 && R02 <= 1000$ | +| R03: A -> C | $R03 >= -1000 && R03 <= 1000$ | +| R04: C -> B | $R04 >= -1000 && R04 <= 1000$ | +| R05: B -> D | $R05 >= 0 && R05 <= 1000$ | +| R06: D -> E | $R06 >= 0 && R06 <= 1000$ | +| R07: E -> F | $R07 == 0.2$ | +| R08: F -> I | $R08 >= 0 && R08 <= 1000$ | +| R09: D -> G | $R09 >= 0 && R09 <= 1000$ | +| R10: G -> H | $R10 == 0.3$ | +| R11: H -> I | $R11 >= 0 && R11 <= 1000$ | +| R12: I -> J | $R12 >= 0 && R12 <= 1000$ | +| R13: J -> K | $R13 >= 0 && R13 <= 1000$ | +| R14: K -> L | $R14 >= -1000 && R14 <= 1000$ | +| R15: L -> Q | $R15 >= 0 && R15 <= 1000$ | +| R16: J -> M | $R16 >= 0 && R16 <= 1000$ | +| R17: M -> N | $R17 >= 0 && R17 <= 1000$ | +| R18: N -> Q | $R18 >= 0 && R18 <= 1000$ | +| R19: K -> O | $R19 >= -1000 && R19 <= 1000$ | +| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ | +| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ | +| R22: Q -> R | $R22 >= 0 && R22 <= 1000$ | +| R23: R -> S | $R23 >= -1000 && R23 <= 1000$ | +| R24: R -> S | $R24 >= 0 && R24 <= 1000$ | +| R25: A + T -> 0.5S + U | $R25 == 0.4$ | +| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |] + diff --git a/latest/cases/01196/l2v5/index.heta b/latest/cases/01196/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01196/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01196/l3v2/build.log b/latest/cases/01196/l3v2/build.log new file mode 100644 index 000000000..983b52795 --- /dev/null +++ b/latest/cases/01196/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01196/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01196/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01196/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01196/l3v2/index.heta b/latest/cases/01196/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01196/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01196/model-sbml-l3v2.xml b/latest/cases/01196/model-sbml-l3v2.xml new file mode 100644 index 000000000..5e6e12a06 --- /dev/null +++ b/latest/cases/01196/model-sbml-l3v2.xml @@ -0,0 +1,633 @@ + + + + + +

+ Infeasible solution, should return a nan +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:22Z + + + 2012-12-21T10:05:22Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01196/synopsis.txt b/latest/cases/01196/synopsis.txt new file mode 100644 index 000000000..b861bd438 --- /dev/null +++ b/latest/cases/01196/synopsis.txt @@ -0,0 +1,50 @@ + +category: Test +synopsis: Infeasible solution, should return a nan +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + + Infeasible solution, should return a nan + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions, and 52 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $R16 >= 0 && R16 <= 1000$ | +| R14: K -> L | $R14 >= -1000 && R14 <= 1000$ | +| R15: L -> Q | $R15 >= 0 && R15 <= 1000$ | +| R12: I -> J | $R12 >= 0 && R12 <= 1000$ | +| R07: E -> F | $R07 >= 2 && R07 <= 1000$ | +| R13: J -> K | $R13 >= 0 && R13 <= 1000$ | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R17: M -> N | $R17 >= 0 && R17 <= 1000$ | +| R03: A -> C | $R03 >= -1000 && R03 <= 1000$ | +| R02: A -> B | $R02 >= -1000 && R02 <= 1000$ | +| R05: B -> D | $R05 >= 0 && R05 <= 1000$ | +| R04: C -> B | $R04 >= -1000 && R04 <= 1000$ | +| R10: G -> H | $R10 >= 0 && R10 <= 1000$ | +| R06: D -> E | $R06 >= 0 && R06 <= 1000$ | +| R09: D -> G | $R09 >= 0 && R09 <= 1000$ | +| R08: F -> I | $R08 >= 0 && R08 <= 1000$ | +| R11: H -> I | $R11 >= 0 && R11 <= 1000$ | +| R18: N -> Q | $R18 >= 0 && R18 <= 1000$ | +| R19: K -> O | $R19 >= -1000 && R19 <= 1000$ | +| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ | +| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ | +| R24: R -> S | $R24 >= 0 && R24 <= 1000$ | +| R23: R -> S | $R23 >= -1000 && R23 <= 1000$ | +| R22: Q -> R | $R22 >= 0 && R22 <= 1000$ | +| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ | +| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ |] + diff --git a/latest/cases/01197/l2v5/index.heta b/latest/cases/01197/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01197/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01197/l3v2/heta-code/output.heta b/latest/cases/01197/l3v2/heta-code/output.heta new file mode 100644 index 000000000..41c229463 --- /dev/null +++ b/latest/cases/01197/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 4; + diff --git a/latest/cases/01197/l3v2/index.heta b/latest/cases/01197/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01197/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01197/l3v2/json/output.json b/latest/cases/01197/l3v2/json/output.json new file mode 100644 index 000000000..07c39ca5f --- /dev/null +++ b/latest/cases/01197/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "4" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01197/model-sbml-l3v2.xml b/latest/cases/01197/model-sbml-l3v2.xml new file mode 100644 index 000000000..ebb976386 --- /dev/null +++ b/latest/cases/01197/model-sbml-l3v2.xml @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/latest/cases/01197/output.heta b/latest/cases/01197/output.heta new file mode 100644 index 000000000..23290807d --- /dev/null +++ b/latest/cases/01197/output.heta @@ -0,0 +1,30 @@ +/* +category: Test +synopsis: Compartment with spatial dimensions of 7. +componentTags: Compartment +testTags: NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains only a compartment, but it has a spatial dimension of 7. The numerics are not affected at all; this simply tests that the existence of this dimensionality doesn't affect the simulation. + +The model contains: +* 1 compartment (c) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial volume of compartment 'c' | $4$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 4; + diff --git a/latest/cases/01197/synopsis.txt b/latest/cases/01197/synopsis.txt new file mode 100644 index 000000000..6a975b639 --- /dev/null +++ b/latest/cases/01197/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: Compartment with spatial dimensions of 7. +componentTags: Compartment +testTags: NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains only a compartment, but it has a spatial dimension of 7. The numerics are not affected at all; this simply tests that the existence of this dimensionality doesn't affect the simulation. + +The model contains: +* 1 compartment (c) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial volume of compartment 'c' | $4$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01198/l2v5/heta-code/output.heta b/latest/cases/01198/l2v5/heta-code/output.heta new file mode 100644 index 000000000..641f8650d --- /dev/null +++ b/latest/cases/01198/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01198/l2v5/index.heta b/latest/cases/01198/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01198/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01198/l2v5/json/output.json b/latest/cases/01198/l2v5/json/output.json new file mode 100644 index 000000000..07a046a46 --- /dev/null +++ b/latest/cases/01198/l2v5/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01198/l3v2/heta-code/output.heta b/latest/cases/01198/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c31a4df1a --- /dev/null +++ b/latest/cases/01198/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01198/l3v2/index.heta b/latest/cases/01198/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01198/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01198/l3v2/json/output.json b/latest/cases/01198/l3v2/json/output.json new file mode 100644 index 000000000..2d1e885ae --- /dev/null +++ b/latest/cases/01198/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01198/model-sbml-l2v5.xml b/latest/cases/01198/model-sbml-l2v5.xml new file mode 100644 index 000000000..bb55e312d --- /dev/null +++ b/latest/cases/01198/model-sbml-l2v5.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01198/model-sbml-l3v2.xml b/latest/cases/01198/model-sbml-l3v2.xml new file mode 100644 index 000000000..2c536139d --- /dev/null +++ b/latest/cases/01198/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01198/output.heta b/latest/cases/01198/output.heta new file mode 100644 index 000000000..a53c85e2a --- /dev/null +++ b/latest/cases/01198/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: A species and a compartment both under control of a rate rule. +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01198/synopsis.txt b/latest/cases/01198/synopsis.txt new file mode 100644 index 000000000..408ef3417 --- /dev/null +++ b/latest/cases/01198/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule. +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01199/l2v5/heta-code/output.heta b/latest/cases/01199/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8ebfc0894 --- /dev/null +++ b/latest/cases/01199/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := 1; + +x @Record { } .= 0; +z @Record { }; +z := (((x >= 0.49) ? true : false) ? 1 : 0); + diff --git a/latest/cases/01199/l2v5/index.heta b/latest/cases/01199/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01199/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01199/l2v5/json/output.json b/latest/cases/01199/l2v5/json/output.json new file mode 100644 index 000000000..294465d3f --- /dev/null +++ b/latest/cases/01199/l2v5/json/output.json @@ -0,0 +1,57 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "(((x >= 0.49) ? true : false) ? 1 : 0)" + } + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01199/l3v2/heta-code/output.heta b/latest/cases/01199/l3v2/heta-code/output.heta new file mode 100644 index 000000000..94ca77903 --- /dev/null +++ b/latest/cases/01199/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := 1; + +x @Record { } .= 0; +z @Record { }; +z := (((x >= 0.49) ? true : false) ? 1 : 0); + diff --git a/latest/cases/01199/l3v2/index.heta b/latest/cases/01199/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01199/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01199/l3v2/json/output.json b/latest/cases/01199/l3v2/json/output.json new file mode 100644 index 000000000..38785eb8c --- /dev/null +++ b/latest/cases/01199/l3v2/json/output.json @@ -0,0 +1,32 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "(((x >= 0.49) ? true : false) ? 1 : 0)" + } + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01199/model-sbml-l2v5.xml b/latest/cases/01199/model-sbml-l2v5.xml new file mode 100644 index 000000000..a9cf597bf --- /dev/null +++ b/latest/cases/01199/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + 1 + + + + + + + 1 + + + + + + x + 0.49 + + + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01199/model-sbml-l3v2.xml b/latest/cases/01199/model-sbml-l3v2.xml new file mode 100644 index 000000000..1b4910a54 --- /dev/null +++ b/latest/cases/01199/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + 1 + + + + + + + 1 + + + + + + x + 0.49 + + + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01199/output.heta b/latest/cases/01199/output.heta new file mode 100644 index 000000000..7065895ce --- /dev/null +++ b/latest/cases/01199/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: Nested piecewise in conditional. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The assignment rule for parameter 'z' has a nested piecewise function in the conditional part of the piecewise function, that returns 'true' or 'false'. It is functionally equivalent to simply having the nested conditional there directly, and is there merely to test the presence of the nesting itself. + +The model contains: +* 2 parameters (x, z) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $1$ | +| Assignment | z | $piecewise(1, piecewise(true, x >= 0.49, false), 0)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $0$ | variable | +| Initial value of parameter z | $piecewise(1, piecewise(true, geq(x, 0.49), false), 0)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := 1; + +x @Record { } .= 0; +z @Record { }; +z := (((x >= 0.49) ? true : false) ? 1 : 0); + diff --git a/latest/cases/01199/synopsis.txt b/latest/cases/01199/synopsis.txt new file mode 100644 index 000000000..7bf248bb6 --- /dev/null +++ b/latest/cases/01199/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Nested piecewise in conditional. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The assignment rule for parameter 'z' has a nested piecewise function in the conditional part of the piecewise function, that returns 'true' or 'false'. It is functionally equivalent to simply having the nested conditional there directly, and is there merely to test the presence of the nesting itself. + +The model contains: +* 2 parameters (x, z) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $1$ | +| Assignment | z | $piecewise(1, piecewise(true, x >= 0.49, false), 0)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $0$ | variable | +| Initial value of parameter z | $piecewise(1, piecewise(true, geq(x, 0.49), false), 0)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01200/l2v5/heta-code/output.heta b/latest/cases/01200/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9bcdc07f1 --- /dev/null +++ b/latest/cases/01200/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := ((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : 0); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01200/l2v5/index.heta b/latest/cases/01200/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01200/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01200/l2v5/json/output.json b/latest/cases/01200/l2v5/json/output.json new file mode 100644 index 000000000..6e2867793 --- /dev/null +++ b/latest/cases/01200/l2v5/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : 0)" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01200/l3v2/heta-code/output.heta b/latest/cases/01200/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5103b1b0b --- /dev/null +++ b/latest/cases/01200/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := ((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : 0); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01200/l3v2/index.heta b/latest/cases/01200/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01200/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01200/l3v2/json/output.json b/latest/cases/01200/l3v2/json/output.json new file mode 100644 index 000000000..736732e68 --- /dev/null +++ b/latest/cases/01200/l3v2/json/output.json @@ -0,0 +1,52 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : 0)" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01200/model-sbml-l2v5.xml b/latest/cases/01200/model-sbml-l2v5.xml new file mode 100644 index 000000000..f849b668f --- /dev/null +++ b/latest/cases/01200/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + 2 + + + y + 1.49 + + + + 1 + + + + + x + 0.49 + + + + 0 + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01200/model-sbml-l3v2.xml b/latest/cases/01200/model-sbml-l3v2.xml new file mode 100644 index 000000000..134421fa4 --- /dev/null +++ b/latest/cases/01200/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + 2 + + + y + 1.49 + + + + 1 + + + + + x + 0.49 + + + + 0 + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01200/output.heta b/latest/cases/01200/output.heta new file mode 100644 index 000000000..7f2b8a523 --- /dev/null +++ b/latest/cases/01200/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Nested piecewise in return. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model has a nested 'piecewise' function, with the nested piecewise in the 'returned value' part of the function. + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(piecewise(2, gt(y, 1.49), 1), leq(x, 0.49), 0)$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(piecewise(2, gt(y, 1.49), 1), leq(x, 0.49), 0)$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := ((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : 0); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01200/synopsis.txt b/latest/cases/01200/synopsis.txt new file mode 100644 index 000000000..d505e8bd3 --- /dev/null +++ b/latest/cases/01200/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Nested piecewise in return. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model has a nested 'piecewise' function, with the nested piecewise in the 'returned value' part of the function. + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(piecewise(2, gt(y, 1.49), 1), leq(x, 0.49), 0)$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(piecewise(2, gt(y, 1.49), 1), leq(x, 0.49), 0)$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01201/l2v5/heta-code/output.heta b/latest/cases/01201/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1e89c345c --- /dev/null +++ b/latest/cases/01201/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := (((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : 0); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01201/l2v5/index.heta b/latest/cases/01201/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01201/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01201/l2v5/json/output.json b/latest/cases/01201/l2v5/json/output.json new file mode 100644 index 000000000..131b19714 --- /dev/null +++ b/latest/cases/01201/l2v5/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "(((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : 0)" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01201/l3v2/heta-code/output.heta b/latest/cases/01201/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b8a172a39 --- /dev/null +++ b/latest/cases/01201/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := (((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : 0); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01201/l3v2/index.heta b/latest/cases/01201/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01201/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01201/l3v2/json/output.json b/latest/cases/01201/l3v2/json/output.json new file mode 100644 index 000000000..735b7d728 --- /dev/null +++ b/latest/cases/01201/l3v2/json/output.json @@ -0,0 +1,52 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "(((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : 0)" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01201/model-sbml-l2v5.xml b/latest/cases/01201/model-sbml-l2v5.xml new file mode 100644 index 000000000..1b88855cf --- /dev/null +++ b/latest/cases/01201/model-sbml-l2v5.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + 2 + + + y + 1.49 + + + + 1 + + + + + + + + x + 0.49 + + + + + + + + + 0 + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01201/model-sbml-l3v2.xml b/latest/cases/01201/model-sbml-l3v2.xml new file mode 100644 index 000000000..3f56f34b0 --- /dev/null +++ b/latest/cases/01201/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + 2 + + + y + 1.49 + + + + 1 + + + + + + + + x + 0.49 + + + + + + + + + 0 + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01201/output.heta b/latest/cases/01201/output.heta new file mode 100644 index 000000000..232ab2ddd --- /dev/null +++ b/latest/cases/01201/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Nested piecewise in conditional and return +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A combination of cases 01199 and 01200, with piecewise functions nested inside a piecewise function as both a conditional and as a return value. Tests the combination of nesting piecewise functions. + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), 0)$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), 0)$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := (((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : 0); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01201/synopsis.txt b/latest/cases/01201/synopsis.txt new file mode 100644 index 000000000..8bfce3842 --- /dev/null +++ b/latest/cases/01201/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Nested piecewise in conditional and return +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A combination of cases 01199 and 01200, with piecewise functions nested inside a piecewise function as both a conditional and as a return value. Tests the combination of nesting piecewise functions. + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), 0)$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), 0)$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01202/l2v5/heta-code/output.heta b/latest/cases/01202/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4061e84be --- /dev/null +++ b/latest/cases/01202/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := 1; +y_proc @Process { actors: = y, }; +y_proc := (-2); + +z @Record { }; +z := ((x <= 0.49) ? 2 : ((y > 0.49) ? 1 : 0)); +x @Record { } .= 0; +y @Record { } .= 2; + diff --git a/latest/cases/01202/l2v5/index.heta b/latest/cases/01202/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01202/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01202/l2v5/json/output.json b/latest/cases/01202/l2v5/json/output.json new file mode 100644 index 000000000..8f3086b8e --- /dev/null +++ b/latest/cases/01202/l2v5/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "((x <= 0.49) ? 2 : ((y > 0.49) ? 1 : 0))" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01202/l3v2/heta-code/output.heta b/latest/cases/01202/l3v2/heta-code/output.heta new file mode 100644 index 000000000..623752082 --- /dev/null +++ b/latest/cases/01202/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := 1; +y_proc @Process { actors: = y, }; +y_proc := (-2); + +z @Record { }; +z := ((x <= 0.49) ? 2 : ((y > 0.49) ? 1 : 0)); +x @Record { } .= 0; +y @Record { } .= 2; + diff --git a/latest/cases/01202/l3v2/index.heta b/latest/cases/01202/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01202/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01202/l3v2/json/output.json b/latest/cases/01202/l3v2/json/output.json new file mode 100644 index 000000000..372288d04 --- /dev/null +++ b/latest/cases/01202/l3v2/json/output.json @@ -0,0 +1,52 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "((x <= 0.49) ? 2 : ((y > 0.49) ? 1 : 0))" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01202/model-sbml-l2v5.xml b/latest/cases/01202/model-sbml-l2v5.xml new file mode 100644 index 000000000..68a5b2c9c --- /dev/null +++ b/latest/cases/01202/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + 2 + + + x + 0.49 + + + + + + 1 + + + y + 0.49 + + + + 0 + + + + + + + + + 1 + + + + + -2 + + + + + diff --git a/latest/cases/01202/model-sbml-l3v2.xml b/latest/cases/01202/model-sbml-l3v2.xml new file mode 100644 index 000000000..d22d93cfe --- /dev/null +++ b/latest/cases/01202/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + 2 + + + x + 0.49 + + + + + + 1 + + + y + 0.49 + + + + 0 + + + + + + + + + 1 + + + + + -2 + + + + + diff --git a/latest/cases/01202/output.heta b/latest/cases/01202/output.heta new file mode 100644 index 000000000..e281447f9 --- /dev/null +++ b/latest/cases/01202/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Nested piecewise in otherwise. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The assignment rule for parameter 'z' has a nested piecewise function in the 'otherwise' part of the piecewise function. + +The model contains: +* 3 parameters (z, x, y) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(2, x <= 0.49, piecewise(1, y > 0.49, 0))$ | +| Rate | x | $1$ | +| Rate | y | $-2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(2, x <= 0.49, piecewise(1, y > 0.49, 0))$ | variable | +| Initial value of parameter x | $0$ | variable | +| Initial value of parameter y | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := 1; +y_proc @Process { actors: = y, }; +y_proc := (-2); + +z @Record { }; +z := ((x <= 0.49) ? 2 : ((y > 0.49) ? 1 : 0)); +x @Record { } .= 0; +y @Record { } .= 2; + diff --git a/latest/cases/01202/synopsis.txt b/latest/cases/01202/synopsis.txt new file mode 100644 index 000000000..548721aab --- /dev/null +++ b/latest/cases/01202/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Nested piecewise in otherwise. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The assignment rule for parameter 'z' has a nested piecewise function in the 'otherwise' part of the piecewise function. + +The model contains: +* 3 parameters (z, x, y) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(2, x <= 0.49, piecewise(1, y > 0.49, 0))$ | +| Rate | x | $1$ | +| Rate | y | $-2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(2, x <= 0.49, piecewise(1, y > 0.49, 0))$ | variable | +| Initial value of parameter x | $0$ | variable | +| Initial value of parameter y | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01203/l2v5/heta-code/output.heta b/latest/cases/01203/l2v5/heta-code/output.heta new file mode 100644 index 000000000..31de07120 --- /dev/null +++ b/latest/cases/01203/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := ((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0)); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01203/l2v5/index.heta b/latest/cases/01203/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01203/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01203/l2v5/json/output.json b/latest/cases/01203/l2v5/json/output.json new file mode 100644 index 000000000..e1ff8da07 --- /dev/null +++ b/latest/cases/01203/l2v5/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0))" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01203/l3v2/heta-code/output.heta b/latest/cases/01203/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3c66030ad --- /dev/null +++ b/latest/cases/01203/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := ((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0)); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01203/l3v2/index.heta b/latest/cases/01203/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01203/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01203/l3v2/json/output.json b/latest/cases/01203/l3v2/json/output.json new file mode 100644 index 000000000..a308ae10e --- /dev/null +++ b/latest/cases/01203/l3v2/json/output.json @@ -0,0 +1,52 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0))" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01203/model-sbml-l2v5.xml b/latest/cases/01203/model-sbml-l2v5.xml new file mode 100644 index 000000000..6d979cd92 --- /dev/null +++ b/latest/cases/01203/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + 2 + + + y + 1.49 + + + + 1 + + + + + x + 0.49 + + + + + + 1 + + + y + 0.49 + + + + 0 + + + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01203/model-sbml-l3v2.xml b/latest/cases/01203/model-sbml-l3v2.xml new file mode 100644 index 000000000..d1d56aee0 --- /dev/null +++ b/latest/cases/01203/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + 2 + + + y + 1.49 + + + + 1 + + + + + x + 0.49 + + + + + + 1 + + + y + 0.49 + + + + 0 + + + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01203/output.heta b/latest/cases/01203/output.heta new file mode 100644 index 000000000..4dcc7e556 --- /dev/null +++ b/latest/cases/01203/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Nested piecewise in return and otherwise. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The assignment rule for parameter 'z' has two nested piecewise functions in the return and otherwise parts of the containing piecewise function. A combination of cases 01200 and 01202 + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(piecewise(2, y > 1.49, 1), x <= 0.49, piecewise(1, y > 0.49, 0))$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(piecewise(2, y > 1.49, 1), x <= 0.49, piecewise(1, y > 0.49, 0))$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := ((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0)); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01203/synopsis.txt b/latest/cases/01203/synopsis.txt new file mode 100644 index 000000000..90eb8dd3f --- /dev/null +++ b/latest/cases/01203/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Nested piecewise in return and otherwise. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The assignment rule for parameter 'z' has two nested piecewise functions in the return and otherwise parts of the containing piecewise function. A combination of cases 01200 and 01202 + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(piecewise(2, y > 1.49, 1), x <= 0.49, piecewise(1, y > 0.49, 0))$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(piecewise(2, y > 1.49, 1), x <= 0.49, piecewise(1, y > 0.49, 0))$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01204/l2v5/heta-code/output.heta b/latest/cases/01204/l2v5/heta-code/output.heta new file mode 100644 index 000000000..434498af9 --- /dev/null +++ b/latest/cases/01204/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := (((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0)); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01204/l2v5/index.heta b/latest/cases/01204/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01204/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01204/l2v5/json/output.json b/latest/cases/01204/l2v5/json/output.json new file mode 100644 index 000000000..670be6f54 --- /dev/null +++ b/latest/cases/01204/l2v5/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "(((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0))" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01204/l3v2/heta-code/output.heta b/latest/cases/01204/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0352a190b --- /dev/null +++ b/latest/cases/01204/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := (((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0)); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01204/l3v2/index.heta b/latest/cases/01204/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01204/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01204/l3v2/json/output.json b/latest/cases/01204/l3v2/json/output.json new file mode 100644 index 000000000..e3a569cee --- /dev/null +++ b/latest/cases/01204/l3v2/json/output.json @@ -0,0 +1,52 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "(((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0))" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "2" + } + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "y_proc", + "assignments": { + "ode_": "(-2)" + }, + "actors": [ + { + "target": "y", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01204/model-sbml-l2v5.xml b/latest/cases/01204/model-sbml-l2v5.xml new file mode 100644 index 000000000..c0c6286c0 --- /dev/null +++ b/latest/cases/01204/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + 2 + + + y + 1.49 + + + + 1 + + + + + + + + x + 0.49 + + + + + + + + + + + 1 + + + y + 0.49 + + + + 0 + + + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01204/model-sbml-l3v2.xml b/latest/cases/01204/model-sbml-l3v2.xml new file mode 100644 index 000000000..1ae061aa7 --- /dev/null +++ b/latest/cases/01204/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + 2 + + + y + 1.49 + + + + 1 + + + + + + + + x + 0.49 + + + + + + + + + + + 1 + + + y + 0.49 + + + + 0 + + + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01204/output.heta b/latest/cases/01204/output.heta new file mode 100644 index 000000000..6547abebf --- /dev/null +++ b/latest/cases/01204/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: Nested piecewise in return, conditional, and otherwise. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The assignment rule for parameter 'z' has three nested piecewise functions in the return, conditional, and otherwise parts of the containing piecewise function. A combination of 01199, 01200, and 01202, and functionally equivalent to 01203. + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), piecewise(1, y > 0.49, 0))$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), piecewise(1, y > 0.49, 0))$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +y_proc @Process { actors: = y, }; +y_proc := (-2); +x_proc @Process { actors: = x, }; +x_proc := 1; + +z @Record { }; +z := (((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0)); +y @Record { } .= 2; +x @Record { } .= 0; + diff --git a/latest/cases/01204/synopsis.txt b/latest/cases/01204/synopsis.txt new file mode 100644 index 000000000..bc22fca2b --- /dev/null +++ b/latest/cases/01204/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Nested piecewise in return, conditional, and otherwise. +componentTags: AssignmentRule, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The assignment rule for parameter 'z' has three nested piecewise functions in the return, conditional, and otherwise parts of the containing piecewise function. A combination of 01199, 01200, and 01202, and functionally equivalent to 01203. + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), piecewise(1, y > 0.49, 0))$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), piecewise(1, y > 0.49, 0))$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01205/l2v5/heta-code/output.heta b/latest/cases/01205/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6af59e686 --- /dev/null +++ b/latest/cases/01205/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { boundary: true, } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01205/l2v5/index.heta b/latest/cases/01205/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01205/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01205/l2v5/json/output.json b/latest/cases/01205/l2v5/json/output.json new file mode 100644 index 000000000..e7f1af736 --- /dev/null +++ b/latest/cases/01205/l2v5/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01205/l3v2/heta-code/output.heta b/latest/cases/01205/l3v2/heta-code/output.heta new file mode 100644 index 000000000..393e3ab37 --- /dev/null +++ b/latest/cases/01205/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +C1 @Compartment { boundary: true, } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01205/l3v2/index.heta b/latest/cases/01205/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01205/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01205/l3v2/json/output.json b/latest/cases/01205/l3v2/json/output.json new file mode 100644 index 000000000..5fc28cb26 --- /dev/null +++ b/latest/cases/01205/l3v2/json/output.json @@ -0,0 +1,41 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01205/model-sbml-l2v5.xml b/latest/cases/01205/model-sbml-l2v5.xml new file mode 100644 index 000000000..47c08f41e --- /dev/null +++ b/latest/cases/01205/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + S1 + + + + + diff --git a/latest/cases/01205/model-sbml-l3v2.xml b/latest/cases/01205/model-sbml-l3v2.xml new file mode 100644 index 000000000..6548c8257 --- /dev/null +++ b/latest/cases/01205/model-sbml-l3v2.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + S1 + + + + + diff --git a/latest/cases/01205/output.heta b/latest/cases/01205/output.heta new file mode 100644 index 000000000..d0a8fb071 --- /dev/null +++ b/latest/cases/01205/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: A species concentration under control of a rate rule. +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species is under control of a rate rule, and set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by this rate of change, but the volume of the compartment stays constant. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { boundary: true, } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01205/synopsis.txt b/latest/cases/01205/synopsis.txt new file mode 100644 index 000000000..17f06c934 --- /dev/null +++ b/latest/cases/01205/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A species concentration under control of a rate rule. +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species is under control of a rate rule, and set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by this rate of change, but the volume of the compartment stays constant. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01206/l2v5/heta-code/output.heta b/latest/cases/01206/l2v5/heta-code/output.heta new file mode 100644 index 000000000..88505cb12 --- /dev/null +++ b/latest/cases/01206/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 3 / C1; + +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01206/l2v5/index.heta b/latest/cases/01206/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01206/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01206/l2v5/json/output.json b/latest/cases/01206/l2v5/json/output.json new file mode 100644 index 000000000..c21474935 --- /dev/null +++ b/latest/cases/01206/l2v5/json/output.json @@ -0,0 +1,65 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3 / C1" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01206/l3v2/heta-code/output.heta b/latest/cases/01206/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c773a0c42 --- /dev/null +++ b/latest/cases/01206/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 3 / C1; + +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01206/l3v2/index.heta b/latest/cases/01206/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01206/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01206/l3v2/json/output.json b/latest/cases/01206/l3v2/json/output.json new file mode 100644 index 000000000..5f035c82a --- /dev/null +++ b/latest/cases/01206/l3v2/json/output.json @@ -0,0 +1,40 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3 / C1" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01206/model-sbml-l2v5.xml b/latest/cases/01206/model-sbml-l2v5.xml new file mode 100644 index 000000000..d3ed0d362 --- /dev/null +++ b/latest/cases/01206/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01206/model-sbml-l3v2.xml b/latest/cases/01206/model-sbml-l3v2.xml new file mode 100644 index 000000000..de5cefc96 --- /dev/null +++ b/latest/cases/01206/model-sbml-l3v2.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01206/output.heta b/latest/cases/01206/output.heta new file mode 100644 index 000000000..4cde8b244 --- /dev/null +++ b/latest/cases/01206/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Constant-amount species in variable compartment. +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the compartment size varies, making the species concentration change (which is assigned to 'x'), but the species amount does not. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $3$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 3 / C1; + +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01206/synopsis.txt b/latest/cases/01206/synopsis.txt new file mode 100644 index 000000000..dcd47eb2a --- /dev/null +++ b/latest/cases/01206/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Constant-amount species in variable compartment. +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the compartment size varies, making the species concentration change (which is assigned to 'x'), but the species amount does not. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $3$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01207/l2v5/heta-code/output.heta b/latest/cases/01207/l2v5/heta-code/output.heta new file mode 100644 index 000000000..cbd32bdb6 --- /dev/null +++ b/latest/cases/01207/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, isAmount: true, } .= 3; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1 / C1; + diff --git a/latest/cases/01207/l2v5/index.heta b/latest/cases/01207/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01207/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01207/l2v5/json/output.json b/latest/cases/01207/l2v5/json/output.json new file mode 100644 index 000000000..04e652f56 --- /dev/null +++ b/latest/cases/01207/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C1", + "isAmount": true + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1 / C1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01207/l3v2/heta-code/output.heta b/latest/cases/01207/l3v2/heta-code/output.heta new file mode 100644 index 000000000..be5c088e2 --- /dev/null +++ b/latest/cases/01207/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, isAmount: true, } .= 3; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1 / C1; + diff --git a/latest/cases/01207/l3v2/index.heta b/latest/cases/01207/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01207/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01207/l3v2/json/output.json b/latest/cases/01207/l3v2/json/output.json new file mode 100644 index 000000000..b23c4ff4c --- /dev/null +++ b/latest/cases/01207/l3v2/json/output.json @@ -0,0 +1,54 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C1", + "isAmount": true + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1 / C1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01207/model-sbml-l2v5.xml b/latest/cases/01207/model-sbml-l2v5.xml new file mode 100644 index 000000000..077e9cca6 --- /dev/null +++ b/latest/cases/01207/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + 0 + + + + + 0.2 + + + + + + + S1 + C1 + + + + + + diff --git a/latest/cases/01207/model-sbml-l3v2.xml b/latest/cases/01207/model-sbml-l3v2.xml new file mode 100644 index 000000000..bae0e6f25 --- /dev/null +++ b/latest/cases/01207/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + 0 + + + + + 0.2 + + + + + + + S1 + C1 + + + + + + diff --git a/latest/cases/01207/output.heta b/latest/cases/01207/output.heta new file mode 100644 index 000000000..3b4a52fad --- /dev/null +++ b/latest/cases/01207/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Variable compartment with explicitly fixed species +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model is exactly the same as model 1206, but the species is interpreted as an amount, not a concentration, and that amount is explicitly set to change by zero, instead of that change being implied as in 1206. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1 / C1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $3$ | variable | +| Initial value of parameter x | $S1 / C1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, isAmount: true, } .= 3; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1 / C1; + diff --git a/latest/cases/01207/synopsis.txt b/latest/cases/01207/synopsis.txt new file mode 100644 index 000000000..f25215b3b --- /dev/null +++ b/latest/cases/01207/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Variable compartment with explicitly fixed species +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model is exactly the same as model 1206, but the species is interpreted as an amount, not a concentration, and that amount is explicitly set to change by zero, instead of that change being implied as in 1206. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1 / C1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $3$ | variable | +| Initial value of parameter x | $S1 / C1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01208/l2v5/heta-code/output.heta b/latest/cases/01208/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2eb566284 --- /dev/null +++ b/latest/cases/01208/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 3 / C1; + +S1_proc @Process { actors: = S1, }; +S1_proc := ((-0.2) * S1) / C1; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01208/l2v5/index.heta b/latest/cases/01208/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01208/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01208/l2v5/json/output.json b/latest/cases/01208/l2v5/json/output.json new file mode 100644 index 000000000..74266e585 --- /dev/null +++ b/latest/cases/01208/l2v5/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3 / C1" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "((-0.2) * S1) / C1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01208/l3v2/heta-code/output.heta b/latest/cases/01208/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a64b29b4c --- /dev/null +++ b/latest/cases/01208/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 3 / C1; + +S1_proc @Process { actors: = S1, }; +S1_proc := ((-0.2) * S1) / C1; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01208/l3v2/index.heta b/latest/cases/01208/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01208/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01208/l3v2/json/output.json b/latest/cases/01208/l3v2/json/output.json new file mode 100644 index 000000000..23074d8f1 --- /dev/null +++ b/latest/cases/01208/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3 / C1" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "((-0.2) * S1) / C1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01208/model-sbml-l2v5.xml b/latest/cases/01208/model-sbml-l2v5.xml new file mode 100644 index 000000000..f5e8eabef --- /dev/null +++ b/latest/cases/01208/model-sbml-l2v5.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + -0.2 + S1 + + C1 + + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01208/model-sbml-l3v2.xml b/latest/cases/01208/model-sbml-l3v2.xml new file mode 100644 index 000000000..11b486133 --- /dev/null +++ b/latest/cases/01208/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + -0.2 + S1 + + C1 + + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01208/output.heta b/latest/cases/01208/output.heta new file mode 100644 index 000000000..d8ddfa5d3 --- /dev/null +++ b/latest/cases/01208/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Variable compartment with variable species concentration +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model ends up exactly the same as model 1206 and 1207, with a variable compartment, and an explicit rate of change of the species concentration that ends up with the species amount not changing. + +If A is the amount of S1, and V is the volume: +d(A/V)/dt = [V dA/dt - A dV/dt]/V^2 + = -A/V^2 dV/dt + = -A/V * .2 / V + = -.2*A/V / V + = -.2*S1/V + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $(-0.2 * S1) / C1$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $3$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 3 / C1; + +S1_proc @Process { actors: = S1, }; +S1_proc := ((-0.2) * S1) / C1; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01208/synopsis.txt b/latest/cases/01208/synopsis.txt new file mode 100644 index 000000000..acac798c8 --- /dev/null +++ b/latest/cases/01208/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Variable compartment with variable species concentration +componentTags: AssignmentRule, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model ends up exactly the same as model 1206 and 1207, with a variable compartment, and an explicit rate of change of the species concentration that ends up with the species amount not changing. + +If A is the amount of S1, and V is the volume: +d(A/V)/dt = [V dA/dt - A dV/dt]/V^2 + = -A/V^2 dV/dt + = -A/V * .2 / V + = -.2*A/V / V + = -.2*S1/V + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $(-0.2 * S1) / C1$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $3$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01209/l2v5/heta-code/output.heta b/latest/cases/01209/l2v5/heta-code/output.heta new file mode 100644 index 000000000..30a6c2f3c --- /dev/null +++ b/latest/cases/01209/l2v5/heta-code/output.heta @@ -0,0 +1,11 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x @Record { } .= ((1 < 2) ? 1 : 3); + diff --git a/latest/cases/01209/l2v5/index.heta b/latest/cases/01209/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01209/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01209/l2v5/json/output.json b/latest/cases/01209/l2v5/json/output.json new file mode 100644 index 000000000..316bc99e1 --- /dev/null +++ b/latest/cases/01209/l2v5/json/output.json @@ -0,0 +1,37 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "((1 < 2) ? 1 : 3)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01209/l3v2/build.log b/latest/cases/01209/l3v2/build.log new file mode 100644 index 000000000..50063cac9 --- /dev/null +++ b/latest/cases/01209/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01209/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01209/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01209/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 80 +[error] No required "num" property for "x" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01209/l3v2/index.heta b/latest/cases/01209/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01209/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01209/model-sbml-l2v5.xml b/latest/cases/01209/model-sbml-l2v5.xml new file mode 100644 index 000000000..8edc243db --- /dev/null +++ b/latest/cases/01209/model-sbml-l2v5.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 1 + 2 + 1 + + + + 3 + + + + + + + diff --git a/latest/cases/01209/model-sbml-l3v2.xml b/latest/cases/01209/model-sbml-l3v2.xml new file mode 100644 index 000000000..b4430e820 --- /dev/null +++ b/latest/cases/01209/model-sbml-l3v2.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 1 + 2 + 1 + + + + 3 + + + + + + + diff --git a/latest/cases/01209/output.heta b/latest/cases/01209/output.heta new file mode 100644 index 000000000..d6bb1a1d7 --- /dev/null +++ b/latest/cases/01209/output.heta @@ -0,0 +1,35 @@ +/* +category: Test +synopsis: An initial assignment with an nary relational element. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as less than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. + +The model contains: +* 1 parameter (x) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $piecewise(1, lt(1, 2, 1), 3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x @Record { } .= ((1 < 2) ? 1 : 3); + diff --git a/latest/cases/01209/synopsis.txt b/latest/cases/01209/synopsis.txt new file mode 100644 index 000000000..a5261cbf7 --- /dev/null +++ b/latest/cases/01209/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: An initial assignment with an nary relational element. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as less than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. + +The model contains: +* 1 parameter (x) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $piecewise(1, lt(1, 2, 1), 3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01210/l2v5/heta-code/output.heta b/latest/cases/01210/l2v5/heta-code/output.heta new file mode 100644 index 000000000..19e15f245 --- /dev/null +++ b/latest/cases/01210/l2v5/heta-code/output.heta @@ -0,0 +1,12 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x @Record { }; +x := ((2 > 1) ? 1 : 3); + diff --git a/latest/cases/01210/l2v5/index.heta b/latest/cases/01210/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01210/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01210/l2v5/json/output.json b/latest/cases/01210/l2v5/json/output.json new file mode 100644 index 000000000..5d0657384 --- /dev/null +++ b/latest/cases/01210/l2v5/json/output.json @@ -0,0 +1,37 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "((2 > 1) ? 1 : 3)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01210/l3v2/heta-code/output.heta b/latest/cases/01210/l3v2/heta-code/output.heta new file mode 100644 index 000000000..454f6fdde --- /dev/null +++ b/latest/cases/01210/l3v2/heta-code/output.heta @@ -0,0 +1,7 @@ + + +t @TimeScale { }; + +x @Record { }; +x := ((2 > 1) ? 1 : 3); + diff --git a/latest/cases/01210/l3v2/index.heta b/latest/cases/01210/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01210/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01210/l3v2/json/output.json b/latest/cases/01210/l3v2/json/output.json new file mode 100644 index 000000000..b96ac7716 --- /dev/null +++ b/latest/cases/01210/l3v2/json/output.json @@ -0,0 +1,12 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "((2 > 1) ? 1 : 3)" + } + } +] \ No newline at end of file diff --git a/latest/cases/01210/model-sbml-l2v5.xml b/latest/cases/01210/model-sbml-l2v5.xml new file mode 100644 index 000000000..bec805df4 --- /dev/null +++ b/latest/cases/01210/model-sbml-l2v5.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 2 + 1 + 2 + + + + 3 + + + + + + + diff --git a/latest/cases/01210/model-sbml-l3v2.xml b/latest/cases/01210/model-sbml-l3v2.xml new file mode 100644 index 000000000..e555685bd --- /dev/null +++ b/latest/cases/01210/model-sbml-l3v2.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 2 + 1 + 2 + + + + 3 + + + + + + + diff --git a/latest/cases/01210/output.heta b/latest/cases/01210/output.heta new file mode 100644 index 000000000..ceb60415d --- /dev/null +++ b/latest/cases/01210/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: An assignment rule with an nary relational element. +componentTags: AssignmentRule, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. + +The model contains: +* 1 parameter (x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $piecewise(1, gt(2, 1, 2), 3)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $piecewise(1, gt(2, 1, 2), 3)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { }; +x := ((2 > 1) ? 1 : 3); + diff --git a/latest/cases/01210/synopsis.txt b/latest/cases/01210/synopsis.txt new file mode 100644 index 000000000..ee56b548f --- /dev/null +++ b/latest/cases/01210/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An assignment rule with an nary relational element. +componentTags: AssignmentRule, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. + +The model contains: +* 1 parameter (x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $piecewise(1, gt(2, 1, 2), 3)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $piecewise(1, gt(2, 1, 2), 3)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01211/l2v5/heta-code/output.heta b/latest/cases/01211/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7d20db5bb --- /dev/null +++ b/latest/cases/01211/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x @Record { } .= 3; +x [_E0]= 5; + +_E0 @DSwitcher { trigger: t > 0.21 and 5 <= 5, }; + diff --git a/latest/cases/01211/l2v5/index.heta b/latest/cases/01211/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01211/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01211/l2v5/json/output.json b/latest/cases/01211/l2v5/json/output.json new file mode 100644 index 000000000..a01865e21 --- /dev/null +++ b/latest/cases/01211/l2v5/json/output.json @@ -0,0 +1,43 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "_E0": "5" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 0.21 and 5 <= 5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01211/l3v2/heta-code/output.heta b/latest/cases/01211/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ccbae6a5d --- /dev/null +++ b/latest/cases/01211/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [_E0]= 5; + +_E0 @DSwitcher { trigger: t > 0.21 and 5 <= 5, }; + diff --git a/latest/cases/01211/l3v2/index.heta b/latest/cases/01211/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01211/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01211/l3v2/json/output.json b/latest/cases/01211/l3v2/json/output.json new file mode 100644 index 000000000..a9020d7a6 --- /dev/null +++ b/latest/cases/01211/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "_E0": "5" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 0.21 and 5 <= 5" + } +] \ No newline at end of file diff --git a/latest/cases/01211/model-sbml-l2v5.xml b/latest/cases/01211/model-sbml-l2v5.xml new file mode 100644 index 000000000..87d976363 --- /dev/null +++ b/latest/cases/01211/model-sbml-l2v5.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + time + 0.21 + + + + 5 + 5 + 2 + + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01211/model-sbml-l3v2.xml b/latest/cases/01211/model-sbml-l3v2.xml new file mode 100644 index 000000000..7990b44ab --- /dev/null +++ b/latest/cases/01211/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + time + 0.21 + + + + 5 + 5 + 2 + + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01211/output.heta b/latest/cases/01211/output.heta new file mode 100644 index 000000000..41057c567 --- /dev/null +++ b/latest/cases/01211/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A trigger with an nary relational element. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the trigger such that it never fires. + +The model contains: +* 1 parameter (x) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 0.21 && leq(5, 5, 2)$ | $x = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [_E0]= 5; + +_E0 @DSwitcher { trigger: t > 0.21 and 5 <= 5, }; + diff --git a/latest/cases/01211/synopsis.txt b/latest/cases/01211/synopsis.txt new file mode 100644 index 000000000..da6476e5e --- /dev/null +++ b/latest/cases/01211/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A trigger with an nary relational element. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the trigger such that it never fires. + +The model contains: +* 1 parameter (x) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 0.21 && leq(5, 5, 2)$ | $x = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01212/l2v5/index.heta b/latest/cases/01212/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01212/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01212/l3v2/heta-code/output.heta b/latest/cases/01212/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1c13db152 --- /dev/null +++ b/latest/cases/01212/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E0]= 5; +x [E1]= 7; + +E0 @DSwitcher { trigger: t > 0.01, }; +E1 @DSwitcher { trigger: t > 0.01, }; + diff --git a/latest/cases/01212/l3v2/index.heta b/latest/cases/01212/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01212/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01212/l3v2/json/output.json b/latest/cases/01212/l3v2/json/output.json new file mode 100644 index 000000000..250a49473 --- /dev/null +++ b/latest/cases/01212/l3v2/json/output.json @@ -0,0 +1,24 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E0": "5", + "E1": "7" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 0.01" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 0.01" + } +] \ No newline at end of file diff --git a/latest/cases/01212/model-sbml-l3v2.xml b/latest/cases/01212/model-sbml-l3v2.xml new file mode 100644 index 000000000..1c5c566cd --- /dev/null +++ b/latest/cases/01212/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + time + 0.01 + + + + + + + + 1 + + + 1 + 2 + 1 + + + + 10 + + + + + + + + 5 + + + + + + + + + + time + 0.01 + + + + + + + + 10 + + + 1 + 2 + 1 + + + + 1 + + + + + + + + 7 + + + + + + + diff --git a/latest/cases/01212/output.heta b/latest/cases/01212/output.heta new file mode 100644 index 000000000..2e03ba4ec --- /dev/null +++ b/latest/cases/01212/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Priorities with nary relational elements. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the priorities on the competing events such that E0 should have the higher priority, firing first, and E1 has the lower priority, firing second, and assigning the value of '7' to x moving forward. + +The model contains: +* 1 parameter (x) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 0.01$ | $piecewise(1, leq(1, 2, 1), 10)$ | $x = 5$ | +| E1 | $time > 0.01$ | $piecewise(10, leq(1, 2, 1), 1)$ | $x = 7$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E0]= 5; +x [E1]= 7; + +E0 @DSwitcher { trigger: t > 0.01, }; +E1 @DSwitcher { trigger: t > 0.01, }; + diff --git a/latest/cases/01212/synopsis.txt b/latest/cases/01212/synopsis.txt new file mode 100644 index 000000000..b3dda79d5 --- /dev/null +++ b/latest/cases/01212/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Priorities with nary relational elements. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the priorities on the competing events such that E0 should have the higher priority, firing first, and E1 has the lower priority, firing second, and assigning the value of '7' to x moving forward. + +The model contains: +* 1 parameter (x) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 0.01$ | $piecewise(1, leq(1, 2, 1), 10)$ | $x = 5$ | +| E1 | $time > 0.01$ | $piecewise(10, leq(1, 2, 1), 1)$ | $x = 7$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01213/l2v5/build.log b/latest/cases/01213/l2v5/build.log new file mode 100644 index 000000000..6054843a5 --- /dev/null +++ b/latest/cases/01213/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01213/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01213/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01213/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01213/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01213/l2v5/index.heta b/latest/cases/01213/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01213/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01213/l3v2/build.log b/latest/cases/01213/l3v2/build.log new file mode 100644 index 000000000..edbc0ab42 --- /dev/null +++ b/latest/cases/01213/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01213/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01213/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01213/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01213/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01213/l3v2/index.heta b/latest/cases/01213/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01213/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01213/model-sbml-l2v5.xml b/latest/cases/01213/model-sbml-l2v5.xml new file mode 100644 index 000000000..f00ecd286 --- /dev/null +++ b/latest/cases/01213/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + time + 0.01 + + + + + + + + 0.5 + + + 1 + 2 + 1 + + + + 0.3 + + + + + + + + 7 + + + + + + + diff --git a/latest/cases/01213/model-sbml-l3v2.xml b/latest/cases/01213/model-sbml-l3v2.xml new file mode 100644 index 000000000..ba495bf76 --- /dev/null +++ b/latest/cases/01213/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + time + 0.01 + + + + + + + + 0.5 + + + 1 + 2 + 1 + + + + 0.3 + + + + + + + + 7 + + + + + + + diff --git a/latest/cases/01213/synopsis.txt b/latest/cases/01213/synopsis.txt new file mode 100644 index 000000000..87a20c36c --- /dev/null +++ b/latest/cases/01213/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A delay with an nary relational element. +componentTags: CSymbolTime, EventWithDelay, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as less than. This model checks to make sure interpreters notice the third argument, which changes the delay on the event to be 0.3, and not 0.5. + +The model contains: +* 1 parameter (x) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time > 0.01$ | $piecewise(0.5, leq(1, 2, 1), 0.3)$ | $x = 7$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01214/l2v5/heta-code/output.heta b/latest/cases/01214/l2v5/heta-code/output.heta new file mode 100644 index 000000000..235fa5822 --- /dev/null +++ b/latest/cases/01214/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x @Record { } .= 3; +x [E0]= ((1 == 1) ? 5 : 7); + +E0 @DSwitcher { trigger: t > 0.01, }; + diff --git a/latest/cases/01214/l2v5/index.heta b/latest/cases/01214/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01214/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01214/l2v5/json/output.json b/latest/cases/01214/l2v5/json/output.json new file mode 100644 index 000000000..bdd16bf56 --- /dev/null +++ b/latest/cases/01214/l2v5/json/output.json @@ -0,0 +1,43 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E0": "((1 == 1) ? 5 : 7)" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 0.01" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01214/l3v2/heta-code/output.heta b/latest/cases/01214/l3v2/heta-code/output.heta new file mode 100644 index 000000000..327e6f7a4 --- /dev/null +++ b/latest/cases/01214/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E0]= ((1 == 1) ? 5 : 7); + +E0 @DSwitcher { trigger: t > 0.01, }; + diff --git a/latest/cases/01214/l3v2/index.heta b/latest/cases/01214/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01214/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01214/l3v2/json/output.json b/latest/cases/01214/l3v2/json/output.json new file mode 100644 index 000000000..f9482c9b8 --- /dev/null +++ b/latest/cases/01214/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E0": "((1 == 1) ? 5 : 7)" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 0.01" + } +] \ No newline at end of file diff --git a/latest/cases/01214/model-sbml-l2v5.xml b/latest/cases/01214/model-sbml-l2v5.xml new file mode 100644 index 000000000..1a2029f1f --- /dev/null +++ b/latest/cases/01214/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + time + 0.01 + + + + + + + + + 5 + + + 1 + 1 + 2 + + + + 7 + + + + + + + + + diff --git a/latest/cases/01214/model-sbml-l3v2.xml b/latest/cases/01214/model-sbml-l3v2.xml new file mode 100644 index 000000000..f03ad7832 --- /dev/null +++ b/latest/cases/01214/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + time + 0.01 + + + + + + + + + 5 + + + 1 + 1 + 2 + + + + 7 + + + + + + + + + diff --git a/latest/cases/01214/output.heta b/latest/cases/01214/output.heta new file mode 100644 index 000000000..717946d6f --- /dev/null +++ b/latest/cases/01214/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A delay with an nary relational element. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as equals. This model checks to make sure interpreters notice the third argument, which changes the event assignment to be 7, not 5. + +The model contains: +* 1 parameter (x) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 0.01$ | $x = piecewise(5, eq(1, 1, 2), 7)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E0]= ((1 == 1) ? 5 : 7); + +E0 @DSwitcher { trigger: t > 0.01, }; + diff --git a/latest/cases/01214/synopsis.txt b/latest/cases/01214/synopsis.txt new file mode 100644 index 000000000..267879959 --- /dev/null +++ b/latest/cases/01214/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A delay with an nary relational element. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as equals. This model checks to make sure interpreters notice the third argument, which changes the event assignment to be 7, not 5. + +The model contains: +* 1 parameter (x) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 0.01$ | $x = piecewise(5, eq(1, 1, 2), 7)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01215/l2v5/heta-code/output.heta b/latest/cases/01215/l2v5/heta-code/output.heta new file mode 100644 index 000000000..efed28105 --- /dev/null +++ b/latest/cases/01215/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := ((2 > 1) ? 1 : 0); + +x @Record { } .= 3; + diff --git a/latest/cases/01215/l2v5/index.heta b/latest/cases/01215/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01215/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01215/l2v5/json/output.json b/latest/cases/01215/l2v5/json/output.json new file mode 100644 index 000000000..388096c7e --- /dev/null +++ b/latest/cases/01215/l2v5/json/output.json @@ -0,0 +1,50 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3" + } + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "((2 > 1) ? 1 : 0)" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01215/l3v2/heta-code/output.heta b/latest/cases/01215/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4368969b0 --- /dev/null +++ b/latest/cases/01215/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := ((2 > 1) ? 1 : 0); + +x @Record { } .= 3; + diff --git a/latest/cases/01215/l3v2/index.heta b/latest/cases/01215/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01215/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01215/l3v2/json/output.json b/latest/cases/01215/l3v2/json/output.json new file mode 100644 index 000000000..103d07021 --- /dev/null +++ b/latest/cases/01215/l3v2/json/output.json @@ -0,0 +1,25 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3" + } + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "((2 > 1) ? 1 : 0)" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01215/model-sbml-l2v5.xml b/latest/cases/01215/model-sbml-l2v5.xml new file mode 100644 index 000000000..6a4fb613d --- /dev/null +++ b/latest/cases/01215/model-sbml-l2v5.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 2 + 1 + 2 + + + + 0 + + + + + + + diff --git a/latest/cases/01215/model-sbml-l3v2.xml b/latest/cases/01215/model-sbml-l3v2.xml new file mode 100644 index 000000000..6b531b23e --- /dev/null +++ b/latest/cases/01215/model-sbml-l3v2.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 2 + 1 + 2 + + + + 0 + + + + + + + diff --git a/latest/cases/01215/output.heta b/latest/cases/01215/output.heta new file mode 100644 index 000000000..b0cfe784f --- /dev/null +++ b/latest/cases/01215/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A rate rule with an nary relational element. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the rate rule from 1 to 0. + +The model contains: +* 1 parameter (x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $piecewise(1, gt(2, 1, 2), 0)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := ((2 > 1) ? 1 : 0); + +x @Record { } .= 3; + diff --git a/latest/cases/01215/synopsis.txt b/latest/cases/01215/synopsis.txt new file mode 100644 index 000000000..dcd676d56 --- /dev/null +++ b/latest/cases/01215/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A rate rule with an nary relational element. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the rate rule from 1 to 0. + +The model contains: +* 1 parameter (x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $piecewise(1, gt(2, 1, 2), 0)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01216/l2v5/build.log b/latest/cases/01216/l2v5/build.log new file mode 100644 index 000000000..8337a2607 --- /dev/null +++ b/latest/cases/01216/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01216/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01216/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01216/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 93 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01216/l2v5/index.heta b/latest/cases/01216/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01216/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01216/l3v2/build.log b/latest/cases/01216/l3v2/build.log new file mode 100644 index 000000000..938812dd5 --- /dev/null +++ b/latest/cases/01216/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01216/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01216/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01216/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01216/l3v2/index.heta b/latest/cases/01216/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01216/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01216/model-sbml-l2v5.xml b/latest/cases/01216/model-sbml-l2v5.xml new file mode 100644 index 000000000..a62b94073 --- /dev/null +++ b/latest/cases/01216/model-sbml-l2v5.xml @@ -0,0 +1,217 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + 2 + 1 + 2 + + + + 3 + + + + + + + + + 1 + + + 1 + 2 + 1 + + + + 4 + + + + + + + + + 1 + + + 2 + 1 + 2 + + + + 5 + + + + + + + + + 1 + + + 1 + 2 + 1 + + + + 6 + + + + + + + + + 1 + + + 1 + 1 + 2 + + + + 7 + + + + + + + + + 1 + + + 2 + 1 + 0 + 0 + -1 + + + + 8 + + + + + + + + + 1 + + + 1 + 2 + 3 + 3 + 4 + + + + 9 + + + + + + + + + 1 + + + 2 + 1 + 0 + 1 + -1 + + + + 10 + + + + + + + + + 1 + + + 1 + 2 + 3 + 2 + 4 + + + + 11 + + + + + + + + + 1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 2 + 1 + 1 + 1 + + + + 12 + + + + + + + diff --git a/latest/cases/01216/model-sbml-l3v2.xml b/latest/cases/01216/model-sbml-l3v2.xml new file mode 100644 index 000000000..ea1d8fceb --- /dev/null +++ b/latest/cases/01216/model-sbml-l3v2.xml @@ -0,0 +1,217 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + 2 + 1 + 2 + + + + 3 + + + + + + + + + 1 + + + 1 + 2 + 1 + + + + 4 + + + + + + + + + 1 + + + 2 + 1 + 2 + + + + 5 + + + + + + + + + 1 + + + 1 + 2 + 1 + + + + 6 + + + + + + + + + 1 + + + 1 + 1 + 2 + + + + 7 + + + + + + + + + 1 + + + 2 + 1 + 0 + 0 + -1 + + + + 8 + + + + + + + + + 1 + + + 1 + 2 + 3 + 3 + 4 + + + + 9 + + + + + + + + + 1 + + + 2 + 1 + 0 + 1 + -1 + + + + 10 + + + + + + + + + 1 + + + 1 + 2 + 3 + 2 + 4 + + + + 11 + + + + + + + + + 1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 2 + 1 + 1 + 1 + + + + 12 + + + + + + + diff --git a/latest/cases/01216/synopsis.txt b/latest/cases/01216/synopsis.txt new file mode 100644 index 000000000..d58771ed7 --- /dev/null +++ b/latest/cases/01216/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Assignment rules with nary relational elements. +componentTags: AssignmentRule, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third and further arguments of all five relational functions, which change the results of various 'piecewise' tests. The model is constructed so that you can't just take the first and second arguments of the function, nor the first and last arguments, but must check each successive pair of variables. + +The model contains: +* 10 parameters (a, b, c, d, e, f, g, h, i, j) + +There are 10 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | a | $piecewise(1, gt(2, 1, 2), 3)$ | +| Assignment | b | $piecewise(1, lt(1, 2, 1), 4)$ | +| Assignment | c | $piecewise(1, geq(2, 1, 2), 5)$ | +| Assignment | d | $piecewise(1, leq(1, 2, 1), 6)$ | +| Assignment | e | $piecewise(1, eq(1, 1, 2), 7)$ | +| Assignment | f | $piecewise(1, gt(2, 1, 0, 0, -1), 8)$ | +| Assignment | g | $piecewise(1, lt(1, 2, 3, 3, 4), 9)$ | +| Assignment | h | $piecewise(1, geq(2, 1, 0, 1, -1), 10)$ | +| Assignment | i | $piecewise(1, leq(1, 2, 3, 2, 4), 11)$ | +| Assignment | j | $piecewise(1, eq(1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1), 12)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $piecewise(1, gt(2, 1, 2), 3)$ | variable | +| Initial value of parameter b | $piecewise(1, lt(1, 2, 1), 4)$ | variable | +| Initial value of parameter c | $piecewise(1, geq(2, 1, 2), 5)$ | variable | +| Initial value of parameter d | $piecewise(1, leq(1, 2, 1), 6)$ | variable | +| Initial value of parameter e | $piecewise(1, eq(1, 1, 2), 7)$ | variable | +| Initial value of parameter f | $piecewise(1, gt(2, 1, 0, 0, -1), 8)$ | variable | +| Initial value of parameter g | $piecewise(1, lt(1, 2, 3, 3, 4), 9)$ | variable | +| Initial value of parameter h | $piecewise(1, geq(2, 1, 0, 1, -1), 10)$ | variable | +| Initial value of parameter i | $piecewise(1, leq(1, 2, 3, 2, 4), 11)$ | variable | +| Initial value of parameter j | $piecewise(1, eq(1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1), 12)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01217/l2v5/build.log b/latest/cases/01217/l2v5/build.log new file mode 100644 index 000000000..1e15ab762 --- /dev/null +++ b/latest/cases/01217/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01217/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01217/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01217/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 89 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01217/l2v5/index.heta b/latest/cases/01217/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01217/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01217/l3v2/build.log b/latest/cases/01217/l3v2/build.log new file mode 100644 index 000000000..66df6755c --- /dev/null +++ b/latest/cases/01217/l3v2/build.log @@ -0,0 +1,13 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01217/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01217/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01217/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "c" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01217/l3v2/index.heta b/latest/cases/01217/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01217/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01217/model-sbml-l2v5.xml b/latest/cases/01217/model-sbml-l2v5.xml new file mode 100644 index 000000000..10abbd0a2 --- /dev/null +++ b/latest/cases/01217/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + b + 1 + + + + + + + + d + 1 + + + + + + + + f + 1 + + + + + + + + + + c + 1 + + + + + + + + e + 1 + + + + + + + + 4 + 2 + + + + + + diff --git a/latest/cases/01217/model-sbml-l3v2.xml b/latest/cases/01217/model-sbml-l3v2.xml new file mode 100644 index 000000000..2eb02ce21 --- /dev/null +++ b/latest/cases/01217/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + b + 1 + + + + + + + + d + 1 + + + + + + + + f + 1 + + + + + + + + + + c + 1 + + + + + + + + e + 1 + + + + + + + + 4 + 2 + + + + + + diff --git a/latest/cases/01217/synopsis.txt b/latest/cases/01217/synopsis.txt new file mode 100644 index 000000000..146c033d2 --- /dev/null +++ b/latest/cases/01217/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Mixed assignment rule and initial assignment dependencies +componentTags: AssignmentRule, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a chain of dependencies is invoked to determine the parameter's various initial values: each depends on a successive parameter, whose initial value is set by an initial assignment or assignment rule, alternately. This ensures that the simulator takes into account the entire system of equations, both initial assignments and assignment rules, when determining initial values. + +This model is equivalent to 01218, but with the variables in reverse order, in case a simulator relies on listed order to determine values. + +The model contains: +* 6 parameters (a, b, c, d, e, f) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | b | $c + 1$ | +| Assignment | d | $e + 1$ | +| Assignment | f | $4 / 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $b + 1$ | constant | +| Initial value of parameter c | $d + 1$ | constant | +| Initial value of parameter e | $f + 1$ | constant | +| Initial value of parameter b | $c + 1$ | variable | +| Initial value of parameter d | $e + 1$ | variable | +| Initial value of parameter f | $4 / 2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01218/l2v5/build.log b/latest/cases/01218/l2v5/build.log new file mode 100644 index 000000000..109c881c4 --- /dev/null +++ b/latest/cases/01218/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01218/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01218/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01218/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 89 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01218/l2v5/index.heta b/latest/cases/01218/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01218/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01218/l3v2/build.log b/latest/cases/01218/l3v2/build.log new file mode 100644 index 000000000..fb5f3c092 --- /dev/null +++ b/latest/cases/01218/l3v2/build.log @@ -0,0 +1,13 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01218/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01218/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01218/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "c" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01218/l3v2/index.heta b/latest/cases/01218/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01218/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01218/model-sbml-l2v5.xml b/latest/cases/01218/model-sbml-l2v5.xml new file mode 100644 index 000000000..3a436f822 --- /dev/null +++ b/latest/cases/01218/model-sbml-l2v5.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + 4 + 2 + + + + + + + + b + 1 + + + + + + + + d + 1 + + + + + + + + + + a + 1 + + + + + + + + c + 1 + + + + + + + + e + 1 + + + + + + diff --git a/latest/cases/01218/model-sbml-l3v2.xml b/latest/cases/01218/model-sbml-l3v2.xml new file mode 100644 index 000000000..3f17bfee7 --- /dev/null +++ b/latest/cases/01218/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + 4 + 2 + + + + + + + + b + 1 + + + + + + + + d + 1 + + + + + + + + + + a + 1 + + + + + + + + c + 1 + + + + + + + + e + 1 + + + + + + diff --git a/latest/cases/01218/synopsis.txt b/latest/cases/01218/synopsis.txt new file mode 100644 index 000000000..b3aac942f --- /dev/null +++ b/latest/cases/01218/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Mixed assignment rule and initial assignment dependencies +componentTags: AssignmentRule, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a chain of dependencies is invoked to determine the parameter's various initial values: each depends on a successive parameter, whose initial value is set by an initial assignment or assignment rule, alternately. This ensures that the simulator takes into account the entire system of equations, both initial assignments and assignment rules, when determining initial values. + +This model is equivalent to 01217, but with the variables in reverse order, in case a simulator relies on listed order to determine values. + + +The model contains: +* 6 parameters (a, b, c, d, e, f) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | b | $a + 1$ | +| Assignment | d | $c + 1$ | +| Assignment | f | $e + 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $4 / 2$ | constant | +| Initial value of parameter c | $b + 1$ | constant | +| Initial value of parameter e | $d + 1$ | constant | +| Initial value of parameter b | $a + 1$ | variable | +| Initial value of parameter d | $c + 1$ | variable | +| Initial value of parameter f | $e + 1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01219/l2v5/heta-code/output.heta b/latest/cases/01219/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d98ffc23f --- /dev/null +++ b/latest/cases/01219/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01219/l2v5/index.heta b/latest/cases/01219/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01219/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01219/l2v5/json/output.json b/latest/cases/01219/l2v5/json/output.json new file mode 100644 index 000000000..a242ad79a --- /dev/null +++ b/latest/cases/01219/l2v5/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1.2" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01219/l3v2/heta-code/output.heta b/latest/cases/01219/l3v2/heta-code/output.heta new file mode 100644 index 000000000..65ab8cda9 --- /dev/null +++ b/latest/cases/01219/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01219/l3v2/index.heta b/latest/cases/01219/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01219/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01219/l3v2/json/output.json b/latest/cases/01219/l3v2/json/output.json new file mode 100644 index 000000000..c21663741 --- /dev/null +++ b/latest/cases/01219/l3v2/json/output.json @@ -0,0 +1,35 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1.2" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01219/model-sbml-l2v5.xml b/latest/cases/01219/model-sbml-l2v5.xml new file mode 100644 index 000000000..13309fbea --- /dev/null +++ b/latest/cases/01219/model-sbml-l2v5.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01219/model-sbml-l3v2.xml b/latest/cases/01219/model-sbml-l3v2.xml new file mode 100644 index 000000000..ca3df7274 --- /dev/null +++ b/latest/cases/01219/model-sbml-l3v2.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01219/output.heta b/latest/cases/01219/output.heta new file mode 100644 index 000000000..d32924ce3 --- /dev/null +++ b/latest/cases/01219/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: A boundary substance-only species in non-unit compartment under control of a rate rule. +componentTags: Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In this model, a boundary species with 'hasOnlySubstanceUnits=true' is in a non-unity compartment, and changes according to a rate rule. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1.2$ | variable | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01219/synopsis.txt b/latest/cases/01219/synopsis.txt new file mode 100644 index 000000000..fa04d87e8 --- /dev/null +++ b/latest/cases/01219/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A boundary substance-only species in non-unit compartment under control of a rate rule. +componentTags: Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In this model, a boundary species with 'hasOnlySubstanceUnits=true' is in a non-unity compartment, and changes according to a rate rule. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1.2$ | variable | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01220/l2v5/heta-code/output.heta b/latest/cases/01220/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d99149922 --- /dev/null +++ b/latest/cases/01220/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: c, isAmount: true, } .= 0.6 * c; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01220/l2v5/index.heta b/latest/cases/01220/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01220/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01220/l2v5/json/output.json b/latest/cases/01220/l2v5/json/output.json new file mode 100644 index 000000000..445c8ceca --- /dev/null +++ b/latest/cases/01220/l2v5/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0.6 * c" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01220/l3v2/heta-code/output.heta b/latest/cases/01220/l3v2/heta-code/output.heta new file mode 100644 index 000000000..eb66373af --- /dev/null +++ b/latest/cases/01220/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: c, isAmount: true, } .= 0.6 * c; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01220/l3v2/index.heta b/latest/cases/01220/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01220/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01220/l3v2/json/output.json b/latest/cases/01220/l3v2/json/output.json new file mode 100644 index 000000000..4ff998e5c --- /dev/null +++ b/latest/cases/01220/l3v2/json/output.json @@ -0,0 +1,35 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0.6 * c" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01220/model-sbml-l2v5.xml b/latest/cases/01220/model-sbml-l2v5.xml new file mode 100644 index 000000000..363ffc4b5 --- /dev/null +++ b/latest/cases/01220/model-sbml-l2v5.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01220/model-sbml-l3v2.xml b/latest/cases/01220/model-sbml-l3v2.xml new file mode 100644 index 000000000..ca603dcb0 --- /dev/null +++ b/latest/cases/01220/model-sbml-l3v2.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01220/output.heta b/latest/cases/01220/output.heta new file mode 100644 index 000000000..88575394d --- /dev/null +++ b/latest/cases/01220/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: A boundary substance-only species in non-unit compartment under control of a rate rule. +componentTags: Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In this model, a boundary species with 'hasOnlySubstanceUnits=true' is in a non-unity compartment, and changes according to a rate rule. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. This model is exactly the same as test 1219, but the Species initial value is set by its concentration, not its amount. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0.6$ | variable | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: c, isAmount: true, } .= 0.6 * c; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01220/synopsis.txt b/latest/cases/01220/synopsis.txt new file mode 100644 index 000000000..5cbe24888 --- /dev/null +++ b/latest/cases/01220/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A boundary substance-only species in non-unit compartment under control of a rate rule. +componentTags: Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In this model, a boundary species with 'hasOnlySubstanceUnits=true' is in a non-unity compartment, and changes according to a rate rule. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. This model is exactly the same as test 1219, but the Species initial value is set by its concentration, not its amount. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0.6$ | variable | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01221/l2v5/heta-code/output.heta b/latest/cases/01221/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b7425a04f --- /dev/null +++ b/latest/cases/01221/l2v5/heta-code/output.heta @@ -0,0 +1,18 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { } .= 2; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; +c_proc @Process { actors: = c, }; +c_proc := 1; + diff --git a/latest/cases/01221/l2v5/index.heta b/latest/cases/01221/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01221/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01221/l2v5/json/output.json b/latest/cases/01221/l2v5/json/output.json new file mode 100644 index 000000000..1a0e834dc --- /dev/null +++ b/latest/cases/01221/l2v5/json/output.json @@ -0,0 +1,72 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1.2" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "c_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01221/l3v2/heta-code/output.heta b/latest/cases/01221/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7e2fee45f --- /dev/null +++ b/latest/cases/01221/l3v2/heta-code/output.heta @@ -0,0 +1,13 @@ + + +t @TimeScale { }; + +c @Compartment { } .= 2; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; +c_proc @Process { actors: = c, }; +c_proc := 1; + diff --git a/latest/cases/01221/l3v2/index.heta b/latest/cases/01221/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01221/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01221/l3v2/json/output.json b/latest/cases/01221/l3v2/json/output.json new file mode 100644 index 000000000..fc8f9fddd --- /dev/null +++ b/latest/cases/01221/l3v2/json/output.json @@ -0,0 +1,47 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1.2" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "c_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "c", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01221/model-sbml-l2v5.xml b/latest/cases/01221/model-sbml-l2v5.xml new file mode 100644 index 000000000..60f3c9647 --- /dev/null +++ b/latest/cases/01221/model-sbml-l2v5.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + 1 + + + + + 1 + + + + + diff --git a/latest/cases/01221/model-sbml-l3v2.xml b/latest/cases/01221/model-sbml-l3v2.xml new file mode 100644 index 000000000..b5bfb590f --- /dev/null +++ b/latest/cases/01221/model-sbml-l3v2.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + 1 + + + + + 1 + + + + + diff --git a/latest/cases/01221/output.heta b/latest/cases/01221/output.heta new file mode 100644 index 000000000..c6a480bfa --- /dev/null +++ b/latest/cases/01221/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: A boundary substance-only species in varying compartment under control of a rate rule. +componentTags: Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a boundary species with 'hasOnlySubstanceUnits=true' is changing according to a rate rule, and is in a compartment which itself is changing due to a rate rule. However, since the species is always described in terms of amount, the fact that its compartment is changing does not affect it. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ | +| Rate | c | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1.2$ | variable | +| Initial volume of compartment 'c' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { } .= 2; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; +c_proc @Process { actors: = c, }; +c_proc := 1; + diff --git a/latest/cases/01221/synopsis.txt b/latest/cases/01221/synopsis.txt new file mode 100644 index 000000000..fdc79fc5f --- /dev/null +++ b/latest/cases/01221/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A boundary substance-only species in varying compartment under control of a rate rule. +componentTags: Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a boundary species with 'hasOnlySubstanceUnits=true' is changing according to a rate rule, and is in a compartment which itself is changing due to a rate rule. However, since the species is always described in terms of amount, the fact that its compartment is changing does not affect it. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ | +| Rate | c | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1.2$ | variable | +| Initial volume of compartment 'c' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01222/l2v5/heta-code/output.heta b/latest/cases/01222/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3696e5ae1 --- /dev/null +++ b/latest/cases/01222/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { } .= 2; +c [_E0]= 4; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01222/l2v5/index.heta b/latest/cases/01222/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01222/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01222/l2v5/json/output.json b/latest/cases/01222/l2v5/json/output.json new file mode 100644 index 000000000..251760584 --- /dev/null +++ b/latest/cases/01222/l2v5/json/output.json @@ -0,0 +1,65 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2", + "_E0": "4" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1.2" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 5.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01222/l3v2/heta-code/output.heta b/latest/cases/01222/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6535c2ffd --- /dev/null +++ b/latest/cases/01222/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +c @Compartment { } .= 2; +c [_E0]= 4; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01222/l3v2/index.heta b/latest/cases/01222/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01222/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01222/l3v2/json/output.json b/latest/cases/01222/l3v2/json/output.json new file mode 100644 index 000000000..3763cbdc1 --- /dev/null +++ b/latest/cases/01222/l3v2/json/output.json @@ -0,0 +1,40 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2", + "_E0": "4" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1.2" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01222/model-sbml-l2v5.xml b/latest/cases/01222/model-sbml-l2v5.xml new file mode 100644 index 000000000..9f6f6e164 --- /dev/null +++ b/latest/cases/01222/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + 1 + + + + + + + + + + time + 5.5 + + + + + + + 4 + + + + + + + diff --git a/latest/cases/01222/model-sbml-l3v2.xml b/latest/cases/01222/model-sbml-l3v2.xml new file mode 100644 index 000000000..51addbe50 --- /dev/null +++ b/latest/cases/01222/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + 1 + + + + + + + + + + time + 5.5 + + + + + + + 4 + + + + + + + diff --git a/latest/cases/01222/output.heta b/latest/cases/01222/output.heta new file mode 100644 index 000000000..40e57f209 --- /dev/null +++ b/latest/cases/01222/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A boundary substance-only species in varying compartment under control of a rate rule. +componentTags: CSymbolTime, Compartment, EventNoDelay, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a boundary species with 'hasOnlySubstanceUnits=true' is changing according to a rate rule, and is in a compartment which itself changes due to an event. However, since the species is always described in terms of amount, the fact that its compartment changes does not affect it. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $c = 4$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1.2$ | variable | +| Initial volume of compartment 'c' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { } .= 2; +c [_E0]= 4; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01222/synopsis.txt b/latest/cases/01222/synopsis.txt new file mode 100644 index 000000000..c0267be8d --- /dev/null +++ b/latest/cases/01222/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A boundary substance-only species in varying compartment under control of a rate rule. +componentTags: CSymbolTime, Compartment, EventNoDelay, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a boundary species with 'hasOnlySubstanceUnits=true' is changing according to a rate rule, and is in a compartment which itself changes due to an event. However, since the species is always described in terms of amount, the fact that its compartment changes does not affect it. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $c = 4$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1.2$ | variable | +| Initial volume of compartment 'c' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01223/l2v5/heta-code/output.heta b/latest/cases/01223/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1f687ea95 --- /dev/null +++ b/latest/cases/01223/l2v5/heta-code/output.heta @@ -0,0 +1,17 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { }; +c := 1 * t + 2; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01223/l2v5/index.heta b/latest/cases/01223/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01223/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01223/l2v5/json/output.json b/latest/cases/01223/l2v5/json/output.json new file mode 100644 index 000000000..bb149a648 --- /dev/null +++ b/latest/cases/01223/l2v5/json/output.json @@ -0,0 +1,59 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "ode_": "1 * t + 2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1.2" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01223/l3v2/heta-code/output.heta b/latest/cases/01223/l3v2/heta-code/output.heta new file mode 100644 index 000000000..026033038 --- /dev/null +++ b/latest/cases/01223/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +c @Compartment { }; +c := 1 * t + 2; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01223/l3v2/index.heta b/latest/cases/01223/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01223/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01223/l3v2/json/output.json b/latest/cases/01223/l3v2/json/output.json new file mode 100644 index 000000000..83d6fb9c9 --- /dev/null +++ b/latest/cases/01223/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "ode_": "1 * t + 2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1.2" + }, + "compartment": "c", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01223/model-sbml-l2v5.xml b/latest/cases/01223/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef240079d --- /dev/null +++ b/latest/cases/01223/model-sbml-l2v5.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + 1 + + + + + + + + + 1 + time + + 2 + + + + + + diff --git a/latest/cases/01223/model-sbml-l3v2.xml b/latest/cases/01223/model-sbml-l3v2.xml new file mode 100644 index 000000000..ebeb4de35 --- /dev/null +++ b/latest/cases/01223/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + 1 + + + + + + + + + 1 + time + + 2 + + + + + + diff --git a/latest/cases/01223/output.heta b/latest/cases/01223/output.heta new file mode 100644 index 000000000..e693a5b98 --- /dev/null +++ b/latest/cases/01223/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: A boundary substance-only species in varying compartment under control of a rate rule. +componentTags: AssignmentRule, CSymbolTime, Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a boundary species with 'hasOnlySubstanceUnits=true' is changing according to a rate rule, and is in a compartment which itself changes due to an assignment rule. However, since the species is always described in terms of amount, the fact that its compartment changes does not affect it. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ | +| Assignment | c | $1 * time + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1.2$ | variable | +| Initial volume of compartment 'c' | $1 * time + 2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { }; +c := 1 * t + 2; + +S1 @Species { compartment: c, isAmount: true, } .= 1.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01223/synopsis.txt b/latest/cases/01223/synopsis.txt new file mode 100644 index 000000000..b2d23515c --- /dev/null +++ b/latest/cases/01223/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A boundary substance-only species in varying compartment under control of a rate rule. +componentTags: AssignmentRule, CSymbolTime, Compartment, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a boundary species with 'hasOnlySubstanceUnits=true' is changing according to a rate rule, and is in a compartment which itself changes due to an assignment rule. However, since the species is always described in terms of amount, the fact that its compartment changes does not affect it. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ | +| Assignment | c | $1 * time + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1.2$ | variable | +| Initial volume of compartment 'c' | $1 * time + 2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01224/l2v5/heta-code/output.heta b/latest/cases/01224/l2v5/heta-code/output.heta new file mode 100644 index 000000000..6f9ea1601 --- /dev/null +++ b/latest/cases/01224/l2v5/heta-code/output.heta @@ -0,0 +1,18 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; + +p1 @Record { } .= J0; + diff --git a/latest/cases/01224/l2v5/index.heta b/latest/cases/01224/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01224/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01224/l2v5/json/output.json b/latest/cases/01224/l2v5/json/output.json new file mode 100644 index 000000000..bf1e30ac3 --- /dev/null +++ b/latest/cases/01224/l2v5/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "J0" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01224/l3v2/heta-code/output.heta b/latest/cases/01224/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ff0f46dcf --- /dev/null +++ b/latest/cases/01224/l3v2/heta-code/output.heta @@ -0,0 +1,13 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; + +p1 @Record { } .= J0; + diff --git a/latest/cases/01224/l3v2/index.heta b/latest/cases/01224/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01224/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01224/l3v2/json/output.json b/latest/cases/01224/l3v2/json/output.json new file mode 100644 index 000000000..55a432492 --- /dev/null +++ b/latest/cases/01224/l3v2/json/output.json @@ -0,0 +1,42 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "J0" + } + } +] \ No newline at end of file diff --git a/latest/cases/01224/model-sbml-l2v5.xml b/latest/cases/01224/model-sbml-l2v5.xml new file mode 100644 index 000000000..a3f761192 --- /dev/null +++ b/latest/cases/01224/model-sbml-l2v5.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + J0 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01224/model-sbml-l3v2.xml b/latest/cases/01224/model-sbml-l3v2.xml new file mode 100644 index 000000000..b08cac689 --- /dev/null +++ b/latest/cases/01224/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + J0 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01224/output.heta b/latest/cases/01224/output.heta new file mode 100644 index 000000000..8d71204b6 --- /dev/null +++ b/latest/cases/01224/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: A simple reaction whose identifier is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in an initial assignment. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter p1 | $J0$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; + +p1 @Record { } .= J0; + diff --git a/latest/cases/01224/synopsis.txt b/latest/cases/01224/synopsis.txt new file mode 100644 index 000000000..c9ec5fc78 --- /dev/null +++ b/latest/cases/01224/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A simple reaction whose identifier is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in an initial assignment. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter p1 | $J0$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01225/l2v5/heta-code/output.heta b/latest/cases/01225/l2v5/heta-code/output.heta new file mode 100644 index 000000000..93fa79a78 --- /dev/null +++ b/latest/cases/01225/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; + +p1 @Record { }; +p1 := J0; + diff --git a/latest/cases/01225/l2v5/index.heta b/latest/cases/01225/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01225/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01225/l2v5/json/output.json b/latest/cases/01225/l2v5/json/output.json new file mode 100644 index 000000000..ef9a549f3 --- /dev/null +++ b/latest/cases/01225/l2v5/json/output.json @@ -0,0 +1,67 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "ode_": "J0" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01225/l3v2/heta-code/output.heta b/latest/cases/01225/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a36794a6e --- /dev/null +++ b/latest/cases/01225/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; + +p1 @Record { }; +p1 := J0; + diff --git a/latest/cases/01225/l3v2/index.heta b/latest/cases/01225/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01225/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01225/l3v2/json/output.json b/latest/cases/01225/l3v2/json/output.json new file mode 100644 index 000000000..3c41d3455 --- /dev/null +++ b/latest/cases/01225/l3v2/json/output.json @@ -0,0 +1,42 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "ode_": "J0" + } + } +] \ No newline at end of file diff --git a/latest/cases/01225/model-sbml-l2v5.xml b/latest/cases/01225/model-sbml-l2v5.xml new file mode 100644 index 000000000..9684b1855 --- /dev/null +++ b/latest/cases/01225/model-sbml-l2v5.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + J0 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01225/model-sbml-l3v2.xml b/latest/cases/01225/model-sbml-l3v2.xml new file mode 100644 index 000000000..b20bb0c23 --- /dev/null +++ b/latest/cases/01225/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + J0 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01225/output.heta b/latest/cases/01225/output.heta new file mode 100644 index 000000000..e883e3f05 --- /dev/null +++ b/latest/cases/01225/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: A simple reaction whose identifier is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in an assignment rule. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter p1 | $J0$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; + +p1 @Record { }; +p1 := J0; + diff --git a/latest/cases/01225/synopsis.txt b/latest/cases/01225/synopsis.txt new file mode 100644 index 000000000..a092b679a --- /dev/null +++ b/latest/cases/01225/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A simple reaction whose identifier is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in an assignment rule. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter p1 | $J0$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01226/l2v5/heta-code/output.heta b/latest/cases/01226/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1088995fc --- /dev/null +++ b/latest/cases/01226/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; +p1_proc @Process { actors: = p1, }; +p1_proc := J0; + +p1 @Record { } .= 0; + diff --git a/latest/cases/01226/l2v5/index.heta b/latest/cases/01226/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01226/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01226/l2v5/json/output.json b/latest/cases/01226/l2v5/json/output.json new file mode 100644 index 000000000..ae145c7e2 --- /dev/null +++ b/latest/cases/01226/l2v5/json/output.json @@ -0,0 +1,80 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "p1_proc", + "assignments": { + "ode_": "J0" + }, + "actors": [ + { + "target": "p1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01226/l3v2/heta-code/output.heta b/latest/cases/01226/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4970e4550 --- /dev/null +++ b/latest/cases/01226/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; +p1_proc @Process { actors: = p1, }; +p1_proc := J0; + +p1 @Record { } .= 0; + diff --git a/latest/cases/01226/l3v2/index.heta b/latest/cases/01226/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01226/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01226/l3v2/json/output.json b/latest/cases/01226/l3v2/json/output.json new file mode 100644 index 000000000..877569ea8 --- /dev/null +++ b/latest/cases/01226/l3v2/json/output.json @@ -0,0 +1,55 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "p1_proc", + "assignments": { + "ode_": "J0" + }, + "actors": [ + { + "target": "p1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01226/model-sbml-l2v5.xml b/latest/cases/01226/model-sbml-l2v5.xml new file mode 100644 index 000000000..821e14e77 --- /dev/null +++ b/latest/cases/01226/model-sbml-l2v5.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + J0 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01226/model-sbml-l3v2.xml b/latest/cases/01226/model-sbml-l3v2.xml new file mode 100644 index 000000000..54c0c2e51 --- /dev/null +++ b/latest/cases/01226/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + J0 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01226/output.heta b/latest/cases/01226/output.heta new file mode 100644 index 000000000..5f178296c --- /dev/null +++ b/latest/cases/01226/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: A simple reaction whose identifier is used in a rate rule. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in a rate rule. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter p1 | $0$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; +p1_proc @Process { actors: = p1, }; +p1_proc := J0; + +p1 @Record { } .= 0; + diff --git a/latest/cases/01226/synopsis.txt b/latest/cases/01226/synopsis.txt new file mode 100644 index 000000000..4963c6693 --- /dev/null +++ b/latest/cases/01226/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A simple reaction whose identifier is used in a rate rule. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in a rate rule. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter p1 | $0$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01227/l2v5/heta-code/output.heta b/latest/cases/01227/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0dc4639bf --- /dev/null +++ b/latest/cases/01227/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; + +k1 @Record { } .= 1.5; +k1 [_E0]= 2; + +_E0 @DSwitcher { trigger: t > J0, }; + diff --git a/latest/cases/01227/l2v5/index.heta b/latest/cases/01227/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01227/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01227/l2v5/json/output.json b/latest/cases/01227/l2v5/json/output.json new file mode 100644 index 000000000..9843a134d --- /dev/null +++ b/latest/cases/01227/l2v5/json/output.json @@ -0,0 +1,73 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1.5", + "_E0": "2" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > J0" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01227/l3v2/heta-code/output.heta b/latest/cases/01227/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d0c38ed5f --- /dev/null +++ b/latest/cases/01227/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; + +k1 @Record { } .= 1.5; +k1 [_E0]= 2; + +_E0 @DSwitcher { trigger: t > J0, }; + diff --git a/latest/cases/01227/l3v2/index.heta b/latest/cases/01227/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01227/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01227/l3v2/json/output.json b/latest/cases/01227/l3v2/json/output.json new file mode 100644 index 000000000..7c078d5b5 --- /dev/null +++ b/latest/cases/01227/l3v2/json/output.json @@ -0,0 +1,48 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1.5", + "_E0": "2" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > J0" + } +] \ No newline at end of file diff --git a/latest/cases/01227/model-sbml-l2v5.xml b/latest/cases/01227/model-sbml-l2v5.xml new file mode 100644 index 000000000..7548b0e81 --- /dev/null +++ b/latest/cases/01227/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + time + J0 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01227/model-sbml-l3v2.xml b/latest/cases/01227/model-sbml-l3v2.xml new file mode 100644 index 000000000..e5f6e36fc --- /dev/null +++ b/latest/cases/01227/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + time + J0 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01227/output.heta b/latest/cases/01227/output.heta new file mode 100644 index 000000000..e07725a9c --- /dev/null +++ b/latest/cases/01227/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: A simple reaction whose identifier is used in a trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in a trigger. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > J0$ | $k1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $1.5$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; + +k1 @Record { } .= 1.5; +k1 [_E0]= 2; + +_E0 @DSwitcher { trigger: t > J0, }; + diff --git a/latest/cases/01227/synopsis.txt b/latest/cases/01227/synopsis.txt new file mode 100644 index 000000000..81f670960 --- /dev/null +++ b/latest/cases/01227/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A simple reaction whose identifier is used in a trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in a trigger. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > J0$ | $k1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $1.5$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01228/l2v5/heta-code/output.heta b/latest/cases/01228/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9def1cdee --- /dev/null +++ b/latest/cases/01228/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; + +k1 @Record { } .= 1; +k1 [_E0]= 1 + J0; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01228/l2v5/index.heta b/latest/cases/01228/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01228/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01228/l2v5/json/output.json b/latest/cases/01228/l2v5/json/output.json new file mode 100644 index 000000000..44fd12108 --- /dev/null +++ b/latest/cases/01228/l2v5/json/output.json @@ -0,0 +1,73 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1", + "_E0": "1 + J0" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 5.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01228/l3v2/heta-code/output.heta b/latest/cases/01228/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6bc15ffd5 --- /dev/null +++ b/latest/cases/01228/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; + +k1 @Record { } .= 1; +k1 [_E0]= 1 + J0; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01228/l3v2/index.heta b/latest/cases/01228/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01228/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01228/l3v2/json/output.json b/latest/cases/01228/l3v2/json/output.json new file mode 100644 index 000000000..c6f6a1d63 --- /dev/null +++ b/latest/cases/01228/l3v2/json/output.json @@ -0,0 +1,48 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1", + "_E0": "1 + J0" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01228/model-sbml-l2v5.xml b/latest/cases/01228/model-sbml-l2v5.xml new file mode 100644 index 000000000..78e5c8c07 --- /dev/null +++ b/latest/cases/01228/model-sbml-l2v5.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + time + 5.5 + + + + + + + + + 1 + J0 + + + + + + + + diff --git a/latest/cases/01228/model-sbml-l3v2.xml b/latest/cases/01228/model-sbml-l3v2.xml new file mode 100644 index 000000000..b6d245005 --- /dev/null +++ b/latest/cases/01228/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + time + 5.5 + + + + + + + + + 1 + J0 + + + + + + + + diff --git a/latest/cases/01228/output.heta b/latest/cases/01228/output.heta new file mode 100644 index 000000000..a980a1868 --- /dev/null +++ b/latest/cases/01228/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: A simple reaction whose identifier is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in an event assignment. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $k1 = 1 + J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; + +k1 @Record { } .= 1; +k1 [_E0]= 1 + J0; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01228/synopsis.txt b/latest/cases/01228/synopsis.txt new file mode 100644 index 000000000..859bf89d9 --- /dev/null +++ b/latest/cases/01228/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A simple reaction whose identifier is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in an event assignment. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $k1 = 1 + J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01229/l2v5/index.heta b/latest/cases/01229/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01229/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01229/l3v2/heta-code/output.heta b/latest/cases/01229/l3v2/heta-code/output.heta new file mode 100644 index 000000000..80672e191 --- /dev/null +++ b/latest/cases/01229/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; + +k1 @Record { } .= 1; +k1 [E0]= 10; +k1 [E1]= 2; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01229/l3v2/index.heta b/latest/cases/01229/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01229/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01229/l3v2/json/output.json b/latest/cases/01229/l3v2/json/output.json new file mode 100644 index 000000000..e9da0feea --- /dev/null +++ b/latest/cases/01229/l3v2/json/output.json @@ -0,0 +1,54 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1", + "E0": "10", + "E1": "2" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 5.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01229/model-sbml-l3v2.xml b/latest/cases/01229/model-sbml-l3v2.xml new file mode 100644 index 000000000..344537d14 --- /dev/null +++ b/latest/cases/01229/model-sbml-l3v2.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + time + 5.5 + + + + + + J0 + + + + + + 10 + + + + + + + + + + time + 5.5 + + + + + + + + J0 + 1 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01229/output.heta b/latest/cases/01229/output.heta new file mode 100644 index 000000000..87090cc1c --- /dev/null +++ b/latest/cases/01229/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: A simple reaction whose identifier is used in an event priority. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in an event priority. E1 has a lower priority, and thus executes after E0, leaving k1 with a value of 2 instead of 10. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $J0$ | $k1 = 10$ | +| E1 | $time > 5.5$ | $J0 - 1$ | $k1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; + +k1 @Record { } .= 1; +k1 [E0]= 10; +k1 [E1]= 2; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01229/synopsis.txt b/latest/cases/01229/synopsis.txt new file mode 100644 index 000000000..b2dfae764 --- /dev/null +++ b/latest/cases/01229/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A simple reaction whose identifier is used in an event priority. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in an event priority. E1 has a lower priority, and thus executes after E0, leaving k1 with a value of 2 instead of 10. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $J0$ | $k1 = 10$ | +| E1 | $time > 5.5$ | $J0 - 1$ | $k1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01230/l2v5/build.log b/latest/cases/01230/l2v5/build.log new file mode 100644 index 000000000..7197e3c04 --- /dev/null +++ b/latest/cases/01230/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01230/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01230/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01230/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01230/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01230/l2v5/index.heta b/latest/cases/01230/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01230/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01230/l3v2/build.log b/latest/cases/01230/l3v2/build.log new file mode 100644 index 000000000..e4f3f87d4 --- /dev/null +++ b/latest/cases/01230/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01230/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01230/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01230/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01230/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01230/l3v2/index.heta b/latest/cases/01230/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01230/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01230/model-sbml-l2v5.xml b/latest/cases/01230/model-sbml-l2v5.xml new file mode 100644 index 000000000..867dabeca --- /dev/null +++ b/latest/cases/01230/model-sbml-l2v5.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + time + 4.5 + + + + + + + + 1 + J0 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01230/model-sbml-l3v2.xml b/latest/cases/01230/model-sbml-l3v2.xml new file mode 100644 index 000000000..bea99d9df --- /dev/null +++ b/latest/cases/01230/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + time + 4.5 + + + + + + + + 1 + J0 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01230/synopsis.txt b/latest/cases/01230/synopsis.txt new file mode 100644 index 000000000..e0950f033 --- /dev/null +++ b/latest/cases/01230/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A simple reaction whose identifier is used in an event delay. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in an event delay. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time > 4.5$ | $1 * J0$ | $k1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01231/l2v5/heta-code/output.heta b/latest/cases/01231/l2v5/heta-code/output.heta new file mode 100644 index 000000000..20da71d2d --- /dev/null +++ b/latest/cases/01231/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; +S2 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; +J1 @Reaction { actors: = S2, reversible: false, }; +J1 := J0 + 1; + +k1 @Record { } .= 1; + diff --git a/latest/cases/01231/l2v5/index.heta b/latest/cases/01231/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01231/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01231/l2v5/json/output.json b/latest/cases/01231/l2v5/json/output.json new file mode 100644 index 000000000..16b7827ad --- /dev/null +++ b/latest/cases/01231/l2v5/json/output.json @@ -0,0 +1,89 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "J0 + 1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01231/l3v2/heta-code/output.heta b/latest/cases/01231/l3v2/heta-code/output.heta new file mode 100644 index 000000000..216c4bbd1 --- /dev/null +++ b/latest/cases/01231/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; +S2 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; +J1 @Reaction { actors: = S2, reversible: false, }; +J1 := J0 + 1; + +k1 @Const { } = 1; + diff --git a/latest/cases/01231/l3v2/index.heta b/latest/cases/01231/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01231/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01231/l3v2/json/output.json b/latest/cases/01231/l3v2/json/output.json new file mode 100644 index 000000000..3dff7ec51 --- /dev/null +++ b/latest/cases/01231/l3v2/json/output.json @@ -0,0 +1,62 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "J0 + 1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "k1", + "num": 1 + } +] \ No newline at end of file diff --git a/latest/cases/01231/model-sbml-l2v5.xml b/latest/cases/01231/model-sbml-l2v5.xml new file mode 100644 index 000000000..78351af36 --- /dev/null +++ b/latest/cases/01231/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + + J0 + 1 + + + + + + + diff --git a/latest/cases/01231/model-sbml-l3v2.xml b/latest/cases/01231/model-sbml-l3v2.xml new file mode 100644 index 000000000..2f92d796e --- /dev/null +++ b/latest/cases/01231/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + + J0 + 1 + + + + + + + diff --git a/latest/cases/01231/output.heta b/latest/cases/01231/output.heta new file mode 100644 index 000000000..e714da379 --- /dev/null +++ b/latest/cases/01231/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A simple reaction whose identifier is used in another reaction's kinetic law. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in another reaction (J1). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k1) +* 1 compartment (c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ | +| J1: -> S2 | $J0 + 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; +S2 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; +J1 @Reaction { actors: = S2, reversible: false, }; +J1 := J0 + 1; + +k1 @Const { } = 1; + diff --git a/latest/cases/01231/synopsis.txt b/latest/cases/01231/synopsis.txt new file mode 100644 index 000000000..c8f1255a0 --- /dev/null +++ b/latest/cases/01231/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A simple reaction whose identifier is used in another reaction's kinetic law. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in another reaction (J1). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k1) +* 1 compartment (c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ | +| J1: -> S2 | $J0 + 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial value of parameter k1 | $1$ | constant | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01232/l2v5/heta-code/output.heta b/latest/cases/01232/l2v5/heta-code/output.heta new file mode 100644 index 000000000..487a033fe --- /dev/null +++ b/latest/cases/01232/l2v5/heta-code/output.heta @@ -0,0 +1,23 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; +S2 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; +J1 @Reaction { actors: = S2, reversible: false, }; +J1 := J0__J1_local; + +k1 @Record { } .= 1; + +J0__J1_local @Const { } = 2; + diff --git a/latest/cases/01232/l2v5/index.heta b/latest/cases/01232/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01232/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01232/l2v5/json/output.json b/latest/cases/01232/l2v5/json/output.json new file mode 100644 index 000000000..a0efe6125 --- /dev/null +++ b/latest/cases/01232/l2v5/json/output.json @@ -0,0 +1,94 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "J0__J1_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "J0__J1_local" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01232/l3v2/heta-code/output.heta b/latest/cases/01232/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e176d7dab --- /dev/null +++ b/latest/cases/01232/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; +S2 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; +J1 @Reaction { actors: = S2, reversible: false, }; +J1 := J0__J1_local; + +k1 @Record { } .= 1; + +J0__J1_local @Const { } = 2; + diff --git a/latest/cases/01232/l3v2/index.heta b/latest/cases/01232/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01232/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01232/l3v2/json/output.json b/latest/cases/01232/l3v2/json/output.json new file mode 100644 index 000000000..6be5ff9e6 --- /dev/null +++ b/latest/cases/01232/l3v2/json/output.json @@ -0,0 +1,69 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Const", + "id": "J0__J1_local", + "num": 2 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "J0__J1_local" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1" + } + } +] \ No newline at end of file diff --git a/latest/cases/01232/model-sbml-l2v5.xml b/latest/cases/01232/model-sbml-l2v5.xml new file mode 100644 index 000000000..6ff778f6b --- /dev/null +++ b/latest/cases/01232/model-sbml-l2v5.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + J0 + + + + + + + + + diff --git a/latest/cases/01232/model-sbml-l3v2.xml b/latest/cases/01232/model-sbml-l3v2.xml new file mode 100644 index 000000000..5eb9a4874 --- /dev/null +++ b/latest/cases/01232/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + J0 + + + + + + + + + diff --git a/latest/cases/01232/output.heta b/latest/cases/01232/output.heta new file mode 100644 index 000000000..2559887e3 --- /dev/null +++ b/latest/cases/01232/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: A simple reaction whose identifier is shadowed by another reaction's local parameter. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check shadowing the identifier of a reaction (J0) with a local parameter of another reaction (J1). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k1) +* 1 local parameter (J1.J0) +* 1 compartment (c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ | +| J1: -> S2 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial value of local parameter 'J1.J0' | $2$ | constant | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; +S2 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := k1; +J1 @Reaction { actors: = S2, reversible: false, }; +J1 := J0__J1_local; + +k1 @Record { } .= 1; + +J0__J1_local @Const { } = 2; + diff --git a/latest/cases/01232/synopsis.txt b/latest/cases/01232/synopsis.txt new file mode 100644 index 000000000..f02f80dfb --- /dev/null +++ b/latest/cases/01232/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A simple reaction whose identifier is shadowed by another reaction's local parameter. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check shadowing the identifier of a reaction (J0) with a local parameter of another reaction (J1). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k1) +* 1 local parameter (J1.J0) +* 1 compartment (c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ | +| J1: -> S2 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial value of local parameter 'J1.J0' | $2$ | constant | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01233/l2v5/heta-code/output.heta b/latest/cases/01233/l2v5/heta-code/output.heta new file mode 100644 index 000000000..146c24e5d --- /dev/null +++ b/latest/cases/01233/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +addone #defineFunction { arguments: [x], math: x + 1, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; + +p1 @Record { } .= addone(J0); + diff --git a/latest/cases/01233/l2v5/index.heta b/latest/cases/01233/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01233/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01233/l2v5/json/output.json b/latest/cases/01233/l2v5/json/output.json new file mode 100644 index 000000000..7ed63dbc4 --- /dev/null +++ b/latest/cases/01233/l2v5/json/output.json @@ -0,0 +1,75 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "addone(J0)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "addone", + "arguments": [ + "x" + ], + "math": "x + 1", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01233/l3v2/heta-code/output.heta b/latest/cases/01233/l3v2/heta-code/output.heta new file mode 100644 index 000000000..953137d48 --- /dev/null +++ b/latest/cases/01233/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + +addone #defineFunction { arguments: [x], math: x + 1, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; + +p1 @Record { } .= addone(J0); + diff --git a/latest/cases/01233/l3v2/index.heta b/latest/cases/01233/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01233/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01233/l3v2/json/output.json b/latest/cases/01233/l3v2/json/output.json new file mode 100644 index 000000000..99559b890 --- /dev/null +++ b/latest/cases/01233/l3v2/json/output.json @@ -0,0 +1,50 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "addone(J0)" + } + }, + { + "id": "addone", + "arguments": [ + "x" + ], + "math": "x + 1", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01233/model-sbml-l2v5.xml b/latest/cases/01233/model-sbml-l2v5.xml new file mode 100644 index 000000000..ccd2bdac0 --- /dev/null +++ b/latest/cases/01233/model-sbml-l2v5.xml @@ -0,0 +1,52 @@ + + + + + + + + + x + + + + x + 1 + + + + + + + + + + + + + + + + + + + addone + J0 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01233/model-sbml-l3v2.xml b/latest/cases/01233/model-sbml-l3v2.xml new file mode 100644 index 000000000..b7de0ef43 --- /dev/null +++ b/latest/cases/01233/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + x + + + + x + 1 + + + + + + + + + + + + + + + + + + + addone + J0 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01233/output.heta b/latest/cases/01233/output.heta new file mode 100644 index 000000000..e555536fe --- /dev/null +++ b/latest/cases/01233/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: A simple reaction whose identifier is used in an initial assignment. +componentTags: Compartment, FunctionDefinition, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in a function within an initial assignment. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addone | x | $x + 1$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter p1 | $addone(J0)$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +addone #defineFunction { arguments: [x], math: x + 1, }; + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 0; + +J0 @Reaction { actors: = S1, reversible: false, }; +J0 := 1; + +p1 @Record { } .= addone(J0); + diff --git a/latest/cases/01233/synopsis.txt b/latest/cases/01233/synopsis.txt new file mode 100644 index 000000000..5b9dce218 --- /dev/null +++ b/latest/cases/01233/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A simple reaction whose identifier is used in an initial assignment. +componentTags: Compartment, FunctionDefinition, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to check using the identifier of a reaction (J0) in a function within an initial assignment. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addone | x | $x + 1$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter p1 | $addone(J0)$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01234/l2v5/index.heta b/latest/cases/01234/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01234/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01234/l3v2/heta-code/output.heta b/latest/cases/01234/l3v2/heta-code/output.heta new file mode 100644 index 000000000..07ff4360c --- /dev/null +++ b/latest/cases/01234/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +p @Const { } = 3; + diff --git a/latest/cases/01234/l3v2/index.heta b/latest/cases/01234/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01234/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01234/l3v2/json/output.json b/latest/cases/01234/l3v2/json/output.json new file mode 100644 index 000000000..a0e7ddb29 --- /dev/null +++ b/latest/cases/01234/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "p", + "num": 3 + } +] \ No newline at end of file diff --git a/latest/cases/01234/model-sbml-l3v2.xml b/latest/cases/01234/model-sbml-l3v2.xml new file mode 100644 index 000000000..0b11748bc --- /dev/null +++ b/latest/cases/01234/model-sbml-l3v2.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/latest/cases/01234/output.heta b/latest/cases/01234/output.heta new file mode 100644 index 000000000..c8a998090 --- /dev/null +++ b/latest/cases/01234/output.heta @@ -0,0 +1,30 @@ +/* +category: Test +synopsis: An InitialAssignment with missing MathML. +componentTags: InitialAssignment, Parameter +testTags: NoMathML +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an InitialAssignment with no Math child is encountered, it is ignored. + +The model contains: +* 1 parameter (p) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p @Const { } = 3; + diff --git a/latest/cases/01234/synopsis.txt b/latest/cases/01234/synopsis.txt new file mode 100644 index 000000000..f2f0137d4 --- /dev/null +++ b/latest/cases/01234/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: An InitialAssignment with missing MathML. +componentTags: InitialAssignment, Parameter +testTags: NoMathML +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an InitialAssignment with no Math child is encountered, it is ignored. + +The model contains: +* 1 parameter (p) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01235/l2v5/index.heta b/latest/cases/01235/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01235/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01235/l3v2/heta-code/output.heta b/latest/cases/01235/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8784140e5 --- /dev/null +++ b/latest/cases/01235/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +p @Record { } .= 3; + diff --git a/latest/cases/01235/l3v2/index.heta b/latest/cases/01235/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01235/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01235/l3v2/json/output.json b/latest/cases/01235/l3v2/json/output.json new file mode 100644 index 000000000..99e2d5bf4 --- /dev/null +++ b/latest/cases/01235/l3v2/json/output.json @@ -0,0 +1,12 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p", + "assignments": { + "start_": "3" + } + } +] \ No newline at end of file diff --git a/latest/cases/01235/model-sbml-l3v2.xml b/latest/cases/01235/model-sbml-l3v2.xml new file mode 100644 index 000000000..b4ee59099 --- /dev/null +++ b/latest/cases/01235/model-sbml-l3v2.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/latest/cases/01235/output.heta b/latest/cases/01235/output.heta new file mode 100644 index 000000000..14a7821f2 --- /dev/null +++ b/latest/cases/01235/output.heta @@ -0,0 +1,36 @@ +/* +category: Test +synopsis: An AssignmentRule with missing MathML. +componentTags: AssignmentRule, Parameter +testTags: NoMathML +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an AssignmentRule with no Math child is encountered, it is ignored. + +The model contains: +* 1 parameter (p) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p @Record { } .= 3; + diff --git a/latest/cases/01235/synopsis.txt b/latest/cases/01235/synopsis.txt new file mode 100644 index 000000000..dc9cdfd2f --- /dev/null +++ b/latest/cases/01235/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An AssignmentRule with missing MathML. +componentTags: AssignmentRule, Parameter +testTags: NoMathML +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an AssignmentRule with no Math child is encountered, it is ignored. + +The model contains: +* 1 parameter (p) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01236/l2v5/index.heta b/latest/cases/01236/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01236/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01236/l3v2/build.log b/latest/cases/01236/l3v2/build.log new file mode 100644 index 000000000..d0245b350 --- /dev/null +++ b/latest/cases/01236/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01236/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01236/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01236/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] Record "p_proc" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01236/l3v2/index.heta b/latest/cases/01236/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01236/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01236/model-sbml-l3v2.xml b/latest/cases/01236/model-sbml-l3v2.xml new file mode 100644 index 000000000..c55d2777c --- /dev/null +++ b/latest/cases/01236/model-sbml-l3v2.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/latest/cases/01236/synopsis.txt b/latest/cases/01236/synopsis.txt new file mode 100644 index 000000000..5a68b14a1 --- /dev/null +++ b/latest/cases/01236/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A RateRule with missing MathML. +componentTags: Parameter, RateRule +testTags: NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if a RateRule with no Math child is encountered, it is ignored. + +The model contains: +* 1 parameter (p) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01237/l2v5/index.heta b/latest/cases/01237/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01237/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01237/l3v2/heta-code/output.heta b/latest/cases/01237/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4064640e7 --- /dev/null +++ b/latest/cases/01237/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +p @Record { } .= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01237/l3v2/index.heta b/latest/cases/01237/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01237/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01237/l3v2/json/output.json b/latest/cases/01237/l3v2/json/output.json new file mode 100644 index 000000000..94c4fbb78 --- /dev/null +++ b/latest/cases/01237/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p", + "assignments": { + "start_": "3" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01237/model-sbml-l3v2.xml b/latest/cases/01237/model-sbml-l3v2.xml new file mode 100644 index 000000000..613093d10 --- /dev/null +++ b/latest/cases/01237/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + time + 5.5 + + + + + + + + + + diff --git a/latest/cases/01237/output.heta b/latest/cases/01237/output.heta new file mode 100644 index 000000000..9b5bfa198 --- /dev/null +++ b/latest/cases/01237/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: An EventAssignment with missing MathML. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an EventAssignment with no Math child is encountered, it is ignored. + +The model contains: +* 1 parameter (p) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 5.5$ | $p = $ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p @Record { } .= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01237/synopsis.txt b/latest/cases/01237/synopsis.txt new file mode 100644 index 000000000..7a19e5843 --- /dev/null +++ b/latest/cases/01237/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An EventAssignment with missing MathML. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an EventAssignment with no Math child is encountered, it is ignored. + +The model contains: +* 1 parameter (p) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 5.5$ | $p = $ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01238/l2v5/index.heta b/latest/cases/01238/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01238/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01238/l3v2/build.log b/latest/cases/01238/l3v2/build.log new file mode 100644 index 000000000..0d837df52 --- /dev/null +++ b/latest/cases/01238/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01238/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01238/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01238/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] No required "trigger" property for "E0" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01238/l3v2/index.heta b/latest/cases/01238/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01238/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01238/model-sbml-l3v2.xml b/latest/cases/01238/model-sbml-l3v2.xml new file mode 100644 index 000000000..09badfb04 --- /dev/null +++ b/latest/cases/01238/model-sbml-l3v2.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01238/synopsis.txt b/latest/cases/01238/synopsis.txt new file mode 100644 index 000000000..8b58ac81d --- /dev/null +++ b/latest/cases/01238/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An Event Trigger with missing MathML. +componentTags: EventNoDelay, Parameter +testTags: NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an Event Trigger with no Math child is encountered, the Event is ignored. + +The model contains: +* 1 parameter (p) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $(unset)$ | $p = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01239/l2v5/index.heta b/latest/cases/01239/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01239/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01239/l3v2/build.log b/latest/cases/01239/l3v2/build.log new file mode 100644 index 000000000..d76181b70 --- /dev/null +++ b/latest/cases/01239/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01239/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01239/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01239/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] No required "trigger" property for "E0" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01239/l3v2/index.heta b/latest/cases/01239/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01239/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01239/model-sbml-l3v2.xml b/latest/cases/01239/model-sbml-l3v2.xml new file mode 100644 index 000000000..86f8abf43 --- /dev/null +++ b/latest/cases/01239/model-sbml-l3v2.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01239/synopsis.txt b/latest/cases/01239/synopsis.txt new file mode 100644 index 000000000..3042c7e09 --- /dev/null +++ b/latest/cases/01239/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An Event with missing Trigger. +componentTags: EventNoDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an Event with no Trigger is encountered, the Event is ignored. + +The model contains: +* 1 parameter (p) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $(unset)$ | $p = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01240/l2v5/index.heta b/latest/cases/01240/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01240/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01240/l3v2/heta-code/output.heta b/latest/cases/01240/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4064640e7 --- /dev/null +++ b/latest/cases/01240/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +p @Record { } .= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01240/l3v2/index.heta b/latest/cases/01240/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01240/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01240/l3v2/json/output.json b/latest/cases/01240/l3v2/json/output.json new file mode 100644 index 000000000..94c4fbb78 --- /dev/null +++ b/latest/cases/01240/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p", + "assignments": { + "start_": "3" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01240/model-sbml-l3v2.xml b/latest/cases/01240/model-sbml-l3v2.xml new file mode 100644 index 000000000..8ba162609 --- /dev/null +++ b/latest/cases/01240/model-sbml-l3v2.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + time + 5.5 + + + + + + + diff --git a/latest/cases/01240/output.heta b/latest/cases/01240/output.heta new file mode 100644 index 000000000..da654cc06 --- /dev/null +++ b/latest/cases/01240/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: An Event with no EventAssignments. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This test was written to ensure that if no EventAssignments are found in an Event, it is ignored. + +The model contains: +* 1 parameter (p) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 5.5$ | |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p @Record { } .= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01240/synopsis.txt b/latest/cases/01240/synopsis.txt new file mode 100644 index 000000000..f4843bcc0 --- /dev/null +++ b/latest/cases/01240/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An Event with no EventAssignments. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This test was written to ensure that if no EventAssignments are found in an Event, it is ignored. + +The model contains: +* 1 parameter (p) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 5.5$ | |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01241/l2v5/index.heta b/latest/cases/01241/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01241/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01241/l3v2/build.log b/latest/cases/01241/l3v2/build.log new file mode 100644 index 000000000..21730c26d --- /dev/null +++ b/latest/cases/01241/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01241/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01241/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01241/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01241/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01241/l3v2/index.heta b/latest/cases/01241/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01241/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01241/model-sbml-l3v2.xml b/latest/cases/01241/model-sbml-l3v2.xml new file mode 100644 index 000000000..abda6e510 --- /dev/null +++ b/latest/cases/01241/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + time + 5.5 + + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01241/synopsis.txt b/latest/cases/01241/synopsis.txt new file mode 100644 index 000000000..0a308445b --- /dev/null +++ b/latest/cases/01241/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An Event Delay with missing MathML. +componentTags: CSymbolTime, EventWithDelay, Parameter +testTags: NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an Event Delay with no MathML is encountered, the Delay is ignored. + +The model contains: +* 1 parameter (p) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| _E0 | $time > 5.5$ | $0$ | $p = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01242/l2v5/index.heta b/latest/cases/01242/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01242/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01242/l3v2/heta-code/output.heta b/latest/cases/01242/l3v2/heta-code/output.heta new file mode 100644 index 000000000..932894d8a --- /dev/null +++ b/latest/cases/01242/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +p @Record { } .= 3; +p [_E0]= 5; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01242/l3v2/index.heta b/latest/cases/01242/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01242/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01242/l3v2/json/output.json b/latest/cases/01242/l3v2/json/output.json new file mode 100644 index 000000000..13512eacb --- /dev/null +++ b/latest/cases/01242/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p", + "assignments": { + "start_": "3", + "_E0": "5" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01242/model-sbml-l3v2.xml b/latest/cases/01242/model-sbml-l3v2.xml new file mode 100644 index 000000000..79631e456 --- /dev/null +++ b/latest/cases/01242/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + time + 5.5 + + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01242/output.heta b/latest/cases/01242/output.heta new file mode 100644 index 000000000..d404d85b5 --- /dev/null +++ b/latest/cases/01242/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: An Event Priority with missing MathML. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an Event Priority with no MathML is encountered, the Priority is ignored. + +The model contains: +* 1 parameter (p) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| _E0 | $time > 5.5$ | (unset) | $p = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p @Record { } .= 3; +p [_E0]= 5; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01242/synopsis.txt b/latest/cases/01242/synopsis.txt new file mode 100644 index 000000000..a4c6749b3 --- /dev/null +++ b/latest/cases/01242/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An Event Priority with missing MathML. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an Event Priority with no MathML is encountered, the Priority is ignored. + +The model contains: +* 1 parameter (p) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| _E0 | $time > 5.5$ | (unset) | $p = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01243/l2v5/index.heta b/latest/cases/01243/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01243/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01243/l3v2/heta-code/output.heta b/latest/cases/01243/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b795668d2 --- /dev/null +++ b/latest/cases/01243/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +p @Record { } .= 3; +p [_E0]= 5; +d @Record { } .= 5; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01243/l3v2/index.heta b/latest/cases/01243/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01243/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01243/l3v2/json/output.json b/latest/cases/01243/l3v2/json/output.json new file mode 100644 index 000000000..98272312e --- /dev/null +++ b/latest/cases/01243/l3v2/json/output.json @@ -0,0 +1,25 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p", + "assignments": { + "start_": "3", + "_E0": "5" + } + }, + { + "class": "Record", + "id": "d", + "assignments": { + "start_": "5" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01243/model-sbml-l3v2.xml b/latest/cases/01243/model-sbml-l3v2.xml new file mode 100644 index 000000000..803458a43 --- /dev/null +++ b/latest/cases/01243/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + time + 5.5 + + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01243/output.heta b/latest/cases/01243/output.heta new file mode 100644 index 000000000..b916b3537 --- /dev/null +++ b/latest/cases/01243/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Two EventAssignments, one with missing MathML. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that even if one EventAssignment is to be ignored due to it having missing MathML, there may be other EventAssignments that are normal. + +The model contains: +* 2 parameters (p, d) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $d = $ | +| | | $p = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable | +| Initial value of parameter d | $5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p @Record { } .= 3; +p [_E0]= 5; +d @Record { } .= 5; + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01243/synopsis.txt b/latest/cases/01243/synopsis.txt new file mode 100644 index 000000000..99f0973c5 --- /dev/null +++ b/latest/cases/01243/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Two EventAssignments, one with missing MathML. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that even if one EventAssignment is to be ignored due to it having missing MathML, there may be other EventAssignments that are normal. + +The model contains: +* 2 parameters (p, d) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $d = $ | +| | | $p = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable | +| Initial value of parameter d | $5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01244/l2v5/index.heta b/latest/cases/01244/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01244/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01244/l3v2/build.log b/latest/cases/01244/l3v2/build.log new file mode 100644 index 000000000..ab48591b2 --- /dev/null +++ b/latest/cases/01244/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01244/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01244/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01244/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01244/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01244/l3v2/index.heta b/latest/cases/01244/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01244/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01244/model-sbml-l3v2.xml b/latest/cases/01244/model-sbml-l3v2.xml new file mode 100644 index 000000000..1409f5e58 --- /dev/null +++ b/latest/cases/01244/model-sbml-l3v2.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/latest/cases/01244/synopsis.txt b/latest/cases/01244/synopsis.txt new file mode 100644 index 000000000..0b7e3f365 --- /dev/null +++ b/latest/cases/01244/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An AlgebraicRule with missing MathML. +componentTags: AlgebraicRule, Parameter +testTags: NoMathML +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that if an AlgebraicRule with no Math child is encountered, it is ignored. + +The model contains: +* 1 parameter (p) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01245/l2v5/index.heta b/latest/cases/01245/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01245/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01245/l3v2/heta-code/output.heta b/latest/cases/01245/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ee52852dd --- /dev/null +++ b/latest/cases/01245/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 2 / c; + +J0 @Reaction { actors: = , }; +J0 := 2; + diff --git a/latest/cases/01245/l3v2/index.heta b/latest/cases/01245/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01245/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01245/l3v2/json/output.json b/latest/cases/01245/l3v2/json/output.json new file mode 100644 index 000000000..6da6a1577 --- /dev/null +++ b/latest/cases/01245/l3v2/json/output.json @@ -0,0 +1,29 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / c" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "2" + }, + "actors": [] + } +] \ No newline at end of file diff --git a/latest/cases/01245/model-sbml-l3v2.xml b/latest/cases/01245/model-sbml-l3v2.xml new file mode 100644 index 000000000..57089e7b7 --- /dev/null +++ b/latest/cases/01245/model-sbml-l3v2.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + 2 + + + + + + diff --git a/latest/cases/01245/output.heta b/latest/cases/01245/output.heta new file mode 100644 index 000000000..4ff6344dc --- /dev/null +++ b/latest/cases/01245/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: A Reaction with no reactants or products. +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that a Reaction with no reactants nor produts is treated properly. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 2 / c; + +J0 @Reaction { actors: = , }; +J0 := 2; + diff --git a/latest/cases/01245/synopsis.txt b/latest/cases/01245/synopsis.txt new file mode 100644 index 000000000..08559a3f9 --- /dev/null +++ b/latest/cases/01245/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A Reaction with no reactants or products. +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that a Reaction with no reactants nor produts is treated properly. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01246/l2v5/index.heta b/latest/cases/01246/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01246/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01246/l3v2/heta-code/output.heta b/latest/cases/01246/l3v2/heta-code/output.heta new file mode 100644 index 000000000..632fe0ca8 --- /dev/null +++ b/latest/cases/01246/l3v2/heta-code/output.heta @@ -0,0 +1,13 @@ + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 2 / c; + +J0 @Reaction { actors: = , reversible: false, }; +J0 := 2; +J1 @Reaction { actors: = S1, reversible: false, }; +J1 := 1; + diff --git a/latest/cases/01246/l3v2/index.heta b/latest/cases/01246/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01246/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01246/l3v2/json/output.json b/latest/cases/01246/l3v2/json/output.json new file mode 100644 index 000000000..61e221a05 --- /dev/null +++ b/latest/cases/01246/l3v2/json/output.json @@ -0,0 +1,44 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / c" + }, + "compartment": "c" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "2" + }, + "actors": [], + "reversible": false + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ], + "reversible": false + } +] \ No newline at end of file diff --git a/latest/cases/01246/model-sbml-l3v2.xml b/latest/cases/01246/model-sbml-l3v2.xml new file mode 100644 index 000000000..d1acd1966 --- /dev/null +++ b/latest/cases/01246/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + 2 + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01246/output.heta b/latest/cases/01246/output.heta new file mode 100644 index 000000000..b9861a0ef --- /dev/null +++ b/latest/cases/01246/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: Two Reactions; one with no reactants or products. +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that a Reaction with no reactants nor produts is treated properly when another normal Reaction is present. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $2$ | +| J1: -> S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +c @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: c, } .= 2 / c; + +J0 @Reaction { actors: = , reversible: false, }; +J0 := 2; +J1 @Reaction { actors: = S1, reversible: false, }; +J1 := 1; + diff --git a/latest/cases/01246/synopsis.txt b/latest/cases/01246/synopsis.txt new file mode 100644 index 000000000..9ff5554fc --- /dev/null +++ b/latest/cases/01246/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Two Reactions; one with no reactants or products. +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that a Reaction with no reactants nor produts is treated properly when another normal Reaction is present. + +The model contains: +* 1 species (S1) +* 1 compartment (c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $2$ | +| J1: -> S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01247/l2v5/index.heta b/latest/cases/01247/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01247/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01247/l3v2/heta-code/output.heta b/latest/cases/01247/l3v2/heta-code/output.heta new file mode 100644 index 000000000..07ff4360c --- /dev/null +++ b/latest/cases/01247/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +p @Const { } = 3; + diff --git a/latest/cases/01247/l3v2/index.heta b/latest/cases/01247/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01247/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01247/l3v2/json/output.json b/latest/cases/01247/l3v2/json/output.json new file mode 100644 index 000000000..a0e7ddb29 --- /dev/null +++ b/latest/cases/01247/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "p", + "num": 3 + } +] \ No newline at end of file diff --git a/latest/cases/01247/model-sbml-l3v2.xml b/latest/cases/01247/model-sbml-l3v2.xml new file mode 100644 index 000000000..f337efce0 --- /dev/null +++ b/latest/cases/01247/model-sbml-l3v2.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/latest/cases/01247/output.heta b/latest/cases/01247/output.heta new file mode 100644 index 000000000..bc8089fb1 --- /dev/null +++ b/latest/cases/01247/output.heta @@ -0,0 +1,31 @@ +/* +category: Test +synopsis: A Constraint with no MathML. +componentTags: Parameter +testTags: NoMathML +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that a Constraint with no MathML is properly ignored. + +The model contains: +* 1 parameter (p) + +It also contains 1 constraints ((unset)) The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p @Const { } = 3; + diff --git a/latest/cases/01247/synopsis.txt b/latest/cases/01247/synopsis.txt new file mode 100644 index 000000000..aa5bbcac4 --- /dev/null +++ b/latest/cases/01247/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: A Constraint with no MathML. +componentTags: Parameter +testTags: NoMathML +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This test was written to ensure that a Constraint with no MathML is properly ignored. + +The model contains: +* 1 parameter (p) + +It also contains 1 constraints ((unset)) The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01248/l2v5/index.heta b/latest/cases/01248/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01248/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01248/l3v2/build.log b/latest/cases/01248/l3v2/build.log new file mode 100644 index 000000000..a13150f03 --- /dev/null +++ b/latest/cases/01248/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01248/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01248/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01248/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01248/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01248/l3v2/index.heta b/latest/cases/01248/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01248/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01248/model-sbml-l3v2.xml b/latest/cases/01248/model-sbml-l3v2.xml new file mode 100644 index 000000000..491d30d2c --- /dev/null +++ b/latest/cases/01248/model-sbml-l3v2.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + rateOf + p1 + + + + + + diff --git a/latest/cases/01248/synopsis.txt b/latest/cases/01248/synopsis.txt new file mode 100644 index 000000000..9061191ed --- /dev/null +++ b/latest/cases/01248/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: The rateOf csymbol with a constant parameter. +componentTags: CSymbolRateOf, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The rateOf csymbol is used here in an initial assignment that references a constant parameter. Hence, the rate is zero. + +The model contains: +* 2 parameters (p1, p2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | constant | +| Initial value of parameter p2 | $rateOf(p1)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01249/l2v5/index.heta b/latest/cases/01249/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01249/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01249/l3v2/build.log b/latest/cases/01249/l3v2/build.log new file mode 100644 index 000000000..79e75322c --- /dev/null +++ b/latest/cases/01249/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01249/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01249/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01249/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01249/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01249/l3v2/index.heta b/latest/cases/01249/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01249/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01249/model-sbml-l3v2.xml b/latest/cases/01249/model-sbml-l3v2.xml new file mode 100644 index 000000000..7cde6ee4a --- /dev/null +++ b/latest/cases/01249/model-sbml-l3v2.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + rateOf + p1 + + + + + + diff --git a/latest/cases/01249/synopsis.txt b/latest/cases/01249/synopsis.txt new file mode 100644 index 000000000..e419f5661 --- /dev/null +++ b/latest/cases/01249/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: The rateOf csymbol with a constant parameter. +componentTags: CSymbolRateOf, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The rateOf csymbol is used here in an initial assignment that references a constant parameter. Hence, the rate is zero. The parameter in question is flagged 'constant=false', however, even though it does not actually change. + +The model contains: +* 2 parameters (p1, p2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $rateOf(p1)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01250/l2v5/index.heta b/latest/cases/01250/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01250/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01250/l3v2/build.log b/latest/cases/01250/l3v2/build.log new file mode 100644 index 000000000..c947702ed --- /dev/null +++ b/latest/cases/01250/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01250/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01250/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01250/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01250/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01250/l3v2/index.heta b/latest/cases/01250/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01250/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01250/model-sbml-l3v2.xml b/latest/cases/01250/model-sbml-l3v2.xml new file mode 100644 index 000000000..b6896cc3f --- /dev/null +++ b/latest/cases/01250/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + rateOf + p1 + + + + + + + + 1 + + + + + diff --git a/latest/cases/01250/synopsis.txt b/latest/cases/01250/synopsis.txt new file mode 100644 index 000000000..03288fa32 --- /dev/null +++ b/latest/cases/01250/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: The rateOf csymbol for a parameter that changes due to a rate rule. +componentTags: CSymbolRateOf, InitialAssignment, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The rateOf csymbol is used here in an initial assignment that references a parameter changing due to a rate rule, and thus takes the value of that rate rule. + +The model contains: +* 2 parameters (p1, p2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p2 | $rateOf(p1)$ | constant | +| Initial value of parameter p1 | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01251/l2v5/index.heta b/latest/cases/01251/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01251/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01251/l3v2/build.log b/latest/cases/01251/l3v2/build.log new file mode 100644 index 000000000..1f0cde697 --- /dev/null +++ b/latest/cases/01251/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01251/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01251/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01251/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01251/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01251/l3v2/index.heta b/latest/cases/01251/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01251/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01251/model-sbml-l3v2.xml b/latest/cases/01251/model-sbml-l3v2.xml new file mode 100644 index 000000000..70e029703 --- /dev/null +++ b/latest/cases/01251/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01251/synopsis.txt b/latest/cases/01251/synopsis.txt new file mode 100644 index 000000000..4725e4bb5 --- /dev/null +++ b/latest/cases/01251/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: The rateOf csymbol for a species that changes due to a reaction. +componentTags: CSymbolRateOf, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The rateOf csymbol is used here in an initial assignment that references a species changing due to a reaction, and thus takes the value of the negative of that reaction's kinetic law, since it's a reactant. + +The model contains: +* 1 species (S1) +* 1 parameter (p2) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $100$ | variable | +| Initial value of parameter p2 | $rateOf(S1)$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01252/l2v5/index.heta b/latest/cases/01252/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01252/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01252/l3v2/build.log b/latest/cases/01252/l3v2/build.log new file mode 100644 index 000000000..0010b7f7a --- /dev/null +++ b/latest/cases/01252/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01252/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01252/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01252/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01252/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01252/l3v2/index.heta b/latest/cases/01252/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01252/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01252/model-sbml-l3v2.xml b/latest/cases/01252/model-sbml-l3v2.xml new file mode 100644 index 000000000..ea9596df2 --- /dev/null +++ b/latest/cases/01252/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01252/synopsis.txt b/latest/cases/01252/synopsis.txt new file mode 100644 index 000000000..a7a14024a --- /dev/null +++ b/latest/cases/01252/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: The rateOf csymbol for a species that changes due to a reaction. +componentTags: CSymbolRateOf, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The rateOf csymbol is used here in an initial assignment that references a species changing due to a reaction, and thus takes the value of the reaction's kinetic law, since it's a product. + +The model contains: +* 1 species (S1) +* 1 parameter (p2) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $100$ | variable | +| Initial value of parameter p2 | $rateOf(S1)$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01253/l2v5/index.heta b/latest/cases/01253/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01253/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01253/l3v2/build.log b/latest/cases/01253/l3v2/build.log new file mode 100644 index 000000000..d5fe8fc0e --- /dev/null +++ b/latest/cases/01253/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01253/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01253/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01253/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01253/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01253/l3v2/index.heta b/latest/cases/01253/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01253/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01253/model-sbml-l3v2.xml b/latest/cases/01253/model-sbml-l3v2.xml new file mode 100644 index 000000000..196c175eb --- /dev/null +++ b/latest/cases/01253/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01253/synopsis.txt b/latest/cases/01253/synopsis.txt new file mode 100644 index 000000000..b787d20e0 --- /dev/null +++ b/latest/cases/01253/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: The rateOf csymbol for a species that changes due to two reactions. +componentTags: CSymbolRateOf, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The rateOf csymbol is used here in an initial assignment that references a species changing due to two reactions. The reactions cancel each other out, leaving a net rate of change of zero. + +The model contains: +* 1 species (S1) +* 1 parameter (p2) +* 1 compartment (c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ | +| J1: S1 -> | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $100$ | variable | +| Initial value of parameter p2 | $rateOf(S1)$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01254/l2v5/index.heta b/latest/cases/01254/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01254/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01254/l3v2/build.log b/latest/cases/01254/l3v2/build.log new file mode 100644 index 000000000..693075b42 --- /dev/null +++ b/latest/cases/01254/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01254/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01254/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01254/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01254/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01254/l3v2/index.heta b/latest/cases/01254/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01254/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01254/model-sbml-l3v2.xml b/latest/cases/01254/model-sbml-l3v2.xml new file mode 100644 index 000000000..525e0af12 --- /dev/null +++ b/latest/cases/01254/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + + + + + 0.5 + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01254/synopsis.txt b/latest/cases/01254/synopsis.txt new file mode 100644 index 000000000..2b2c79eda --- /dev/null +++ b/latest/cases/01254/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: The rateOf csymbol for a species that changes due to two reactions. +componentTags: CSymbolRateOf, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The rateOf csymbol is used here in an initial assignment that references a species changing due to two reactions. The reactions combine to give a net rate of change of S1 of -0.5. + +The model contains: +* 1 species (S1) +* 1 parameter (p2) +* 1 compartment (c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $0.5$ | +| J1: S1 -> | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $100$ | variable | +| Initial value of parameter p2 | $rateOf(S1)$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01255/l2v5/index.heta b/latest/cases/01255/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01255/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01255/l3v2/build.log b/latest/cases/01255/l3v2/build.log new file mode 100644 index 000000000..597dc27bf --- /dev/null +++ b/latest/cases/01255/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01255/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01255/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01255/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01255/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01255/l3v2/index.heta b/latest/cases/01255/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01255/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01255/model-sbml-l3v2.xml b/latest/cases/01255/model-sbml-l3v2.xml new file mode 100644 index 000000000..17575d908 --- /dev/null +++ b/latest/cases/01255/model-sbml-l3v2.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + rateOf + p1 + + + + + + diff --git a/latest/cases/01255/synopsis.txt b/latest/cases/01255/synopsis.txt new file mode 100644 index 000000000..3ab519849 --- /dev/null +++ b/latest/cases/01255/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: The rateOf csymbol for a parameter whose rate of change is not constant. +componentTags: AssignmentRule, CSymbolRateOf, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The rateOf csymbol is used here in an assignment rule that references a parameter changing due to a non-constant rate rule. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ | +| Assignment | p2 | $rateOf(p1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $rateOf(p1)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01256/l2v5/index.heta b/latest/cases/01256/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01256/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01256/l3v2/build.log b/latest/cases/01256/l3v2/build.log new file mode 100644 index 000000000..ac10e0e75 --- /dev/null +++ b/latest/cases/01256/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01256/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01256/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01256/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01256/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01256/l3v2/index.heta b/latest/cases/01256/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01256/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01256/model-sbml-l3v2.xml b/latest/cases/01256/model-sbml-l3v2.xml new file mode 100644 index 000000000..bb761e4d4 --- /dev/null +++ b/latest/cases/01256/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + + + + + + + 0.01 + S1 + + + + + + + diff --git a/latest/cases/01256/synopsis.txt b/latest/cases/01256/synopsis.txt new file mode 100644 index 000000000..e83c1c265 --- /dev/null +++ b/latest/cases/01256/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: The rateOf csymbol for a species that changes due to a reaction with a non-constant kinetic law. +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + The rateOf csymbol is used here in an assignment rule that references a species changing due to a reactions with a non-constant kinetic law. + +The model contains: +* 1 species (S1) +* 1 parameter (p2) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $0.01 * S1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p2 | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter p2 | $rateOf(S1)$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01257/l2v5/index.heta b/latest/cases/01257/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01257/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01257/l3v2/build.log b/latest/cases/01257/l3v2/build.log new file mode 100644 index 000000000..ad875013f --- /dev/null +++ b/latest/cases/01257/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01257/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01257/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01257/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01257/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01257/l3v2/index.heta b/latest/cases/01257/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01257/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01257/model-sbml-l3v2.xml b/latest/cases/01257/model-sbml-l3v2.xml new file mode 100644 index 000000000..5f59dda4b --- /dev/null +++ b/latest/cases/01257/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + rateOf + S1 + + + rateOf + p1 + + + + + + + + + + + + + + + 0.01 + S1 + + + + + + + diff --git a/latest/cases/01257/synopsis.txt b/latest/cases/01257/synopsis.txt new file mode 100644 index 000000000..f1fc7b6db --- /dev/null +++ b/latest/cases/01257/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Two rateOf csymbols for a species and parameter. +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +Two rateOf csymbols are used here in an assignment rule: one that references a species changing due to a reactions with a non-constant kinetic law, and one that references a parameter changing due to a rate rule. + +The model contains: +* 1 species (S1) +* 2 parameters (p1, p2) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $0.01 * S1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ | +| Assignment | p2 | $rateOf(S1) + rateOf(p1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $rateOf(S1) + rateOf(p1)$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01258/l2v5/index.heta b/latest/cases/01258/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01258/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01258/l3v2/build.log b/latest/cases/01258/l3v2/build.log new file mode 100644 index 000000000..0acaa221b --- /dev/null +++ b/latest/cases/01258/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01258/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01258/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01258/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01258/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01258/l3v2/index.heta b/latest/cases/01258/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01258/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01258/model-sbml-l3v2.xml b/latest/cases/01258/model-sbml-l3v2.xml new file mode 100644 index 000000000..3e288cc62 --- /dev/null +++ b/latest/cases/01258/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + 1 + + + + + + rateOf + p1 + + + + + + diff --git a/latest/cases/01258/synopsis.txt b/latest/cases/01258/synopsis.txt new file mode 100644 index 000000000..420e38071 --- /dev/null +++ b/latest/cases/01258/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A rateOf csymbol in a rate rule. +componentTags: CSymbolRateOf, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A rateOf csymbols is used here in a rate rule, defining the rate of change of p2 the same as the rate of change of p1. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $1$ | +| Rate | p2 | $rateOf(p1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01259/l2v5/index.heta b/latest/cases/01259/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01259/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01259/l3v2/build.log b/latest/cases/01259/l3v2/build.log new file mode 100644 index 000000000..3fe9e9af5 --- /dev/null +++ b/latest/cases/01259/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01259/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01259/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01259/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01259/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01259/l3v2/index.heta b/latest/cases/01259/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01259/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01259/model-sbml-l3v2.xml b/latest/cases/01259/model-sbml-l3v2.xml new file mode 100644 index 000000000..23e736102 --- /dev/null +++ b/latest/cases/01259/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + rateOf + p1 + + + + + + + diff --git a/latest/cases/01259/synopsis.txt b/latest/cases/01259/synopsis.txt new file mode 100644 index 000000000..dfa34779e --- /dev/null +++ b/latest/cases/01259/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A rateOf csymbol in a kinetic law. +componentTags: CSymbolRateOf, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A rateOf csymbols is used here in a kinetic law, defining it to be the same as the rate of change of p1. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $rateOf(p1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial value of parameter p1 | $2$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01260/l2v5/index.heta b/latest/cases/01260/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01260/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01260/l3v2/build.log b/latest/cases/01260/l3v2/build.log new file mode 100644 index 000000000..88529aa1d --- /dev/null +++ b/latest/cases/01260/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01260/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01260/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01260/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01260/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01260/l3v2/index.heta b/latest/cases/01260/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01260/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01260/model-sbml-l3v2.xml b/latest/cases/01260/model-sbml-l3v2.xml new file mode 100644 index 000000000..12b713501 --- /dev/null +++ b/latest/cases/01260/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + 1 + + + + + + + + + + time + 5.5 + + + + + + + + rateOf + p1 + + + + + + + + diff --git a/latest/cases/01260/synopsis.txt b/latest/cases/01260/synopsis.txt new file mode 100644 index 000000000..f2ae0648f --- /dev/null +++ b/latest/cases/01260/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A rateOf csymbol in an event assignment. +componentTags: CSymbolRateOf, CSymbolTime, EventNoDelay, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A rateOf csymbols is used here in an event assignment for p2. + +The model contains: +* 2 parameters (p1, p2) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $p2 = rateOf(p1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01261/l2v5/index.heta b/latest/cases/01261/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01261/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01261/l3v2/build.log b/latest/cases/01261/l3v2/build.log new file mode 100644 index 000000000..7060d9970 --- /dev/null +++ b/latest/cases/01261/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01261/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01261/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01261/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01261/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01261/l3v2/index.heta b/latest/cases/01261/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01261/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01261/model-sbml-l3v2.xml b/latest/cases/01261/model-sbml-l3v2.xml new file mode 100644 index 000000000..83d14e7fc --- /dev/null +++ b/latest/cases/01261/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + rateOf + p1 + + + + + + + + + + + + rateOf + p1 + + 0.0105 + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01261/synopsis.txt b/latest/cases/01261/synopsis.txt new file mode 100644 index 000000000..3f3dd8fba --- /dev/null +++ b/latest/cases/01261/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A rateOf csymbol in an event trigger. +componentTags: AssignmentRule, CSymbolRateOf, EventNoDelay, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + A rateOf csymbol is used here in an event trigger that assigns to p2. + +The model contains: +* 3 parameters (p1, p3, p2) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $rateOf(p1) > 0.0105$ | $p2 = 5$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ | +| Assignment | p3 | $rateOf(p1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p3 | $rateOf(p1)$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + diff --git a/latest/cases/01262/l2v5/index.heta b/latest/cases/01262/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01262/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01262/l3v2/heta-code/output.heta b/latest/cases/01262/l3v2/heta-code/output.heta new file mode 100644 index 000000000..be25d2b7e --- /dev/null +++ b/latest/cases/01262/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +p1_proc @Process { actors: = p1, }; +p1_proc := 1; + +p1 @Record { } .= 1; +p2 @Record { } .= 10; +p2 [E0]= 5; +p2 [E1]= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01262/l3v2/index.heta b/latest/cases/01262/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01262/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01262/l3v2/json/output.json b/latest/cases/01262/l3v2/json/output.json new file mode 100644 index 000000000..5ba0df458 --- /dev/null +++ b/latest/cases/01262/l3v2/json/output.json @@ -0,0 +1,44 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "start_": "10", + "E0": "5", + "E1": "3" + } + }, + { + "class": "Process", + "id": "p1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "p1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 5.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01262/model-sbml-l3v2.xml b/latest/cases/01262/model-sbml-l3v2.xml new file mode 100644 index 000000000..50929ec2e --- /dev/null +++ b/latest/cases/01262/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + 1 + + + + + + + + + + time + 5.5 + + + + + + 1.01 + + + + + + 5 + + + + + + + + + + time + 5.5 + + + + + + + rateOf + p1 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01262/output.heta b/latest/cases/01262/output.heta new file mode 100644 index 000000000..9ad364900 --- /dev/null +++ b/latest/cases/01262/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: A rateOf csymbol in an event priority. +componentTags: CSymbolRateOf, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + A rateOf csymbol is used here in an event priority that assigns to p2. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $1.01$ | $p2 = 5$ | +| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + +*/ + + + +t @TimeScale { }; + +p1_proc @Process { actors: = p1, }; +p1_proc := 1; + +p1 @Record { } .= 1; +p2 @Record { } .= 10; +p2 [E0]= 5; +p2 [E1]= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01262/synopsis.txt b/latest/cases/01262/synopsis.txt new file mode 100644 index 000000000..e8162525d --- /dev/null +++ b/latest/cases/01262/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A rateOf csymbol in an event priority. +componentTags: CSymbolRateOf, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + A rateOf csymbol is used here in an event priority that assigns to p2. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $1.01$ | $p2 = 5$ | +| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + diff --git a/latest/cases/01263/l2v5/index.heta b/latest/cases/01263/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01263/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01263/l3v2/build.log b/latest/cases/01263/l3v2/build.log new file mode 100644 index 000000000..139aeb128 --- /dev/null +++ b/latest/cases/01263/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01263/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01263/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01263/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01263/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01263/l3v2/index.heta b/latest/cases/01263/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01263/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01263/model-sbml-l3v2.xml b/latest/cases/01263/model-sbml-l3v2.xml new file mode 100644 index 000000000..3269491d4 --- /dev/null +++ b/latest/cases/01263/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + 1 + + + + + + + + + + time + 4.5 + + + + + + + rateOf + p1 + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01263/synopsis.txt b/latest/cases/01263/synopsis.txt new file mode 100644 index 000000000..2ac5741f0 --- /dev/null +++ b/latest/cases/01263/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A rateOf csymbol in an event delay. +componentTags: CSymbolRateOf, CSymbolTime, EventWithDelay, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A rateOf csymbol is used here in an event delay that assigns to p2. + +The model contains: +* 2 parameters (p1, p2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time > 4.5$ | $rateOf(p1)$ | $p2 = 5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01264/l2v5/index.heta b/latest/cases/01264/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01264/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01264/l3v2/build.log b/latest/cases/01264/l3v2/build.log new file mode 100644 index 000000000..be105afa5 --- /dev/null +++ b/latest/cases/01264/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01264/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01264/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01264/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01264/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01264/l3v2/index.heta b/latest/cases/01264/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01264/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01264/model-sbml-l3v2.xml b/latest/cases/01264/model-sbml-l3v2.xml new file mode 100644 index 000000000..6722aadc3 --- /dev/null +++ b/latest/cases/01264/model-sbml-l3v2.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + rateOf + p1 + + + + + + diff --git a/latest/cases/01264/synopsis.txt b/latest/cases/01264/synopsis.txt new file mode 100644 index 000000000..e6e0d18d1 --- /dev/null +++ b/latest/cases/01264/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: A variable rateOf csymbol in a rate rule. +componentTags: CSymbolRateOf, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + A variable rateOf csymbols is used here in a rate rule, defining the rate of change of p2 the same as the rate of change of p1. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ | +| Rate | p2 | $rateOf(p1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + diff --git a/latest/cases/01265/l2v5/index.heta b/latest/cases/01265/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01265/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01265/l3v2/build.log b/latest/cases/01265/l3v2/build.log new file mode 100644 index 000000000..c699c94f6 --- /dev/null +++ b/latest/cases/01265/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01265/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01265/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01265/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01265/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01265/l3v2/index.heta b/latest/cases/01265/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01265/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01265/model-sbml-l3v2.xml b/latest/cases/01265/model-sbml-l3v2.xml new file mode 100644 index 000000000..0f38417c2 --- /dev/null +++ b/latest/cases/01265/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + + + + + rateOf + p1 + + + + + + + diff --git a/latest/cases/01265/synopsis.txt b/latest/cases/01265/synopsis.txt new file mode 100644 index 000000000..d55910c48 --- /dev/null +++ b/latest/cases/01265/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A variable rateOf csymbol in a kinetic law. +componentTags: CSymbolRateOf, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A variable rateOf csymbol is used here in a kinetic law, defining it to be the same as the rate of change of p1. + +The model contains: +* 1 species (S1) +* 1 parameter (p1) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $rateOf(p1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial value of parameter p1 | $2$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01266/l2v5/index.heta b/latest/cases/01266/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01266/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01266/l3v2/build.log b/latest/cases/01266/l3v2/build.log new file mode 100644 index 000000000..71143dbb1 --- /dev/null +++ b/latest/cases/01266/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01266/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01266/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01266/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01266/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01266/l3v2/index.heta b/latest/cases/01266/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01266/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01266/model-sbml-l3v2.xml b/latest/cases/01266/model-sbml-l3v2.xml new file mode 100644 index 000000000..ea7eb2d9b --- /dev/null +++ b/latest/cases/01266/model-sbml-l3v2.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + + + time + 5.5 + + + + + + + + rateOf + p1 + + + + + + + + diff --git a/latest/cases/01266/synopsis.txt b/latest/cases/01266/synopsis.txt new file mode 100644 index 000000000..7224440fd --- /dev/null +++ b/latest/cases/01266/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A variable rateOf csymbol in an event assignment. +componentTags: CSymbolRateOf, CSymbolTime, EventNoDelay, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +A variable rateOf csymbols is used here in an event assignment for p2. + +The model contains: +* 2 parameters (p1, p2) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $p2 = rateOf(p1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + diff --git a/latest/cases/01267/l2v5/index.heta b/latest/cases/01267/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01267/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01267/l3v2/heta-code/output.heta b/latest/cases/01267/l3v2/heta-code/output.heta new file mode 100644 index 000000000..325cdfba4 --- /dev/null +++ b/latest/cases/01267/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +p1_proc @Process { actors: = p1, }; +p1_proc := 0.01 * p1; + +p1 @Record { } .= 2; +p2 @Record { } .= 10; +p2 [E0]= 5; +p2 [E1]= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01267/l3v2/index.heta b/latest/cases/01267/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01267/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01267/l3v2/json/output.json b/latest/cases/01267/l3v2/json/output.json new file mode 100644 index 000000000..9dfffcc5b --- /dev/null +++ b/latest/cases/01267/l3v2/json/output.json @@ -0,0 +1,44 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "2" + } + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "start_": "10", + "E0": "5", + "E1": "3" + } + }, + { + "class": "Process", + "id": "p1_proc", + "assignments": { + "ode_": "0.01 * p1" + }, + "actors": [ + { + "target": "p1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 5.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01267/model-sbml-l3v2.xml b/latest/cases/01267/model-sbml-l3v2.xml new file mode 100644 index 000000000..2c2d5cb50 --- /dev/null +++ b/latest/cases/01267/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + + + time + 5.5 + + + + + + 0.021 + + + + + + 5 + + + + + + + + + + time + 5.5 + + + + + + + rateOf + p1 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01267/output.heta b/latest/cases/01267/output.heta new file mode 100644 index 000000000..b6baa90a0 --- /dev/null +++ b/latest/cases/01267/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: A variable rateOf csymbol in an event priority. +componentTags: CSymbolRateOf, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A variable rateOf csymbol is used here in an event priority that assigns to p2. At the time the event triggers, the priority is greater than .021, meaning that it fires first, and E0 fires second, leaving the value of p2 at 5. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $0.021$ | $p2 = 5$ | +| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p1_proc @Process { actors: = p1, }; +p1_proc := 0.01 * p1; + +p1 @Record { } .= 2; +p2 @Record { } .= 10; +p2 [E0]= 5; +p2 [E1]= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01267/synopsis.txt b/latest/cases/01267/synopsis.txt new file mode 100644 index 000000000..7d5dfc9da --- /dev/null +++ b/latest/cases/01267/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A variable rateOf csymbol in an event priority. +componentTags: CSymbolRateOf, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A variable rateOf csymbol is used here in an event priority that assigns to p2. At the time the event triggers, the priority is greater than .021, meaning that it fires first, and E0 fires second, leaving the value of p2 at 5. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $0.021$ | $p2 = 5$ | +| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01268/l2v5/index.heta b/latest/cases/01268/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01268/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01268/l3v2/build.log b/latest/cases/01268/l3v2/build.log new file mode 100644 index 000000000..9d800bbfa --- /dev/null +++ b/latest/cases/01268/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01268/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01268/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01268/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01268/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01268/l3v2/index.heta b/latest/cases/01268/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01268/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01268/model-sbml-l3v2.xml b/latest/cases/01268/model-sbml-l3v2.xml new file mode 100644 index 000000000..5e2cbcff5 --- /dev/null +++ b/latest/cases/01268/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + + + time + 5.9 + + + + + + + + 100 + + rateOf + p1 + + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01268/synopsis.txt b/latest/cases/01268/synopsis.txt new file mode 100644 index 000000000..c537e6638 --- /dev/null +++ b/latest/cases/01268/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A variable rateOf csymbol in an event delay. +componentTags: CSymbolRateOf, CSymbolTime, EventWithDelay, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A variable rateOf csymbol is used here in an event delay that assigns to p2. + +The model contains: +* 2 parameters (p1, p2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time > 5.9$ | $100 * rateOf(p1)$ | $p2 = 5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01269/l2v5/index.heta b/latest/cases/01269/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01269/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01269/l3v2/build.log b/latest/cases/01269/l3v2/build.log new file mode 100644 index 000000000..90e932abd --- /dev/null +++ b/latest/cases/01269/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01269/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01269/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01269/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01269/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01269/l3v2/index.heta b/latest/cases/01269/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01269/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01269/model-sbml-l3v2.xml b/latest/cases/01269/model-sbml-l3v2.xml new file mode 100644 index 000000000..123b5a4c2 --- /dev/null +++ b/latest/cases/01269/model-sbml-l3v2.xml @@ -0,0 +1,119 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + rateOf + p1 + + + + + + + + + + + + time + 4.5 + + + + + + + rateOf + p1 + + + + + + 3 + + + + + + + + + rateOf + p1 + + 2 + + + + + + + + + + + time + 4.5 + + + + + + + rateOf + p1 + + + + + + + rateOf + p1 + + + + + + + + + + rateOf + p1 + + 5 + + + + + + + + diff --git a/latest/cases/01269/synopsis.txt b/latest/cases/01269/synopsis.txt new file mode 100644 index 000000000..bfff46ae2 --- /dev/null +++ b/latest/cases/01269/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: A rateOf csymbol used everywhere. +componentTags: CSymbolRateOf, CSymbolTime, Compartment, EventPriority, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +A rateOf csymbol is used in all MathML contexts in the same model. + +The model contains: +* 1 species (S1) +* 2 parameters (p1, p2) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $rateOf(p1)$ |] + + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Delay* | *Event Assignments* | +| _E0 | $time > 4.5$ | $3$ | $rateOf(p1)$ | $p2 = rateOf(p1) + 2$ | +| _E1 | $time > 4.5$ | $rateOf(p1)$ | $rateOf(p1)$ | $p2 = rateOf(p1) + 5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial value of parameter p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01270/l2v5/index.heta b/latest/cases/01270/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01270/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01270/l3v2/build.log b/latest/cases/01270/l3v2/build.log new file mode 100644 index 000000000..132d888d9 --- /dev/null +++ b/latest/cases/01270/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01270/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01270/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01270/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01270/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01270/l3v2/index.heta b/latest/cases/01270/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01270/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01270/model-sbml-l3v2.xml b/latest/cases/01270/model-sbml-l3v2.xml new file mode 100644 index 000000000..462dec2f8 --- /dev/null +++ b/latest/cases/01270/model-sbml-l3v2.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + + + + + rateOf + p1 + + + + + + + + + + + + time + 4.5 + + + + + + + rateOf + p1 + + + + + + 0.02 + + + + + + + + + rateOf + p1 + + 2 + + + + + + + + + + + time + 4.5 + + + + + + + rateOf + p1 + + + + + + + rateOf + p1 + + + + + + + + + + rateOf + p1 + + 5 + + + + + + + + diff --git a/latest/cases/01270/synopsis.txt b/latest/cases/01270/synopsis.txt new file mode 100644 index 000000000..70ab9dcff --- /dev/null +++ b/latest/cases/01270/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: A variable rateOf csymbol in several contexts at once. +componentTags: CSymbolRateOf, CSymbolTime, Compartment, EventPriority, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +A variable rateOf csymbol is used in all valid MathML contexts. + +The model contains: +* 1 species (S1) +* 2 parameters (p1, p2) +* 1 compartment (c) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $rateOf(p1)$ |] + + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Delay* | *Event Assignments* | +| _E0 | $time > 4.5$ | $0.02$ | $rateOf(p1)$ | $p2 = rateOf(p1) + 2$ | +| _E1 | $time > 4.5$ | $rateOf(p1)$ | $rateOf(p1)$ | $p2 = rateOf(p1) + 5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $0.01 * p1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial value of parameter p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'c' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01271/l2v5/index.heta b/latest/cases/01271/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01271/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01271/l3v2/build.log b/latest/cases/01271/l3v2/build.log new file mode 100644 index 000000000..2900fca73 --- /dev/null +++ b/latest/cases/01271/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01271/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01271/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01271/model-sbml-l3v2.xml"... +[error] Heta does not support empty or "foo" elements in FunctionDefinition, when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01271/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01271/l3v2/index.heta b/latest/cases/01271/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01271/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01271/model-sbml-l3v2.xml b/latest/cases/01271/model-sbml-l3v2.xml new file mode 100644 index 000000000..18a6fd873 --- /dev/null +++ b/latest/cases/01271/model-sbml-l3v2.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/latest/cases/01271/synopsis.txt b/latest/cases/01271/synopsis.txt new file mode 100644 index 000000000..24c3cdb1f --- /dev/null +++ b/latest/cases/01271/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: A FunctionDefinition with no MathML. +componentTags: FunctionDefinition, Parameter +testTags: NoMathML +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +An unused FunctionDefinition with no MathML child is present in the model. + +The model contains: +* 1 parameter (p1) +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | foo | | $$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $2$ | constant |] + diff --git a/latest/cases/01272/l2v5/index.heta b/latest/cases/01272/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01272/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01272/l3v2/build.log b/latest/cases/01272/l3v2/build.log new file mode 100644 index 000000000..b186583a3 --- /dev/null +++ b/latest/cases/01272/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01272/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01272/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01272/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 80 +[error] No required "num" property for "p1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01272/l3v2/index.heta b/latest/cases/01272/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01272/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01272/model-sbml-l3v2.xml b/latest/cases/01272/model-sbml-l3v2.xml new file mode 100644 index 000000000..80def18dd --- /dev/null +++ b/latest/cases/01272/model-sbml-l3v2.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 9 + 2 + + + + + + diff --git a/latest/cases/01272/synopsis.txt b/latest/cases/01272/synopsis.txt new file mode 100644 index 000000000..9ea582f5f --- /dev/null +++ b/latest/cases/01272/synopsis.txt @@ -0,0 +1,19 @@ + +category: Test +synopsis: Use of the 'quotient' MathML in an initial assignment. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, L3v2MathML +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +In this model, the 'quotient' MathML symbol is used in an initial assignment. + +The model contains: +* 1 parameter (p1) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $quotient(9, 2)$ | constant |] + diff --git a/latest/cases/01273/l2v5/index.heta b/latest/cases/01273/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01273/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01273/l3v2/build.log b/latest/cases/01273/l3v2/build.log new file mode 100644 index 000000000..55b8ff023 --- /dev/null +++ b/latest/cases/01273/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01273/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01273/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01273/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 80 +[error] No required "num" property for "p1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01273/l3v2/index.heta b/latest/cases/01273/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01273/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01273/model-sbml-l3v2.xml b/latest/cases/01273/model-sbml-l3v2.xml new file mode 100644 index 000000000..fe2011c1d --- /dev/null +++ b/latest/cases/01273/model-sbml-l3v2.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 9 + 2 + + + + + + diff --git a/latest/cases/01273/synopsis.txt b/latest/cases/01273/synopsis.txt new file mode 100644 index 000000000..036d1816d --- /dev/null +++ b/latest/cases/01273/synopsis.txt @@ -0,0 +1,19 @@ + +category: Test +synopsis: Use of the 'rem' MathML in an initial assignment. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, L3v2MathML +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +In this model, the 'rem' MathML symbol is used in an initial assignment. + +The model contains: +* 1 parameter (p1) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $rem(9, 2)$ | constant |] + diff --git a/latest/cases/01274/l2v5/index.heta b/latest/cases/01274/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01274/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01274/l3v2/build.log b/latest/cases/01274/l3v2/build.log new file mode 100644 index 000000000..b25328b1e --- /dev/null +++ b/latest/cases/01274/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01274/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01274/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01274/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 83 +[error] No required "num" property for "p1" of Const. +[error] No required "num" property for "p2" of Const. +[error] No required "num" property for "p3" of Const. +[error] No required "num" property for "p4" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01274/l3v2/index.heta b/latest/cases/01274/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01274/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01274/model-sbml-l3v2.xml b/latest/cases/01274/model-sbml-l3v2.xml new file mode 100644 index 000000000..1711a8b6e --- /dev/null +++ b/latest/cases/01274/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01274/synopsis.txt b/latest/cases/01274/synopsis.txt new file mode 100644 index 000000000..42aa45910 --- /dev/null +++ b/latest/cases/01274/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: Use of the 'implies' MathML in initial assignments. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, L3v2MathML +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the 'implies' MathML symbol is used in an initial assignment. 'Implies' means 'if A is true, then B is also true', or '(not A) or B'. With the automatic translation (in l3v2) of boolean values to numeric values, this means that p1, p3, and p4 are '1' (true), while p2 is '0' (false). + +The model contains: +* 4 parameters (p1, p2, p3, p4) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $implies(true, true)$ | constant | +| Initial value of parameter p2 | $implies(true, false)$ | constant | +| Initial value of parameter p3 | $implies(false, true)$ | constant | +| Initial value of parameter p4 | $implies(false, false)$ | constant |] + diff --git a/latest/cases/01275/l2v5/index.heta b/latest/cases/01275/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01275/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01275/l3v2/build.log b/latest/cases/01275/l3v2/build.log new file mode 100644 index 000000000..e32d0dcb4 --- /dev/null +++ b/latest/cases/01275/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01275/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01275/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01275/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 82 +[error] No required "num" property for "p1" of Const. +[error] No required "num" property for "p2" of Const. +[error] No required "num" property for "p3" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01275/l3v2/index.heta b/latest/cases/01275/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01275/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01275/model-sbml-l3v2.xml b/latest/cases/01275/model-sbml-l3v2.xml new file mode 100644 index 000000000..74d6432e4 --- /dev/null +++ b/latest/cases/01275/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + -1 + -10 + + + + + + + + 30 + + + + + + + + 2 + 200 + 20 + + + + + + diff --git a/latest/cases/01275/synopsis.txt b/latest/cases/01275/synopsis.txt new file mode 100644 index 000000000..cdabc5d4f --- /dev/null +++ b/latest/cases/01275/synopsis.txt @@ -0,0 +1,21 @@ + +category: Test +synopsis: Use of the 'max' MathML in initial assignments. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, L3v2MathML +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +Three tests of the 'max' MathML construct. + +The model contains: +* 3 parameters (p1, p2, p3) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $max(-1, -10)$ | constant | +| Initial value of parameter p2 | $max(30)$ | constant | +| Initial value of parameter p3 | $max(2, 200, 20)$ | constant |] + diff --git a/latest/cases/01276/l2v5/index.heta b/latest/cases/01276/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01276/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01276/l3v2/build.log b/latest/cases/01276/l3v2/build.log new file mode 100644 index 000000000..42c9fe329 --- /dev/null +++ b/latest/cases/01276/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01276/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01276/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01276/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 82 +[error] No required "num" property for "p1" of Const. +[error] No required "num" property for "p2" of Const. +[error] No required "num" property for "p3" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01276/l3v2/index.heta b/latest/cases/01276/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01276/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01276/model-sbml-l3v2.xml b/latest/cases/01276/model-sbml-l3v2.xml new file mode 100644 index 000000000..36526aceb --- /dev/null +++ b/latest/cases/01276/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + -1 + -10 + + + + + + + + 30 + + + + + + + + 20 + 200 + 2 + 2000 + + + + + + diff --git a/latest/cases/01276/synopsis.txt b/latest/cases/01276/synopsis.txt new file mode 100644 index 000000000..543b0439f --- /dev/null +++ b/latest/cases/01276/synopsis.txt @@ -0,0 +1,21 @@ + +category: Test +synopsis: Use of the 'min' MathML in initial assignments. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned, L3v2MathML +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +Three tests of the 'min' MathML construct. + +The model contains: +* 3 parameters (p1, p2, p3) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $min(-1, -10)$ | constant | +| Initial value of parameter p2 | $min(30)$ | constant | +| Initial value of parameter p3 | $min(20, 200, 2, 2000)$ | constant |] + diff --git a/latest/cases/01277/l2v5/index.heta b/latest/cases/01277/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01277/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01277/l3v2/build.log b/latest/cases/01277/l3v2/build.log new file mode 100644 index 000000000..6f5f0d16d --- /dev/null +++ b/latest/cases/01277/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01277/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01277/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01277/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 80 +[error] FunctionDef "quotient" is not found as expected here: p1 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01277/l3v2/index.heta b/latest/cases/01277/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01277/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01277/model-sbml-l3v2.xml b/latest/cases/01277/model-sbml-l3v2.xml new file mode 100644 index 000000000..a1ff8570e --- /dev/null +++ b/latest/cases/01277/model-sbml-l3v2.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + time + 2 + + + + + + diff --git a/latest/cases/01277/synopsis.txt b/latest/cases/01277/synopsis.txt new file mode 100644 index 000000000..584c27a27 --- /dev/null +++ b/latest/cases/01277/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Use of the 'quotient' MathML in an assignment rule. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +In this model, the 'quotient' MathML symbol is used in an assignment rule. + +The model contains: +* 1 parameter (p1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $quotient(time, 2)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $quotient(time, 2)$ | variable |] + diff --git a/latest/cases/01278/l2v5/index.heta b/latest/cases/01278/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01278/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01278/l3v2/build.log b/latest/cases/01278/l3v2/build.log new file mode 100644 index 000000000..9a2dd0de1 --- /dev/null +++ b/latest/cases/01278/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01278/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01278/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01278/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 80 +[error] FunctionDef "rem" is not found as expected here: p1 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01278/l3v2/index.heta b/latest/cases/01278/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01278/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01278/model-sbml-l3v2.xml b/latest/cases/01278/model-sbml-l3v2.xml new file mode 100644 index 000000000..63cfc51bc --- /dev/null +++ b/latest/cases/01278/model-sbml-l3v2.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + time + 2 + + + + + + diff --git a/latest/cases/01278/synopsis.txt b/latest/cases/01278/synopsis.txt new file mode 100644 index 000000000..2d94dc4e7 --- /dev/null +++ b/latest/cases/01278/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Use of the 'rem' MathML in an assignment rule. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +In this model, the 'rem' MathML symbol is used in an assignment rule. + +The model contains: +* 1 parameter (p1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $rem(time, 2)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $rem(time, 2)$ | variable |] + diff --git a/latest/cases/01279/l2v5/index.heta b/latest/cases/01279/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01279/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01279/l3v2/build.log b/latest/cases/01279/l3v2/build.log new file mode 100644 index 000000000..d43b6c84a --- /dev/null +++ b/latest/cases/01279/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01279/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01279/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01279/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 83 +[error] FunctionDef "implies" is not found as expected here: p1 { math: undefined }; +[error] FunctionDef "implies" is not found as expected here: p2 { math: undefined }; +[error] FunctionDef "implies" is not found as expected here: p3 { math: undefined }; +[error] FunctionDef "implies" is not found as expected here: p4 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01279/l3v2/index.heta b/latest/cases/01279/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01279/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01279/model-sbml-l3v2.xml b/latest/cases/01279/model-sbml-l3v2.xml new file mode 100644 index 000000000..4f4e8dd11 --- /dev/null +++ b/latest/cases/01279/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + time + 5.5 + + + + time + 2.5 + + + + + + + + + + + time + 5.5 + + + + time + 2.5 + + + + + + + + + + + time + 5.5 + + + + time + 2.5 + + + + + + + + + + + time + 5.5 + + + + time + 2.5 + + + + + + + diff --git a/latest/cases/01279/synopsis.txt b/latest/cases/01279/synopsis.txt new file mode 100644 index 000000000..cb4d42899 --- /dev/null +++ b/latest/cases/01279/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Use of the 'implies' MathML in assignment rules. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the 'implies' MathML symbol is used in assignment rules. 'Implies' means 'if A is true, then B is also true', or '(not A) or B'. With the automatic translation (in l3v2) of boolean values to numeric values, this means that p1 is always 1 (true); p2 becomes 0 (false) halfway through the run; p3 becomes 0 only from 2.5 5.5), (time > 2.5))$ | +| Assignment | p2 | $implies((time > 5.5), (time < 2.5))$ | +| Assignment | p3 | $implies((time < 5.5), (time > 2.5))$ | +| Assignment | p4 | $implies((time < 5.5), (time < 2.5))$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $implies((time > 5.5), (time > 2.5))$ | variable | +| Initial value of parameter p2 | $implies((time > 5.5), (time < 2.5))$ | variable | +| Initial value of parameter p3 | $implies((time < 5.5), (time > 2.5))$ | variable | +| Initial value of parameter p4 | $implies((time < 5.5), (time < 2.5))$ | variable |] + diff --git a/latest/cases/01280/l2v5/index.heta b/latest/cases/01280/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01280/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01280/l3v2/heta-code/output.heta b/latest/cases/01280/l3v2/heta-code/output.heta new file mode 100644 index 000000000..54c6fca58 --- /dev/null +++ b/latest/cases/01280/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +p1 @Record { }; +p1 := max((-5), (-t)); +p2 @Record { }; +p2 := max(t); +p3 @Record { }; +p3 := max(5, t); + diff --git a/latest/cases/01280/l3v2/index.heta b/latest/cases/01280/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01280/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01280/l3v2/json/output.json b/latest/cases/01280/l3v2/json/output.json new file mode 100644 index 000000000..a2f1a6aa2 --- /dev/null +++ b/latest/cases/01280/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "ode_": "max((-5), (-t))" + } + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "ode_": "max(t)" + } + }, + { + "class": "Record", + "id": "p3", + "assignments": { + "ode_": "max(5, t)" + } + } +] \ No newline at end of file diff --git a/latest/cases/01280/model-sbml-l3v2.xml b/latest/cases/01280/model-sbml-l3v2.xml new file mode 100644 index 000000000..f4f430c71 --- /dev/null +++ b/latest/cases/01280/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + -5 + + + time + + + + + + + + + time + + + + + + + + 5 + time + + + + + + diff --git a/latest/cases/01280/output.heta b/latest/cases/01280/output.heta new file mode 100644 index 000000000..dc01790b2 --- /dev/null +++ b/latest/cases/01280/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Use of the 'max' MathML in assignment rules. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +Three tests of the 'max' MathML construct in assignment rules. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $max(-5, -time)$ | +| Assignment | p2 | $max(time)$ | +| Assignment | p3 | $max(5, time)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $max(-5, -time)$ | variable | +| Initial value of parameter p2 | $max(time)$ | variable | +| Initial value of parameter p3 | $max(5, time)$ | variable |] + +*/ + + + +t @TimeScale { }; + +p1 @Record { }; +p1 := max((-5), (-t)); +p2 @Record { }; +p2 := max(t); +p3 @Record { }; +p3 := max(5, t); + diff --git a/latest/cases/01280/synopsis.txt b/latest/cases/01280/synopsis.txt new file mode 100644 index 000000000..bb898f456 --- /dev/null +++ b/latest/cases/01280/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Use of the 'max' MathML in assignment rules. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +Three tests of the 'max' MathML construct in assignment rules. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $max(-5, -time)$ | +| Assignment | p2 | $max(time)$ | +| Assignment | p3 | $max(5, time)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $max(-5, -time)$ | variable | +| Initial value of parameter p2 | $max(time)$ | variable | +| Initial value of parameter p3 | $max(5, time)$ | variable |] + diff --git a/latest/cases/01281/l2v5/index.heta b/latest/cases/01281/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01281/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01281/l3v2/heta-code/output.heta b/latest/cases/01281/l3v2/heta-code/output.heta new file mode 100644 index 000000000..06d3818e0 --- /dev/null +++ b/latest/cases/01281/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +p1 @Record { }; +p1 := min((-5), (-t)); +p2 @Record { }; +p2 := min(t); +p3 @Record { }; +p3 := min(5, t, 7); + diff --git a/latest/cases/01281/l3v2/index.heta b/latest/cases/01281/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01281/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01281/l3v2/json/output.json b/latest/cases/01281/l3v2/json/output.json new file mode 100644 index 000000000..5d32d863c --- /dev/null +++ b/latest/cases/01281/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "ode_": "min((-5), (-t))" + } + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "ode_": "min(t)" + } + }, + { + "class": "Record", + "id": "p3", + "assignments": { + "ode_": "min(5, t, 7)" + } + } +] \ No newline at end of file diff --git a/latest/cases/01281/model-sbml-l3v2.xml b/latest/cases/01281/model-sbml-l3v2.xml new file mode 100644 index 000000000..1395aceee --- /dev/null +++ b/latest/cases/01281/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + -5 + + + time + + + + + + + + + time + + + + + + + + 5 + time + 7 + + + + + + diff --git a/latest/cases/01281/output.heta b/latest/cases/01281/output.heta new file mode 100644 index 000000000..54f6c3211 --- /dev/null +++ b/latest/cases/01281/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Use of the 'min' MathML in assignment rules. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +Three tests of the 'min' MathML construct in assignment rules. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $min(-5, -time)$ | +| Assignment | p2 | $min(time)$ | +| Assignment | p3 | $min(5, time, 7)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $min(-5, time)$ | variable | +| Initial value of parameter p2 | $min(time)$ | variable | +| Initial value of parameter p3 | $min(5, time, 7)$ | variable |] + +*/ + + + +t @TimeScale { }; + +p1 @Record { }; +p1 := min((-5), (-t)); +p2 @Record { }; +p2 := min(t); +p3 @Record { }; +p3 := min(5, t, 7); + diff --git a/latest/cases/01281/synopsis.txt b/latest/cases/01281/synopsis.txt new file mode 100644 index 000000000..fadf53864 --- /dev/null +++ b/latest/cases/01281/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Use of the 'min' MathML in assignment rules. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +Three tests of the 'min' MathML construct in assignment rules. + +The model contains: +* 3 parameters (p1, p2, p3) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $min(-5, -time)$ | +| Assignment | p2 | $min(time)$ | +| Assignment | p3 | $min(5, time, 7)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $min(-5, time)$ | variable | +| Initial value of parameter p2 | $min(time)$ | variable | +| Initial value of parameter p3 | $min(5, time, 7)$ | variable |] + diff --git a/latest/cases/01282/l2v5/index.heta b/latest/cases/01282/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01282/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01282/l3v2/build.log b/latest/cases/01282/l3v2/build.log new file mode 100644 index 000000000..fcb1ac2be --- /dev/null +++ b/latest/cases/01282/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01282/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01282/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01282/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 82 +[error] No required "num" property for "p1" of Const. +[error] No required "num" property for "p2" of Const. +[error] No required "num" property for "p3" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01282/l3v2/index.heta b/latest/cases/01282/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01282/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01282/model-sbml-l3v2.xml b/latest/cases/01282/model-sbml-l3v2.xml new file mode 100644 index 000000000..d7eea92a4 --- /dev/null +++ b/latest/cases/01282/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + 0 + 5 + + + 1 + + + + + + + + + + + + 0 + 0.0 + + + + + + + + + 0 + + + 1 + 1 + + + + 0 + 3 + + + + + + + diff --git a/latest/cases/01282/synopsis.txt b/latest/cases/01282/synopsis.txt new file mode 100644 index 000000000..7525231ce --- /dev/null +++ b/latest/cases/01282/synopsis.txt @@ -0,0 +1,21 @@ + +category: Test +synopsis: Use of numbers in boolean contexts. +componentTags: InitialAssignment, Parameter +testTags: BoolNumericSwap, InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +Three initial assignments that use numeric valus in Boolean contexts. + +The model contains: +* 3 parameters (p1, p2, p3) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $piecewise(0, 5, 1)$ | constant | +| Initial value of parameter p2 | $true && (0 || 0.0)$ | constant | +| Initial value of parameter p3 | $0 || (1 - 1) || (0^3)$ | constant |] + diff --git a/latest/cases/01283/l2v5/index.heta b/latest/cases/01283/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01283/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01283/l3v2/build.log b/latest/cases/01283/l3v2/build.log new file mode 100644 index 000000000..af049f9e7 --- /dev/null +++ b/latest/cases/01283/l3v2/build.log @@ -0,0 +1,13 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01283/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01283/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01283/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 84 +[error] No required "num" property for "p1" of Const. +[error] No required "num" property for "p2" of Const. +[error] No required "num" property for "p3" of Const. +[error] No required "num" property for "p4" of Const. +[error] No required "num" property for "p5" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01283/l3v2/index.heta b/latest/cases/01283/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01283/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01283/model-sbml-l3v2.xml b/latest/cases/01283/model-sbml-l3v2.xml new file mode 100644 index 000000000..d06f6ae3f --- /dev/null +++ b/latest/cases/01283/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 3 + + + + + + + + + + + 5 + + + + + + 2 + + + 2 + + + + + + + diff --git a/latest/cases/01283/synopsis.txt b/latest/cases/01283/synopsis.txt new file mode 100644 index 000000000..4bd95ba86 --- /dev/null +++ b/latest/cases/01283/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: Use of numbers in boolean contexts. +componentTags: InitialAssignment, Parameter +testTags: BoolNumericSwap, InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +Three initial assignments that use numeric valus in Boolean contexts. + +The model contains: +* 5 parameters (p1, p2, p3, p4, p5) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $piecewise(false, true, true)$ | constant | +| Initial value of parameter p2 | $true$ | constant | +| Initial value of parameter p3 | $false$ | constant | +| Initial value of parameter p4 | $true + 3$ | constant | +| Initial value of parameter p5 | $false / 5 - (2 * true)^2$ | constant |] + diff --git a/latest/cases/01284/l2v5/index.heta b/latest/cases/01284/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01284/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01284/l3v2/build.log b/latest/cases/01284/l3v2/build.log new file mode 100644 index 000000000..9650e5a79 --- /dev/null +++ b/latest/cases/01284/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01284/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01284/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01284/model-sbml-l3v2.xml"... +[error] DSwitcher trigger "E0" should be a boolean expression. +[info] Setting references in elements, total length 81 +[error] No required "trigger" property for "E0" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01284/l3v2/index.heta b/latest/cases/01284/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01284/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01284/model-sbml-l3v2.xml b/latest/cases/01284/model-sbml-l3v2.xml new file mode 100644 index 000000000..09bfb8bff --- /dev/null +++ b/latest/cases/01284/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + 3 + + + + + + 2 + + + + + + + diff --git a/latest/cases/01284/synopsis.txt b/latest/cases/01284/synopsis.txt new file mode 100644 index 000000000..9e3cea63b --- /dev/null +++ b/latest/cases/01284/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Use of a number in a trigger. +componentTags: EventNoDelay, Parameter +testTags: BoolNumericSwap, EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + The trigger for this event is simply '3', which is always 'true' in a Boolean context. Because the event's initialValue is 'false', this results in the event triggering at t0. + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| _E0 | $3$ | false | $p1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | variable |] + diff --git a/latest/cases/01285/l2v5/index.heta b/latest/cases/01285/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01285/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01285/l3v2/build.log b/latest/cases/01285/l3v2/build.log new file mode 100644 index 000000000..70557ed83 --- /dev/null +++ b/latest/cases/01285/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01285/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01285/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01285/model-sbml-l3v2.xml"... +[error] Record assignments "p1" should be a numeric expression. +[info] Setting references in elements, total length 81 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01285/l3v2/index.heta b/latest/cases/01285/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01285/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01285/model-sbml-l3v2.xml b/latest/cases/01285/model-sbml-l3v2.xml new file mode 100644 index 000000000..a681b769f --- /dev/null +++ b/latest/cases/01285/model-sbml-l3v2.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + time + 5.5 + + + + + + + + + + + + + + diff --git a/latest/cases/01285/synopsis.txt b/latest/cases/01285/synopsis.txt new file mode 100644 index 000000000..28474dc65 --- /dev/null +++ b/latest/cases/01285/synopsis.txt @@ -0,0 +1,25 @@ + +category: Test +synopsis: Use of a Boolean in an event assignment. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: BoolNumericSwap, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +This event assigns a value of 'true' to the parameter p1. + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 5.5$ | $p1 = true$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | variable |] + diff --git a/latest/cases/01286/l2v5/index.heta b/latest/cases/01286/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01286/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01286/l3v2/heta-code/output.heta b/latest/cases/01286/l3v2/heta-code/output.heta new file mode 100644 index 000000000..679fa5f1c --- /dev/null +++ b/latest/cases/01286/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +p1 @Record { } .= 5; +p1 [E0]= 10; +p1 [E1]= 20; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01286/l3v2/index.heta b/latest/cases/01286/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01286/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01286/l3v2/json/output.json b/latest/cases/01286/l3v2/json/output.json new file mode 100644 index 000000000..0ba4dcc14 --- /dev/null +++ b/latest/cases/01286/l3v2/json/output.json @@ -0,0 +1,24 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "5", + "E0": "10", + "E1": "20" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 5.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01286/model-sbml-l3v2.xml b/latest/cases/01286/model-sbml-l3v2.xml new file mode 100644 index 000000000..79bc32cae --- /dev/null +++ b/latest/cases/01286/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + time + 5.5 + + + + + + + + + + + + 10 + + + + + + + + + + time + 5.5 + + + + + + + + + + + + 20 + + + + + + + diff --git a/latest/cases/01286/output.heta b/latest/cases/01286/output.heta new file mode 100644 index 000000000..31284e342 --- /dev/null +++ b/latest/cases/01286/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Use of a Boolean in an event priority. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: BoolNumericSwap, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The two events have priorities of 'true' and 'false', causing the 'true' priority to fire first. + +The model contains: +* 1 parameter (p1) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $true$ | $p1 = 10$ | +| E1 | $time > 5.5$ | $false$ | $p1 = 20$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p1 @Record { } .= 5; +p1 [E0]= 10; +p1 [E1]= 20; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01286/synopsis.txt b/latest/cases/01286/synopsis.txt new file mode 100644 index 000000000..161cfb7ef --- /dev/null +++ b/latest/cases/01286/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Use of a Boolean in an event priority. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: BoolNumericSwap, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The two events have priorities of 'true' and 'false', causing the 'true' priority to fire first. + +The model contains: +* 1 parameter (p1) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $true$ | $p1 = 10$ | +| E1 | $time > 5.5$ | $false$ | $p1 = 20$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01287/l2v5/index.heta b/latest/cases/01287/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01287/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01287/l3v2/build.log b/latest/cases/01287/l3v2/build.log new file mode 100644 index 000000000..a1813eaa2 --- /dev/null +++ b/latest/cases/01287/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01287/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01287/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01287/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01287/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01287/l3v2/index.heta b/latest/cases/01287/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01287/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01287/model-sbml-l3v2.xml b/latest/cases/01287/model-sbml-l3v2.xml new file mode 100644 index 000000000..1eff59f4f --- /dev/null +++ b/latest/cases/01287/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + time + 5.5 + + + + + + + + + + + + 10 + + + + + + + + + + time + 5.5 + + + + + + + + + + + + 20 + + + + + + + diff --git a/latest/cases/01287/synopsis.txt b/latest/cases/01287/synopsis.txt new file mode 100644 index 000000000..9582b39c5 --- /dev/null +++ b/latest/cases/01287/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Use of a Boolean in event delays. +componentTags: CSymbolTime, EventWithDelay, Parameter +testTags: BoolNumericSwap, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The two events have delays of 'true' and 'false', causing the 'false' delay to fire first. + +The model contains: +* 1 parameter (p1) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time > 5.5$ | $true$ | $p1 = 10$ | +| E1 | $time > 5.5$ | $false$ | $p1 = 20$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01288/l2v5/index.heta b/latest/cases/01288/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01288/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01288/l3v2/build.log b/latest/cases/01288/l3v2/build.log new file mode 100644 index 000000000..aba53d24b --- /dev/null +++ b/latest/cases/01288/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01288/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01288/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01288/model-sbml-l3v2.xml"... +[error] Record assignments "J0" should be a numeric expression. +[error] Record assignments "J1" should be a numeric expression. +[info] Setting references in elements, total length 83 +[error] Record "J0" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "J1" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01288/l3v2/index.heta b/latest/cases/01288/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01288/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01288/model-sbml-l3v2.xml b/latest/cases/01288/model-sbml-l3v2.xml new file mode 100644 index 000000000..3a59a7e21 --- /dev/null +++ b/latest/cases/01288/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01288/synopsis.txt b/latest/cases/01288/synopsis.txt new file mode 100644 index 000000000..42df55f47 --- /dev/null +++ b/latest/cases/01288/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Use of a Boolean in kinetic laws. +componentTags: Compartment, Reaction, Species +testTags: Amount, BoolNumericSwap +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The two reactions have kinetic laws of 'true' and 'false', causing the former to have a rate of 1, and the latter a rate of 0. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> | $false$ | +| J1: -> S1 | $true$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01289/l2v5/index.heta b/latest/cases/01289/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01289/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01289/l3v2/build.log b/latest/cases/01289/l3v2/build.log new file mode 100644 index 000000000..30d762754 --- /dev/null +++ b/latest/cases/01289/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01289/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01289/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01289/model-sbml-l3v2.xml"... +[error] Function math "gt5" should be a numeric expression. +[info] Setting references in elements, total length 81 +[error] No required "num" property for "p1" of Const. +[error] No required "num" property for "p2" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01289/l3v2/index.heta b/latest/cases/01289/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01289/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01289/model-sbml-l3v2.xml b/latest/cases/01289/model-sbml-l3v2.xml new file mode 100644 index 000000000..fccd62405 --- /dev/null +++ b/latest/cases/01289/model-sbml-l3v2.xml @@ -0,0 +1,44 @@ + + + + + + + + + + x + + + + x + 5 + + + + + + + + + + + + + + gt5 + 3 + + + + + + + gt5 + 8 + + + + + + diff --git a/latest/cases/01289/synopsis.txt b/latest/cases/01289/synopsis.txt new file mode 100644 index 000000000..714bd4ae7 --- /dev/null +++ b/latest/cases/01289/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Use of a Boolean in a function definition. +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: BoolNumericSwap, InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The function definition returns 'true' if the passed-in argument is greater than 5, and 'false' otherwise. This function is used to set the initial assignment of two parameters. + +The model contains: +* 2 parameters (p1, p2) +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | gt5 | x | $x > 5$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $gt5(3)$ | constant | +| Initial value of parameter p2 | $gt5(8)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01290/l2v5/index.heta b/latest/cases/01290/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01290/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01290/l3v2/build.log b/latest/cases/01290/l3v2/build.log new file mode 100644 index 000000000..1cf81e072 --- /dev/null +++ b/latest/cases/01290/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01290/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01290/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01290/model-sbml-l3v2.xml"... +[error] Record assignments "p1_proc" should be a numeric expression. +[error] Record assignments "p2_proc" should be a numeric expression. +[info] Setting references in elements, total length 83 +[error] Record "p1_proc" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "p2_proc" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01290/l3v2/index.heta b/latest/cases/01290/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01290/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01290/model-sbml-l3v2.xml b/latest/cases/01290/model-sbml-l3v2.xml new file mode 100644 index 000000000..a524297f9 --- /dev/null +++ b/latest/cases/01290/model-sbml-l3v2.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01290/synopsis.txt b/latest/cases/01290/synopsis.txt new file mode 100644 index 000000000..528604460 --- /dev/null +++ b/latest/cases/01290/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Use of a Boolean in rate rules. +componentTags: Parameter, RateRule +testTags: BoolNumericSwap, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The two rate rules have values of 'true' and 'false', yielding a rate of 1 for the first, and 0 for the second. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $true$ | +| Rate | p2 | $false$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01291/l2v5/index.heta b/latest/cases/01291/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01291/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01291/l3v2/build.log b/latest/cases/01291/l3v2/build.log new file mode 100644 index 000000000..1f99cc505 --- /dev/null +++ b/latest/cases/01291/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01291/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01291/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01291/model-sbml-l3v2.xml"... +[error] Record assignments "p1" should be a numeric expression. +[error] Record assignments "p2" should be a numeric expression. +[info] Setting references in elements, total length 81 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01291/l3v2/index.heta b/latest/cases/01291/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01291/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01291/model-sbml-l3v2.xml b/latest/cases/01291/model-sbml-l3v2.xml new file mode 100644 index 000000000..630e2c80e --- /dev/null +++ b/latest/cases/01291/model-sbml-l3v2.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01291/synopsis.txt b/latest/cases/01291/synopsis.txt new file mode 100644 index 000000000..e00e6616e --- /dev/null +++ b/latest/cases/01291/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Use of a Boolean in assignment rules. +componentTags: AssignmentRule, Parameter +testTags: BoolNumericSwap, InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The two assignment rules have values of 'true' and 'false', yielding values of 1 for the first, and 0 for the second. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $true$ | +| Assignment | p2 | $false$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $true$ | variable | +| Initial value of parameter p2 | $false$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01292/l2v5/index.heta b/latest/cases/01292/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01292/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01292/l3v2/build.log b/latest/cases/01292/l3v2/build.log new file mode 100644 index 000000000..119efdb79 --- /dev/null +++ b/latest/cases/01292/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01292/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01292/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01292/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01292/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01292/l3v2/index.heta b/latest/cases/01292/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01292/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01292/model-sbml-l3v2.xml b/latest/cases/01292/model-sbml-l3v2.xml new file mode 100644 index 000000000..7e9567c16 --- /dev/null +++ b/latest/cases/01292/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + p1 + + + + + + + + + p2 + + + + + + + diff --git a/latest/cases/01292/synopsis.txt b/latest/cases/01292/synopsis.txt new file mode 100644 index 000000000..1c4906725 --- /dev/null +++ b/latest/cases/01292/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Use of a Boolean in algebraic rules. +componentTags: AlgebraicRule, Parameter +testTags: BoolNumericSwap, InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The two algebraic rules have values of 'true' and 'false' in them. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $p1 - true$ | +| Algebraic | $0$ | $p2 - false$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $unknown$ | variable | +| Initial value of parameter p2 | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01293/l2v5/index.heta b/latest/cases/01293/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01293/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01293/l3v2/build.log b/latest/cases/01293/l3v2/build.log new file mode 100644 index 000000000..7aa344771 --- /dev/null +++ b/latest/cases/01293/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01293/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01293/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01293/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01293/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01293/l3v2/index.heta b/latest/cases/01293/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01293/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01293/model-sbml-l3v2.xml b/latest/cases/01293/model-sbml-l3v2.xml new file mode 100644 index 000000000..63b8a88bf --- /dev/null +++ b/latest/cases/01293/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + 0.01 + S1 + + + + + + + + + + + + + + 100 + + rateOf + S1 + + + 1.05 + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01293/synopsis.txt b/latest/cases/01293/synopsis.txt new file mode 100644 index 000000000..1d0a6ce27 --- /dev/null +++ b/latest/cases/01293/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A rateOf csymbol in an event trigger. +componentTags: CSymbolRateOf, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +A rateOf csymbol is used here in an event trigger that assigns to p2. This model is the same as model 01261, with S1 changing as a species in a reaction, instead of in a rate rule. + +The model contains: +* 1 species (S1) +* 1 parameter (p2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $0.01 * S1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $(100 * rateOf(S1)) > 1.05$ | $p2 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01294/l2v5/index.heta b/latest/cases/01294/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01294/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01294/l3v2/heta-code/output.heta b/latest/cases/01294/l3v2/heta-code/output.heta new file mode 100644 index 000000000..954ca7613 --- /dev/null +++ b/latest/cases/01294/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +p1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = p1, }; +J0 := 1; + +p2 @Record { } .= 10; +p2 [E0]= 5; +p2 [E1]= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01294/l3v2/index.heta b/latest/cases/01294/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01294/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01294/l3v2/json/output.json b/latest/cases/01294/l3v2/json/output.json new file mode 100644 index 000000000..98d6ce7d9 --- /dev/null +++ b/latest/cases/01294/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "p1", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "p1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "start_": "10", + "E0": "5", + "E1": "3" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 5.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01294/model-sbml-l3v2.xml b/latest/cases/01294/model-sbml-l3v2.xml new file mode 100644 index 000000000..b8688fcf1 --- /dev/null +++ b/latest/cases/01294/model-sbml-l3v2.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + time + 5.5 + + + + + + 1.01 + + + + + + 5 + + + + + + + + + + time + 5.5 + + + + + + + rateOf + p1 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01294/output.heta b/latest/cases/01294/output.heta new file mode 100644 index 000000000..98c123c94 --- /dev/null +++ b/latest/cases/01294/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: A rateOf csymbol in an event priority. +componentTags: CSymbolRateOf, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + A rateOf csymbol is used here in an event priority that assigns to p2. This is exactly the same model as 01262, with p1 changing as a species in a reaction, instead of in a rate rule. + +The model contains: +* 1 species (p1) +* 1 parameter (p2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> p1 | $1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $1.01$ | $p2 = 5$ | +| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species p1 | $1$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +p1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = p1, }; +J0 := 1; + +p2 @Record { } .= 10; +p2 [E0]= 5; +p2 [E1]= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01294/synopsis.txt b/latest/cases/01294/synopsis.txt new file mode 100644 index 000000000..5a1b79e2d --- /dev/null +++ b/latest/cases/01294/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A rateOf csymbol in an event priority. +componentTags: CSymbolRateOf, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + A rateOf csymbol is used here in an event priority that assigns to p2. This is exactly the same model as 01262, with p1 changing as a species in a reaction, instead of in a rate rule. + +The model contains: +* 1 species (p1) +* 1 parameter (p2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> p1 | $1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $1.01$ | $p2 = 5$ | +| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species p1 | $1$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01295/l2v5/index.heta b/latest/cases/01295/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01295/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01295/l3v2/build.log b/latest/cases/01295/l3v2/build.log new file mode 100644 index 000000000..15937da6b --- /dev/null +++ b/latest/cases/01295/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01295/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01295/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01295/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01295/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01295/l3v2/index.heta b/latest/cases/01295/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01295/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01295/model-sbml-l3v2.xml b/latest/cases/01295/model-sbml-l3v2.xml new file mode 100644 index 000000000..8fe29d143 --- /dev/null +++ b/latest/cases/01295/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + time + 4.5 + + + + + + + rateOf + p1 + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01295/synopsis.txt b/latest/cases/01295/synopsis.txt new file mode 100644 index 000000000..d2acafce4 --- /dev/null +++ b/latest/cases/01295/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A rateOf csymbol in an event delay. +componentTags: CSymbolRateOf, CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + A rateOf csymbol is used here in an event delay that assigns to p2. This is exactly the same model as 01263, with p1 changing as a species in a reaction, instead of in a rate rule. + +The model contains: +* 1 species (p1) +* 1 parameter (p2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> p1 | $1$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time > 4.5$ | $rateOf(p1)$ | $p2 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species p1 | $1$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01296/l2v5/index.heta b/latest/cases/01296/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01296/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01296/l3v2/build.log b/latest/cases/01296/l3v2/build.log new file mode 100644 index 000000000..b6b073ff2 --- /dev/null +++ b/latest/cases/01296/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01296/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01296/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01296/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01296/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01296/l3v2/index.heta b/latest/cases/01296/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01296/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01296/model-sbml-l3v2.xml b/latest/cases/01296/model-sbml-l3v2.xml new file mode 100644 index 000000000..f3032677e --- /dev/null +++ b/latest/cases/01296/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + + + + + + + rateOf + p1 + + + + + + + diff --git a/latest/cases/01296/synopsis.txt b/latest/cases/01296/synopsis.txt new file mode 100644 index 000000000..cc0ac001e --- /dev/null +++ b/latest/cases/01296/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A variable rateOf csymbol in a kinetic law. +componentTags: CSymbolRateOf, Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + A variable rateOf csymbols is used here in a kinetic law, defining the rate of change of p2 the same as the rate of change of p1. This is exactly the same model as 01264, with p1 and p2 changing as species in reactions, instead of in a rate rule. + +The model contains: +* 2 species (p1, p2) +* 1 compartment (C) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> p1 | $0.01 * p1$ | +| J1: -> p2 | $rateOf(p1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species p1 | $2$ | variable | +| Initial concentration of species p2 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01297/l2v5/index.heta b/latest/cases/01297/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01297/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01297/l3v2/build.log b/latest/cases/01297/l3v2/build.log new file mode 100644 index 000000000..c97bcfed0 --- /dev/null +++ b/latest/cases/01297/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01297/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01297/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01297/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01297/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01297/l3v2/index.heta b/latest/cases/01297/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01297/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01297/model-sbml-l3v2.xml b/latest/cases/01297/model-sbml-l3v2.xml new file mode 100644 index 000000000..8f5e8cfcc --- /dev/null +++ b/latest/cases/01297/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + + + + time + 5.5 + + + + + + + + rateOf + p1 + + + + + + + + diff --git a/latest/cases/01297/synopsis.txt b/latest/cases/01297/synopsis.txt new file mode 100644 index 000000000..6c185be9f --- /dev/null +++ b/latest/cases/01297/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A variable rateOf csymbol in an event assignment. +componentTags: CSymbolRateOf, CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +A variable rateOf csymbols is used here in an event assignment for p2. This is exactly the same model as 01266, with p1 changing as a species in a reaction, instead of in a rate rule. + +The model contains: +* 1 species (p1) +* 1 parameter (p2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> p1 | $0.01 * p1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $p2 = rateOf(p1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01298/l2v5/index.heta b/latest/cases/01298/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01298/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01298/l3v2/heta-code/output.heta b/latest/cases/01298/l3v2/heta-code/output.heta new file mode 100644 index 000000000..99cf64c1d --- /dev/null +++ b/latest/cases/01298/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +p1 @Species { compartment: C, } .= 2; + +J0 @Reaction { actors: = p1, }; +J0 := 0.01 * p1; + +p2 @Record { } .= 10; +p2 [E0]= 5; +p2 [E1]= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01298/l3v2/index.heta b/latest/cases/01298/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01298/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01298/l3v2/json/output.json b/latest/cases/01298/l3v2/json/output.json new file mode 100644 index 000000000..1bf3b1d06 --- /dev/null +++ b/latest/cases/01298/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "p1", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01 * p1" + }, + "actors": [ + { + "target": "p1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "start_": "10", + "E0": "5", + "E1": "3" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 5.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01298/model-sbml-l3v2.xml b/latest/cases/01298/model-sbml-l3v2.xml new file mode 100644 index 000000000..271faebc3 --- /dev/null +++ b/latest/cases/01298/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + + + + time + 5.5 + + + + + + 0.021 + + + + + + 5 + + + + + + + + + + time + 5.5 + + + + + + + rateOf + p1 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01298/output.heta b/latest/cases/01298/output.heta new file mode 100644 index 000000000..e1c83b971 --- /dev/null +++ b/latest/cases/01298/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: A variable rateOf csymbol in an event priority. +componentTags: CSymbolRateOf, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A variable rateOf csymbol is used here in an event priority that assigns to p2. At the time the event triggers, the priority is greater than .021, meaning that it fires first, and E0 fires second, leaving the value of p2 at 5. This is exactly the same model as 01267, with p1 changing as a species in a reaction, instead of in a rate rule. + +The model contains: +* 1 species (p1) +* 1 parameter (p2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> p1 | $0.01 * p1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $0.021$ | $p2 = 5$ | +| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +p1 @Species { compartment: C, } .= 2; + +J0 @Reaction { actors: = p1, }; +J0 := 0.01 * p1; + +p2 @Record { } .= 10; +p2 [E0]= 5; +p2 [E1]= 3; + +E0 @DSwitcher { trigger: t > 5.5, }; +E1 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01298/synopsis.txt b/latest/cases/01298/synopsis.txt new file mode 100644 index 000000000..234097867 --- /dev/null +++ b/latest/cases/01298/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A variable rateOf csymbol in an event priority. +componentTags: CSymbolRateOf, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A variable rateOf csymbol is used here in an event priority that assigns to p2. At the time the event triggers, the priority is greater than .021, meaning that it fires first, and E0 fires second, leaving the value of p2 at 5. This is exactly the same model as 01267, with p1 changing as a species in a reaction, instead of in a rate rule. + +The model contains: +* 1 species (p1) +* 1 parameter (p2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> p1 | $0.01 * p1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 5.5$ | $0.021$ | $p2 = 5$ | +| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01299/l2v5/index.heta b/latest/cases/01299/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01299/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01299/l3v2/build.log b/latest/cases/01299/l3v2/build.log new file mode 100644 index 000000000..351826dfe --- /dev/null +++ b/latest/cases/01299/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01299/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01299/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01299/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01299/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01299/l3v2/index.heta b/latest/cases/01299/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01299/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01299/model-sbml-l3v2.xml b/latest/cases/01299/model-sbml-l3v2.xml new file mode 100644 index 000000000..74d886fd1 --- /dev/null +++ b/latest/cases/01299/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + 0.01 + p1 + + + + + + + + + + + + time + 5.9 + + + + + + + + 100 + + rateOf + p1 + + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01299/synopsis.txt b/latest/cases/01299/synopsis.txt new file mode 100644 index 000000000..c69e5b02d --- /dev/null +++ b/latest/cases/01299/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A variable rateOf csymbol in an event delay. +componentTags: CSymbolRateOf, CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A variable rateOf csymbol is used here in an event delay that assigns to p2. This is exactly the same model as 01268, with p1 changing as a species in a reaction, instead of in a rate rule. + +The model contains: +* 1 species (p1) +* 1 parameter (p2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> p1 | $0.01 * p1$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time > 5.9$ | $100 * rateOf(p1)$ | $p2 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species p1 | $2$ | variable | +| Initial value of parameter p2 | $10$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01300/l2v5/index.heta b/latest/cases/01300/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01300/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01300/l3v2/heta-code/output.heta b/latest/cases/01300/l3v2/heta-code/output.heta new file mode 100644 index 000000000..70f861801 --- /dev/null +++ b/latest/cases/01300/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; + +p1 @Record { } .= J0; + diff --git a/latest/cases/01300/l3v2/index.heta b/latest/cases/01300/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01300/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01300/l3v2/json/output.json b/latest/cases/01300/l3v2/json/output.json new file mode 100644 index 000000000..d175df1ab --- /dev/null +++ b/latest/cases/01300/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "3" + }, + "actors": [] + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "J0" + } + } +] \ No newline at end of file diff --git a/latest/cases/01300/model-sbml-l3v2.xml b/latest/cases/01300/model-sbml-l3v2.xml new file mode 100644 index 000000000..7d0dc471d --- /dev/null +++ b/latest/cases/01300/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + J0 + + + + + + + + 3 + + + + + + diff --git a/latest/cases/01300/output.heta b/latest/cases/01300/output.heta new file mode 100644 index 000000000..24104c8b6 --- /dev/null +++ b/latest/cases/01300/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: An empty reaction's identifier used in an initial assignment. +componentTags: InitialAssignment, Parameter, Reaction +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an initial assignment. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $J0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; + +p1 @Record { } .= J0; + diff --git a/latest/cases/01300/synopsis.txt b/latest/cases/01300/synopsis.txt new file mode 100644 index 000000000..e18ddbfd1 --- /dev/null +++ b/latest/cases/01300/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An empty reaction's identifier used in an initial assignment. +componentTags: InitialAssignment, Parameter, Reaction +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an initial assignment. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $J0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01301/l2v5/index.heta b/latest/cases/01301/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01301/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01301/l3v2/heta-code/output.heta b/latest/cases/01301/l3v2/heta-code/output.heta new file mode 100644 index 000000000..deeb3c6f5 --- /dev/null +++ b/latest/cases/01301/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; + +p1 @Record { }; +p1 := J0; + diff --git a/latest/cases/01301/l3v2/index.heta b/latest/cases/01301/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01301/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01301/l3v2/json/output.json b/latest/cases/01301/l3v2/json/output.json new file mode 100644 index 000000000..4f575a4eb --- /dev/null +++ b/latest/cases/01301/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "3" + }, + "actors": [] + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "ode_": "J0" + } + } +] \ No newline at end of file diff --git a/latest/cases/01301/model-sbml-l3v2.xml b/latest/cases/01301/model-sbml-l3v2.xml new file mode 100644 index 000000000..abce2163d --- /dev/null +++ b/latest/cases/01301/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + J0 + + + + + + + + 3 + + + + + + diff --git a/latest/cases/01301/output.heta b/latest/cases/01301/output.heta new file mode 100644 index 000000000..aec1fd53b --- /dev/null +++ b/latest/cases/01301/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: An empty reaction's identifier used in an assignment rule. +componentTags: AssignmentRule, Parameter, Reaction +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an assignment rule. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $J0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; + +p1 @Record { }; +p1 := J0; + diff --git a/latest/cases/01301/synopsis.txt b/latest/cases/01301/synopsis.txt new file mode 100644 index 000000000..7e3760359 --- /dev/null +++ b/latest/cases/01301/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: An empty reaction's identifier used in an assignment rule. +componentTags: AssignmentRule, Parameter, Reaction +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an assignment rule. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $J0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01302/l2v5/index.heta b/latest/cases/01302/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01302/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01302/l3v2/heta-code/output.heta b/latest/cases/01302/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ab41f48fb --- /dev/null +++ b/latest/cases/01302/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; +p1_proc @Process { actors: = p1, }; +p1_proc := J0; + +p1 @Record { } .= 0; + diff --git a/latest/cases/01302/l3v2/index.heta b/latest/cases/01302/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01302/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01302/l3v2/json/output.json b/latest/cases/01302/l3v2/json/output.json new file mode 100644 index 000000000..63834f868 --- /dev/null +++ b/latest/cases/01302/l3v2/json/output.json @@ -0,0 +1,33 @@ +[ + { + "id": "t" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "3" + }, + "actors": [] + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "p1_proc", + "assignments": { + "ode_": "J0" + }, + "actors": [ + { + "target": "p1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01302/model-sbml-l3v2.xml b/latest/cases/01302/model-sbml-l3v2.xml new file mode 100644 index 000000000..79a5307c9 --- /dev/null +++ b/latest/cases/01302/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + J0 + + + + + + + + 3 + + + + + + diff --git a/latest/cases/01302/output.heta b/latest/cases/01302/output.heta new file mode 100644 index 000000000..a9ee51adf --- /dev/null +++ b/latest/cases/01302/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: An empty reaction's identifier used in a rate rule. +componentTags: Parameter, RateRule, Reaction +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in a rate rule. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; +p1_proc @Process { actors: = p1, }; +p1_proc := J0; + +p1 @Record { } .= 0; + diff --git a/latest/cases/01302/synopsis.txt b/latest/cases/01302/synopsis.txt new file mode 100644 index 000000000..14b4c3371 --- /dev/null +++ b/latest/cases/01302/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: An empty reaction's identifier used in a rate rule. +componentTags: Parameter, RateRule, Reaction +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in a rate rule. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01303/l2v5/index.heta b/latest/cases/01303/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01303/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01303/l3v2/heta-code/output.heta b/latest/cases/01303/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0a90f3230 --- /dev/null +++ b/latest/cases/01303/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; + +p1 @Record { } .= 0; +p1 [_E0]= J0; + +_E0 @DSwitcher { trigger: t > 4.5, }; + diff --git a/latest/cases/01303/l3v2/index.heta b/latest/cases/01303/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01303/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01303/l3v2/json/output.json b/latest/cases/01303/l3v2/json/output.json new file mode 100644 index 000000000..c64c9eecc --- /dev/null +++ b/latest/cases/01303/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "3" + }, + "actors": [] + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "0", + "_E0": "J0" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 4.5" + } +] \ No newline at end of file diff --git a/latest/cases/01303/model-sbml-l3v2.xml b/latest/cases/01303/model-sbml-l3v2.xml new file mode 100644 index 000000000..674c51720 --- /dev/null +++ b/latest/cases/01303/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + 3 + + + + + + + + + + + time + 4.5 + + + + + + + J0 + + + + + + + diff --git a/latest/cases/01303/output.heta b/latest/cases/01303/output.heta new file mode 100644 index 000000000..2d5d72786 --- /dev/null +++ b/latest/cases/01303/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: An empty reaction's identifier used in an event assignment. +componentTags: CSymbolTime, EventNoDelay, Parameter, Reaction +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an event assignment. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 4.5$ | $p1 = J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; + +p1 @Record { } .= 0; +p1 [_E0]= J0; + +_E0 @DSwitcher { trigger: t > 4.5, }; + diff --git a/latest/cases/01303/synopsis.txt b/latest/cases/01303/synopsis.txt new file mode 100644 index 000000000..fe788d725 --- /dev/null +++ b/latest/cases/01303/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: An empty reaction's identifier used in an event assignment. +componentTags: CSymbolTime, EventNoDelay, Parameter, Reaction +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an event assignment. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 4.5$ | $p1 = J0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01304/l2v5/index.heta b/latest/cases/01304/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01304/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01304/l3v2/heta-code/output.heta b/latest/cases/01304/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a62744236 --- /dev/null +++ b/latest/cases/01304/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; + +p1 @Record { } .= 0; +p1 [E0]= 5; + +E0 @DSwitcher { trigger: t > (J0 + 1.5), }; + diff --git a/latest/cases/01304/l3v2/index.heta b/latest/cases/01304/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01304/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01304/l3v2/json/output.json b/latest/cases/01304/l3v2/json/output.json new file mode 100644 index 000000000..0a541114d --- /dev/null +++ b/latest/cases/01304/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "3" + }, + "actors": [] + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "0", + "E0": "5" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > (J0 + 1.5)" + } +] \ No newline at end of file diff --git a/latest/cases/01304/model-sbml-l3v2.xml b/latest/cases/01304/model-sbml-l3v2.xml new file mode 100644 index 000000000..a1016e242 --- /dev/null +++ b/latest/cases/01304/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + 3 + + + + + + + + + + + time + + + J0 + 1.5 + + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01304/output.heta b/latest/cases/01304/output.heta new file mode 100644 index 000000000..51c1d5da7 --- /dev/null +++ b/latest/cases/01304/output.heta @@ -0,0 +1,48 @@ +/* +category: Test +synopsis: An empty reaction's identifier used in an event trigger. +componentTags: CSymbolTime, EventNoDelay, Parameter, Reaction +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an event trigger. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > (J0 + 1.5)$ | $p1 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := 3; + +p1 @Record { } .= 0; +p1 [E0]= 5; + +E0 @DSwitcher { trigger: t > (J0 + 1.5), }; + diff --git a/latest/cases/01304/synopsis.txt b/latest/cases/01304/synopsis.txt new file mode 100644 index 000000000..d242534e9 --- /dev/null +++ b/latest/cases/01304/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: An empty reaction's identifier used in an event trigger. +componentTags: CSymbolTime, EventNoDelay, Parameter, Reaction +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an event trigger. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > (J0 + 1.5)$ | $p1 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01305/l2v5/index.heta b/latest/cases/01305/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01305/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01305/l3v2/build.log b/latest/cases/01305/l3v2/build.log new file mode 100644 index 000000000..66d82aeb2 --- /dev/null +++ b/latest/cases/01305/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01305/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01305/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01305/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01305/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01305/l3v2/index.heta b/latest/cases/01305/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01305/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01305/model-sbml-l3v2.xml b/latest/cases/01305/model-sbml-l3v2.xml new file mode 100644 index 000000000..24da5177c --- /dev/null +++ b/latest/cases/01305/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + 3 + + + + + + + + + + + time + 1.5 + + + + + + J0 + + + + + + 5 + + + + + + + diff --git a/latest/cases/01305/synopsis.txt b/latest/cases/01305/synopsis.txt new file mode 100644 index 000000000..e6b26cc50 --- /dev/null +++ b/latest/cases/01305/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: An empty reaction's identifier used in an event delay. +componentTags: CSymbolTime, EventWithDelay, Parameter, Reaction +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an event delay. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $3$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| _E0 | $time > 1.5$ | $J0$ | $p1 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01306/l2v5/index.heta b/latest/cases/01306/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01306/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01306/l3v2/heta-code/output.heta b/latest/cases/01306/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6fdb3233f --- /dev/null +++ b/latest/cases/01306/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := t; + +p1 @Record { }; +p1 := J0 + 1; + diff --git a/latest/cases/01306/l3v2/index.heta b/latest/cases/01306/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01306/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01306/l3v2/json/output.json b/latest/cases/01306/l3v2/json/output.json new file mode 100644 index 000000000..84e4ccfe0 --- /dev/null +++ b/latest/cases/01306/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "t" + }, + "actors": [] + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "ode_": "J0 + 1" + } + } +] \ No newline at end of file diff --git a/latest/cases/01306/model-sbml-l3v2.xml b/latest/cases/01306/model-sbml-l3v2.xml new file mode 100644 index 000000000..8e89085e5 --- /dev/null +++ b/latest/cases/01306/model-sbml-l3v2.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + J0 + 1 + + + + + + + + + time + + + + + + diff --git a/latest/cases/01306/output.heta b/latest/cases/01306/output.heta new file mode 100644 index 000000000..013ffffeb --- /dev/null +++ b/latest/cases/01306/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: An empty reaction's identifier used in an assignment rule. +componentTags: AssignmentRule, CSymbolTime, Parameter, Reaction +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an assignment rule. Differs from test 01301 because the kinetic law is non-constant. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $time$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $J0 + 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $J0 + 1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J0 @Reaction { actors: = , }; +J0 := t; + +p1 @Record { }; +p1 := J0 + 1; + diff --git a/latest/cases/01306/synopsis.txt b/latest/cases/01306/synopsis.txt new file mode 100644 index 000000000..665b266e7 --- /dev/null +++ b/latest/cases/01306/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: An empty reaction's identifier used in an assignment rule. +componentTags: AssignmentRule, CSymbolTime, Parameter, Reaction +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an assignment rule. Differs from test 01301 because the kinetic law is non-constant. + +The model contains: +* 1 parameter (p1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> | $time$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $J0 + 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $J0 + 1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01307/l2v5/heta-code/output.heta b/latest/cases/01307/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b374541f1 --- /dev/null +++ b/latest/cases/01307/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 3; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +J0 @Reaction { actors: = S1, }; +J0 := 1; + diff --git a/latest/cases/01307/l2v5/index.heta b/latest/cases/01307/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01307/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01307/l2v5/json/output.json b/latest/cases/01307/l2v5/json/output.json new file mode 100644 index 000000000..dc261a998 --- /dev/null +++ b/latest/cases/01307/l2v5/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01307/l3v2/heta-code/output.heta b/latest/cases/01307/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6014090ce --- /dev/null +++ b/latest/cases/01307/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 3; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +J0 @Reaction { actors: = S1, }; +J0 := 1; + diff --git a/latest/cases/01307/l3v2/index.heta b/latest/cases/01307/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01307/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01307/l3v2/json/output.json b/latest/cases/01307/l3v2/json/output.json new file mode 100644 index 000000000..1aab8c800 --- /dev/null +++ b/latest/cases/01307/l3v2/json/output.json @@ -0,0 +1,35 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01307/model-sbml-l2v5.xml b/latest/cases/01307/model-sbml-l2v5.xml new file mode 100644 index 000000000..14f7da060 --- /dev/null +++ b/latest/cases/01307/model-sbml-l2v5.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01307/model-sbml-l3v2.xml b/latest/cases/01307/model-sbml-l3v2.xml new file mode 100644 index 000000000..6950caf14 --- /dev/null +++ b/latest/cases/01307/model-sbml-l3v2.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01307/output.heta b/latest/cases/01307/output.heta new file mode 100644 index 000000000..a211e3e27 --- /dev/null +++ b/latest/cases/01307/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: A species always used as amount, with requested output in concentration +componentTags: Compartment, Reaction, Species +testTags: Concentration, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this simple model, a species whose level is always used in terms of amount in the model (initialAmount, hasOnlySubstanceUnits=true) has requested output in terms of concentration. This is more a test of the test suite system itself than a modeling test per se. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 3; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +J0 @Reaction { actors: = S1, }; +J0 := 1; + diff --git a/latest/cases/01307/synopsis.txt b/latest/cases/01307/synopsis.txt new file mode 100644 index 000000000..555cce4fb --- /dev/null +++ b/latest/cases/01307/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A species always used as amount, with requested output in concentration +componentTags: Compartment, Reaction, Species +testTags: Concentration, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this simple model, a species whose level is always used in terms of amount in the model (initialAmount, hasOnlySubstanceUnits=true) has requested output in terms of concentration. This is more a test of the test suite system itself than a modeling test per se. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01308/l2v5/heta-code/output.heta b/latest/cases/01308/l2v5/heta-code/output.heta new file mode 100644 index 000000000..395ade238 --- /dev/null +++ b/latest/cases/01308/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 3; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01308/l2v5/index.heta b/latest/cases/01308/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01308/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01308/l2v5/json/output.json b/latest/cases/01308/l2v5/json/output.json new file mode 100644 index 000000000..dc9f5f38d --- /dev/null +++ b/latest/cases/01308/l2v5/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01308/l3v2/heta-code/output.heta b/latest/cases/01308/l3v2/heta-code/output.heta new file mode 100644 index 000000000..38e573976 --- /dev/null +++ b/latest/cases/01308/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 3; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01308/l3v2/index.heta b/latest/cases/01308/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01308/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01308/l3v2/json/output.json b/latest/cases/01308/l3v2/json/output.json new file mode 100644 index 000000000..604595603 --- /dev/null +++ b/latest/cases/01308/l3v2/json/output.json @@ -0,0 +1,35 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01308/model-sbml-l2v5.xml b/latest/cases/01308/model-sbml-l2v5.xml new file mode 100644 index 000000000..23dbd029d --- /dev/null +++ b/latest/cases/01308/model-sbml-l2v5.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01308/model-sbml-l3v2.xml b/latest/cases/01308/model-sbml-l3v2.xml new file mode 100644 index 000000000..9e35c8132 --- /dev/null +++ b/latest/cases/01308/model-sbml-l3v2.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01308/output.heta b/latest/cases/01308/output.heta new file mode 100644 index 000000000..d93b8479b --- /dev/null +++ b/latest/cases/01308/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: A species always used as amount, with requested output in concentration +componentTags: Compartment, RateRule, Species +testTags: Concentration, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this simple model, a species whose level is always used in terms of amount in the model (initialAmount, hasOnlySubstanceUnits=true) has requested output in terms of concentration. This is more a test of the test suite system itself than a modeling test per se. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 3; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 1; + diff --git a/latest/cases/01308/synopsis.txt b/latest/cases/01308/synopsis.txt new file mode 100644 index 000000000..758afc66e --- /dev/null +++ b/latest/cases/01308/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A species always used as amount, with requested output in concentration +componentTags: Compartment, RateRule, Species +testTags: Concentration, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this simple model, a species whose level is always used in terms of amount in the model (initialAmount, hasOnlySubstanceUnits=true) has requested output in terms of concentration. This is more a test of the test suite system itself than a modeling test per se. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01309/l2v5/heta-code/output.heta b/latest/cases/01309/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2579b8984 --- /dev/null +++ b/latest/cases/01309/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { } .= 3; + +S1 @Species { boundary: true, compartment: C, isAmount: true, } .= 2; + +C_proc @Process { actors: = C, }; +C_proc := 1; + diff --git a/latest/cases/01309/l2v5/index.heta b/latest/cases/01309/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01309/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01309/l2v5/json/output.json b/latest/cases/01309/l2v5/json/output.json new file mode 100644 index 000000000..c7af5a29e --- /dev/null +++ b/latest/cases/01309/l2v5/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "3" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "boundary": true, + "compartment": "C", + "isAmount": true + }, + { + "class": "Process", + "id": "C_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01309/l3v2/heta-code/output.heta b/latest/cases/01309/l3v2/heta-code/output.heta new file mode 100644 index 000000000..294623339 --- /dev/null +++ b/latest/cases/01309/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { } .= 3; + +S1 @Species { boundary: true, compartment: C, isAmount: true, } .= 2; + +C_proc @Process { actors: = C, }; +C_proc := 1; + diff --git a/latest/cases/01309/l3v2/index.heta b/latest/cases/01309/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01309/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01309/l3v2/json/output.json b/latest/cases/01309/l3v2/json/output.json new file mode 100644 index 000000000..a873ef664 --- /dev/null +++ b/latest/cases/01309/l3v2/json/output.json @@ -0,0 +1,35 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "3" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "boundary": true, + "compartment": "C", + "isAmount": true + }, + { + "class": "Process", + "id": "C_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "C", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01309/model-sbml-l2v5.xml b/latest/cases/01309/model-sbml-l2v5.xml new file mode 100644 index 000000000..1027f04c0 --- /dev/null +++ b/latest/cases/01309/model-sbml-l2v5.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01309/model-sbml-l3v2.xml b/latest/cases/01309/model-sbml-l3v2.xml new file mode 100644 index 000000000..f88f07a88 --- /dev/null +++ b/latest/cases/01309/model-sbml-l3v2.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + 1 + + + + + diff --git a/latest/cases/01309/output.heta b/latest/cases/01309/output.heta new file mode 100644 index 000000000..1e695b4d5 --- /dev/null +++ b/latest/cases/01309/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: A species always used as amount, with requested output in concentration +componentTags: Compartment, RateRule, Species +testTags: Concentration, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this simple model, a species whose level is always used in terms of amount in the model (initialAmount, hasOnlySubstanceUnits=true) has requested output in terms of concentration. This is more a test of the test suite system itself than a modeling test per se. In this model, it is the compartment size that changes, not the species amount. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { } .= 3; + +S1 @Species { boundary: true, compartment: C, isAmount: true, } .= 2; + +C_proc @Process { actors: = C, }; +C_proc := 1; + diff --git a/latest/cases/01309/synopsis.txt b/latest/cases/01309/synopsis.txt new file mode 100644 index 000000000..7a1b52eb6 --- /dev/null +++ b/latest/cases/01309/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A species always used as amount, with requested output in concentration +componentTags: Compartment, RateRule, Species +testTags: Concentration, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this simple model, a species whose level is always used in terms of amount in the model (initialAmount, hasOnlySubstanceUnits=true) has requested output in terms of concentration. This is more a test of the test suite system itself than a modeling test per se. In this model, it is the compartment size that changes, not the species amount. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | C | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01310/l2v5/index.heta b/latest/cases/01310/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01310/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01310/l3v2/heta-code/output.heta b/latest/cases/01310/l3v2/heta-code/output.heta new file mode 100644 index 000000000..41c229463 --- /dev/null +++ b/latest/cases/01310/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 4; + diff --git a/latest/cases/01310/l3v2/index.heta b/latest/cases/01310/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01310/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01310/l3v2/json/output.json b/latest/cases/01310/l3v2/json/output.json new file mode 100644 index 000000000..07c39ca5f --- /dev/null +++ b/latest/cases/01310/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "4" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01310/model-sbml-l3v2.xml b/latest/cases/01310/model-sbml-l3v2.xml new file mode 100644 index 000000000..0c722daa8 --- /dev/null +++ b/latest/cases/01310/model-sbml-l3v2.xml @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/latest/cases/01310/output.heta b/latest/cases/01310/output.heta new file mode 100644 index 000000000..1f0d82f82 --- /dev/null +++ b/latest/cases/01310/output.heta @@ -0,0 +1,30 @@ +/* +category: Test +synopsis: Compartment with spatial dimensions of 2.7. +componentTags: Compartment +testTags: NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains only a compartment, but it has a spatial dimension of 2.7. The numerics are not affected at all; this simply tests that the existence of this dimensionality doesn't affect the simulation. + +The model contains: +* 1 compartment (C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial volume of compartment 'C' | $4$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 4; + diff --git a/latest/cases/01310/synopsis.txt b/latest/cases/01310/synopsis.txt new file mode 100644 index 000000000..0ee8fd403 --- /dev/null +++ b/latest/cases/01310/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: Compartment with spatial dimensions of 2.7. +componentTags: Compartment +testTags: NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains only a compartment, but it has a spatial dimension of 2.7. The numerics are not affected at all; this simply tests that the existence of this dimensionality doesn't affect the simulation. + +The model contains: +* 1 compartment (C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial volume of compartment 'C' | $4$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01311/l2v5/heta-code/output.heta b/latest/cases/01311/l2v5/heta-code/output.heta new file mode 100644 index 000000000..17fd5d183 --- /dev/null +++ b/latest/cases/01311/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +three #defineFunction { arguments: [], math: 3, }; +getthree #defineFunction { arguments: [], math: three(), }; +getgetthree #defineFunction { arguments: [], math: getthree(), }; + +t @TimeScale { }; + +p1 @Record { } .= getgetthree(); + diff --git a/latest/cases/01311/l2v5/index.heta b/latest/cases/01311/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01311/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01311/l2v5/json/output.json b/latest/cases/01311/l2v5/json/output.json new file mode 100644 index 000000000..0b10491d3 --- /dev/null +++ b/latest/cases/01311/l2v5/json/output.json @@ -0,0 +1,52 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "getgetthree()" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "three", + "math": "3", + "action": "defineFunction" + }, + { + "id": "getthree", + "math": "three()", + "action": "defineFunction" + }, + { + "id": "getgetthree", + "math": "getthree()", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01311/l3v2/build.log b/latest/cases/01311/l3v2/build.log new file mode 100644 index 000000000..a90ee5398 --- /dev/null +++ b/latest/cases/01311/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01311/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01311/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01311/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 83 +[error] No required "num" property for "p1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01311/l3v2/index.heta b/latest/cases/01311/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01311/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01311/model-sbml-l2v5.xml b/latest/cases/01311/model-sbml-l2v5.xml new file mode 100644 index 000000000..51ea60be6 --- /dev/null +++ b/latest/cases/01311/model-sbml-l2v5.xml @@ -0,0 +1,44 @@ + + + + + + + + 3 + + + + + + + + three + + + + + + + + + getthree + + + + + + + + + + + + + getgetthree + + + + + + diff --git a/latest/cases/01311/model-sbml-l3v2.xml b/latest/cases/01311/model-sbml-l3v2.xml new file mode 100644 index 000000000..472cccd8b --- /dev/null +++ b/latest/cases/01311/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + 3 + + + + + + + + three + + + + + + + + + getthree + + + + + + + + + + + + + getgetthree + + + + + + diff --git a/latest/cases/01311/output.heta b/latest/cases/01311/output.heta new file mode 100644 index 000000000..26dd01937 --- /dev/null +++ b/latest/cases/01311/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A very simple model that calls a function defintion with no arguments, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | three | | $3$ | + | getthree | | $three()$ | + | getgetthree | | $getthree()$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $getgetthree()$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +three #defineFunction { arguments: [], math: 3, }; +getthree #defineFunction { arguments: [], math: three(), }; +getgetthree #defineFunction { arguments: [], math: getthree(), }; + +t @TimeScale { }; + +p1 @Record { } .= getgetthree(); + diff --git a/latest/cases/01311/synopsis.txt b/latest/cases/01311/synopsis.txt new file mode 100644 index 000000000..661bd6cd7 --- /dev/null +++ b/latest/cases/01311/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A very simple model that calls a function defintion with no arguments, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | three | | $3$ | + | getthree | | $three()$ | + | getgetthree | | $getthree()$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $getgetthree()$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01312/l2v5/heta-code/output.heta b/latest/cases/01312/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9bc7f7e89 --- /dev/null +++ b/latest/cases/01312/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +this #defineFunction { arguments: [x], math: x, }; +getthis #defineFunction { arguments: [x], math: this(x), }; +getgetthis #defineFunction { arguments: [x], math: getthis(x), }; + +t @TimeScale { }; + +p1 @Record { } .= getgetthis(3); + diff --git a/latest/cases/01312/l2v5/index.heta b/latest/cases/01312/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01312/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01312/l2v5/json/output.json b/latest/cases/01312/l2v5/json/output.json new file mode 100644 index 000000000..865625cac --- /dev/null +++ b/latest/cases/01312/l2v5/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "getgetthis(3)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "this", + "arguments": [ + "x" + ], + "math": "x", + "action": "defineFunction" + }, + { + "id": "getthis", + "arguments": [ + "x" + ], + "math": "this(x)", + "action": "defineFunction" + }, + { + "id": "getgetthis", + "arguments": [ + "x" + ], + "math": "getthis(x)", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01312/l3v2/build.log b/latest/cases/01312/l3v2/build.log new file mode 100644 index 000000000..eaea2347d --- /dev/null +++ b/latest/cases/01312/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01312/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01312/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01312/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 83 +[error] No required "num" property for "p1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01312/l3v2/index.heta b/latest/cases/01312/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01312/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01312/model-sbml-l2v5.xml b/latest/cases/01312/model-sbml-l2v5.xml new file mode 100644 index 000000000..4bab553c9 --- /dev/null +++ b/latest/cases/01312/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + x + + x + + + + + + + + x + + + this + x + + + + + + + + + x + + + getthis + x + + + + + + + + + + + + + getgetthis + 3 + + + + + + diff --git a/latest/cases/01312/model-sbml-l3v2.xml b/latest/cases/01312/model-sbml-l3v2.xml new file mode 100644 index 000000000..99fb786e5 --- /dev/null +++ b/latest/cases/01312/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + x + + x + + + + + + + + x + + + this + x + + + + + + + + + x + + + getthis + x + + + + + + + + + + + + + getgetthis + 3 + + + + + + diff --git a/latest/cases/01312/output.heta b/latest/cases/01312/output.heta new file mode 100644 index 000000000..f35e45617 --- /dev/null +++ b/latest/cases/01312/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A very simple model that calls a function defintion with one argument, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | this | x | $x$ | + | getthis | x | $this(x)$ | + | getgetthis | x | $getthis(x)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $getgetthis(3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +this #defineFunction { arguments: [x], math: x, }; +getthis #defineFunction { arguments: [x], math: this(x), }; +getgetthis #defineFunction { arguments: [x], math: getthis(x), }; + +t @TimeScale { }; + +p1 @Record { } .= getgetthis(3); + diff --git a/latest/cases/01312/synopsis.txt b/latest/cases/01312/synopsis.txt new file mode 100644 index 000000000..6f7b02e87 --- /dev/null +++ b/latest/cases/01312/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A very simple model that calls a function defintion with one argument, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | this | x | $x$ | + | getthis | x | $this(x)$ | + | getgetthis | x | $getthis(x)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $getgetthis(3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01313/l2v5/heta-code/output.heta b/latest/cases/01313/l2v5/heta-code/output.heta new file mode 100644 index 000000000..531f7bcfa --- /dev/null +++ b/latest/cases/01313/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +addone #defineFunction { arguments: [x], math: x + 1, }; +addoneagain #defineFunction { arguments: [x], math: addone(x) + 1, }; +addoneagainagain #defineFunction { arguments: [x], math: addoneagain(x) + 1, }; + +t @TimeScale { }; + +p1 @Record { } .= addoneagainagain(3); + diff --git a/latest/cases/01313/l2v5/index.heta b/latest/cases/01313/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01313/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01313/l2v5/json/output.json b/latest/cases/01313/l2v5/json/output.json new file mode 100644 index 000000000..e75d0ac34 --- /dev/null +++ b/latest/cases/01313/l2v5/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "addoneagainagain(3)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "addone", + "arguments": [ + "x" + ], + "math": "x + 1", + "action": "defineFunction" + }, + { + "id": "addoneagain", + "arguments": [ + "x" + ], + "math": "addone(x) + 1", + "action": "defineFunction" + }, + { + "id": "addoneagainagain", + "arguments": [ + "x" + ], + "math": "addoneagain(x) + 1", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01313/l3v2/build.log b/latest/cases/01313/l3v2/build.log new file mode 100644 index 000000000..200c9c990 --- /dev/null +++ b/latest/cases/01313/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01313/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01313/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01313/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 83 +[error] No required "num" property for "p1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01313/l3v2/index.heta b/latest/cases/01313/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01313/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01313/model-sbml-l2v5.xml b/latest/cases/01313/model-sbml-l2v5.xml new file mode 100644 index 000000000..363da84a2 --- /dev/null +++ b/latest/cases/01313/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + x + + + + x + 1 + + + + + + + + + x + + + + + addone + x + + 1 + + + + + + + + + x + + + + + addoneagain + x + + 1 + + + + + + + + + + + + + addoneagainagain + 3 + + + + + + diff --git a/latest/cases/01313/model-sbml-l3v2.xml b/latest/cases/01313/model-sbml-l3v2.xml new file mode 100644 index 000000000..4536e1fa1 --- /dev/null +++ b/latest/cases/01313/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + x + + + + x + 1 + + + + + + + + + x + + + + + addone + x + + 1 + + + + + + + + + x + + + + + addoneagain + x + + 1 + + + + + + + + + + + + + addoneagainagain + 3 + + + + + + diff --git a/latest/cases/01313/output.heta b/latest/cases/01313/output.heta new file mode 100644 index 000000000..92c689864 --- /dev/null +++ b/latest/cases/01313/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A very simple model that calls a function defintion with one argument, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addone | x | $x + 1$ | + | addoneagain | x | $addone(x) + 1$ | + | addoneagainagain | x | $addoneagain(x) + 1$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $addoneagainagain(3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +addone #defineFunction { arguments: [x], math: x + 1, }; +addoneagain #defineFunction { arguments: [x], math: addone(x) + 1, }; +addoneagainagain #defineFunction { arguments: [x], math: addoneagain(x) + 1, }; + +t @TimeScale { }; + +p1 @Record { } .= addoneagainagain(3); + diff --git a/latest/cases/01313/synopsis.txt b/latest/cases/01313/synopsis.txt new file mode 100644 index 000000000..3057fb38c --- /dev/null +++ b/latest/cases/01313/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A very simple model that calls a function defintion with one argument, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addone | x | $x + 1$ | + | addoneagain | x | $addone(x) + 1$ | + | addoneagainagain | x | $addoneagain(x) + 1$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $addoneagainagain(3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01314/l2v5/heta-code/output.heta b/latest/cases/01314/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0ec0abe2f --- /dev/null +++ b/latest/cases/01314/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +addone #defineFunction { arguments: [x], math: x + 1, }; +addoneagain #defineFunction { arguments: [x], math: addone(x) + 1, }; +addoneagainandagain #defineFunction { arguments: [x], math: addoneagain(x) + addone(x) + 1, }; + +t @TimeScale { }; + +p1 @Record { } .= addoneagainandagain(3); + diff --git a/latest/cases/01314/l2v5/index.heta b/latest/cases/01314/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01314/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01314/l2v5/json/output.json b/latest/cases/01314/l2v5/json/output.json new file mode 100644 index 000000000..e5821c508 --- /dev/null +++ b/latest/cases/01314/l2v5/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "addoneagainandagain(3)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "addone", + "arguments": [ + "x" + ], + "math": "x + 1", + "action": "defineFunction" + }, + { + "id": "addoneagain", + "arguments": [ + "x" + ], + "math": "addone(x) + 1", + "action": "defineFunction" + }, + { + "id": "addoneagainandagain", + "arguments": [ + "x" + ], + "math": "addoneagain(x) + addone(x) + 1", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01314/l3v2/build.log b/latest/cases/01314/l3v2/build.log new file mode 100644 index 000000000..1ac504fa0 --- /dev/null +++ b/latest/cases/01314/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01314/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01314/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01314/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 83 +[error] No required "num" property for "p1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01314/l3v2/index.heta b/latest/cases/01314/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01314/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01314/model-sbml-l2v5.xml b/latest/cases/01314/model-sbml-l2v5.xml new file mode 100644 index 000000000..a822a0a3c --- /dev/null +++ b/latest/cases/01314/model-sbml-l2v5.xml @@ -0,0 +1,72 @@ + + + + + + + + + x + + + + x + 1 + + + + + + + + + x + + + + + addone + x + + 1 + + + + + + + + + x + + + + + addoneagain + x + + + addone + x + + 1 + + + + + + + + + + + + + addoneagainandagain + 3 + + + + + + diff --git a/latest/cases/01314/model-sbml-l3v2.xml b/latest/cases/01314/model-sbml-l3v2.xml new file mode 100644 index 000000000..44b921e13 --- /dev/null +++ b/latest/cases/01314/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + x + + + + x + 1 + + + + + + + + + x + + + + + addone + x + + 1 + + + + + + + + + x + + + + + addoneagain + x + + + addone + x + + 1 + + + + + + + + + + + + + addoneagainandagain + 3 + + + + + + diff --git a/latest/cases/01314/output.heta b/latest/cases/01314/output.heta new file mode 100644 index 000000000..3dd114480 --- /dev/null +++ b/latest/cases/01314/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A slightly complicated nested function definition, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addone | x | $x + 1$ | + | addoneagain | x | $addone(x) + 1$ | + | addoneagainandagain | x | $addoneagain(x) + addone(x) + 1$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $addoneagainandagain(3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +addone #defineFunction { arguments: [x], math: x + 1, }; +addoneagain #defineFunction { arguments: [x], math: addone(x) + 1, }; +addoneagainandagain #defineFunction { arguments: [x], math: addoneagain(x) + addone(x) + 1, }; + +t @TimeScale { }; + +p1 @Record { } .= addoneagainandagain(3); + diff --git a/latest/cases/01314/synopsis.txt b/latest/cases/01314/synopsis.txt new file mode 100644 index 000000000..53310e75a --- /dev/null +++ b/latest/cases/01314/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A slightly complicated nested function definition, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addone | x | $x + 1$ | + | addoneagain | x | $addone(x) + 1$ | + | addoneagainandagain | x | $addoneagain(x) + addone(x) + 1$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $addoneagainandagain(3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01315/l2v5/heta-code/output.heta b/latest/cases/01315/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e573419c5 --- /dev/null +++ b/latest/cases/01315/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +addone #defineFunction { arguments: [x], math: x + 1, }; +addoneagain2x #defineFunction { arguments: [x], math: addone(x) + addone(x) + 1, }; +addoneagainandagain2x #defineFunction { arguments: [x], math: addoneagain2x(x) + addoneagain2x(x) + addone(x) + addone(x) + 1, }; + +t @TimeScale { }; + +p1 @Record { } .= addoneagainandagain2x(3); + diff --git a/latest/cases/01315/l2v5/index.heta b/latest/cases/01315/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01315/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01315/l2v5/json/output.json b/latest/cases/01315/l2v5/json/output.json new file mode 100644 index 000000000..bf02bb7bf --- /dev/null +++ b/latest/cases/01315/l2v5/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "addoneagainandagain2x(3)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "addone", + "arguments": [ + "x" + ], + "math": "x + 1", + "action": "defineFunction" + }, + { + "id": "addoneagain2x", + "arguments": [ + "x" + ], + "math": "addone(x) + addone(x) + 1", + "action": "defineFunction" + }, + { + "id": "addoneagainandagain2x", + "arguments": [ + "x" + ], + "math": "addoneagain2x(x) + addoneagain2x(x) + addone(x) + addone(x) + 1", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01315/l3v2/build.log b/latest/cases/01315/l3v2/build.log new file mode 100644 index 000000000..62002d5ac --- /dev/null +++ b/latest/cases/01315/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01315/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01315/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01315/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 83 +[error] No required "num" property for "p1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01315/l3v2/index.heta b/latest/cases/01315/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01315/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01315/model-sbml-l2v5.xml b/latest/cases/01315/model-sbml-l2v5.xml new file mode 100644 index 000000000..9b1987c4f --- /dev/null +++ b/latest/cases/01315/model-sbml-l2v5.xml @@ -0,0 +1,84 @@ + + + + + + + + + x + + + + x + 1 + + + + + + + + + x + + + + + addone + x + + + addone + x + + 1 + + + + + + + + + x + + + + + addoneagain2x + x + + + addoneagain2x + x + + + addone + x + + + addone + x + + 1 + + + + + + + + + + + + + addoneagainandagain2x + 3 + + + + + + diff --git a/latest/cases/01315/model-sbml-l3v2.xml b/latest/cases/01315/model-sbml-l3v2.xml new file mode 100644 index 000000000..1c8cc07db --- /dev/null +++ b/latest/cases/01315/model-sbml-l3v2.xml @@ -0,0 +1,85 @@ + + + + + + + + + + x + + + + x + 1 + + + + + + + + + x + + + + + addone + x + + + addone + x + + 1 + + + + + + + + + x + + + + + addoneagain2x + x + + + addoneagain2x + x + + + addone + x + + + addone + x + + 1 + + + + + + + + + + + + + addoneagainandagain2x + 3 + + + + + + diff --git a/latest/cases/01315/output.heta b/latest/cases/01315/output.heta new file mode 100644 index 000000000..f3872182e --- /dev/null +++ b/latest/cases/01315/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A slightly complicated nested function definition, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addone | x | $x + 1$ | + | addoneagain2x | x | $addone(x) + addone(x) + 1$ | + | addoneagainandagain2x | x | $addoneagain2x(x) + addoneagain2x(x) + addone(x) + addone(x) + 1$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $addoneagainandagain2x(3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +addone #defineFunction { arguments: [x], math: x + 1, }; +addoneagain2x #defineFunction { arguments: [x], math: addone(x) + addone(x) + 1, }; +addoneagainandagain2x #defineFunction { arguments: [x], math: addoneagain2x(x) + addoneagain2x(x) + addone(x) + addone(x) + 1, }; + +t @TimeScale { }; + +p1 @Record { } .= addoneagainandagain2x(3); + diff --git a/latest/cases/01315/synopsis.txt b/latest/cases/01315/synopsis.txt new file mode 100644 index 000000000..671456aeb --- /dev/null +++ b/latest/cases/01315/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Nested function definitions +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A slightly complicated nested function definition, nested three deep. + +The model contains: +* 1 parameter (p1) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addone | x | $x + 1$ | + | addoneagain2x | x | $addone(x) + addone(x) + 1$ | + | addoneagainandagain2x | x | $addoneagain2x(x) + addoneagain2x(x) + addone(x) + addone(x) + 1$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $addoneagainandagain2x(3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01316/l2v5/index.heta b/latest/cases/01316/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01316/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01316/l3v2/build.log b/latest/cases/01316/l3v2/build.log new file mode 100644 index 000000000..76361a93b --- /dev/null +++ b/latest/cases/01316/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01316/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01316/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01316/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] No required "num" property for "p2" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01316/l3v2/index.heta b/latest/cases/01316/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01316/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01316/model-sbml-l3v2.xml b/latest/cases/01316/model-sbml-l3v2.xml new file mode 100644 index 000000000..8ebc5e8fe --- /dev/null +++ b/latest/cases/01316/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + 1 + + + p1 + 1 24 + + + + + + + diff --git a/latest/cases/01316/synopsis.txt b/latest/cases/01316/synopsis.txt new file mode 100644 index 000000000..e8eeb6bdb --- /dev/null +++ b/latest/cases/01316/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: Use of a csymbol whose putative ID shadows another parameter. +componentTags: CSymbolAvogadro, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model the 'avogadro' csymbol is given the ID of another parameter. This ID should be ignored. + +The model contains: +* 2 parameters (p1, p2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | constant | +| Initial value of parameter p2 | $1 + avogadro / 1.000000e+24$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01317/l2v5/heta-code/output.heta b/latest/cases/01317/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b5a55e0df --- /dev/null +++ b/latest/cases/01317/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +p1 @Record { } .= 5; +p2 @Record { }; +p2 := 1 + t; + diff --git a/latest/cases/01317/l2v5/index.heta b/latest/cases/01317/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01317/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01317/l2v5/json/output.json b/latest/cases/01317/l2v5/json/output.json new file mode 100644 index 000000000..5a3989df9 --- /dev/null +++ b/latest/cases/01317/l2v5/json/output.json @@ -0,0 +1,44 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "5" + } + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "ode_": "1 + t" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01317/l3v2/heta-code/output.heta b/latest/cases/01317/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e7ce47103 --- /dev/null +++ b/latest/cases/01317/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +p2 @Record { }; +p2 := 1 + t; + +p1 @Const { } = 5; + diff --git a/latest/cases/01317/l3v2/index.heta b/latest/cases/01317/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01317/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01317/l3v2/json/output.json b/latest/cases/01317/l3v2/json/output.json new file mode 100644 index 000000000..6ce26a7d4 --- /dev/null +++ b/latest/cases/01317/l3v2/json/output.json @@ -0,0 +1,17 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "p1", + "num": 5 + }, + { + "class": "Record", + "id": "p2", + "assignments": { + "ode_": "1 + t" + } + } +] \ No newline at end of file diff --git a/latest/cases/01317/model-sbml-l2v5.xml b/latest/cases/01317/model-sbml-l2v5.xml new file mode 100644 index 000000000..030f05786 --- /dev/null +++ b/latest/cases/01317/model-sbml-l2v5.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + 1 + p1 + + + + + + diff --git a/latest/cases/01317/model-sbml-l3v2.xml b/latest/cases/01317/model-sbml-l3v2.xml new file mode 100644 index 000000000..4693b7fca --- /dev/null +++ b/latest/cases/01317/model-sbml-l3v2.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + 1 + p1 + + + + + + diff --git a/latest/cases/01317/output.heta b/latest/cases/01317/output.heta new file mode 100644 index 000000000..637737914 --- /dev/null +++ b/latest/cases/01317/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Use of a csymbol whose putative ID shadows another parameter. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model the 'time' csymbol is given the ID of another parameter. This ID should be ignored. + +The model contains: +* 2 parameters (p1, p2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p2 | $1 + time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | constant | +| Initial value of parameter p2 | $1 + time$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p2 @Record { }; +p2 := 1 + t; + +p1 @Const { } = 5; + diff --git a/latest/cases/01317/synopsis.txt b/latest/cases/01317/synopsis.txt new file mode 100644 index 000000000..cd7f47dd3 --- /dev/null +++ b/latest/cases/01317/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Use of a csymbol whose putative ID shadows another parameter. +componentTags: AssignmentRule, CSymbolTime, Parameter +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model the 'time' csymbol is given the ID of another parameter. This ID should be ignored. + +The model contains: +* 2 parameters (p1, p2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p2 | $1 + time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | constant | +| Initial value of parameter p2 | $1 + time$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01318/l2v5/build.log b/latest/cases/01318/l2v5/build.log new file mode 100644 index 000000000..e133c29dd --- /dev/null +++ b/latest/cases/01318/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01318/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01318/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01318/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01318/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01318/l2v5/index.heta b/latest/cases/01318/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01318/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01318/l3v2/build.log b/latest/cases/01318/l3v2/build.log new file mode 100644 index 000000000..29bbe9c35 --- /dev/null +++ b/latest/cases/01318/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01318/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01318/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01318/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01318/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01318/l3v2/index.heta b/latest/cases/01318/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01318/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01318/model-sbml-l2v5.xml b/latest/cases/01318/model-sbml-l2v5.xml new file mode 100644 index 000000000..7c3bd0aa7 --- /dev/null +++ b/latest/cases/01318/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + 1 + time + + + + + + + p1 + p2 + 1 + + + + + + diff --git a/latest/cases/01318/model-sbml-l3v2.xml b/latest/cases/01318/model-sbml-l3v2.xml new file mode 100644 index 000000000..2eb37e83f --- /dev/null +++ b/latest/cases/01318/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + 1 + time + + + + + + + p1 + p2 + 1 + + + + + + diff --git a/latest/cases/01318/synopsis.txt b/latest/cases/01318/synopsis.txt new file mode 100644 index 000000000..00ddba722 --- /dev/null +++ b/latest/cases/01318/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Use of a csymbol whose putative ID shadows another parameter. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Parameter +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model the 'delay' csymbol is given the ID of another parameter. This ID should be ignored. + +The model contains: +* 3 parameters (p2, p3, p1) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p2 | $1 + time$ | +| Assignment | p3 | $delay(p2, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | constant | +| Initial value of parameter p2 | $1 + time$ | variable | +| Initial value of parameter p3 | $delay(p2, 1)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01319/l2v5/build.log b/latest/cases/01319/l2v5/build.log new file mode 100644 index 000000000..00ee866dc --- /dev/null +++ b/latest/cases/01319/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01319/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01319/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01319/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01319/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01319/l2v5/index.heta b/latest/cases/01319/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01319/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01319/l3v2/build.log b/latest/cases/01319/l3v2/build.log new file mode 100644 index 000000000..d082faeaf --- /dev/null +++ b/latest/cases/01319/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01319/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01319/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01319/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01319/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01319/l3v2/index.heta b/latest/cases/01319/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01319/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01319/model-sbml-l2v5.xml b/latest/cases/01319/model-sbml-l2v5.xml new file mode 100644 index 000000000..ecdf26b69 --- /dev/null +++ b/latest/cases/01319/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + 1 + time + + + + + + + plus + p2 + 1 + + + + + + diff --git a/latest/cases/01319/model-sbml-l3v2.xml b/latest/cases/01319/model-sbml-l3v2.xml new file mode 100644 index 000000000..029b35e8b --- /dev/null +++ b/latest/cases/01319/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + 1 + time + + + + + + + plus + p2 + 1 + + + + + + diff --git a/latest/cases/01319/synopsis.txt b/latest/cases/01319/synopsis.txt new file mode 100644 index 000000000..d833484ef --- /dev/null +++ b/latest/cases/01319/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Use of a csymbol whose putative ID shadows another parameter. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Parameter +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model the 'delay' csymbol is given the ID of a different function. This ID should be ignored. + +The model contains: +* 3 parameters (p2, p3, p1) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p2 | $1 + time$ | +| Assignment | p3 | $delay(p2, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $5$ | constant | +| Initial value of parameter p2 | $1 + time$ | variable | +| Initial value of parameter p3 | $delay(p2, 1)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01320/l2v5/build.log b/latest/cases/01320/l2v5/build.log new file mode 100644 index 000000000..89b402f83 --- /dev/null +++ b/latest/cases/01320/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01320/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01320/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01320/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01320/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01320/l2v5/index.heta b/latest/cases/01320/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01320/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01320/l3v2/build.log b/latest/cases/01320/l3v2/build.log new file mode 100644 index 000000000..d36c134d3 --- /dev/null +++ b/latest/cases/01320/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01320/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01320/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01320/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01320/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01320/l3v2/index.heta b/latest/cases/01320/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01320/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01320/model-sbml-l2v5.xml b/latest/cases/01320/model-sbml-l2v5.xml new file mode 100644 index 000000000..c0a176cec --- /dev/null +++ b/latest/cases/01320/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + p1 + S1 + 1 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01320/model-sbml-l3v2.xml b/latest/cases/01320/model-sbml-l3v2.xml new file mode 100644 index 000000000..eabfbbf66 --- /dev/null +++ b/latest/cases/01320/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + p1 + S1 + 1 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01320/synopsis.txt b/latest/cases/01320/synopsis.txt new file mode 100644 index 000000000..09cd679ef --- /dev/null +++ b/latest/cases/01320/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Use of a csymbol whose putative ID shadows another parameter. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model the 'delay' csymbol is given the ID of a different parameter. This ID should be ignored. + +The model contains: +* 1 species (S1) +* 2 parameters (p1, p2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p2 | $delay(S1, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter p1 | $5$ | variable | +| Initial value of parameter p2 | $delay(S1, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01321/l2v5/index.heta b/latest/cases/01321/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01321/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01321/l3v2/build.log b/latest/cases/01321/l3v2/build.log new file mode 100644 index 000000000..0926abf9f --- /dev/null +++ b/latest/cases/01321/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01321/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01321/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01321/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01321/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01321/l3v2/index.heta b/latest/cases/01321/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01321/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01321/model-sbml-l3v2.xml b/latest/cases/01321/model-sbml-l3v2.xml new file mode 100644 index 000000000..00e63a6cc --- /dev/null +++ b/latest/cases/01321/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + 2 + + + + + + p1 + p1 + + + + + + diff --git a/latest/cases/01321/synopsis.txt b/latest/cases/01321/synopsis.txt new file mode 100644 index 000000000..1d7bb1eff --- /dev/null +++ b/latest/cases/01321/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Use of a csymbol whose putative ID shadows another parameter. +componentTags: AssignmentRule, CSymbolRateOf, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model the 'rateOf' csymbol is given the ID of a different parameter. This ID should be ignored. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $2$ | +| Assignment | p2 | $rateOf(p1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $rateOf(p1)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01322/l2v5/index.heta b/latest/cases/01322/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01322/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01322/l3v2/build.log b/latest/cases/01322/l3v2/build.log new file mode 100644 index 000000000..23f53ee4b --- /dev/null +++ b/latest/cases/01322/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01322/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01322/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01322/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01322/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01322/l3v2/index.heta b/latest/cases/01322/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01322/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01322/model-sbml-l3v2.xml b/latest/cases/01322/model-sbml-l3v2.xml new file mode 100644 index 000000000..92de1287a --- /dev/null +++ b/latest/cases/01322/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + 2 + + + + + + plus + p1 + + + + + + diff --git a/latest/cases/01322/synopsis.txt b/latest/cases/01322/synopsis.txt new file mode 100644 index 000000000..74edbd24b --- /dev/null +++ b/latest/cases/01322/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Use of a csymbol whose putative ID shadows another parameter. +componentTags: AssignmentRule, CSymbolRateOf, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model the 'rateOf' csymbol is given the ID of a different function. This ID should be ignored. + +The model contains: +* 2 parameters (p1, p2) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $2$ | +| Assignment | p2 | $rateOf(p1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable | +| Initial value of parameter p2 | $rateOf(p1)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01323/l2v5/index.heta b/latest/cases/01323/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01323/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01323/l3v2/build.log b/latest/cases/01323/l3v2/build.log new file mode 100644 index 000000000..7aae6710a --- /dev/null +++ b/latest/cases/01323/l3v2/build.log @@ -0,0 +1,49 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01323/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01323/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01323/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 120 +[error] No required "num" property for "a_sbml" of Const. +[error] No required "num" property for "a_truncated" of Const. +[error] No required "num" property for "a_1865" of Const. +[error] No required "num" property for "a_1873" of Const. +[error] No required "num" property for "a_1890a" of Const. +[error] No required "num" property for "a_1890b" of Const. +[error] No required "num" property for "a_1901" of Const. +[error] No required "num" property for "a_1903" of Const. +[error] No required "num" property for "a_1904" of Const. +[error] No required "num" property for "a_1908" of Const. +[error] No required "num" property for "a_1909" of Const. +[error] No required "num" property for "a_1914a" of Const. +[error] No required "num" property for "a_1914b" of Const. +[error] No required "num" property for "a_1915" of Const. +[error] No required "num" property for "a_1917" of Const. +[error] No required "num" property for "a_1923" of Const. +[error] No required "num" property for "a_1924" of Const. +[error] No required "num" property for "a_1929" of Const. +[error] No required "num" property for "a_1931" of Const. +[error] No required "num" property for "a_1941" of Const. +[error] No required "num" property for "a_1945" of Const. +[error] No required "num" property for "a_1948" of Const. +[error] No required "num" property for "a_1949" of Const. +[error] No required "num" property for "a_1951" of Const. +[error] No required "num" property for "a_1965a" of Const. +[error] No required "num" property for "a_1965b" of Const. +[error] No required "num" property for "a_1973" of Const. +[error] No required "num" property for "a_1974" of Const. +[error] No required "num" property for "a_1987a" of Const. +[error] No required "num" property for "a_1987b" of Const. +[error] No required "num" property for "a_1992" of Const. +[error] No required "num" property for "a_1994" of Const. +[error] No required "num" property for "a_1995" of Const. +[error] No required "num" property for "a_1999" of Const. +[error] No required "num" property for "a_2000" of Const. +[error] No required "num" property for "a_2001" of Const. +[error] No required "num" property for "a_2002" of Const. +[error] No required "num" property for "a_2003" of Const. +[error] No required "num" property for "a_2006" of Const. +[error] No required "num" property for "a_2011" of Const. +[error] No required "num" property for "a_2015" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01323/l3v2/index.heta b/latest/cases/01323/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01323/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01323/model-sbml-l3v2.xml b/latest/cases/01323/model-sbml-l3v2.xml new file mode 100644 index 000000000..5f025c225 --- /dev/null +++ b/latest/cases/01323/model-sbml-l3v2.xml @@ -0,0 +1,420 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 6.02214179 23 + avogadro + + + + + + + + 6.022142 23 + avogadro + + + + + + + + 7.2 24 + avogadro + + + + + + + + 1.1 24 + avogadro + + + + + + + + 7 23 + avogadro + + + + + + + + 6.08 23 + avogadro + + + + + + + + 6.16 23 + avogadro + + + + + + + + 9.3 23 + avogadro + + + + + + + + 8.7 23 + avogadro + + + + + + + + 6 23 + avogadro + + + + + + + + 6.16 23 + avogadro + + + + + + + + 6 23 + avogadro + + + + + + + + 5.91 23 + avogadro + + + + + + + + 6.06 23 + avogadro + + + + + + + + 6.064 23 + avogadro + + + + + + + + 5.9 23 + avogadro + + + + + + + + 6.004 23 + avogadro + + + + + + + + 6.0644 23 + avogadro + + + + + + + + 6.019 23 + avogadro + + + + + + + + 6.02283 23 + avogadro + + + + + + + + 6.02338 23 + avogadro + + + + + + + + 6.0232 23 + avogadro + + + + + + + + 6.02403 23 + avogadro + + + + + + + + 6.02544 23 + avogadro + + + + + + + + 6.022088 23 + avogadro + + + + + + + + 6.02252 23 + avogadro + + + + + + + + 6.022045 23 + avogadro + + + + + + + + 6.0220943 23 + avogadro + + + + + + + + 6.022134 23 + avogadro + + + + + + + + 6.0221367 23 + avogadro + + + + + + + + 6.0221363 23 + avogadro + + + + + + + + 6.0221379 23 + avogadro + + + + + + + + 6.0221365 23 + avogadro + + + + + + + + 6.022155 23 + avogadro + + + + + + + + 6.02214199 23 + avogadro + + + + + + + + 6.0221339 23 + avogadro + + + + + + + + 6.0221415 23 + avogadro + + + + + + + + 6.0221353 23 + avogadro + + + + + + + + 6.02214179 23 + avogadro + + + + + + + + 6.02214129 23 + avogadro + + + + + + + + 6.022140857 23 + avogadro + + + + + + diff --git a/latest/cases/01323/synopsis.txt b/latest/cases/01323/synopsis.txt new file mode 100644 index 000000000..10cf54232 --- /dev/null +++ b/latest/cases/01323/synopsis.txt @@ -0,0 +1,68 @@ + +category: Test +synopsis: Initial assignments that test that the appropriate value for avogadro is being used. +componentTags: CSymbolAvogadro, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +Since 1865, people have been calculating avogadro's number with increasing accuracy. In 2010, when the SBML Level 3 specification came out, the most accurate value anyone had calculated was 6.02214179e23, and this value was taken as canonical for all SBML files. Since (and before) then, avogadro has taken other values. However, none of them should be used. This file checks that you use the value of avogadro from the correct year, by dividing the literal value of avogadro in different years by the csymbol 'avogadro'. If you fail this test, but get a value of '1' for one of your parameters, you are using the value of avogadro established in that year, and not as it had been determined to be in 2010. + +Another possibility is that the test itself is going wrong because your program has truncated the values from which avogadro is being subtracted: if you get the same result for 'a_truncated' as you get for 'a_2006', this probably means you're either using the infix output of libsbml version 5.14.0 or earlier, which truncated all 'e-notation' values to seven significant digits, or a similar scheme that does the same thing. + +I don't really think that you're likely to be accidentally using the value of avogadro from 1865, but those values are provided here to sate your historical curiosity. + +Values before and including 2001 were found in http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.408.199&rep=rep1&type=pdf, while values after that were found through direct citations, and by using the Internet Archive's copies of CODATA's recommended value for Avogadro: http://web.archive.org/web/20040215162824*/http://physics.nist.gov/cgi-bin/cuu/Value?na + +The model contains: +* 41 parameters (a_sbml, a_truncated, a_1865, a_1873, a_1890a, a_1890b, a_1901, a_1903, a_1904, a_1908, a_1909, a_1914a, a_1914b, a_1915, a_1917, a_1923, a_1924, a_1929, a_1931, a_1941, a_1945, a_1948, a_1949, a_1951, a_1965a, a_1965b, a_1973, a_1974, a_1987a, a_1987b, a_1992, a_1994, a_1995, a_1999, a_2000, a_2001, a_2002, a_2003, a_2006, a_2011, a_2015) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a_sbml | $6.02214179e23 / avogadro$ | constant | +| Initial value of parameter a_truncated | $6.022142e23 / avogadro$ | constant | +| Initial value of parameter a_1865 | $7.2e24 / avogadro$ | constant | +| Initial value of parameter a_1873 | $1.1e24 / avogadro$ | constant | +| Initial value of parameter a_1890a | $7e23 / avogadro$ | constant | +| Initial value of parameter a_1890b | $6.08e23 / avogadro$ | constant | +| Initial value of parameter a_1901 | $6.16e23 / avogadro$ | constant | +| Initial value of parameter a_1903 | $9.3e23 / avogadro$ | constant | +| Initial value of parameter a_1904 | $8.7e23 / avogadro$ | constant | +| Initial value of parameter a_1908 | $6e23 / avogadro$ | constant | +| Initial value of parameter a_1909 | $6.16e23 / avogadro$ | constant | +| Initial value of parameter a_1914a | $6e23 / avogadro$ | constant | +| Initial value of parameter a_1914b | $5.91e23 / avogadro$ | constant | +| Initial value of parameter a_1915 | $6.06e23 / avogadro$ | constant | +| Initial value of parameter a_1917 | $6.064e23 / avogadro$ | constant | +| Initial value of parameter a_1923 | $5.9e23 / avogadro$ | constant | +| Initial value of parameter a_1924 | $6.004e23 / avogadro$ | constant | +| Initial value of parameter a_1929 | $6.0644e23 / avogadro$ | constant | +| Initial value of parameter a_1931 | $6.019e23 / avogadro$ | constant | +| Initial value of parameter a_1941 | $6.02283e23 / avogadro$ | constant | +| Initial value of parameter a_1945 | $6.02338e23 / avogadro$ | constant | +| Initial value of parameter a_1948 | $6.0232e23 / avogadro$ | constant | +| Initial value of parameter a_1949 | $6.02403e23 / avogadro$ | constant | +| Initial value of parameter a_1951 | $6.02544e23 / avogadro$ | constant | +| Initial value of parameter a_1965a | $6.022088e23 / avogadro$ | constant | +| Initial value of parameter a_1965b | $6.02252e23 / avogadro$ | constant | +| Initial value of parameter a_1973 | $6.022045e23 / avogadro$ | constant | +| Initial value of parameter a_1974 | $6.0220943e23 / avogadro$ | constant | +| Initial value of parameter a_1987a | $6.022134e23 / avogadro$ | constant | +| Initial value of parameter a_1987b | $6.0221367e23 / avogadro$ | constant | +| Initial value of parameter a_1992 | $6.0221363e23 / avogadro$ | constant | +| Initial value of parameter a_1994 | $6.0221379e23 / avogadro$ | constant | +| Initial value of parameter a_1995 | $6.0221365e23 / avogadro$ | constant | +| Initial value of parameter a_1999 | $6.022155e23 / avogadro$ | constant | +| Initial value of parameter a_2000 | $6.02214199e23 / avogadro$ | constant | +| Initial value of parameter a_2001 | $6.0221339e23 / avogadro$ | constant | +| Initial value of parameter a_2002 | $6.0221415e23 / avogadro$ | constant | +| Initial value of parameter a_2003 | $6.0221353e23 / avogadro$ | constant | +| Initial value of parameter a_2006 | $6.02214179e23 / avogadro$ | constant | +| Initial value of parameter a_2011 | $6.02214129e23 / avogadro$ | constant | +| Initial value of parameter a_2015 | $6.022140857e23 / avogadro$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01324/l2v5/build.log b/latest/cases/01324/l2v5/build.log new file mode 100644 index 000000000..5bc6262d9 --- /dev/null +++ b/latest/cases/01324/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01324/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01324/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01324/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01324/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01324/l2v5/index.heta b/latest/cases/01324/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01324/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01324/l3v2/build.log b/latest/cases/01324/l3v2/build.log new file mode 100644 index 000000000..efe68db0e --- /dev/null +++ b/latest/cases/01324/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01324/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01324/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01324/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01324/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01324/l3v2/index.heta b/latest/cases/01324/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01324/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01324/model-sbml-l2v5.xml b/latest/cases/01324/model-sbml-l2v5.xml new file mode 100644 index 000000000..2eb3f9fd9 --- /dev/null +++ b/latest/cases/01324/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + 1 + + + + + + + + + + x + 3.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01324/model-sbml-l3v2.xml b/latest/cases/01324/model-sbml-l3v2.xml new file mode 100644 index 000000000..7766b60c8 --- /dev/null +++ b/latest/cases/01324/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + 1 + + + + + + + + + + x + 3.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01324/synopsis.txt b/latest/cases/01324/synopsis.txt new file mode 100644 index 000000000..2b7741f07 --- /dev/null +++ b/latest/cases/01324/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A delayed event using trigger-time values. +componentTags: EventWithDelay, Parameter, RateRule +testTags: EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses trigger-time values, which makes a difference to the results. + +The model contains: +* 2 parameters (x, y) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $x >= 3.5$ | $2$ | $y = x$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $1$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01325/l2v5/build.log b/latest/cases/01325/l2v5/build.log new file mode 100644 index 000000000..00b02f44d --- /dev/null +++ b/latest/cases/01325/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01325/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01325/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01325/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01325/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01325/l2v5/index.heta b/latest/cases/01325/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01325/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01325/l3v2/build.log b/latest/cases/01325/l3v2/build.log new file mode 100644 index 000000000..7f40c75bf --- /dev/null +++ b/latest/cases/01325/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01325/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01325/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01325/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01325/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01325/l3v2/index.heta b/latest/cases/01325/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01325/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01325/model-sbml-l2v5.xml b/latest/cases/01325/model-sbml-l2v5.xml new file mode 100644 index 000000000..a1d353500 --- /dev/null +++ b/latest/cases/01325/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + 1 + + + + + + + + + + x + 3.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01325/model-sbml-l3v2.xml b/latest/cases/01325/model-sbml-l3v2.xml new file mode 100644 index 000000000..d66c2b4ef --- /dev/null +++ b/latest/cases/01325/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + 1 + + + + + + + + + + x + 3.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01325/synopsis.txt b/latest/cases/01325/synopsis.txt new file mode 100644 index 000000000..7106bc104 --- /dev/null +++ b/latest/cases/01325/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A delayed event using assignment-time values. +componentTags: EventWithDelay, Parameter, RateRule +testTags: EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses assignment-time values, which makes a difference to the results. + +The model contains: +* 2 parameters (x, y) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $x >= 3.5$ | Assignment time | $2$ | $y = x$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $1$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01326/l2v5/build.log b/latest/cases/01326/l2v5/build.log new file mode 100644 index 000000000..58632deab --- /dev/null +++ b/latest/cases/01326/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01326/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01326/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01326/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01326/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01326/l2v5/index.heta b/latest/cases/01326/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01326/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01326/l3v2/build.log b/latest/cases/01326/l3v2/build.log new file mode 100644 index 000000000..255108832 --- /dev/null +++ b/latest/cases/01326/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01326/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01326/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01326/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01326/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01326/l3v2/index.heta b/latest/cases/01326/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01326/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01326/model-sbml-l2v5.xml b/latest/cases/01326/model-sbml-l2v5.xml new file mode 100644 index 000000000..701a78487 --- /dev/null +++ b/latest/cases/01326/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + x + 3.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01326/model-sbml-l3v2.xml b/latest/cases/01326/model-sbml-l3v2.xml new file mode 100644 index 000000000..ac0fe69aa --- /dev/null +++ b/latest/cases/01326/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + x + 3.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01326/synopsis.txt b/latest/cases/01326/synopsis.txt new file mode 100644 index 000000000..bad25c5f7 --- /dev/null +++ b/latest/cases/01326/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A delayed event using trigger-time values. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses trigger-time values, which makes a difference to the results. This model is the same as 01324, but with a reaction instead of a rate rule. + +The model contains: +* 1 species (x) +* 1 parameter (y) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> x | $1$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $x >= 3.5$ | $2$ | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species x | $1$ | variable | +| Initial value of parameter y | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01327/l2v5/build.log b/latest/cases/01327/l2v5/build.log new file mode 100644 index 000000000..c22cd96e5 --- /dev/null +++ b/latest/cases/01327/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01327/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01327/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01327/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01327/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01327/l2v5/index.heta b/latest/cases/01327/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01327/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01327/l3v2/build.log b/latest/cases/01327/l3v2/build.log new file mode 100644 index 000000000..94635df49 --- /dev/null +++ b/latest/cases/01327/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01327/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01327/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01327/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01327/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01327/l3v2/index.heta b/latest/cases/01327/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01327/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01327/model-sbml-l2v5.xml b/latest/cases/01327/model-sbml-l2v5.xml new file mode 100644 index 000000000..72472dbae --- /dev/null +++ b/latest/cases/01327/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + x + 3.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01327/model-sbml-l3v2.xml b/latest/cases/01327/model-sbml-l3v2.xml new file mode 100644 index 000000000..44ff99c27 --- /dev/null +++ b/latest/cases/01327/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + x + 3.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01327/synopsis.txt b/latest/cases/01327/synopsis.txt new file mode 100644 index 000000000..e06a6d22f --- /dev/null +++ b/latest/cases/01327/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A delayed event using assignment-time values. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses assignment-time values, which makes a difference to the results. This model is the same as 01325, but with a reaction instead of a rate rule. + +The model contains: +* 1 species (x) +* 1 parameter (y) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> x | $1$ |] + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $x >= 3.5$ | Assignment time | $2$ | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species x | $1$ | variable | +| Initial value of parameter y | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01328/l2v5/build.log b/latest/cases/01328/l2v5/build.log new file mode 100644 index 000000000..fc60eec1d --- /dev/null +++ b/latest/cases/01328/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01328/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01328/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01328/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01328/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01328/l2v5/index.heta b/latest/cases/01328/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01328/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01328/l3v2/build.log b/latest/cases/01328/l3v2/build.log new file mode 100644 index 000000000..cef8a9d70 --- /dev/null +++ b/latest/cases/01328/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01328/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01328/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01328/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01328/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01328/l3v2/index.heta b/latest/cases/01328/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01328/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01328/model-sbml-l2v5.xml b/latest/cases/01328/model-sbml-l2v5.xml new file mode 100644 index 000000000..318d4a91f --- /dev/null +++ b/latest/cases/01328/model-sbml-l2v5.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + time + 3.5 + + + + + + + 7 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01328/model-sbml-l3v2.xml b/latest/cases/01328/model-sbml-l3v2.xml new file mode 100644 index 000000000..7d1fe99e3 --- /dev/null +++ b/latest/cases/01328/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + time + 3.5 + + + + + + + 7 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01328/synopsis.txt b/latest/cases/01328/synopsis.txt new file mode 100644 index 000000000..76216bd03 --- /dev/null +++ b/latest/cases/01328/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A delayed event using trigger-time values. +componentTags: CSymbolTime, EventNoDelay, EventWithDelay, Parameter +testTags: EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses trigger-time values, which makes a difference to the results. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E1 | $time > 3.5$ | $0$ | $x = 7$ | +| E0 | $time > 2.5$ | $2$ | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $1$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01329/l2v5/build.log b/latest/cases/01329/l2v5/build.log new file mode 100644 index 000000000..dcdc637ca --- /dev/null +++ b/latest/cases/01329/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01329/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01329/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01329/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01329/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01329/l2v5/index.heta b/latest/cases/01329/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01329/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01329/l3v2/build.log b/latest/cases/01329/l3v2/build.log new file mode 100644 index 000000000..ab3ffd9e5 --- /dev/null +++ b/latest/cases/01329/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01329/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01329/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01329/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01329/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01329/l3v2/index.heta b/latest/cases/01329/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01329/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01329/model-sbml-l2v5.xml b/latest/cases/01329/model-sbml-l2v5.xml new file mode 100644 index 000000000..d46be5584 --- /dev/null +++ b/latest/cases/01329/model-sbml-l2v5.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + time + 3.5 + + + + + + + 7 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01329/model-sbml-l3v2.xml b/latest/cases/01329/model-sbml-l3v2.xml new file mode 100644 index 000000000..76d14a010 --- /dev/null +++ b/latest/cases/01329/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + time + 3.5 + + + + + + + 7 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + x + + + + + + + diff --git a/latest/cases/01329/synopsis.txt b/latest/cases/01329/synopsis.txt new file mode 100644 index 000000000..eebca46dc --- /dev/null +++ b/latest/cases/01329/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A delayed event using assignment-time values. +componentTags: CSymbolTime, EventNoDelay, EventWithDelay, Parameter +testTags: EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses assignment-time values, which makes a difference to the results. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E1 | $time > 3.5$ | Trigger time | $0$ | $x = 7$ | +| E0 | $time > 2.5$ | Assignment time | $2$ | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $1$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01330/l2v5/index.heta b/latest/cases/01330/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01330/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01330/l3v2/heta-code/output.heta b/latest/cases/01330/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0f9c5867b --- /dev/null +++ b/latest/cases/01330/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +y @Record { } .= 0; +y [E2]= x; + +E1 @DSwitcher { trigger: t > 3.5, }; +E2 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01330/l3v2/index.heta b/latest/cases/01330/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01330/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01330/l3v2/json/output.json b/latest/cases/01330/l3v2/json/output.json new file mode 100644 index 000000000..cad978cda --- /dev/null +++ b/latest/cases/01330/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E1": "7" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "0", + "E2": "x" + } + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 3.5" + }, + { + "class": "DSwitcher", + "id": "E2", + "trigger": "t > 3.5" + } +] \ No newline at end of file diff --git a/latest/cases/01330/model-sbml-l3v2.xml b/latest/cases/01330/model-sbml-l3v2.xml new file mode 100644 index 000000000..74e5393d9 --- /dev/null +++ b/latest/cases/01330/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + time + 3.5 + + + + + + 10 + + + + + + 7 + + + + + + + + + + time + 3.5 + + + + + + 5 + + + + + + x + + + + + + + diff --git a/latest/cases/01330/output.heta b/latest/cases/01330/output.heta new file mode 100644 index 000000000..f349588c0 --- /dev/null +++ b/latest/cases/01330/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: A simultaneous event using trigger-time values. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses trigger-time values, which makes a difference to the results. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E1 | $time > 3.5$ | $10$ | $x = 7$ | +| E2 | $time > 3.5$ | $5$ | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +y @Record { } .= 0; +y [E2]= x; + +E1 @DSwitcher { trigger: t > 3.5, }; +E2 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01330/synopsis.txt b/latest/cases/01330/synopsis.txt new file mode 100644 index 000000000..02f4d599e --- /dev/null +++ b/latest/cases/01330/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A simultaneous event using trigger-time values. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses trigger-time values, which makes a difference to the results. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E1 | $time > 3.5$ | $10$ | $x = 7$ | +| E2 | $time > 3.5$ | $5$ | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01331/l2v5/index.heta b/latest/cases/01331/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01331/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01331/l3v2/heta-code/output.heta b/latest/cases/01331/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0f9c5867b --- /dev/null +++ b/latest/cases/01331/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +y @Record { } .= 0; +y [E2]= x; + +E1 @DSwitcher { trigger: t > 3.5, }; +E2 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01331/l3v2/index.heta b/latest/cases/01331/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01331/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01331/l3v2/json/output.json b/latest/cases/01331/l3v2/json/output.json new file mode 100644 index 000000000..cad978cda --- /dev/null +++ b/latest/cases/01331/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E1": "7" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "0", + "E2": "x" + } + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 3.5" + }, + { + "class": "DSwitcher", + "id": "E2", + "trigger": "t > 3.5" + } +] \ No newline at end of file diff --git a/latest/cases/01331/model-sbml-l3v2.xml b/latest/cases/01331/model-sbml-l3v2.xml new file mode 100644 index 000000000..918925080 --- /dev/null +++ b/latest/cases/01331/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + time + 3.5 + + + + + + 10 + + + + + + 7 + + + + + + + + + + time + 3.5 + + + + + + 5 + + + + + + x + + + + + + + diff --git a/latest/cases/01331/output.heta b/latest/cases/01331/output.heta new file mode 100644 index 000000000..4a95169d3 --- /dev/null +++ b/latest/cases/01331/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: A simultaneous event using assignment-time values. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses assignment-time values, which makes a difference to the results. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Use values from:* | *Event Assignments* | +| E1 | $time > 3.5$ | $10$ | Trigger time | $x = 7$ | +| E2 | $time > 3.5$ | $5$ | Assignment time | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +y @Record { } .= 0; +y [E2]= x; + +E1 @DSwitcher { trigger: t > 3.5, }; +E2 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01331/synopsis.txt b/latest/cases/01331/synopsis.txt new file mode 100644 index 000000000..d08232dbe --- /dev/null +++ b/latest/cases/01331/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A simultaneous event using assignment-time values. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses assignment-time values, which makes a difference to the results. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Use values from:* | *Event Assignments* | +| E1 | $time > 3.5$ | $10$ | Trigger time | $x = 7$ | +| E2 | $time > 3.5$ | $5$ | Assignment time | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01332/l2v5/index.heta b/latest/cases/01332/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01332/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01332/l3v2/heta-code/output.heta b/latest/cases/01332/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e4bd71b6a --- /dev/null +++ b/latest/cases/01332/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +x [E2]= 5; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01332/l3v2/index.heta b/latest/cases/01332/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01332/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01332/l3v2/json/output.json b/latest/cases/01332/l3v2/json/output.json new file mode 100644 index 000000000..5834fd9c5 --- /dev/null +++ b/latest/cases/01332/l3v2/json/output.json @@ -0,0 +1,24 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E1": "7", + "E2": "5" + } + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "x > 2" + }, + { + "class": "DSwitcher", + "id": "E2", + "trigger": "x > 2" + } +] \ No newline at end of file diff --git a/latest/cases/01332/model-sbml-l3v2.xml b/latest/cases/01332/model-sbml-l3v2.xml new file mode 100644 index 000000000..efa9adfd4 --- /dev/null +++ b/latest/cases/01332/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + x + 2 + + + + + + 10 + + + + + + 7 + + + + + + + + + + x + 2 + + + + + + 5 + + + + + + 5 + + + + + + + diff --git a/latest/cases/01332/output.heta b/latest/cases/01332/output.heta new file mode 100644 index 000000000..fbaa85992 --- /dev/null +++ b/latest/cases/01332/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Two events that fire at t0 with different priorities. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events both fire at t0, with different priorities. Since both assign to the same variable, the one with the lower priority sets the value going forward in time. + +The model contains: +* 1 parameter (x) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | false | $x = 7$ | +| E2 | $x > 2$ | $5$ | false | $x = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +x [E2]= 5; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01332/synopsis.txt b/latest/cases/01332/synopsis.txt new file mode 100644 index 000000000..9058e2810 --- /dev/null +++ b/latest/cases/01332/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Two events that fire at t0 with different priorities. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events both fire at t0, with different priorities. Since both assign to the same variable, the one with the lower priority sets the value going forward in time. + +The model contains: +* 1 parameter (x) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | false | $x = 7$ | +| E2 | $x > 2$ | $5$ | false | $x = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01333/l2v5/index.heta b/latest/cases/01333/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01333/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01333/l3v2/heta-code/output.heta b/latest/cases/01333/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c550c9f35 --- /dev/null +++ b/latest/cases/01333/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +y @Record { } .= 0; +y [E2]= x; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01333/l3v2/index.heta b/latest/cases/01333/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01333/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01333/l3v2/json/output.json b/latest/cases/01333/l3v2/json/output.json new file mode 100644 index 000000000..f37b5bca5 --- /dev/null +++ b/latest/cases/01333/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E1": "7" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "0", + "E2": "x" + } + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "x > 2" + }, + { + "class": "DSwitcher", + "id": "E2", + "trigger": "x > 2" + } +] \ No newline at end of file diff --git a/latest/cases/01333/model-sbml-l3v2.xml b/latest/cases/01333/model-sbml-l3v2.xml new file mode 100644 index 000000000..e9e408792 --- /dev/null +++ b/latest/cases/01333/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + x + 2 + + + + + + 10 + + + + + + 7 + + + + + + + + + + x + 2 + + + + + + 5 + + + + + + x + + + + + + + diff --git a/latest/cases/01333/output.heta b/latest/cases/01333/output.heta new file mode 100644 index 000000000..11e965bce --- /dev/null +++ b/latest/cases/01333/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Two events that fire at t0 with different priorities. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventT0Firing, EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events both fire at t0, with different priorities. The first assigns a new value to 'x', and the second assigns the value of 'x' to y, but uses the *trigger* time value, meaning that afterwards, both x and y end up with new values. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | false | $x = 7$ | +| E2 | $x > 2$ | $5$ | false | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +y @Record { } .= 0; +y [E2]= x; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01333/synopsis.txt b/latest/cases/01333/synopsis.txt new file mode 100644 index 000000000..516317987 --- /dev/null +++ b/latest/cases/01333/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Two events that fire at t0 with different priorities. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventT0Firing, EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events both fire at t0, with different priorities. The first assigns a new value to 'x', and the second assigns the value of 'x' to y, but uses the *trigger* time value, meaning that afterwards, both x and y end up with new values. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | false | $x = 7$ | +| E2 | $x > 2$ | $5$ | false | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01334/l2v5/index.heta b/latest/cases/01334/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01334/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01334/l3v2/heta-code/output.heta b/latest/cases/01334/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c550c9f35 --- /dev/null +++ b/latest/cases/01334/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +y @Record { } .= 0; +y [E2]= x; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01334/l3v2/index.heta b/latest/cases/01334/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01334/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01334/l3v2/json/output.json b/latest/cases/01334/l3v2/json/output.json new file mode 100644 index 000000000..f37b5bca5 --- /dev/null +++ b/latest/cases/01334/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E1": "7" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "0", + "E2": "x" + } + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "x > 2" + }, + { + "class": "DSwitcher", + "id": "E2", + "trigger": "x > 2" + } +] \ No newline at end of file diff --git a/latest/cases/01334/model-sbml-l3v2.xml b/latest/cases/01334/model-sbml-l3v2.xml new file mode 100644 index 000000000..8315aa5e7 --- /dev/null +++ b/latest/cases/01334/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + x + 2 + + + + + + 10 + + + + + + 7 + + + + + + + + + + x + 2 + + + + + + 5 + + + + + + x + + + + + + + diff --git a/latest/cases/01334/output.heta b/latest/cases/01334/output.heta new file mode 100644 index 000000000..2ef132587 --- /dev/null +++ b/latest/cases/01334/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Two events that fire at t0 with different priorities. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventT0Firing, EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events both fire at t0, with different priorities. The first assigns a new value to 'x', and the second assigns the value of 'x' to y, using the *assignment* time value, meaning that afterwards, both x and y end up with the same value. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Use values from:* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | false | Trigger time | $x = 7$ | +| E2 | $x > 2$ | $5$ | false | Assignment time | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 7; +y @Record { } .= 0; +y [E2]= x; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01334/synopsis.txt b/latest/cases/01334/synopsis.txt new file mode 100644 index 000000000..976fa1471 --- /dev/null +++ b/latest/cases/01334/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Two events that fire at t0 with different priorities. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventT0Firing, EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events both fire at t0, with different priorities. The first assigns a new value to 'x', and the second assigns the value of 'x' to y, using the *assignment* time value, meaning that afterwards, both x and y end up with the same value. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Use values from:* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | false | Trigger time | $x = 7$ | +| E2 | $x > 2$ | $5$ | false | Assignment time | $y = x$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01335/l2v5/index.heta b/latest/cases/01335/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01335/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01335/l3v2/build.log b/latest/cases/01335/l3v2/build.log new file mode 100644 index 000000000..3758b7515 --- /dev/null +++ b/latest/cases/01335/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01335/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01335/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01335/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01335/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01335/l3v2/index.heta b/latest/cases/01335/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01335/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01335/model-sbml-l3v2.xml b/latest/cases/01335/model-sbml-l3v2.xml new file mode 100644 index 000000000..e5f6f5937 --- /dev/null +++ b/latest/cases/01335/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + x + 2 + + + + + + 2.5 + + + + + + 7 + + + + + + + diff --git a/latest/cases/01335/synopsis.txt b/latest/cases/01335/synopsis.txt new file mode 100644 index 000000000..c7995754e --- /dev/null +++ b/latest/cases/01335/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event delay after triggering at t0. +componentTags: EventWithDelay, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event triggers at t0, and executes after a delay. + +The model contains: +* 1 parameter (x) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Delay* | *Event Assignments* | +| E1 | $x > 2$ | false | $2.5$ | $x = 7$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01336/l2v5/index.heta b/latest/cases/01336/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01336/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01336/l3v2/heta-code/output.heta b/latest/cases/01336/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e94f3dd0a --- /dev/null +++ b/latest/cases/01336/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 0; +y @Record { } .= 6; +y [E2]= 7; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01336/l3v2/index.heta b/latest/cases/01336/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01336/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01336/l3v2/json/output.json b/latest/cases/01336/l3v2/json/output.json new file mode 100644 index 000000000..0cef6b81c --- /dev/null +++ b/latest/cases/01336/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E1": "0" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "6", + "E2": "7" + } + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "x > 2" + }, + { + "class": "DSwitcher", + "id": "E2", + "trigger": "x > 2" + } +] \ No newline at end of file diff --git a/latest/cases/01336/model-sbml-l3v2.xml b/latest/cases/01336/model-sbml-l3v2.xml new file mode 100644 index 000000000..dceff03a1 --- /dev/null +++ b/latest/cases/01336/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + x + 2 + + + + + + 10 + + + + + + 0 + + + + + + + + + + x + 2 + + + + + + 5 + + + + + + 7 + + + + + + + diff --git a/latest/cases/01336/output.heta b/latest/cases/01336/output.heta new file mode 100644 index 000000000..383f928d2 --- /dev/null +++ b/latest/cases/01336/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: Two events that trigger at t0, one of which cancels the other. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events trigger at t0, but the first reverses the trigger of the second, which is set persistent=false, cancelling the event's execution. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *initialValue* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | true | false | $x = 0$ | +| E2 | $x > 2$ | $5$ | false | false | $y = 7$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $6$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 0; +y @Record { } .= 6; +y [E2]= 7; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01336/synopsis.txt b/latest/cases/01336/synopsis.txt new file mode 100644 index 000000000..0b2f68cac --- /dev/null +++ b/latest/cases/01336/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Two events that trigger at t0, one of which cancels the other. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events trigger at t0, but the first reverses the trigger of the second, which is set persistent=false, cancelling the event's execution. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *initialValue* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | true | false | $x = 0$ | +| E2 | $x > 2$ | $5$ | false | false | $y = 7$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $6$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01337/l2v5/index.heta b/latest/cases/01337/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01337/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01337/l3v2/heta-code/output.heta b/latest/cases/01337/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e94f3dd0a --- /dev/null +++ b/latest/cases/01337/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 0; +y @Record { } .= 6; +y [E2]= 7; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01337/l3v2/index.heta b/latest/cases/01337/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01337/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01337/l3v2/json/output.json b/latest/cases/01337/l3v2/json/output.json new file mode 100644 index 000000000..0cef6b81c --- /dev/null +++ b/latest/cases/01337/l3v2/json/output.json @@ -0,0 +1,31 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3", + "E1": "0" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "start_": "6", + "E2": "7" + } + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "x > 2" + }, + { + "class": "DSwitcher", + "id": "E2", + "trigger": "x > 2" + } +] \ No newline at end of file diff --git a/latest/cases/01337/model-sbml-l3v2.xml b/latest/cases/01337/model-sbml-l3v2.xml new file mode 100644 index 000000000..e4798aba4 --- /dev/null +++ b/latest/cases/01337/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + x + 2 + + + + + + 10 + + + + + + 0 + + + + + + + + + + x + 2 + + + + + + 5 + + + + + + 7 + + + + + + + diff --git a/latest/cases/01337/output.heta b/latest/cases/01337/output.heta new file mode 100644 index 000000000..d02cec778 --- /dev/null +++ b/latest/cases/01337/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: Two events that trigger at t0, one of which fails to cancels the other. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventIsPersistent, EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events trigger at t0, and the first reverses the trigger of the second, but it's not set persistent=false, allowing it to continue. + +This is the best test, because it's test 1337. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | false | $x = 0$ | +| E2 | $x > 2$ | $5$ | false | $y = 7$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $6$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { } .= 3; +x [E1]= 0; +y @Record { } .= 6; +y [E2]= 7; + +E1 @DSwitcher { trigger: x > 2, }; +E2 @DSwitcher { trigger: x > 2, }; + diff --git a/latest/cases/01337/synopsis.txt b/latest/cases/01337/synopsis.txt new file mode 100644 index 000000000..04cf94d0f --- /dev/null +++ b/latest/cases/01337/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: Two events that trigger at t0, one of which fails to cancels the other. +componentTags: EventNoDelay, EventPriority, Parameter +testTags: EventIsPersistent, EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events trigger at t0, and the first reverses the trigger of the second, but it's not set persistent=false, allowing it to continue. + +This is the best test, because it's test 1337. + +The model contains: +* 2 parameters (x, y) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* | +| E1 | $x > 2$ | $10$ | false | $x = 0$ | +| E2 | $x > 2$ | $5$ | false | $y = 7$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable | +| Initial value of parameter y | $6$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01338/l2v5/heta-code/output.heta b/latest/cases/01338/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4f6655ada --- /dev/null +++ b/latest/cases/01338/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1; +k1_proc @Process { actors: = k1, }; +k1_proc := (-1); + +k1 @Record { } .= 5; + diff --git a/latest/cases/01338/l2v5/index.heta b/latest/cases/01338/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01338/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01338/l2v5/json/output.json b/latest/cases/01338/l2v5/json/output.json new file mode 100644 index 000000000..47b2332b7 --- /dev/null +++ b/latest/cases/01338/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "5" + } + }, + { + "class": "Process", + "id": "k1_proc", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01338/l3v2/heta-code/output.heta b/latest/cases/01338/l3v2/heta-code/output.heta new file mode 100644 index 000000000..efd45c873 --- /dev/null +++ b/latest/cases/01338/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1; +k1_proc @Process { actors: = k1, }; +k1_proc := (-1); + +k1 @Record { } .= 5; + diff --git a/latest/cases/01338/l3v2/index.heta b/latest/cases/01338/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01338/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01338/l3v2/json/output.json b/latest/cases/01338/l3v2/json/output.json new file mode 100644 index 000000000..1e83d6909 --- /dev/null +++ b/latest/cases/01338/l3v2/json/output.json @@ -0,0 +1,54 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "5" + } + }, + { + "class": "Process", + "id": "k1_proc", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01338/model-sbml-l2v5.xml b/latest/cases/01338/model-sbml-l2v5.xml new file mode 100644 index 000000000..a56db18cb --- /dev/null +++ b/latest/cases/01338/model-sbml-l2v5.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + -1 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01338/model-sbml-l3v2.xml b/latest/cases/01338/model-sbml-l3v2.xml new file mode 100644 index 000000000..bb2898167 --- /dev/null +++ b/latest/cases/01338/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + -1 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01338/output.heta b/latest/cases/01338/output.heta new file mode 100644 index 000000000..e7b7fa45f --- /dev/null +++ b/latest/cases/01338/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Two events that trigger at t0, one of which fails to cancels the other. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a reaction that produces S1 starts off positive, but then goes negative, due to a parameter under control of a rate rule. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1; +k1_proc @Process { actors: = k1, }; +k1_proc := (-1); + +k1 @Record { } .= 5; + diff --git a/latest/cases/01338/synopsis.txt b/latest/cases/01338/synopsis.txt new file mode 100644 index 000000000..e6e169681 --- /dev/null +++ b/latest/cases/01338/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Two events that trigger at t0, one of which fails to cancels the other. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a reaction that produces S1 starts off positive, but then goes negative, due to a parameter under control of a rate rule. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01339/l2v5/heta-code/output.heta b/latest/cases/01339/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4f96ed042 --- /dev/null +++ b/latest/cases/01339/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1; +k1_proc @Process { actors: = k1, }; +k1_proc := 1; + +k1 @Record { } .= -5; + diff --git a/latest/cases/01339/l2v5/index.heta b/latest/cases/01339/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01339/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01339/l2v5/json/output.json b/latest/cases/01339/l2v5/json/output.json new file mode 100644 index 000000000..42d428f7f --- /dev/null +++ b/latest/cases/01339/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "-5" + } + }, + { + "class": "Process", + "id": "k1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01339/l3v2/heta-code/output.heta b/latest/cases/01339/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0d4fe3fbc --- /dev/null +++ b/latest/cases/01339/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1; +k1_proc @Process { actors: = k1, }; +k1_proc := 1; + +k1 @Record { } .= -5; + diff --git a/latest/cases/01339/l3v2/index.heta b/latest/cases/01339/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01339/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01339/l3v2/json/output.json b/latest/cases/01339/l3v2/json/output.json new file mode 100644 index 000000000..4a4536bda --- /dev/null +++ b/latest/cases/01339/l3v2/json/output.json @@ -0,0 +1,54 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "-5" + } + }, + { + "class": "Process", + "id": "k1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "k1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01339/model-sbml-l2v5.xml b/latest/cases/01339/model-sbml-l2v5.xml new file mode 100644 index 000000000..be96cbce6 --- /dev/null +++ b/latest/cases/01339/model-sbml-l2v5.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01339/model-sbml-l3v2.xml b/latest/cases/01339/model-sbml-l3v2.xml new file mode 100644 index 000000000..1f916c708 --- /dev/null +++ b/latest/cases/01339/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + k1 + + + + + + diff --git a/latest/cases/01339/output.heta b/latest/cases/01339/output.heta new file mode 100644 index 000000000..2153bb8e0 --- /dev/null +++ b/latest/cases/01339/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: A reaction whose rate becomes negative. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a reaction that produces S1 starts off negative, but then goes positive, due to a parameter under control of a rate rule. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $-5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1; +k1_proc @Process { actors: = k1, }; +k1_proc := 1; + +k1 @Record { } .= -5; + diff --git a/latest/cases/01339/synopsis.txt b/latest/cases/01339/synopsis.txt new file mode 100644 index 000000000..2bd8634b7 --- /dev/null +++ b/latest/cases/01339/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A reaction whose rate becomes negative. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, NonConstantParameter, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a reaction that produces S1 starts off negative, but then goes positive, due to a parameter under control of a rate rule. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $-5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01340/l2v5/heta-code/output.heta b/latest/cases/01340/l2v5/heta-code/output.heta new file mode 100644 index 000000000..98d41c830 --- /dev/null +++ b/latest/cases/01340/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1; + +k1 @Record { } .= 1; +k1 [_E0]= (-1); + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01340/l2v5/index.heta b/latest/cases/01340/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01340/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01340/l2v5/json/output.json b/latest/cases/01340/l2v5/json/output.json new file mode 100644 index 000000000..993ec0632 --- /dev/null +++ b/latest/cases/01340/l2v5/json/output.json @@ -0,0 +1,72 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1", + "_E0": "(-1)" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 5.5" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01340/l3v2/heta-code/output.heta b/latest/cases/01340/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5b9e9d602 --- /dev/null +++ b/latest/cases/01340/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1; + +k1 @Record { } .= 1; +k1 [_E0]= (-1); + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01340/l3v2/index.heta b/latest/cases/01340/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01340/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01340/l3v2/json/output.json b/latest/cases/01340/l3v2/json/output.json new file mode 100644 index 000000000..8ca4c8cd1 --- /dev/null +++ b/latest/cases/01340/l3v2/json/output.json @@ -0,0 +1,47 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "1", + "_E0": "(-1)" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 5.5" + } +] \ No newline at end of file diff --git a/latest/cases/01340/model-sbml-l2v5.xml b/latest/cases/01340/model-sbml-l2v5.xml new file mode 100644 index 000000000..91a4e600c --- /dev/null +++ b/latest/cases/01340/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + time + 5.5 + + + + + + + -1 + + + + + + + diff --git a/latest/cases/01340/model-sbml-l3v2.xml b/latest/cases/01340/model-sbml-l3v2.xml new file mode 100644 index 000000000..7b40e9560 --- /dev/null +++ b/latest/cases/01340/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + time + 5.5 + + + + + + + -1 + + + + + + + diff --git a/latest/cases/01340/output.heta b/latest/cases/01340/output.heta new file mode 100644 index 000000000..0d328c1a8 --- /dev/null +++ b/latest/cases/01340/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: A reaction whose rate goes negative due to an event. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a reaction that produces S1 starts off positive, but then goes negative, due to an event. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $k1 = -1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1; + +k1 @Record { } .= 1; +k1 [_E0]= (-1); + +_E0 @DSwitcher { trigger: t > 5.5, }; + diff --git a/latest/cases/01340/synopsis.txt b/latest/cases/01340/synopsis.txt new file mode 100644 index 000000000..5a1bd6978 --- /dev/null +++ b/latest/cases/01340/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A reaction whose rate goes negative due to an event. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, NonConstantParameter, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a reaction that produces S1 starts off positive, but then goes negative, due to an event. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 5.5$ | $k1 = -1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01341/l2v5/heta-code/output.heta b/latest/cases/01341/l2v5/heta-code/output.heta new file mode 100644 index 000000000..d44311908 --- /dev/null +++ b/latest/cases/01341/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2; + diff --git a/latest/cases/01341/l2v5/index.heta b/latest/cases/01341/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01341/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01341/l2v5/json/output.json b/latest/cases/01341/l2v5/json/output.json new file mode 100644 index 000000000..8141aeada --- /dev/null +++ b/latest/cases/01341/l2v5/json/output.json @@ -0,0 +1,46 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01341/l3v2/heta-code/output.heta b/latest/cases/01341/l3v2/heta-code/output.heta new file mode 100644 index 000000000..58e64417f --- /dev/null +++ b/latest/cases/01341/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2; + diff --git a/latest/cases/01341/l3v2/index.heta b/latest/cases/01341/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01341/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01341/l3v2/json/output.json b/latest/cases/01341/l3v2/json/output.json new file mode 100644 index 000000000..535709b43 --- /dev/null +++ b/latest/cases/01341/l3v2/json/output.json @@ -0,0 +1,21 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01341/model-sbml-l2v5.xml b/latest/cases/01341/model-sbml-l2v5.xml new file mode 100644 index 000000000..81ef78d1e --- /dev/null +++ b/latest/cases/01341/model-sbml-l2v5.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01341/model-sbml-l3v2.xml b/latest/cases/01341/model-sbml-l3v2.xml new file mode 100644 index 000000000..a60d0f0e3 --- /dev/null +++ b/latest/cases/01341/model-sbml-l3v2.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/latest/cases/01341/output.heta b/latest/cases/01341/output.heta new file mode 100644 index 000000000..8da5b868a --- /dev/null +++ b/latest/cases/01341/output.heta @@ -0,0 +1,34 @@ +/* +category: Test +synopsis: Just a compartment and a species. +componentTags: Compartment, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model test the simple existence of a species and a compartment. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2; + diff --git a/latest/cases/01341/synopsis.txt b/latest/cases/01341/synopsis.txt new file mode 100644 index 000000000..045b0d894 --- /dev/null +++ b/latest/cases/01341/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Just a compartment and a species. +componentTags: Compartment, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model test the simple existence of a species and a compartment. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01342/l2v5/heta-code/output.heta b/latest/cases/01342/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ef5302e06 --- /dev/null +++ b/latest/cases/01342/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, } .= 2 / C; + diff --git a/latest/cases/01342/l2v5/index.heta b/latest/cases/01342/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01342/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01342/l2v5/json/output.json b/latest/cases/01342/l2v5/json/output.json new file mode 100644 index 000000000..53d678d31 --- /dev/null +++ b/latest/cases/01342/l2v5/json/output.json @@ -0,0 +1,46 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01342/l3v2/heta-code/output.heta b/latest/cases/01342/l3v2/heta-code/output.heta new file mode 100644 index 000000000..212b15e2c --- /dev/null +++ b/latest/cases/01342/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, } .= 2 / C; + diff --git a/latest/cases/01342/l3v2/index.heta b/latest/cases/01342/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01342/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01342/l3v2/json/output.json b/latest/cases/01342/l3v2/json/output.json new file mode 100644 index 000000000..4b6a4ad38 --- /dev/null +++ b/latest/cases/01342/l3v2/json/output.json @@ -0,0 +1,21 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01342/model-sbml-l2v5.xml b/latest/cases/01342/model-sbml-l2v5.xml new file mode 100644 index 000000000..17a38b9de --- /dev/null +++ b/latest/cases/01342/model-sbml-l2v5.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01342/model-sbml-l3v2.xml b/latest/cases/01342/model-sbml-l3v2.xml new file mode 100644 index 000000000..1810cb0d9 --- /dev/null +++ b/latest/cases/01342/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01342/output.heta b/latest/cases/01342/output.heta new file mode 100644 index 000000000..b6390209d --- /dev/null +++ b/latest/cases/01342/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: Just a non-unity compartment and a species. +componentTags: Compartment, Species +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model test the simple existence of a species and a non-unity compartment. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, } .= 2 / C; + diff --git a/latest/cases/01342/synopsis.txt b/latest/cases/01342/synopsis.txt new file mode 100644 index 000000000..79b476485 --- /dev/null +++ b/latest/cases/01342/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Just a non-unity compartment and a species. +componentTags: Compartment, Species +testTags: Amount, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model test the simple existence of a species and a non-unity compartment. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01343/l2v5/build.log b/latest/cases/01343/l2v5/build.log new file mode 100644 index 000000000..405943fb1 --- /dev/null +++ b/latest/cases/01343/l2v5/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01343/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01343/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01343/model-sbml-l2v5.xml"... +[info] Setting references in elements, total length 88 +[error] FunctionDef "tanh" is not found as expected here: P1 { math: undefined }; +[error] FunctionDef "tanh" is not found as expected here: P2 { math: undefined }; +[error] FunctionDef "tanh" is not found as expected here: P3 { math: undefined }; +[error] FunctionDef "tanh" is not found as expected here: P4 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01343/l2v5/index.heta b/latest/cases/01343/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01343/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01343/l3v2/build.log b/latest/cases/01343/l3v2/build.log new file mode 100644 index 000000000..ec8d92d84 --- /dev/null +++ b/latest/cases/01343/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01343/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01343/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01343/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 83 +[error] No required "num" property for "P1" of Const. +[error] FunctionDef "tanh" is not found as expected here: P2 { math: undefined }; +[error] FunctionDef "tanh" is not found as expected here: P3 { math: undefined }; +[error] FunctionDef "tanh" is not found as expected here: P4 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01343/l3v2/index.heta b/latest/cases/01343/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01343/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01343/model-sbml-l2v5.xml b/latest/cases/01343/model-sbml-l2v5.xml new file mode 100644 index 000000000..85b018204 --- /dev/null +++ b/latest/cases/01343/model-sbml-l2v5.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + 0.3 + + + + + + + + + + -0.4 + + + + + + + + time + + + + + + + + + + time + + + + + + + diff --git a/latest/cases/01343/model-sbml-l3v2.xml b/latest/cases/01343/model-sbml-l3v2.xml new file mode 100644 index 000000000..956e74113 --- /dev/null +++ b/latest/cases/01343/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + 0.3 + + + + + + + + + + -0.4 + + + + + + + + time + + + + + + + + + + time + + + + + + + diff --git a/latest/cases/01343/synopsis.txt b/latest/cases/01343/synopsis.txt new file mode 100644 index 000000000..42ef37b04 --- /dev/null +++ b/latest/cases/01343/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A test of 'tanh' in different contexts +componentTags: AssignmentRule, CSymbolTime, InitialAssignment, Parameter +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the 'tanh' MathML function in various contexts. It was mistakenly omitted from tests 957-959. + +The model contains: +* 4 parameters (P1, P2, P3, P4) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P2 | $tanh(-0.4)$ | +| Assignment | P3 | $tanh(time)$ | +| Assignment | P4 | $tanh(-time)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $tanh(0.3)$ | constant | +| Initial value of parameter P2 | $tanh(-0.4)$ | variable | +| Initial value of parameter P3 | $tanh(time)$ | variable | +| Initial value of parameter P4 | $tanh(-time)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01344/l2v5/index.heta b/latest/cases/01344/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01344/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01344/l3v2/heta-code/output.heta b/latest/cases/01344/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e566a1950 --- /dev/null +++ b/latest/cases/01344/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01344/l3v2/index.heta b/latest/cases/01344/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01344/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01344/l3v2/json/output.json b/latest/cases/01344/l3v2/json/output.json new file mode 100644 index 000000000..181be3b22 --- /dev/null +++ b/latest/cases/01344/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01344/model-sbml-l3v2.xml b/latest/cases/01344/model-sbml-l3v2.xml new file mode 100644 index 000000000..e01fa3ca9 --- /dev/null +++ b/latest/cases/01344/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01344/output.heta b/latest/cases/01344/output.heta new file mode 100644 index 000000000..158384cd4 --- /dev/null +++ b/latest/cases/01344/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A replaced reaction whose ID is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel reaction ID is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $J1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01344/synopsis.txt b/latest/cases/01344/synopsis.txt new file mode 100644 index 000000000..6e002a29a --- /dev/null +++ b/latest/cases/01344/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A replaced reaction whose ID is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel reaction ID is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $J1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01345/l2v5/index.heta b/latest/cases/01345/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01345/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01345/l3v2/heta-code/output.heta b/latest/cases/01345/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e566a1950 --- /dev/null +++ b/latest/cases/01345/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01345/l3v2/index.heta b/latest/cases/01345/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01345/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01345/l3v2/json/output.json b/latest/cases/01345/l3v2/json/output.json new file mode 100644 index 000000000..181be3b22 --- /dev/null +++ b/latest/cases/01345/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01345/model-sbml-l3v2.xml b/latest/cases/01345/model-sbml-l3v2.xml new file mode 100644 index 000000000..85f22e236 --- /dev/null +++ b/latest/cases/01345/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + 2 + + + + + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01345/output.heta b/latest/cases/01345/output.heta new file mode 100644 index 000000000..8609e8c57 --- /dev/null +++ b/latest/cases/01345/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: A replaced reaction whose ID is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $J1 + 2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01345/synopsis.txt b/latest/cases/01345/synopsis.txt new file mode 100644 index 000000000..cd434f273 --- /dev/null +++ b/latest/cases/01345/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A replaced reaction whose ID is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $J1 + 2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01346/l2v5/index.heta b/latest/cases/01346/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01346/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01346/l3v2/heta-code/output.heta b/latest/cases/01346/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e566a1950 --- /dev/null +++ b/latest/cases/01346/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01346/l3v2/index.heta b/latest/cases/01346/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01346/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01346/l3v2/json/output.json b/latest/cases/01346/l3v2/json/output.json new file mode 100644 index 000000000..181be3b22 --- /dev/null +++ b/latest/cases/01346/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01346/model-sbml-l3v2.xml b/latest/cases/01346/model-sbml-l3v2.xml new file mode 100644 index 000000000..639c59ba2 --- /dev/null +++ b/latest/cases/01346/model-sbml-l3v2.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + time + + + J0 + 0.5 + + + + + + + + 4 + + + + + + + + diff --git a/latest/cases/01346/output.heta b/latest/cases/01346/output.heta new file mode 100644 index 000000000..d4fb6cace --- /dev/null +++ b/latest/cases/01346/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A replaced reaction whose ID is used in an event trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01346/synopsis.txt b/latest/cases/01346/synopsis.txt new file mode 100644 index 000000000..e67a51f63 --- /dev/null +++ b/latest/cases/01346/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A replaced reaction whose ID is used in an event trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01347/l2v5/index.heta b/latest/cases/01347/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01347/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01347/l3v2/heta-code/output.heta b/latest/cases/01347/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e566a1950 --- /dev/null +++ b/latest/cases/01347/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01347/l3v2/index.heta b/latest/cases/01347/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01347/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01347/l3v2/json/output.json b/latest/cases/01347/l3v2/json/output.json new file mode 100644 index 000000000..181be3b22 --- /dev/null +++ b/latest/cases/01347/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01347/model-sbml-l3v2.xml b/latest/cases/01347/model-sbml-l3v2.xml new file mode 100644 index 000000000..1d6c9f8f0 --- /dev/null +++ b/latest/cases/01347/model-sbml-l3v2.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + time + 5.5 + + + + + + J0 + + + + + + 4 + + + + + + + + + + time + 5.5 + + + + + + 4 + + + + + + 10 + + + + + + + + diff --git a/latest/cases/01347/output.heta b/latest/cases/01347/output.heta new file mode 100644 index 000000000..08c6e6ade --- /dev/null +++ b/latest/cases/01347/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A replaced reaction whose ID is used in am event priority. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an event priority. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ | +| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01347/synopsis.txt b/latest/cases/01347/synopsis.txt new file mode 100644 index 000000000..2fe5cc56a --- /dev/null +++ b/latest/cases/01347/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A replaced reaction whose ID is used in am event priority. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an event priority. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ | +| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01348/l2v5/index.heta b/latest/cases/01348/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01348/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01348/l3v2/heta-code/output.heta b/latest/cases/01348/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e566a1950 --- /dev/null +++ b/latest/cases/01348/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01348/l3v2/index.heta b/latest/cases/01348/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01348/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01348/l3v2/json/output.json b/latest/cases/01348/l3v2/json/output.json new file mode 100644 index 000000000..181be3b22 --- /dev/null +++ b/latest/cases/01348/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01348/model-sbml-l3v2.xml b/latest/cases/01348/model-sbml-l3v2.xml new file mode 100644 index 000000000..769917b2f --- /dev/null +++ b/latest/cases/01348/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + time + 5.5 + + + + + + + J0 + + + + + + + + diff --git a/latest/cases/01348/output.heta b/latest/cases/01348/output.heta new file mode 100644 index 000000000..60b64ee8d --- /dev/null +++ b/latest/cases/01348/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A replaced reaction whose ID is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01348/synopsis.txt b/latest/cases/01348/synopsis.txt new file mode 100644 index 000000000..0e8d7aded --- /dev/null +++ b/latest/cases/01348/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A replaced reaction whose ID is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01349/l2v5/index.heta b/latest/cases/01349/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01349/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01349/l3v2/heta-code/output.heta b/latest/cases/01349/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e566a1950 --- /dev/null +++ b/latest/cases/01349/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01349/l3v2/index.heta b/latest/cases/01349/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01349/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01349/l3v2/json/output.json b/latest/cases/01349/l3v2/json/output.json new file mode 100644 index 000000000..181be3b22 --- /dev/null +++ b/latest/cases/01349/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01349/model-sbml-l3v2.xml b/latest/cases/01349/model-sbml-l3v2.xml new file mode 100644 index 000000000..b8598dfd8 --- /dev/null +++ b/latest/cases/01349/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + time + 0.5 + + + + + + J0 + + + + + + 2 + + + + + + + + diff --git a/latest/cases/01349/output.heta b/latest/cases/01349/output.heta new file mode 100644 index 000000000..9b596c120 --- /dev/null +++ b/latest/cases/01349/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A replaced reaction whose ID is used in an event delay. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an event delay. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01349/synopsis.txt b/latest/cases/01349/synopsis.txt new file mode 100644 index 000000000..befaee53d --- /dev/null +++ b/latest/cases/01349/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A replaced reaction whose ID is used in an event delay. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced reaction ID is used in an event delay. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01350/l2v5/index.heta b/latest/cases/01350/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01350/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01350/l3v2/heta-code/output.heta b/latest/cases/01350/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e566a1950 --- /dev/null +++ b/latest/cases/01350/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01350/l3v2/index.heta b/latest/cases/01350/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01350/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01350/l3v2/json/output.json b/latest/cases/01350/l3v2/json/output.json new file mode 100644 index 000000000..181be3b22 --- /dev/null +++ b/latest/cases/01350/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01350/model-sbml-l3v2.xml b/latest/cases/01350/model-sbml-l3v2.xml new file mode 100644 index 000000000..dc67dcde1 --- /dev/null +++ b/latest/cases/01350/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + x + J0 + + + + + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01350/output.heta b/latest/cases/01350/output.heta new file mode 100644 index 000000000..8797a5a61 --- /dev/null +++ b/latest/cases/01350/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A replaced reaction whose ID is used in an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel reaction ID is used in an algebraic rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $A__x - J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01350/synopsis.txt b/latest/cases/01350/synopsis.txt new file mode 100644 index 000000000..5edbc62c4 --- /dev/null +++ b/latest/cases/01350/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A replaced reaction whose ID is used in an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel reaction ID is used in an algebraic rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $A__x - J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01351/l2v5/index.heta b/latest/cases/01351/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01351/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01351/l3v2/heta-code/output.heta b/latest/cases/01351/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e566a1950 --- /dev/null +++ b/latest/cases/01351/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01351/l3v2/index.heta b/latest/cases/01351/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01351/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01351/l3v2/json/output.json b/latest/cases/01351/l3v2/json/output.json new file mode 100644 index 000000000..181be3b22 --- /dev/null +++ b/latest/cases/01351/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01351/model-sbml-l3v2.xml b/latest/cases/01351/model-sbml-l3v2.xml new file mode 100644 index 000000000..d19e4e32a --- /dev/null +++ b/latest/cases/01351/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + J0 + + + + + + + diff --git a/latest/cases/01351/output.heta b/latest/cases/01351/output.heta new file mode 100644 index 000000000..700d10431 --- /dev/null +++ b/latest/cases/01351/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: A replaced reaction whose ID is used in a reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel reaction ID is used in another reaction. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 compartment (C) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ | +| A__J2: S1 -> | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01351/synopsis.txt b/latest/cases/01351/synopsis.txt new file mode 100644 index 000000000..dd42f60c4 --- /dev/null +++ b/latest/cases/01351/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A replaced reaction whose ID is used in a reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel reaction ID is used in another reaction. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 compartment (C) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ | +| A__J2: S1 -> | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01352/l2v5/index.heta b/latest/cases/01352/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01352/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01352/l3v2/heta-code/output.heta b/latest/cases/01352/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e566a1950 --- /dev/null +++ b/latest/cases/01352/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01352/l3v2/index.heta b/latest/cases/01352/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01352/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01352/l3v2/json/output.json b/latest/cases/01352/l3v2/json/output.json new file mode 100644 index 000000000..181be3b22 --- /dev/null +++ b/latest/cases/01352/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01352/model-sbml-l3v2.xml b/latest/cases/01352/model-sbml-l3v2.xml new file mode 100644 index 000000000..2959e82f7 --- /dev/null +++ b/latest/cases/01352/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01352/output.heta b/latest/cases/01352/output.heta new file mode 100644 index 000000000..745e512f2 --- /dev/null +++ b/latest/cases/01352/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A replaced reaction whose ID is used in a rate rule. +componentTags: Compartment, Parameter, RateRule, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel reaction ID is used in a rate rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = S1, }; +J1 := 5; + diff --git a/latest/cases/01352/synopsis.txt b/latest/cases/01352/synopsis.txt new file mode 100644 index 000000000..55b6d3abe --- /dev/null +++ b/latest/cases/01352/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A replaced reaction whose ID is used in a rate rule. +componentTags: Compartment, Parameter, RateRule, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel reaction ID is used in a rate rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01353/l2v5/index.heta b/latest/cases/01353/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01353/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01353/l3v2/heta-code/output.heta b/latest/cases/01353/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f64ed6e02 --- /dev/null +++ b/latest/cases/01353/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01353/l3v2/index.heta b/latest/cases/01353/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01353/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01353/l3v2/json/output.json b/latest/cases/01353/l3v2/json/output.json new file mode 100644 index 000000000..68d0db6e5 --- /dev/null +++ b/latest/cases/01353/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "J1", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01353/model-sbml-l3v2.xml b/latest/cases/01353/model-sbml-l3v2.xml new file mode 100644 index 000000000..795fd21c0 --- /dev/null +++ b/latest/cases/01353/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + diff --git a/latest/cases/01353/output.heta b/latest/cases/01353/output.heta new file mode 100644 index 000000000..0126d6309 --- /dev/null +++ b/latest/cases/01353/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A replaced parameter whose ID is used in an assignment rule. +componentTags: AssignmentRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel parameter ID is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $J1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01353/synopsis.txt b/latest/cases/01353/synopsis.txt new file mode 100644 index 000000000..95b45141c --- /dev/null +++ b/latest/cases/01353/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A replaced parameter whose ID is used in an assignment rule. +componentTags: AssignmentRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel parameter ID is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $J1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01354/l2v5/index.heta b/latest/cases/01354/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01354/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01354/l3v2/heta-code/output.heta b/latest/cases/01354/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f64ed6e02 --- /dev/null +++ b/latest/cases/01354/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01354/l3v2/index.heta b/latest/cases/01354/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01354/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01354/l3v2/json/output.json b/latest/cases/01354/l3v2/json/output.json new file mode 100644 index 000000000..68d0db6e5 --- /dev/null +++ b/latest/cases/01354/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "J1", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01354/model-sbml-l3v2.xml b/latest/cases/01354/model-sbml-l3v2.xml new file mode 100644 index 000000000..9a8d35d3f --- /dev/null +++ b/latest/cases/01354/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + 2 + + + + + + + diff --git a/latest/cases/01354/output.heta b/latest/cases/01354/output.heta new file mode 100644 index 000000000..e844917ec --- /dev/null +++ b/latest/cases/01354/output.heta @@ -0,0 +1,31 @@ +/* +category: Test +synopsis: A replaced parameter whose ID is used in an initial assignment. +componentTags: InitialAssignment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $J1 + 2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01354/synopsis.txt b/latest/cases/01354/synopsis.txt new file mode 100644 index 000000000..43de57914 --- /dev/null +++ b/latest/cases/01354/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: A replaced parameter whose ID is used in an initial assignment. +componentTags: InitialAssignment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $J1 + 2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01355/l2v5/index.heta b/latest/cases/01355/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01355/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01355/l3v2/heta-code/output.heta b/latest/cases/01355/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f64ed6e02 --- /dev/null +++ b/latest/cases/01355/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01355/l3v2/index.heta b/latest/cases/01355/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01355/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01355/l3v2/json/output.json b/latest/cases/01355/l3v2/json/output.json new file mode 100644 index 000000000..68d0db6e5 --- /dev/null +++ b/latest/cases/01355/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "J1", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01355/model-sbml-l3v2.xml b/latest/cases/01355/model-sbml-l3v2.xml new file mode 100644 index 000000000..e50a12f56 --- /dev/null +++ b/latest/cases/01355/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + J0 + 0.5 + + + + + + + + 4 + + + + + + + + diff --git a/latest/cases/01355/output.heta b/latest/cases/01355/output.heta new file mode 100644 index 000000000..6989123be --- /dev/null +++ b/latest/cases/01355/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A replaced parameter whose ID is used in an event trigger. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01355/synopsis.txt b/latest/cases/01355/synopsis.txt new file mode 100644 index 000000000..d0fa757a0 --- /dev/null +++ b/latest/cases/01355/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A replaced parameter whose ID is used in an event trigger. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01356/l2v5/index.heta b/latest/cases/01356/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01356/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01356/l3v2/heta-code/output.heta b/latest/cases/01356/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f64ed6e02 --- /dev/null +++ b/latest/cases/01356/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01356/l3v2/index.heta b/latest/cases/01356/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01356/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01356/l3v2/json/output.json b/latest/cases/01356/l3v2/json/output.json new file mode 100644 index 000000000..68d0db6e5 --- /dev/null +++ b/latest/cases/01356/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "J1", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01356/model-sbml-l3v2.xml b/latest/cases/01356/model-sbml-l3v2.xml new file mode 100644 index 000000000..56c5ae8d4 --- /dev/null +++ b/latest/cases/01356/model-sbml-l3v2.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 5.5 + + + + + + J0 + + + + + + 4 + + + + + + + + + + time + 5.5 + + + + + + 4 + + + + + + 10 + + + + + + + + diff --git a/latest/cases/01356/output.heta b/latest/cases/01356/output.heta new file mode 100644 index 000000000..c1ef62083 --- /dev/null +++ b/latest/cases/01356/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: A replaced parameter whose ID is used in an event priority. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an event priority. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ | +| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01356/synopsis.txt b/latest/cases/01356/synopsis.txt new file mode 100644 index 000000000..34895e560 --- /dev/null +++ b/latest/cases/01356/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A replaced parameter whose ID is used in an event priority. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an event priority. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ | +| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01357/l2v5/index.heta b/latest/cases/01357/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01357/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01357/l3v2/heta-code/output.heta b/latest/cases/01357/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f64ed6e02 --- /dev/null +++ b/latest/cases/01357/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01357/l3v2/index.heta b/latest/cases/01357/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01357/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01357/l3v2/json/output.json b/latest/cases/01357/l3v2/json/output.json new file mode 100644 index 000000000..68d0db6e5 --- /dev/null +++ b/latest/cases/01357/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "J1", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01357/model-sbml-l3v2.xml b/latest/cases/01357/model-sbml-l3v2.xml new file mode 100644 index 000000000..c99b8a8e7 --- /dev/null +++ b/latest/cases/01357/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 5.5 + + + + + + + J0 + + + + + + + + diff --git a/latest/cases/01357/output.heta b/latest/cases/01357/output.heta new file mode 100644 index 000000000..6801c4a9c --- /dev/null +++ b/latest/cases/01357/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A replaced parameter whose ID is used in an event assignment. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01357/synopsis.txt b/latest/cases/01357/synopsis.txt new file mode 100644 index 000000000..f7443b0ed --- /dev/null +++ b/latest/cases/01357/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A replaced parameter whose ID is used in an event assignment. +componentTags: CSymbolTime, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01358/l2v5/index.heta b/latest/cases/01358/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01358/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01358/l3v2/heta-code/output.heta b/latest/cases/01358/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f64ed6e02 --- /dev/null +++ b/latest/cases/01358/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01358/l3v2/index.heta b/latest/cases/01358/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01358/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01358/l3v2/json/output.json b/latest/cases/01358/l3v2/json/output.json new file mode 100644 index 000000000..68d0db6e5 --- /dev/null +++ b/latest/cases/01358/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "J1", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01358/model-sbml-l3v2.xml b/latest/cases/01358/model-sbml-l3v2.xml new file mode 100644 index 000000000..3dd6f687d --- /dev/null +++ b/latest/cases/01358/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 0.5 + + + + + + J0 + + + + + + 2 + + + + + + + + diff --git a/latest/cases/01358/output.heta b/latest/cases/01358/output.heta new file mode 100644 index 000000000..5083d3317 --- /dev/null +++ b/latest/cases/01358/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A replaced parameter whose ID is used in an event delay. +componentTags: CSymbolTime, EventWithDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an event delay. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01358/synopsis.txt b/latest/cases/01358/synopsis.txt new file mode 100644 index 000000000..59955c75e --- /dev/null +++ b/latest/cases/01358/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A replaced parameter whose ID is used in an event delay. +componentTags: CSymbolTime, EventWithDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced parameter ID is used in an event delay. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01359/l2v5/index.heta b/latest/cases/01359/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01359/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01359/l3v2/heta-code/output.heta b/latest/cases/01359/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f64ed6e02 --- /dev/null +++ b/latest/cases/01359/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01359/l3v2/index.heta b/latest/cases/01359/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01359/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01359/l3v2/json/output.json b/latest/cases/01359/l3v2/json/output.json new file mode 100644 index 000000000..68d0db6e5 --- /dev/null +++ b/latest/cases/01359/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "J1", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01359/model-sbml-l3v2.xml b/latest/cases/01359/model-sbml-l3v2.xml new file mode 100644 index 000000000..5c8b0c30c --- /dev/null +++ b/latest/cases/01359/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + x + J0 + + + + + + + diff --git a/latest/cases/01359/output.heta b/latest/cases/01359/output.heta new file mode 100644 index 000000000..e0c4b5763 --- /dev/null +++ b/latest/cases/01359/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A replaced parameter whose ID is used in an algebraic rule. +componentTags: AlgebraicRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel parameter ID is used in an algebraic rule. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $A__x - J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01359/synopsis.txt b/latest/cases/01359/synopsis.txt new file mode 100644 index 000000000..adf9b95c4 --- /dev/null +++ b/latest/cases/01359/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A replaced parameter whose ID is used in an algebraic rule. +componentTags: AlgebraicRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel parameter ID is used in an algebraic rule. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $A__x - J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01360/l2v5/index.heta b/latest/cases/01360/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01360/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01360/l3v2/heta-code/output.heta b/latest/cases/01360/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2d9455174 --- /dev/null +++ b/latest/cases/01360/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Const { } = 5; + diff --git a/latest/cases/01360/l3v2/index.heta b/latest/cases/01360/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01360/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01360/l3v2/json/output.json b/latest/cases/01360/l3v2/json/output.json new file mode 100644 index 000000000..7f79548f7 --- /dev/null +++ b/latest/cases/01360/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "J1", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01360/model-sbml-l3v2.xml b/latest/cases/01360/model-sbml-l3v2.xml new file mode 100644 index 000000000..bfa434c8c --- /dev/null +++ b/latest/cases/01360/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + + diff --git a/latest/cases/01360/output.heta b/latest/cases/01360/output.heta new file mode 100644 index 000000000..fdd0fc909 --- /dev/null +++ b/latest/cases/01360/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: A replaced parameter whose ID is used in a reaction. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel parameter ID is used in a reaction. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (J1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__J2: -> S1 | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter J1 | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Const { } = 5; + diff --git a/latest/cases/01360/synopsis.txt b/latest/cases/01360/synopsis.txt new file mode 100644 index 000000000..3147f88c8 --- /dev/null +++ b/latest/cases/01360/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A replaced parameter whose ID is used in a reaction. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel parameter ID is used in a reaction. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (J1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__J2: -> S1 | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter J1 | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01361/l2v5/index.heta b/latest/cases/01361/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01361/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01361/l3v2/heta-code/output.heta b/latest/cases/01361/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f64ed6e02 --- /dev/null +++ b/latest/cases/01361/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01361/l3v2/index.heta b/latest/cases/01361/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01361/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01361/l3v2/json/output.json b/latest/cases/01361/l3v2/json/output.json new file mode 100644 index 000000000..68d0db6e5 --- /dev/null +++ b/latest/cases/01361/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "J1", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01361/model-sbml-l3v2.xml b/latest/cases/01361/model-sbml-l3v2.xml new file mode 100644 index 000000000..a8f9ad205 --- /dev/null +++ b/latest/cases/01361/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + diff --git a/latest/cases/01361/output.heta b/latest/cases/01361/output.heta new file mode 100644 index 000000000..bed454f5f --- /dev/null +++ b/latest/cases/01361/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A replaced parameter whose ID is used in a rate rule. +componentTags: Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel parameter ID is used in a rate rule. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Const { } = 5; + diff --git a/latest/cases/01361/synopsis.txt b/latest/cases/01361/synopsis.txt new file mode 100644 index 000000000..e528d72f6 --- /dev/null +++ b/latest/cases/01361/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A replaced parameter whose ID is used in a rate rule. +componentTags: Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel parameter ID is used in a rate rule. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (J1, A__x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter J1 | $5$ | constant | +| Initial value of parameter A__x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01362/l2v5/index.heta b/latest/cases/01362/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01362/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01362/l3v2/heta-code/output.heta b/latest/cases/01362/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9e50fdf9 --- /dev/null +++ b/latest/cases/01362/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01362/l3v2/index.heta b/latest/cases/01362/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01362/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01362/l3v2/json/output.json b/latest/cases/01362/l3v2/json/output.json new file mode 100644 index 000000000..7f1e6722f --- /dev/null +++ b/latest/cases/01362/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01362/model-sbml-l3v2.xml b/latest/cases/01362/model-sbml-l3v2.xml new file mode 100644 index 000000000..3c13872a9 --- /dev/null +++ b/latest/cases/01362/model-sbml-l3v2.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + diff --git a/latest/cases/01362/output.heta b/latest/cases/01362/output.heta new file mode 100644 index 000000000..ad6d3cf58 --- /dev/null +++ b/latest/cases/01362/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: A replaced compartment whose ID is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel compartment ID is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $J1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01362/synopsis.txt b/latest/cases/01362/synopsis.txt new file mode 100644 index 000000000..e406cc85e --- /dev/null +++ b/latest/cases/01362/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A replaced compartment whose ID is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel compartment ID is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $J1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01363/l2v5/index.heta b/latest/cases/01363/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01363/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01363/l3v2/heta-code/output.heta b/latest/cases/01363/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9e50fdf9 --- /dev/null +++ b/latest/cases/01363/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01363/l3v2/index.heta b/latest/cases/01363/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01363/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01363/l3v2/json/output.json b/latest/cases/01363/l3v2/json/output.json new file mode 100644 index 000000000..7f1e6722f --- /dev/null +++ b/latest/cases/01363/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01363/model-sbml-l3v2.xml b/latest/cases/01363/model-sbml-l3v2.xml new file mode 100644 index 000000000..00ab84265 --- /dev/null +++ b/latest/cases/01363/model-sbml-l3v2.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + 2 + + + + + + + diff --git a/latest/cases/01363/output.heta b/latest/cases/01363/output.heta new file mode 100644 index 000000000..5d068728d --- /dev/null +++ b/latest/cases/01363/output.heta @@ -0,0 +1,32 @@ +/* +category: Test +synopsis: A replaced compartment whose ID is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $J1 + 2$ | constant | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01363/synopsis.txt b/latest/cases/01363/synopsis.txt new file mode 100644 index 000000000..a8f49652d --- /dev/null +++ b/latest/cases/01363/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: A replaced compartment whose ID is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $J1 + 2$ | constant | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01364/l2v5/index.heta b/latest/cases/01364/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01364/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01364/l3v2/heta-code/output.heta b/latest/cases/01364/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9e50fdf9 --- /dev/null +++ b/latest/cases/01364/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01364/l3v2/index.heta b/latest/cases/01364/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01364/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01364/l3v2/json/output.json b/latest/cases/01364/l3v2/json/output.json new file mode 100644 index 000000000..7f1e6722f --- /dev/null +++ b/latest/cases/01364/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01364/model-sbml-l3v2.xml b/latest/cases/01364/model-sbml-l3v2.xml new file mode 100644 index 000000000..b2426281e --- /dev/null +++ b/latest/cases/01364/model-sbml-l3v2.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + J0 + 0.5 + + + + + + + + 4 + + + + + + + + diff --git a/latest/cases/01364/output.heta b/latest/cases/01364/output.heta new file mode 100644 index 000000000..921367bc7 --- /dev/null +++ b/latest/cases/01364/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: A replaced compartment whose ID is used in an event trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01364/synopsis.txt b/latest/cases/01364/synopsis.txt new file mode 100644 index 000000000..b2925d704 --- /dev/null +++ b/latest/cases/01364/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A replaced compartment whose ID is used in an event trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01365/l2v5/index.heta b/latest/cases/01365/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01365/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01365/l3v2/heta-code/output.heta b/latest/cases/01365/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9e50fdf9 --- /dev/null +++ b/latest/cases/01365/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01365/l3v2/index.heta b/latest/cases/01365/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01365/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01365/l3v2/json/output.json b/latest/cases/01365/l3v2/json/output.json new file mode 100644 index 000000000..7f1e6722f --- /dev/null +++ b/latest/cases/01365/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01365/model-sbml-l3v2.xml b/latest/cases/01365/model-sbml-l3v2.xml new file mode 100644 index 000000000..ca60d551a --- /dev/null +++ b/latest/cases/01365/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 5.5 + + + + + + J0 + + + + + + 4 + + + + + + + + + + time + 5.5 + + + + + + 4 + + + + + + 10 + + + + + + + + diff --git a/latest/cases/01365/output.heta b/latest/cases/01365/output.heta new file mode 100644 index 000000000..c628510e3 --- /dev/null +++ b/latest/cases/01365/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A replaced compartment whose ID is used in an event priority. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an event priority. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ | +| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01365/synopsis.txt b/latest/cases/01365/synopsis.txt new file mode 100644 index 000000000..73e0c1a94 --- /dev/null +++ b/latest/cases/01365/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A replaced compartment whose ID is used in an event priority. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an event priority. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ | +| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01366/l2v5/index.heta b/latest/cases/01366/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01366/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01366/l3v2/heta-code/output.heta b/latest/cases/01366/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9e50fdf9 --- /dev/null +++ b/latest/cases/01366/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01366/l3v2/index.heta b/latest/cases/01366/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01366/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01366/l3v2/json/output.json b/latest/cases/01366/l3v2/json/output.json new file mode 100644 index 000000000..7f1e6722f --- /dev/null +++ b/latest/cases/01366/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01366/model-sbml-l3v2.xml b/latest/cases/01366/model-sbml-l3v2.xml new file mode 100644 index 000000000..56022eade --- /dev/null +++ b/latest/cases/01366/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 5.5 + + + + + + + J0 + + + + + + + + diff --git a/latest/cases/01366/output.heta b/latest/cases/01366/output.heta new file mode 100644 index 000000000..68ffd59e6 --- /dev/null +++ b/latest/cases/01366/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: A replaced compartment whose ID is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01366/synopsis.txt b/latest/cases/01366/synopsis.txt new file mode 100644 index 000000000..9a666471e --- /dev/null +++ b/latest/cases/01366/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A replaced compartment whose ID is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01367/l2v5/index.heta b/latest/cases/01367/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01367/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01367/l3v2/heta-code/output.heta b/latest/cases/01367/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9e50fdf9 --- /dev/null +++ b/latest/cases/01367/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01367/l3v2/index.heta b/latest/cases/01367/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01367/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01367/l3v2/json/output.json b/latest/cases/01367/l3v2/json/output.json new file mode 100644 index 000000000..7f1e6722f --- /dev/null +++ b/latest/cases/01367/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01367/model-sbml-l3v2.xml b/latest/cases/01367/model-sbml-l3v2.xml new file mode 100644 index 000000000..df43c6705 --- /dev/null +++ b/latest/cases/01367/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 0.5 + + + + + + J0 + + + + + + 2 + + + + + + + + diff --git a/latest/cases/01367/output.heta b/latest/cases/01367/output.heta new file mode 100644 index 000000000..5583a7393 --- /dev/null +++ b/latest/cases/01367/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: A replaced compartment whose ID is used in an event delay. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an event delay. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01367/synopsis.txt b/latest/cases/01367/synopsis.txt new file mode 100644 index 000000000..c52f046c9 --- /dev/null +++ b/latest/cases/01367/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A replaced compartment whose ID is used in an event delay. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced compartment ID is used in an event delay. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01368/l2v5/index.heta b/latest/cases/01368/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01368/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01368/l3v2/heta-code/output.heta b/latest/cases/01368/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9e50fdf9 --- /dev/null +++ b/latest/cases/01368/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01368/l3v2/index.heta b/latest/cases/01368/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01368/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01368/l3v2/json/output.json b/latest/cases/01368/l3v2/json/output.json new file mode 100644 index 000000000..7f1e6722f --- /dev/null +++ b/latest/cases/01368/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01368/model-sbml-l3v2.xml b/latest/cases/01368/model-sbml-l3v2.xml new file mode 100644 index 000000000..800dc8568 --- /dev/null +++ b/latest/cases/01368/model-sbml-l3v2.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + x + J0 + + + + + + + diff --git a/latest/cases/01368/output.heta b/latest/cases/01368/output.heta new file mode 100644 index 000000000..7ac6f043d --- /dev/null +++ b/latest/cases/01368/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: A replaced compartment whose ID is used in an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel compartment ID is used in an algebraic rule. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $A__x - J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $unknown$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01368/synopsis.txt b/latest/cases/01368/synopsis.txt new file mode 100644 index 000000000..8805321ec --- /dev/null +++ b/latest/cases/01368/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A replaced compartment whose ID is used in an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel compartment ID is used in an algebraic rule. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $A__x - J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $unknown$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01369/l2v5/index.heta b/latest/cases/01369/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01369/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01369/l3v2/heta-code/output.heta b/latest/cases/01369/l3v2/heta-code/output.heta new file mode 100644 index 000000000..591f94a8e --- /dev/null +++ b/latest/cases/01369/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +J1 @Compartment { boundary: true, } .= 5; + +S1 @Species { compartment: C, } .= 3; + diff --git a/latest/cases/01369/l3v2/index.heta b/latest/cases/01369/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01369/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01369/l3v2/json/output.json b/latest/cases/01369/l3v2/json/output.json new file mode 100644 index 000000000..d2df532a2 --- /dev/null +++ b/latest/cases/01369/l3v2/json/output.json @@ -0,0 +1,29 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01369/model-sbml-l3v2.xml b/latest/cases/01369/model-sbml-l3v2.xml new file mode 100644 index 000000000..9ea0b89fa --- /dev/null +++ b/latest/cases/01369/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + + diff --git a/latest/cases/01369/output.heta b/latest/cases/01369/output.heta new file mode 100644 index 000000000..16e584511 --- /dev/null +++ b/latest/cases/01369/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: A replaced compartment whose ID is used in a reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel compartment ID is used in a reaction. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 2 compartments (C, J1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__J2: -> S1 | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +J1 @Compartment { boundary: true, } .= 5; + +S1 @Species { compartment: C, } .= 3; + diff --git a/latest/cases/01369/synopsis.txt b/latest/cases/01369/synopsis.txt new file mode 100644 index 000000000..105814c53 --- /dev/null +++ b/latest/cases/01369/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A replaced compartment whose ID is used in a reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel compartment ID is used in a reaction. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 2 compartments (C, J1) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__J2: -> S1 | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01370/l2v5/index.heta b/latest/cases/01370/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01370/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01370/l3v2/heta-code/output.heta b/latest/cases/01370/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f9e50fdf9 --- /dev/null +++ b/latest/cases/01370/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01370/l3v2/index.heta b/latest/cases/01370/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01370/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01370/l3v2/json/output.json b/latest/cases/01370/l3v2/json/output.json new file mode 100644 index 000000000..7f1e6722f --- /dev/null +++ b/latest/cases/01370/l3v2/json/output.json @@ -0,0 +1,13 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01370/model-sbml-l3v2.xml b/latest/cases/01370/model-sbml-l3v2.xml new file mode 100644 index 000000000..782c3b51a --- /dev/null +++ b/latest/cases/01370/model-sbml-l3v2.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + diff --git a/latest/cases/01370/output.heta b/latest/cases/01370/output.heta new file mode 100644 index 000000000..2957e5671 --- /dev/null +++ b/latest/cases/01370/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: A replaced compartment whose ID is used in a rate rule. +componentTags: Compartment, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel compartment ID is used in a rate rule. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $0$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +J1 @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01370/synopsis.txt b/latest/cases/01370/synopsis.txt new file mode 100644 index 000000000..43122907b --- /dev/null +++ b/latest/cases/01370/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A replaced compartment whose ID is used in a rate rule. +componentTags: Compartment, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel compartment ID is used in a rate rule. + +The 'flattened' version of this hierarchical model contains: +* 1 parameter (A__x) +* 1 compartment (J1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter A__x | $0$ | variable | +| Initial volume of compartment 'J1' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01371/l2v5/index.heta b/latest/cases/01371/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01371/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01371/l3v2/heta-code/output.heta b/latest/cases/01371/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a0cbc4a00 --- /dev/null +++ b/latest/cases/01371/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +A_C @Compartment { boundary: true, } .= 1; + +J1 @Species { boundary: true, compartment: A_C, } .= 5; + diff --git a/latest/cases/01371/l3v2/index.heta b/latest/cases/01371/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01371/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01371/l3v2/json/output.json b/latest/cases/01371/l3v2/json/output.json new file mode 100644 index 000000000..39cd00bac --- /dev/null +++ b/latest/cases/01371/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "A_C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true, + "compartment": "A_C" + } +] \ No newline at end of file diff --git a/latest/cases/01371/model-sbml-l3v2.xml b/latest/cases/01371/model-sbml-l3v2.xml new file mode 100644 index 000000000..e62546082 --- /dev/null +++ b/latest/cases/01371/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + diff --git a/latest/cases/01371/output.heta b/latest/cases/01371/output.heta new file mode 100644 index 000000000..cd0b870b2 --- /dev/null +++ b/latest/cases/01371/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: A replaced species whose ID is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species ID is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $J1$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +A_C @Compartment { boundary: true, } .= 1; + +J1 @Species { boundary: true, compartment: A_C, } .= 5; + diff --git a/latest/cases/01371/synopsis.txt b/latest/cases/01371/synopsis.txt new file mode 100644 index 000000000..37b4d58f7 --- /dev/null +++ b/latest/cases/01371/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A replaced species whose ID is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species ID is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $J1$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01372/l2v5/index.heta b/latest/cases/01372/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01372/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01372/l3v2/heta-code/output.heta b/latest/cases/01372/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a0cbc4a00 --- /dev/null +++ b/latest/cases/01372/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +A_C @Compartment { boundary: true, } .= 1; + +J1 @Species { boundary: true, compartment: A_C, } .= 5; + diff --git a/latest/cases/01372/l3v2/index.heta b/latest/cases/01372/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01372/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01372/l3v2/json/output.json b/latest/cases/01372/l3v2/json/output.json new file mode 100644 index 000000000..39cd00bac --- /dev/null +++ b/latest/cases/01372/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "A_C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true, + "compartment": "A_C" + } +] \ No newline at end of file diff --git a/latest/cases/01372/model-sbml-l3v2.xml b/latest/cases/01372/model-sbml-l3v2.xml new file mode 100644 index 000000000..f30d096c1 --- /dev/null +++ b/latest/cases/01372/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + 2 + + + + + + + diff --git a/latest/cases/01372/output.heta b/latest/cases/01372/output.heta new file mode 100644 index 000000000..4ab0ee878 --- /dev/null +++ b/latest/cases/01372/output.heta @@ -0,0 +1,36 @@ +/* +category: Test +synopsis: A replaced species whose ID is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species ID is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $J1 + 2$ | constant | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +A_C @Compartment { boundary: true, } .= 1; + +J1 @Species { boundary: true, compartment: A_C, } .= 5; + diff --git a/latest/cases/01372/synopsis.txt b/latest/cases/01372/synopsis.txt new file mode 100644 index 000000000..859475b4e --- /dev/null +++ b/latest/cases/01372/synopsis.txt @@ -0,0 +1,26 @@ + +category: Test +synopsis: A replaced species whose ID is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species ID is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $J1 + 2$ | constant | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01373/l2v5/index.heta b/latest/cases/01373/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01373/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01373/l3v2/heta-code/output.heta b/latest/cases/01373/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a0cbc4a00 --- /dev/null +++ b/latest/cases/01373/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +A_C @Compartment { boundary: true, } .= 1; + +J1 @Species { boundary: true, compartment: A_C, } .= 5; + diff --git a/latest/cases/01373/l3v2/index.heta b/latest/cases/01373/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01373/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01373/l3v2/json/output.json b/latest/cases/01373/l3v2/json/output.json new file mode 100644 index 000000000..39cd00bac --- /dev/null +++ b/latest/cases/01373/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "A_C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true, + "compartment": "A_C" + } +] \ No newline at end of file diff --git a/latest/cases/01373/model-sbml-l3v2.xml b/latest/cases/01373/model-sbml-l3v2.xml new file mode 100644 index 000000000..31bf6662f --- /dev/null +++ b/latest/cases/01373/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + J0 + 0.5 + + + + + + + + 4 + + + + + + + + diff --git a/latest/cases/01373/output.heta b/latest/cases/01373/output.heta new file mode 100644 index 000000000..fd2543791 --- /dev/null +++ b/latest/cases/01373/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: A replaced species whose ID is used in an event trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species ID is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +A_C @Compartment { boundary: true, } .= 1; + +J1 @Species { boundary: true, compartment: A_C, } .= 5; + diff --git a/latest/cases/01373/synopsis.txt b/latest/cases/01373/synopsis.txt new file mode 100644 index 000000000..d633c5a58 --- /dev/null +++ b/latest/cases/01373/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A replaced species whose ID is used in an event trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species ID is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01374/l2v5/index.heta b/latest/cases/01374/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01374/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01374/l3v2/build.log b/latest/cases/01374/l3v2/build.log new file mode 100644 index 000000000..913d9bca9 --- /dev/null +++ b/latest/cases/01374/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01374/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01374/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01374/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] Record "A_C" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01374/l3v2/index.heta b/latest/cases/01374/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01374/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01374/model-sbml-l3v2.xml b/latest/cases/01374/model-sbml-l3v2.xml new file mode 100644 index 000000000..e663486ca --- /dev/null +++ b/latest/cases/01374/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 5.5 + + + + + + J0 + + + + + + 4 + + + + + + + + + + time + 5.5 + + + + + + 4 + + + + + + 10 + + + + + + + + diff --git a/latest/cases/01374/synopsis.txt b/latest/cases/01374/synopsis.txt new file mode 100644 index 000000000..02d083a1a --- /dev/null +++ b/latest/cases/01374/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A replaced species whose ID is used in an event priority. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species ID is used in an event priority. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ | +| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01375/l2v5/index.heta b/latest/cases/01375/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01375/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01375/l3v2/heta-code/output.heta b/latest/cases/01375/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a0cbc4a00 --- /dev/null +++ b/latest/cases/01375/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +A_C @Compartment { boundary: true, } .= 1; + +J1 @Species { boundary: true, compartment: A_C, } .= 5; + diff --git a/latest/cases/01375/l3v2/index.heta b/latest/cases/01375/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01375/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01375/l3v2/json/output.json b/latest/cases/01375/l3v2/json/output.json new file mode 100644 index 000000000..39cd00bac --- /dev/null +++ b/latest/cases/01375/l3v2/json/output.json @@ -0,0 +1,22 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "A_C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true, + "compartment": "A_C" + } +] \ No newline at end of file diff --git a/latest/cases/01375/model-sbml-l3v2.xml b/latest/cases/01375/model-sbml-l3v2.xml new file mode 100644 index 000000000..b73e00362 --- /dev/null +++ b/latest/cases/01375/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 5.5 + + + + + + + J0 + + + + + + + + diff --git a/latest/cases/01375/output.heta b/latest/cases/01375/output.heta new file mode 100644 index 000000000..2000549b0 --- /dev/null +++ b/latest/cases/01375/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: A replaced species whose ID is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species ID is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +A_C @Compartment { boundary: true, } .= 1; + +J1 @Species { boundary: true, compartment: A_C, } .= 5; + diff --git a/latest/cases/01375/synopsis.txt b/latest/cases/01375/synopsis.txt new file mode 100644 index 000000000..7463b8c75 --- /dev/null +++ b/latest/cases/01375/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A replaced species whose ID is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species ID is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01376/l2v5/index.heta b/latest/cases/01376/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01376/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01376/l3v2/build.log b/latest/cases/01376/l3v2/build.log new file mode 100644 index 000000000..55dc79eee --- /dev/null +++ b/latest/cases/01376/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01376/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01376/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01376/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] Record "A_C" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01376/l3v2/index.heta b/latest/cases/01376/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01376/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01376/model-sbml-l3v2.xml b/latest/cases/01376/model-sbml-l3v2.xml new file mode 100644 index 000000000..d757a4155 --- /dev/null +++ b/latest/cases/01376/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 0.5 + + + + + + J0 + + + + + + 2 + + + + + + + + diff --git a/latest/cases/01376/synopsis.txt b/latest/cases/01376/synopsis.txt new file mode 100644 index 000000000..0d8753764 --- /dev/null +++ b/latest/cases/01376/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A replaced species whose ID is used in an event delay. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species ID is used in an event delay. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01377/l2v5/index.heta b/latest/cases/01377/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01377/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01377/l3v2/build.log b/latest/cases/01377/l3v2/build.log new file mode 100644 index 000000000..5de2792b4 --- /dev/null +++ b/latest/cases/01377/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01377/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01377/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01377/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] Record "A_C" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01377/l3v2/index.heta b/latest/cases/01377/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01377/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01377/model-sbml-l3v2.xml b/latest/cases/01377/model-sbml-l3v2.xml new file mode 100644 index 000000000..9397f3afb --- /dev/null +++ b/latest/cases/01377/model-sbml-l3v2.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x + J0 + + + + + + + diff --git a/latest/cases/01377/synopsis.txt b/latest/cases/01377/synopsis.txt new file mode 100644 index 000000000..c204f7634 --- /dev/null +++ b/latest/cases/01377/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A replaced species whose ID is used in an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, ConstantSpecies, InitialValueReassigned, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species ID is used in an algebraic rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $A__x - J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | constant | +| Initial value of parameter A__x | $unknown$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01378/l2v5/index.heta b/latest/cases/01378/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01378/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01378/l3v2/heta-code/output.heta b/latest/cases/01378/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ab69c064a --- /dev/null +++ b/latest/cases/01378/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; +J1 @Species { boundary: true, compartment: C, } .= 5; + diff --git a/latest/cases/01378/l3v2/index.heta b/latest/cases/01378/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01378/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01378/l3v2/json/output.json b/latest/cases/01378/l3v2/json/output.json new file mode 100644 index 000000000..13ca4657d --- /dev/null +++ b/latest/cases/01378/l3v2/json/output.json @@ -0,0 +1,30 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "J1", + "assignments": { + "start_": "5" + }, + "boundary": true, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01378/model-sbml-l3v2.xml b/latest/cases/01378/model-sbml-l3v2.xml new file mode 100644 index 000000000..6d1616aa3 --- /dev/null +++ b/latest/cases/01378/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + + diff --git a/latest/cases/01378/output.heta b/latest/cases/01378/output.heta new file mode 100644 index 000000000..654b013fb --- /dev/null +++ b/latest/cases/01378/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: A replaced species whose ID is used in a reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species ID is used in a reaction. + +The 'flattened' version of this hierarchical model contains: +* 2 species (S1, J1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__J2: -> S1 | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species J1 | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; +J1 @Species { boundary: true, compartment: C, } .= 5; + diff --git a/latest/cases/01378/synopsis.txt b/latest/cases/01378/synopsis.txt new file mode 100644 index 000000000..5b51958e5 --- /dev/null +++ b/latest/cases/01378/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A replaced species whose ID is used in a reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species ID is used in a reaction. + +The 'flattened' version of this hierarchical model contains: +* 2 species (S1, J1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__J2: -> S1 | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species J1 | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01379/l2v5/index.heta b/latest/cases/01379/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01379/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01379/l3v2/build.log b/latest/cases/01379/l3v2/build.log new file mode 100644 index 000000000..aa2699342 --- /dev/null +++ b/latest/cases/01379/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01379/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01379/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01379/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] Record "A_C" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01379/l3v2/index.heta b/latest/cases/01379/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01379/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01379/model-sbml-l3v2.xml b/latest/cases/01379/model-sbml-l3v2.xml new file mode 100644 index 000000000..34f120112 --- /dev/null +++ b/latest/cases/01379/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0 + + + + + + diff --git a/latest/cases/01379/synopsis.txt b/latest/cases/01379/synopsis.txt new file mode 100644 index 000000000..08734a340 --- /dev/null +++ b/latest/cases/01379/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A replaced species whose ID is used in a rate rule. +componentTags: Compartment, Parameter, RateRule, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, BoundaryCondition, NonConstantParameter, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species ID is used in a rate rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (J1) +* 1 parameter (A__x) +* 1 compartment (A_C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A__x | $J1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species J1 | $5$ | variable | +| Initial value of parameter A__x | $0$ | variable | +| Initial volume of compartment 'A_C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01380/l2v5/index.heta b/latest/cases/01380/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01380/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01380/l3v2/heta-code/output.heta b/latest/cases/01380/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01380/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01380/l3v2/index.heta b/latest/cases/01380/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01380/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01380/l3v2/json/output.json b/latest/cases/01380/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01380/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01380/model-sbml-l3v2.xml b/latest/cases/01380/model-sbml-l3v2.xml new file mode 100644 index 000000000..b83d242d3 --- /dev/null +++ b/latest/cases/01380/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + J0_sr + + + + + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01380/output.heta b/latest/cases/01380/output.heta new file mode 100644 index 000000000..548a06ab0 --- /dev/null +++ b/latest/cases/01380/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A replaced species reference whose ID is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species reference (itself in a replaced reaction) is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $J1_sr$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01380/synopsis.txt b/latest/cases/01380/synopsis.txt new file mode 100644 index 000000000..de60fc4d7 --- /dev/null +++ b/latest/cases/01380/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A replaced species reference whose ID is used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species reference (itself in a replaced reaction) is used in an assignment rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | A__x | $J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $J1_sr$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01381/l2v5/index.heta b/latest/cases/01381/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01381/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01381/l3v2/heta-code/output.heta b/latest/cases/01381/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01381/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01381/l3v2/index.heta b/latest/cases/01381/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01381/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01381/l3v2/json/output.json b/latest/cases/01381/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01381/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01381/model-sbml-l3v2.xml b/latest/cases/01381/model-sbml-l3v2.xml new file mode 100644 index 000000000..70ebbdedd --- /dev/null +++ b/latest/cases/01381/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + J0_sr + 2 + + + + + + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01381/output.heta b/latest/cases/01381/output.heta new file mode 100644 index 000000000..963d7c733 --- /dev/null +++ b/latest/cases/01381/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: A replaced species reference whose ID is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $J1_sr + 2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01381/synopsis.txt b/latest/cases/01381/synopsis.txt new file mode 100644 index 000000000..c3ffb09a0 --- /dev/null +++ b/latest/cases/01381/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A replaced species reference whose ID is used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an initial assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $J1_sr + 2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01382/l2v5/index.heta b/latest/cases/01382/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01382/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01382/l3v2/heta-code/output.heta b/latest/cases/01382/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01382/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01382/l3v2/index.heta b/latest/cases/01382/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01382/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01382/l3v2/json/output.json b/latest/cases/01382/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01382/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01382/model-sbml-l3v2.xml b/latest/cases/01382/model-sbml-l3v2.xml new file mode 100644 index 000000000..fd3fc1d90 --- /dev/null +++ b/latest/cases/01382/model-sbml-l3v2.xml @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + time + + + J0_sr + 0.5 + + + + + + + + 4 + + + + + + + + diff --git a/latest/cases/01382/output.heta b/latest/cases/01382/output.heta new file mode 100644 index 000000000..5ac87125e --- /dev/null +++ b/latest/cases/01382/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A replaced species reference whose ID is used in an event trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1_sr + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01382/synopsis.txt b/latest/cases/01382/synopsis.txt new file mode 100644 index 000000000..ed39d56fc --- /dev/null +++ b/latest/cases/01382/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A replaced species reference whose ID is used in an event trigger. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an event trigger. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > (J1_sr + 0.5)$ | $A__x = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01383/l2v5/index.heta b/latest/cases/01383/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01383/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01383/l3v2/heta-code/output.heta b/latest/cases/01383/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01383/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01383/l3v2/index.heta b/latest/cases/01383/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01383/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01383/l3v2/json/output.json b/latest/cases/01383/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01383/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01383/model-sbml-l3v2.xml b/latest/cases/01383/model-sbml-l3v2.xml new file mode 100644 index 000000000..8f72f0236 --- /dev/null +++ b/latest/cases/01383/model-sbml-l3v2.xml @@ -0,0 +1,114 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + time + 5.5 + + + + + + J0_sr + + + + + + 4 + + + + + + + + + + time + 5.5 + + + + + + 4 + + + + + + 10 + + + + + + + + diff --git a/latest/cases/01383/output.heta b/latest/cases/01383/output.heta new file mode 100644 index 000000000..72e543ae1 --- /dev/null +++ b/latest/cases/01383/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: A replaced species reference whose ID is used in am event priority. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an event priority. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $J1_sr$ | $A__x = 4$ | +| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01383/synopsis.txt b/latest/cases/01383/synopsis.txt new file mode 100644 index 000000000..9204d11ae --- /dev/null +++ b/latest/cases/01383/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A replaced species reference whose ID is used in am event priority. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an event priority. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $J1_sr$ | $A__x = 4$ | +| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01384/l2v5/index.heta b/latest/cases/01384/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01384/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01384/l3v2/heta-code/output.heta b/latest/cases/01384/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01384/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01384/l3v2/index.heta b/latest/cases/01384/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01384/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01384/l3v2/json/output.json b/latest/cases/01384/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01384/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01384/model-sbml-l3v2.xml b/latest/cases/01384/model-sbml-l3v2.xml new file mode 100644 index 000000000..866cd0dd1 --- /dev/null +++ b/latest/cases/01384/model-sbml-l3v2.xml @@ -0,0 +1,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + time + 5.5 + + + + + + + J0_sr + + + + + + + + diff --git a/latest/cases/01384/output.heta b/latest/cases/01384/output.heta new file mode 100644 index 000000000..e9fdcbf9c --- /dev/null +++ b/latest/cases/01384/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A replaced species reference whose ID is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01384/synopsis.txt b/latest/cases/01384/synopsis.txt new file mode 100644 index 000000000..0e6b824c2 --- /dev/null +++ b/latest/cases/01384/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A replaced species reference whose ID is used in an event assignment. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an event assignment. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| A__E0 | $time > 5.5$ | $A__x = J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01385/l2v5/index.heta b/latest/cases/01385/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01385/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01385/l3v2/heta-code/output.heta b/latest/cases/01385/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01385/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01385/l3v2/index.heta b/latest/cases/01385/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01385/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01385/l3v2/json/output.json b/latest/cases/01385/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01385/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01385/model-sbml-l3v2.xml b/latest/cases/01385/model-sbml-l3v2.xml new file mode 100644 index 000000000..d3863533b --- /dev/null +++ b/latest/cases/01385/model-sbml-l3v2.xml @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + time + 0.5 + + + + + + J0_sr + + + + + + 2 + + + + + + + + diff --git a/latest/cases/01385/output.heta b/latest/cases/01385/output.heta new file mode 100644 index 000000000..c2fabe64c --- /dev/null +++ b/latest/cases/01385/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A replaced species reference whose ID is used in an event delay. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an event delay. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| A__E0 | $time > 0.5$ | $J1_sr$ | $A__x = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01385/synopsis.txt b/latest/cases/01385/synopsis.txt new file mode 100644 index 000000000..4f7605610 --- /dev/null +++ b/latest/cases/01385/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A replaced species reference whose ID is used in an event delay. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced species reference (itself in a replaced reaction) is used in an event delay. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| A__E0 | $time > 0.5$ | $J1_sr$ | $A__x = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01386/l2v5/index.heta b/latest/cases/01386/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01386/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01386/l3v2/heta-code/output.heta b/latest/cases/01386/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01386/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01386/l3v2/index.heta b/latest/cases/01386/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01386/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01386/l3v2/json/output.json b/latest/cases/01386/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01386/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01386/model-sbml-l3v2.xml b/latest/cases/01386/model-sbml-l3v2.xml new file mode 100644 index 000000000..414b3c6bb --- /dev/null +++ b/latest/cases/01386/model-sbml-l3v2.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + x + J0_sr + + + + + + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01386/output.heta b/latest/cases/01386/output.heta new file mode 100644 index 000000000..5452d7c0f --- /dev/null +++ b/latest/cases/01386/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A replaced species reference whose ID is used in an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species reference (itself in a replaced reaction) is used in an algebraic rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $A__x - J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01386/synopsis.txt b/latest/cases/01386/synopsis.txt new file mode 100644 index 000000000..99c4352d3 --- /dev/null +++ b/latest/cases/01386/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A replaced species reference whose ID is used in an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species reference (itself in a replaced reaction) is used in an algebraic rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $A__x - J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01387/l2v5/index.heta b/latest/cases/01387/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01387/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01387/l3v2/heta-code/output.heta b/latest/cases/01387/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01387/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01387/l3v2/index.heta b/latest/cases/01387/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01387/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01387/l3v2/json/output.json b/latest/cases/01387/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01387/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01387/model-sbml-l3v2.xml b/latest/cases/01387/model-sbml-l3v2.xml new file mode 100644 index 000000000..382642314 --- /dev/null +++ b/latest/cases/01387/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + J0_sr + + + + + + + diff --git a/latest/cases/01387/output.heta b/latest/cases/01387/output.heta new file mode 100644 index 000000000..4d744d26e --- /dev/null +++ b/latest/cases/01387/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: A replaced species reference (itself in a replaced reaction) whose ID is used in a reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species reference (itself in a replaced reaction) is used in another reaction. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ | +| A__J2: S1 -> | $J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01387/synopsis.txt b/latest/cases/01387/synopsis.txt new file mode 100644 index 000000000..d6d351ffd --- /dev/null +++ b/latest/cases/01387/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A replaced species reference (itself in a replaced reaction) whose ID is used in a reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species reference (itself in a replaced reaction) is used in another reaction. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ | +| A__J2: S1 -> | $J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01388/l2v5/index.heta b/latest/cases/01388/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01388/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01388/l3v2/heta-code/output.heta b/latest/cases/01388/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01388/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01388/l3v2/index.heta b/latest/cases/01388/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01388/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01388/l3v2/json/output.json b/latest/cases/01388/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01388/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01388/model-sbml-l3v2.xml b/latest/cases/01388/model-sbml-l3v2.xml new file mode 100644 index 000000000..31e1c1f8c --- /dev/null +++ b/latest/cases/01388/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + J0_sr + + + + + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01388/output.heta b/latest/cases/01388/output.heta new file mode 100644 index 000000000..cb4f350f4 --- /dev/null +++ b/latest/cases/01388/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: A replaced species reference whose ID is used in a rate rule. +componentTags: Compartment, Parameter, RateRule, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species reference (itself in a replaced reaction) is used in a rate rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A__x | $J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01388/synopsis.txt b/latest/cases/01388/synopsis.txt new file mode 100644 index 000000000..6e9044529 --- /dev/null +++ b/latest/cases/01388/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A replaced species reference whose ID is used in a rate rule. +componentTags: Compartment, Parameter, RateRule, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a replaced submodel species reference (itself in a replaced reaction) is used in a rate rule. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 parameter (A__x) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A__x | $J1_sr$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial value of parameter A__x | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01389/l2v5/index.heta b/latest/cases/01389/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01389/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01389/l3v2/heta-code/output.heta b/latest/cases/01389/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2335a0800 --- /dev/null +++ b/latest/cases/01389/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01389/l3v2/index.heta b/latest/cases/01389/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01389/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01389/l3v2/json/output.json b/latest/cases/01389/l3v2/json/output.json new file mode 100644 index 000000000..24c039f22 --- /dev/null +++ b/latest/cases/01389/l3v2/json/output.json @@ -0,0 +1,34 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 5 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01389/model-sbml-l3v2.xml b/latest/cases/01389/model-sbml-l3v2.xml new file mode 100644 index 000000000..01f811642 --- /dev/null +++ b/latest/cases/01389/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01389/output.heta b/latest/cases/01389/output.heta new file mode 100644 index 000000000..cef28b2de --- /dev/null +++ b/latest/cases/01389/output.heta @@ -0,0 +1,44 @@ +/* +category: Test +synopsis: A replaced species reference in a replaced reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This is the base model for the previous 9 tests: a replaced species reference inside a replaced reaction. Neither the reaction ID nor the species reference ID are used anywhere; this is just to make sure simulator software can handle the situation in general. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 3; + +J1 @Reaction { actors: = 5*S1, }; +J1 := 1; + diff --git a/latest/cases/01389/synopsis.txt b/latest/cases/01389/synopsis.txt new file mode 100644 index 000000000..af43e29de --- /dev/null +++ b/latest/cases/01389/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A replaced species reference in a replaced reaction. +componentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This is the base model for the previous 9 tests: a replaced species reference inside a replaced reaction. Neither the reaction ID nor the species reference ID are used anywhere; this is just to make sure simulator software can handle the situation in general. + +The 'flattened' version of this hierarchical model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (J1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> 5S1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01390/l2v5/index.heta b/latest/cases/01390/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01390/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01390/l3v2/build.log b/latest/cases/01390/l3v2/build.log new file mode 100644 index 000000000..1bf5308f2 --- /dev/null +++ b/latest/cases/01390/l3v2/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01390/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01390/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01390/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[error] No required "num" property for "f" of Const. +[error] No required "num" property for "g" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01390/l3v2/index.heta b/latest/cases/01390/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01390/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01390/model-sbml-l3v2.xml b/latest/cases/01390/model-sbml-l3v2.xml new file mode 100644 index 000000000..c3f48eaf4 --- /dev/null +++ b/latest/cases/01390/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + b + + + + + d + + + + + f + + + + + + + + + + + + + + + + + + + + + + a + + + + + c + + + + + e + + + + + + + + + + + + + + + diff --git a/latest/cases/01390/synopsis.txt b/latest/cases/01390/synopsis.txt new file mode 100644 index 000000000..ff0212078 --- /dev/null +++ b/latest/cases/01390/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A chain of initial assignments that cross the submodel boundary +componentTags: InitialAssignment, Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a chain of initial assignments assign a to b, b to c, c to d, etc. However, every other assignment occurs in the parent model, alternating with assignments in the submodel. This is designed to check simulators that might treat submodels separately from parent models, to make sure they can follow a chain of assignments across the parent/child boundary. + +The 'flattened' version of this hierarchical model contains: +* 7 parameters (a, b, c, d, e, f, g) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $1$ | constant | +| Initial value of parameter b | $a$ | constant | +| Initial value of parameter c | $b$ | constant | +| Initial value of parameter d | $c$ | constant | +| Initial value of parameter e | $d$ | constant | +| Initial value of parameter f | $e$ | constant | +| Initial value of parameter g | $f$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01391/l2v5/index.heta b/latest/cases/01391/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01391/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01391/l3v2/build.log b/latest/cases/01391/l3v2/build.log new file mode 100644 index 000000000..35d2abcbe --- /dev/null +++ b/latest/cases/01391/l3v2/build.log @@ -0,0 +1,14 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01391/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01391/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01391/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[error] Record "b" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "d" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "f" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01391/l3v2/index.heta b/latest/cases/01391/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01391/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01391/model-sbml-l3v2.xml b/latest/cases/01391/model-sbml-l3v2.xml new file mode 100644 index 000000000..60fc7cecc --- /dev/null +++ b/latest/cases/01391/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + b + + + + + d + + + + + f + + + + + + + + + + + + + + + + + + + + + + a + + + + + c + + + + + e + + + + + + + + + + + + + + + diff --git a/latest/cases/01391/synopsis.txt b/latest/cases/01391/synopsis.txt new file mode 100644 index 000000000..3dd5e2d21 --- /dev/null +++ b/latest/cases/01391/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A chain of assignment rules that cross the submodel boundary +componentTags: AssignmentRule, Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a chain of assignment rules assign a to b, b to c, c to d, etc. However, every other assignment occurs in the parent model, alternating with assignments in the submodel. This is designed to check simulators that might treat submodels separately from parent models, to make sure they can follow a chain of assignments across the parent/child boundary. + +The 'flattened' version of this hierarchical model contains: +* 7 parameters (a, b, c, d, e, f, g) + +There are 6 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | c | $b$ | +| Assignment | e | $d$ | +| Assignment | g | $f$ | +| Assignment | b | $a$ | +| Assignment | d | $c$ | +| Assignment | f | $e$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $1$ | constant | +| Initial value of parameter b | $a$ | variable | +| Initial value of parameter c | $b$ | variable | +| Initial value of parameter d | $c$ | variable | +| Initial value of parameter e | $d$ | variable | +| Initial value of parameter f | $e$ | variable | +| Initial value of parameter g | $f$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01392/l2v5/index.heta b/latest/cases/01392/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01392/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01392/l3v2/build.log b/latest/cases/01392/l3v2/build.log new file mode 100644 index 000000000..ca6441b49 --- /dev/null +++ b/latest/cases/01392/l3v2/build.log @@ -0,0 +1,14 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01392/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01392/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01392/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[error] Record "b" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "d" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "f" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01392/l3v2/index.heta b/latest/cases/01392/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01392/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01392/model-sbml-l3v2.xml b/latest/cases/01392/model-sbml-l3v2.xml new file mode 100644 index 000000000..dc4023a57 --- /dev/null +++ b/latest/cases/01392/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + b + + + + + d + + + + + f + + + + + + + + + + + + + + + + + + + + + + a + + + + + c + + + + + e + + + + + + + + + + + + + + + diff --git a/latest/cases/01392/synopsis.txt b/latest/cases/01392/synopsis.txt new file mode 100644 index 000000000..0ba482e5f --- /dev/null +++ b/latest/cases/01392/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A chain of assignments that cross the submodel boundary +componentTags: AssignmentRule, InitialAssignment, Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a chain of assignment rules and initial assignments assign a to b, b to c, c to d, etc. However, every other initial assignment occurs in the parent model, alternating with assignment rules in the submodel. This is designed to check simulators that might treat submodels separately from parent models, to make sure they can follow a chain of assignments across the parent/child boundary. + +The 'flattened' version of this hierarchical model contains: +* 7 parameters (a, b, c, d, e, f, g) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | b | $a$ | +| Assignment | d | $c$ | +| Assignment | f | $e$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $1$ | constant | +| Initial value of parameter b | $a$ | variable | +| Initial value of parameter c | $b$ | variable | +| Initial value of parameter d | $c$ | variable | +| Initial value of parameter e | $d$ | variable | +| Initial value of parameter f | $e$ | variable | +| Initial value of parameter g | $f$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01393/l2v5/index.heta b/latest/cases/01393/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01393/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01393/l3v2/build.log b/latest/cases/01393/l3v2/build.log new file mode 100644 index 000000000..451c16dda --- /dev/null +++ b/latest/cases/01393/l3v2/build.log @@ -0,0 +1,15 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01393/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01393/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01393/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[error] Record "a" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "b" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "d" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "f" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01393/l3v2/index.heta b/latest/cases/01393/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01393/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01393/model-sbml-l3v2.xml b/latest/cases/01393/model-sbml-l3v2.xml new file mode 100644 index 000000000..0e5ef959d --- /dev/null +++ b/latest/cases/01393/model-sbml-l3v2.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + b + + + + + d + + + + + f + + + + + + + + + + + + + + + + + + + + + + time + + + + + a + + + + + c + + + + + e + + + + + + + + + + + + + + + diff --git a/latest/cases/01393/synopsis.txt b/latest/cases/01393/synopsis.txt new file mode 100644 index 000000000..949c19673 --- /dev/null +++ b/latest/cases/01393/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A chain of assignment rules that cross the submodel boundary +componentTags: AssignmentRule, CSymbolTime, Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a chain of assignment rules assign a to b, b to c, c to d, etc. However, every other assignment occurs in the parent model, alternating with assignments in the submodel. This is designed to check simulators that might treat submodels separately from parent models, to make sure they can follow a chain of assignments across the parent/child boundary. In this case, a actually varies in time, unlike previous tests. + +The 'flattened' version of this hierarchical model contains: +* 7 parameters (a, b, c, d, e, f, g) + +There are 7 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | c | $b$ | +| Assignment | e | $d$ | +| Assignment | g | $f$ | +| Assignment | a | $time$ | +| Assignment | b | $a$ | +| Assignment | d | $c$ | +| Assignment | f | $e$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $time$ | variable | +| Initial value of parameter b | $a$ | variable | +| Initial value of parameter c | $b$ | variable | +| Initial value of parameter d | $c$ | variable | +| Initial value of parameter e | $d$ | variable | +| Initial value of parameter f | $e$ | variable | +| Initial value of parameter g | $f$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01394/l2v5/index.heta b/latest/cases/01394/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01394/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01394/l3v2/build.log b/latest/cases/01394/l3v2/build.log new file mode 100644 index 000000000..b7f738013 --- /dev/null +++ b/latest/cases/01394/l3v2/build.log @@ -0,0 +1,14 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01394/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01394/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01394/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[error] Record "b" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "d" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "f" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01394/l3v2/index.heta b/latest/cases/01394/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01394/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01394/model-sbml-l3v2.xml b/latest/cases/01394/model-sbml-l3v2.xml new file mode 100644 index 000000000..311eab2d0 --- /dev/null +++ b/latest/cases/01394/model-sbml-l3v2.xml @@ -0,0 +1,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + b + + + + + f + + + + + + + d + + + + + + + + + + + + + + + + + + + + + + c + + + + + + + a + + + + + e + + + + + + + + + + + + + + + diff --git a/latest/cases/01394/synopsis.txt b/latest/cases/01394/synopsis.txt new file mode 100644 index 000000000..78ff2c866 --- /dev/null +++ b/latest/cases/01394/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A chain of assignments that cross the submodel boundary +componentTags: AssignmentRule, InitialAssignment, Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + In this model, a chain of assignment rules and initial assignments assign a to b, b to c, c to d, etc. However, every other initial assignment or assignment rule occurs in the parent model, alternating with initial assignments and assignment rules in the submodel. This is designed to check simulators that might treat submodels separately from parent models, to make sure they can follow a chain of assignments across the parent/child boundary, where both assignment rules and initial assignments can occur in either parent or child. + +The 'flattened' version of this hierarchical model contains: +* 7 parameters (a, b, c, d, e, f, g) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | e | $d$ | +| Assignment | b | $a$ | +| Assignment | f | $e$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $1$ | constant | +| Initial value of parameter b | $a$ | variable | +| Initial value of parameter c | $b$ | variable | +| Initial value of parameter d | $c$ | variable | +| Initial value of parameter e | $d$ | variable | +| Initial value of parameter f | $e$ | variable | +| Initial value of parameter g | $f$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01395/l2v5/heta-code/output.heta b/latest/cases/01395/l2v5/heta-code/output.heta new file mode 100644 index 000000000..db8a92728 --- /dev/null +++ b/latest/cases/01395/l2v5/heta-code/output.heta @@ -0,0 +1,218 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +DefaultCompartment @Compartment 'DefaultCompartment' { boundary: true, } .= 1; + +pp9_mrna @Species 'pp9_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p9 @Species 'p9' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp8_mrna @Species 'pp8_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p8 @Species 'p8' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp7_mrna @Species 'pp7_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p7 @Species 'p7' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp6_mrna @Species 'pp6_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p6 @Species 'p6' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp5_mrna @Species 'pp5_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p5 @Species 'p5' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp4_mrna @Species 'pp4_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p4 @Species 'p4' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp3_mrna @Species 'pp3_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p3 @Species 'p3' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp2_mrna @Species 'pp2_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p2 @Species 'p2' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp1_mrna @Species 'pp1_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p1 @Species 'p1' { compartment: DefaultCompartment, } .= 5 / DefaultCompartment; + +pp9_v1 @Reaction 'pp9_v1' { actors: = pp9_mrna, reversible: false, }; +pp9_v1 := cod9; +pp9_v2 @Reaction 'pp9_v2' { actors: pp9_mrna = , modifiers: [p9], reversible: false, }; +pp9_v2 := pp9_mrna_degradation_rate * pp9_mrna; +pp9_v3 @Reaction 'pp9_v3' { actors: = p9, modifiers: [pp9_mrna], reversible: false, }; +pp9_v3 := rbs9_strength * pp9_mrna; +pp9_v4 @Reaction 'pp9_v4' { actors: p9 = , reversible: false, }; +pp9_v4 := p9_degradation_rate * p9; +pp8_v1 @Reaction 'pp8_v1' { actors: = pp8_mrna, reversible: false, }; +pp8_v1 := cod8; +pp8_v2 @Reaction 'pp8_v2' { actors: pp8_mrna = , modifiers: [p8], reversible: false, }; +pp8_v2 := pp8_mrna_degradation_rate * pp8_mrna; +pp8_v3 @Reaction 'pp8_v3' { actors: = p8, modifiers: [pp8_mrna], reversible: false, }; +pp8_v3 := rbs8_strength * pp8_mrna; +pp8_v4 @Reaction 'pp8_v4' { actors: p8 = , reversible: false, }; +pp8_v4 := p8_degradation_rate * p8; +pp7_v1 @Reaction 'pp7_v1' { actors: = pp7_mrna, reversible: false, }; +pp7_v1 := cod7; +pp7_v2 @Reaction 'pp7_v2' { actors: pp7_mrna = , modifiers: [p7], reversible: false, }; +pp7_v2 := pp7_mrna_degradation_rate * pp7_mrna; +pp7_v3 @Reaction 'pp7_v3' { actors: = p7, modifiers: [pp7_mrna], reversible: false, }; +pp7_v3 := rbs7_strength * pp7_mrna; +pp7_v4 @Reaction 'pp7_v4' { actors: p7 = , reversible: false, }; +pp7_v4 := p7_degradation_rate * p7; +pp6_v1 @Reaction 'pp6_v1' { actors: = pp6_mrna, reversible: false, }; +pp6_v1 := cod6; +pp6_v2 @Reaction 'pp6_v2' { actors: pp6_mrna = , modifiers: [p6], reversible: false, }; +pp6_v2 := pp6_mrna_degradation_rate * pp6_mrna; +pp6_v3 @Reaction 'pp6_v3' { actors: = p6, modifiers: [pp6_mrna], reversible: false, }; +pp6_v3 := rbs6_strength * pp6_mrna; +pp6_v4 @Reaction 'pp6_v4' { actors: p6 = , reversible: false, }; +pp6_v4 := p6_degradation_rate * p6; +pp5_v1 @Reaction 'pp5_v1' { actors: = pp5_mrna, reversible: false, }; +pp5_v1 := cod5; +pp5_v2 @Reaction 'pp5_v2' { actors: pp5_mrna = , modifiers: [p5], reversible: false, }; +pp5_v2 := pp5_mrna_degradation_rate * pp5_mrna; +pp5_v3 @Reaction 'pp5_v3' { actors: = p5, modifiers: [pp5_mrna], reversible: false, }; +pp5_v3 := rbs5_strength * pp5_mrna; +pp5_v4 @Reaction 'pp5_v4' { actors: p5 = , reversible: false, }; +pp5_v4 := p5_degradation_rate * p5; +pp4_v1 @Reaction 'pp4_v1' { actors: = pp4_mrna, reversible: false, }; +pp4_v1 := cod4; +pp4_v2 @Reaction 'pp4_v2' { actors: pp4_mrna = , modifiers: [p4], reversible: false, }; +pp4_v2 := pp4_mrna_degradation_rate * pp4_mrna; +pp4_v3 @Reaction 'pp4_v3' { actors: = p4, modifiers: [pp4_mrna], reversible: false, }; +pp4_v3 := rbs4_strength * pp4_mrna; +pp4_v4 @Reaction 'pp4_v4' { actors: p4 = , reversible: false, }; +pp4_v4 := p4_degradation_rate * p4; +pp3_v1 @Reaction 'pp3_v1' { actors: = pp3_mrna, reversible: false, }; +pp3_v1 := cod3; +pp3_v2 @Reaction 'pp3_v2' { actors: pp3_mrna = , modifiers: [p3], reversible: false, }; +pp3_v2 := pp3_mrna_degradation_rate * pp3_mrna; +pp3_v3 @Reaction 'pp3_v3' { actors: = p3, modifiers: [pp3_mrna], reversible: false, }; +pp3_v3 := rbs3_strength * pp3_mrna; +pp3_v4 @Reaction 'pp3_v4' { actors: p3 = , reversible: false, }; +pp3_v4 := p3_degradation_rate * p3; +pp2_v1 @Reaction 'pp2_v1' { actors: = pp2_mrna, reversible: false, }; +pp2_v1 := cod2; +pp2_v2 @Reaction 'pp2_v2' { actors: pp2_mrna = , modifiers: [p2], reversible: false, }; +pp2_v2 := pp2_mrna_degradation_rate * pp2_mrna; +pp2_v3 @Reaction 'pp2_v3' { actors: = p2, modifiers: [pp2_mrna], reversible: false, }; +pp2_v3 := rbs2_strength * pp2_mrna; +pp2_v4 @Reaction 'pp2_v4' { actors: p2 = , reversible: false, }; +pp2_v4 := p2_degradation_rate * p2; +pp1_v1 @Reaction 'pp1_v1' { actors: = pp1_mrna, reversible: false, }; +pp1_v1 := cod1; +pp1_v2 @Reaction 'pp1_v2' { actors: pp1_mrna = , modifiers: [p1], reversible: false, }; +pp1_v2 := pp1_mrna_degradation_rate * pp1_mrna; +pp1_v3 @Reaction 'pp1_v3' { actors: = p1, modifiers: [pp1_mrna], reversible: false, }; +pp1_v3 := rbs1_strength * pp1_mrna; +pp1_v4 @Reaction 'pp1_v4' { actors: p1 = , reversible: false, }; +pp1_v4 := p1_degradation_rate * p1; + +pp8_mrna_degradation_rate @Record 'pp8_mrna_degradation_rate' { } .= 1; +pp9_mrna_degradation_rate @Record 'pp9_mrna_degradation_rate' { } .= 1; +p1_degradation_rate @Record 'p1_degradation_rate' { } .= 0.5; +p2_degradation_rate @Record 'p2_degradation_rate' { } .= 0.5; +p3_degradation_rate @Record 'p3_degradation_rate' { } .= 0.5; +p4_degradation_rate @Record 'p4_degradation_rate' { } .= 0.5; +p5_degradation_rate @Record 'p5_degradation_rate' { } .= 0.5; +p6_degradation_rate @Record 'p6_degradation_rate' { } .= 0.5; +p7_degradation_rate @Record 'p7_degradation_rate' { } .= 0.5; +p8_degradation_rate @Record 'p8_degradation_rate' { } .= 0.5; +p9_degradation_rate @Record 'p9_degradation_rate' { } .= 0.5; +v1_Kd @Record 'v1_Kd' { } .= 11.147; +v1_h @Record 'v1_h' { } .= 1; +v2_Kd @Record 'v2_Kd' { } .= 1; +v2_h @Record 'v2_h' { } .= 4; +v3_Kd @Record 'v3_Kd' { } .= 20; +v3_h @Record 'v3_h' { } .= 1; +v4_Kd @Record 'v4_Kd' { } .= 0.2; +v4_h @Record 'v4_h' { } .= 4; +v5_Kd @Record 'v5_Kd' { } .= 0.2; +v5_h @Record 'v5_h' { } .= 4; +v6_Kd @Record 'v6_Kd' { } .= 0.04; +v6_h @Record 'v6_h' { } .= 4; +v7_Kd @Record 'v7_Kd' { } .= 0.02; +v7_h @Record 'v7_h' { } .= 4; +v8_Kd @Record 'v8_Kd' { } .= 0.04; +v8_h @Record 'v8_h' { } .= 4; +v9_Kd @Record 'v9_Kd' { } .= 0.2; +v9_h @Record 'v9_h' { } .= 4; +pp1_mrna_degradation_rate @Record 'pp1_mrna_degradation_rate' { } .= 1; +pp2_mrna_degradation_rate @Record 'pp2_mrna_degradation_rate' { } .= 1; +pro1_strength @Record 'pro1_strength' { } .= 2; +pro2_strength @Record 'pro2_strength' { } .= 4.5077; +pro3_strength @Record 'pro3_strength' { } .= 5; +pro4_strength @Record 'pro4_strength' { } .= 5; +pro5_strength @Record 'pro5_strength' { } .= 5; +pro6_strength @Record 'pro6_strength' { } .= 1.31; +pro7_strength @Record 'pro7_strength' { } .= 1.31; +pro8_strength @Record 'pro8_strength' { } .= 5; +pro9_strength @Record 'pro9_strength' { } .= 5; +pp3_mrna_degradation_rate @Record 'pp3_mrna_degradation_rate' { } .= 1; +v10_Kd @Record 'v10_Kd' { } .= 0.02; +v10_h @Record 'v10_h' { } .= 4; +v11_Kd @Record 'v11_Kd' { } .= 0.1; +v11_h @Record 'v11_h' { } .= 2; +v12_Kd @Record 'v12_Kd' { } .= 0.1; +v12_h @Record 'v12_h' { } .= 2; +v13_Kd @Record 'v13_Kd' { } .= 0.01; +v13_h @Record 'v13_h' { } .= 2; +pp4_mrna_degradation_rate @Record 'pp4_mrna_degradation_rate' { } .= 1; +v14_Kd @Record 'v14_Kd' { } .= 1; +v14_h @Record 'v14_h' { } .= 4; +v15_Kd @Record 'v15_Kd' { } .= 20; +v15_h @Record 'v15_h' { } .= 1; +pp5_mrna_degradation_rate @Record 'pp5_mrna_degradation_rate' { } .= 1; +rbs1_strength @Record 'rbs1_strength' { } .= 0.3668; +rbs2_strength @Record 'rbs2_strength' { } .= 1.4102; +rbs3_strength @Record 'rbs3_strength' { } .= 0.8; +rbs4_strength @Record 'rbs4_strength' { } .= 2.21; +rbs5_strength @Record 'rbs5_strength' { } .= 0.5; +rbs6_strength @Record 'rbs6_strength' { } .= 2; +rbs7_strength @Record 'rbs7_strength' { } .= 5; +rbs8_strength @Record 'rbs8_strength' { } .= 3.6377; +rbs9_strength @Record 'rbs9_strength' { } .= 8; +pp6_mrna_degradation_rate @Record 'pp6_mrna_degradation_rate' { } .= 1; +pp7_mrna_degradation_rate @Record 'pp7_mrna_degradation_rate' { } .= 1; +as8 @Record 'as8' { } .= 1; +as8 := (1 + pow(p5 / v9_Kd, v9_h) - 1) / (1 + pow(p5 / v9_Kd, v9_h)); +cod1 @Record 'cod1' { } .= 1; +cod1 := pro1_strength; +cod2 @Record 'cod2' { } .= 1; +cod2 := pro2_strength * as1 * rs1; +cod3 @Record 'cod3' { } .= 1; +cod3 := pro3_strength * rs2 * rs3; +cod4 @Record 'cod4' { } .= 1; +cod4 := pro4_strength * rs7 * rs6; +cod5 @Record 'cod5' { } .= 1; +cod5 := pro5_strength * as2; +cod6 @Record 'cod6' { } .= 1; +cod6 := pro6_strength * (as3 + as4); +cod7 @Record 'cod7' { } .= 1; +cod7 := pro7_strength * (as7 + as8); +cod8 @Record 'cod8' { } .= 1; +cod8 := pro8_strength * as5 * rs4; +cod9 @Record 'cod9' { } .= 1; +cod9 := pro9_strength * as6 * rs5; +rs1 @Record 'rs1' { } .= 1; +rs1 := 1 / (1 + pow(p9 / v13_Kd, v13_h)); +rs2 @Record 'rs2' { } .= 1; +rs2 := 1 / (1 + pow(p2 / v2_Kd, v2_h)); +rs3 @Record 'rs3' { } .= 1; +rs3 := 1 / (1 + pow(p3 / v3_Kd, v3_h)); +rs4 @Record 'rs4' { } .= 1; +rs4 := 1 / (1 + pow(p8 / v11_Kd, v11_h)); +rs5 @Record 'rs5' { } .= 1; +rs5 := 1 / (1 + pow(p8 / v12_Kd, v12_h)); +rs6 @Record 'rs6' { } .= 1; +rs6 := 1 / (1 + pow(p2 / v14_Kd, v14_h)); +rs7 @Record 'rs7' { } .= 1; +rs7 := 1 / (1 + pow(p3 / v15_Kd, v15_h)); +as1 @Record 'as1' { } .= 1; +as1 := (1 + pow(p1 / v1_Kd, v1_h) - 1) / (1 + pow(p1 / v1_Kd, v1_h)); +as2 @Record 'as2' { } .= 1; +as2 := (1 + pow(p4 / v4_Kd, v4_h) - 1) / (1 + pow(p4 / v4_Kd, v4_h)); +as3 @Record 'as3' { } .= 1; +as3 := (1 + pow(p5 / v5_Kd, v5_h) - 1) / (1 + pow(p5 / v5_Kd, v5_h)); +as4 @Record 'as4' { } .= 1; +as4 := (1 + pow(p6 / v6_Kd, v6_h) - 1) / (1 + pow(p6 / v6_Kd, v6_h)); +as5 @Record 'as5' { } .= 1; +as5 := (1 + pow(p7 / v7_Kd, v7_h) - 1) / (1 + pow(p7 / v7_Kd, v7_h)); +as6 @Record 'as6' { } .= 1; +as6 := (1 + pow(p7 / v10_Kd, v10_h) - 1) / (1 + pow(p7 / v10_Kd, v10_h)); +as7 @Record 'as7' { } .= 1; +as7 := (1 + pow(p6 / v8_Kd, v8_h) - 1) / (1 + pow(p6 / v8_Kd, v8_h)); + diff --git a/latest/cases/01395/l2v5/index.heta b/latest/cases/01395/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01395/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01395/l2v5/json/output.json b/latest/cases/01395/l2v5/json/output.json new file mode 100644 index 000000000..b6409afa1 --- /dev/null +++ b/latest/cases/01395/l2v5/json/output.json @@ -0,0 +1,1575 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "DefaultCompartment", + "title": "DefaultCompartment", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "pp9_mrna", + "title": "pp9_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p9", + "title": "p9", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp8_mrna", + "title": "pp8_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p8", + "title": "p8", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp7_mrna", + "title": "pp7_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p7", + "title": "p7", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp6_mrna", + "title": "pp6_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p6", + "title": "p6", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp5_mrna", + "title": "pp5_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p5", + "title": "p5", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp4_mrna", + "title": "pp4_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p4", + "title": "p4", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp3_mrna", + "title": "pp3_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p3", + "title": "p3", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp2_mrna", + "title": "pp2_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp1_mrna", + "title": "pp1_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "5 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Reaction", + "id": "pp9_v1", + "title": "pp9_v1", + "assignments": { + "ode_": "cod9" + }, + "actors": [ + { + "target": "pp9_mrna", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp9_v2", + "title": "pp9_v2", + "assignments": { + "ode_": "pp9_mrna_degradation_rate * pp9_mrna" + }, + "actors": [ + { + "target": "pp9_mrna", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "p9" + } + ] + }, + { + "class": "Reaction", + "id": "pp9_v3", + "title": "pp9_v3", + "assignments": { + "ode_": "rbs9_strength * pp9_mrna" + }, + "actors": [ + { + "target": "p9", + "stoichiometry": 1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "pp9_mrna" + } + ] + }, + { + "class": "Reaction", + "id": "pp9_v4", + "title": "pp9_v4", + "assignments": { + "ode_": "p9_degradation_rate * p9" + }, + "actors": [ + { + "target": "p9", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp8_v1", + "title": "pp8_v1", + "assignments": { + "ode_": "cod8" + }, + "actors": [ + { + "target": "pp8_mrna", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp8_v2", + "title": "pp8_v2", + "assignments": { + "ode_": "pp8_mrna_degradation_rate * pp8_mrna" + }, + "actors": [ + { + "target": "pp8_mrna", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "p8" + } + ] + }, + { + "class": "Reaction", + "id": "pp8_v3", + "title": "pp8_v3", + "assignments": { + "ode_": "rbs8_strength * pp8_mrna" + }, + "actors": [ + { + "target": "p8", + "stoichiometry": 1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "pp8_mrna" + } + ] + }, + { + "class": "Reaction", + "id": "pp8_v4", + "title": "pp8_v4", + "assignments": { + "ode_": "p8_degradation_rate * p8" + }, + "actors": [ + { + "target": "p8", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp7_v1", + "title": "pp7_v1", + "assignments": { + "ode_": "cod7" + }, + "actors": [ + { + "target": "pp7_mrna", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp7_v2", + "title": "pp7_v2", + "assignments": { + "ode_": "pp7_mrna_degradation_rate * pp7_mrna" + }, + "actors": [ + { + "target": "pp7_mrna", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "p7" + } + ] + }, + { + "class": "Reaction", + "id": "pp7_v3", + "title": "pp7_v3", + "assignments": { + "ode_": "rbs7_strength * pp7_mrna" + }, + "actors": [ + { + "target": "p7", + "stoichiometry": 1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "pp7_mrna" + } + ] + }, + { + "class": "Reaction", + "id": "pp7_v4", + "title": "pp7_v4", + "assignments": { + "ode_": "p7_degradation_rate * p7" + }, + "actors": [ + { + "target": "p7", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp6_v1", + "title": "pp6_v1", + "assignments": { + "ode_": "cod6" + }, + "actors": [ + { + "target": "pp6_mrna", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp6_v2", + "title": "pp6_v2", + "assignments": { + "ode_": "pp6_mrna_degradation_rate * pp6_mrna" + }, + "actors": [ + { + "target": "pp6_mrna", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "p6" + } + ] + }, + { + "class": "Reaction", + "id": "pp6_v3", + "title": "pp6_v3", + "assignments": { + "ode_": "rbs6_strength * pp6_mrna" + }, + "actors": [ + { + "target": "p6", + "stoichiometry": 1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "pp6_mrna" + } + ] + }, + { + "class": "Reaction", + "id": "pp6_v4", + "title": "pp6_v4", + "assignments": { + "ode_": "p6_degradation_rate * p6" + }, + "actors": [ + { + "target": "p6", + "stoichiometry": -1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp5_v1", + "title": "pp5_v1", + "assignments": { + "ode_": "cod5" + }, + "actors": [ + { + "target": "pp5_mrna", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp5_v2", + "title": "pp5_v2", + "assignments": { + "ode_": "pp5_mrna_degradation_rate * pp5_mrna" + }, + "actors": [ + { + "target": "pp5_mrna", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "p5" + } + ] + }, + { + "class": "Reaction", + "id": "pp5_v3", + "title": "pp5_v3", + "assignments": { + "ode_": "rbs5_strength * pp5_mrna" + }, + "actors": [ + { + 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+ "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p2 / v2_Kd, v2_h))" + } + }, + { + "class": "Record", + "id": "rs3", + "title": "rs3", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p3 / v3_Kd, v3_h))" + } + }, + { + "class": "Record", + "id": "rs4", + "title": "rs4", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p8 / v11_Kd, v11_h))" + } + }, + { + "class": "Record", + "id": "rs5", + "title": "rs5", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p8 / v12_Kd, v12_h))" + } + }, + { + "class": "Record", + "id": "rs6", + "title": "rs6", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p2 / v14_Kd, v14_h))" + } + }, + { + "class": "Record", + "id": "rs7", + "title": "rs7", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p3 / v15_Kd, v15_h))" + } + }, + { + "class": "Record", + "id": "as1", + "title": "as1", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p1 / v1_Kd, v1_h) - 1) / (1 + pow(p1 / v1_Kd, v1_h))" + } + }, + { + "class": "Record", + "id": "as2", + "title": "as2", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p4 / v4_Kd, v4_h) - 1) / (1 + pow(p4 / v4_Kd, v4_h))" + } + }, + { + "class": "Record", + "id": "as3", + "title": "as3", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p5 / v5_Kd, v5_h) - 1) / (1 + pow(p5 / v5_Kd, v5_h))" + } + }, + { + "class": "Record", + "id": "as4", + "title": "as4", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p6 / v6_Kd, v6_h) - 1) / (1 + pow(p6 / v6_Kd, v6_h))" + } + }, + { + "class": "Record", + "id": "as5", + "title": "as5", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p7 / v7_Kd, v7_h) - 1) / (1 + pow(p7 / v7_Kd, v7_h))" + } + }, + { + "class": "Record", + "id": "as6", + "title": "as6", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p7 / v10_Kd, v10_h) - 1) / (1 + pow(p7 / v10_Kd, v10_h))" + } + }, + { + "class": "Record", + "id": "as7", + "title": "as7", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p6 / v8_Kd, v8_h) - 1) / (1 + pow(p6 / v8_Kd, v8_h))" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01395/l3v2/heta-code/output.heta b/latest/cases/01395/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7fb8705f0 --- /dev/null +++ b/latest/cases/01395/l3v2/heta-code/output.heta @@ -0,0 +1,214 @@ + + +t @TimeScale { }; + +DefaultCompartment @Compartment 'DefaultCompartment' { boundary: true, } .= 1; + +pp9_mrna @Species 'pp9_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p9 @Species 'p9' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp8_mrna @Species 'pp8_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p8 @Species 'p8' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp7_mrna @Species 'pp7_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p7 @Species 'p7' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp6_mrna @Species 'pp6_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p6 @Species 'p6' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp5_mrna @Species 'pp5_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p5 @Species 'p5' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp4_mrna @Species 'pp4_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p4 @Species 'p4' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp3_mrna @Species 'pp3_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p3 @Species 'p3' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp2_mrna @Species 'pp2_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p2 @Species 'p2' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp1_mrna @Species 'pp1_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p1 @Species 'p1' { compartment: DefaultCompartment, } .= 5 / DefaultCompartment; + +pp9_v1 @Reaction 'pp9_v1' { actors: = pp9_mrna, reversible: false, }; +pp9_v1 := cod9; +pp9_v2 @Reaction 'pp9_v2' { actors: pp9_mrna = , modifiers: [p9], reversible: false, }; +pp9_v2 := pp9_mrna_degradation_rate * pp9_mrna; +pp9_v3 @Reaction 'pp9_v3' { actors: = p9, modifiers: [pp9_mrna], reversible: false, }; +pp9_v3 := rbs9_strength * pp9_mrna; +pp9_v4 @Reaction 'pp9_v4' { actors: p9 = , reversible: false, }; +pp9_v4 := p9_degradation_rate * p9; +pp8_v1 @Reaction 'pp8_v1' { actors: = pp8_mrna, reversible: false, }; +pp8_v1 := cod8; +pp8_v2 @Reaction 'pp8_v2' { actors: pp8_mrna = , modifiers: [p8], reversible: false, }; +pp8_v2 := pp8_mrna_degradation_rate * pp8_mrna; +pp8_v3 @Reaction 'pp8_v3' { actors: = p8, modifiers: [pp8_mrna], reversible: false, }; +pp8_v3 := rbs8_strength * pp8_mrna; +pp8_v4 @Reaction 'pp8_v4' { actors: p8 = , reversible: false, }; +pp8_v4 := p8_degradation_rate * p8; +pp7_v1 @Reaction 'pp7_v1' { actors: = pp7_mrna, reversible: false, }; +pp7_v1 := cod7; +pp7_v2 @Reaction 'pp7_v2' { actors: pp7_mrna = , modifiers: [p7], reversible: false, }; +pp7_v2 := pp7_mrna_degradation_rate * pp7_mrna; +pp7_v3 @Reaction 'pp7_v3' { actors: = p7, modifiers: [pp7_mrna], reversible: false, }; +pp7_v3 := rbs7_strength * pp7_mrna; +pp7_v4 @Reaction 'pp7_v4' { actors: p7 = , reversible: false, }; +pp7_v4 := p7_degradation_rate * p7; +pp6_v1 @Reaction 'pp6_v1' { actors: = pp6_mrna, reversible: false, }; +pp6_v1 := cod6; +pp6_v2 @Reaction 'pp6_v2' { actors: pp6_mrna = , modifiers: [p6], reversible: false, }; +pp6_v2 := pp6_mrna_degradation_rate * pp6_mrna; +pp6_v3 @Reaction 'pp6_v3' { actors: = p6, modifiers: [pp6_mrna], reversible: false, }; +pp6_v3 := rbs6_strength * pp6_mrna; +pp6_v4 @Reaction 'pp6_v4' { actors: p6 = , reversible: false, }; +pp6_v4 := p6_degradation_rate * p6; +pp5_v1 @Reaction 'pp5_v1' { actors: = pp5_mrna, reversible: false, }; +pp5_v1 := cod5; +pp5_v2 @Reaction 'pp5_v2' { actors: pp5_mrna = , modifiers: [p5], reversible: false, }; +pp5_v2 := pp5_mrna_degradation_rate * pp5_mrna; +pp5_v3 @Reaction 'pp5_v3' { actors: = p5, modifiers: [pp5_mrna], reversible: false, }; +pp5_v3 := rbs5_strength * pp5_mrna; +pp5_v4 @Reaction 'pp5_v4' { actors: p5 = , reversible: false, }; +pp5_v4 := p5_degradation_rate * p5; +pp4_v1 @Reaction 'pp4_v1' { actors: = pp4_mrna, reversible: false, }; +pp4_v1 := cod4; +pp4_v2 @Reaction 'pp4_v2' { actors: pp4_mrna = , modifiers: [p4], reversible: false, }; +pp4_v2 := pp4_mrna_degradation_rate * pp4_mrna; +pp4_v3 @Reaction 'pp4_v3' { actors: = p4, modifiers: [pp4_mrna], reversible: false, }; +pp4_v3 := rbs4_strength * pp4_mrna; +pp4_v4 @Reaction 'pp4_v4' { actors: p4 = , reversible: false, }; +pp4_v4 := p4_degradation_rate * p4; +pp3_v1 @Reaction 'pp3_v1' { actors: = pp3_mrna, reversible: false, }; +pp3_v1 := cod3; +pp3_v2 @Reaction 'pp3_v2' { actors: pp3_mrna = , modifiers: [p3], reversible: false, }; +pp3_v2 := pp3_mrna_degradation_rate * pp3_mrna; +pp3_v3 @Reaction 'pp3_v3' { actors: = p3, modifiers: [pp3_mrna], reversible: false, }; +pp3_v3 := rbs3_strength * pp3_mrna; +pp3_v4 @Reaction 'pp3_v4' { actors: p3 = , reversible: false, }; +pp3_v4 := p3_degradation_rate * p3; +pp2_v1 @Reaction 'pp2_v1' { actors: = pp2_mrna, reversible: false, }; +pp2_v1 := cod2; +pp2_v2 @Reaction 'pp2_v2' { actors: pp2_mrna = , modifiers: [p2], reversible: false, }; +pp2_v2 := pp2_mrna_degradation_rate * pp2_mrna; +pp2_v3 @Reaction 'pp2_v3' { actors: = p2, modifiers: [pp2_mrna], reversible: false, }; +pp2_v3 := rbs2_strength * pp2_mrna; +pp2_v4 @Reaction 'pp2_v4' { actors: p2 = , reversible: false, }; +pp2_v4 := p2_degradation_rate * p2; +pp1_v1 @Reaction 'pp1_v1' { actors: = pp1_mrna, reversible: false, }; +pp1_v1 := cod1; +pp1_v2 @Reaction 'pp1_v2' { actors: pp1_mrna = , modifiers: [p1], reversible: false, }; +pp1_v2 := pp1_mrna_degradation_rate * pp1_mrna; +pp1_v3 @Reaction 'pp1_v3' { actors: = p1, modifiers: [pp1_mrna], reversible: false, }; +pp1_v3 := rbs1_strength * pp1_mrna; +pp1_v4 @Reaction 'pp1_v4' { actors: p1 = , reversible: false, }; +pp1_v4 := p1_degradation_rate * p1; + +as8 @Record 'as8' { } .= 1; +as8 := (1 + pow(p5 / v9_Kd, v9_h) - 1) / (1 + pow(p5 / v9_Kd, v9_h)); +cod1 @Record 'cod1' { } .= 1; +cod1 := pro1_strength; +cod2 @Record 'cod2' { } .= 1; +cod2 := pro2_strength * as1 * rs1; +cod3 @Record 'cod3' { } .= 1; +cod3 := pro3_strength * rs2 * rs3; +cod4 @Record 'cod4' { } .= 1; +cod4 := pro4_strength * rs7 * rs6; +cod5 @Record 'cod5' { } .= 1; +cod5 := pro5_strength * as2; +cod6 @Record 'cod6' { } .= 1; +cod6 := pro6_strength * (as3 + as4); +cod7 @Record 'cod7' { } .= 1; +cod7 := pro7_strength * (as7 + as8); +cod8 @Record 'cod8' { } .= 1; +cod8 := pro8_strength * as5 * rs4; +cod9 @Record 'cod9' { } .= 1; +cod9 := pro9_strength * as6 * rs5; +rs1 @Record 'rs1' { } .= 1; +rs1 := 1 / (1 + pow(p9 / v13_Kd, v13_h)); +rs2 @Record 'rs2' { } .= 1; +rs2 := 1 / (1 + pow(p2 / v2_Kd, v2_h)); +rs3 @Record 'rs3' { } .= 1; +rs3 := 1 / (1 + pow(p3 / v3_Kd, v3_h)); +rs4 @Record 'rs4' { } .= 1; +rs4 := 1 / (1 + pow(p8 / v11_Kd, v11_h)); +rs5 @Record 'rs5' { } .= 1; +rs5 := 1 / (1 + pow(p8 / v12_Kd, v12_h)); +rs6 @Record 'rs6' { } .= 1; +rs6 := 1 / (1 + pow(p2 / v14_Kd, v14_h)); +rs7 @Record 'rs7' { } .= 1; +rs7 := 1 / (1 + pow(p3 / v15_Kd, v15_h)); +as1 @Record 'as1' { } .= 1; +as1 := (1 + pow(p1 / v1_Kd, v1_h) - 1) / (1 + pow(p1 / v1_Kd, v1_h)); +as2 @Record 'as2' { } .= 1; +as2 := (1 + pow(p4 / v4_Kd, v4_h) - 1) / (1 + pow(p4 / v4_Kd, v4_h)); +as3 @Record 'as3' { } .= 1; +as3 := (1 + pow(p5 / v5_Kd, v5_h) - 1) / (1 + pow(p5 / v5_Kd, v5_h)); +as4 @Record 'as4' { } .= 1; +as4 := (1 + pow(p6 / v6_Kd, v6_h) - 1) / (1 + pow(p6 / v6_Kd, v6_h)); +as5 @Record 'as5' { } .= 1; +as5 := (1 + pow(p7 / v7_Kd, v7_h) - 1) / (1 + pow(p7 / v7_Kd, v7_h)); +as6 @Record 'as6' { } .= 1; +as6 := (1 + pow(p7 / v10_Kd, v10_h) - 1) / (1 + pow(p7 / v10_Kd, v10_h)); +as7 @Record 'as7' { } .= 1; +as7 := (1 + pow(p6 / v8_Kd, v8_h) - 1) / (1 + pow(p6 / v8_Kd, v8_h)); + +pp8_mrna_degradation_rate @Const 'pp8_mrna_degradation_rate' { } = 1; +pp9_mrna_degradation_rate @Const 'pp9_mrna_degradation_rate' { } = 1; +p1_degradation_rate @Const 'p1_degradation_rate' { } = 0.5; +p2_degradation_rate @Const 'p2_degradation_rate' { } = 0.5; +p3_degradation_rate @Const 'p3_degradation_rate' { } = 0.5; +p4_degradation_rate @Const 'p4_degradation_rate' { } = 0.5; +p5_degradation_rate @Const 'p5_degradation_rate' { } = 0.5; +p6_degradation_rate @Const 'p6_degradation_rate' { } = 0.5; +p7_degradation_rate @Const 'p7_degradation_rate' { } = 0.5; +p8_degradation_rate @Const 'p8_degradation_rate' { } = 0.5; +p9_degradation_rate @Const 'p9_degradation_rate' { } = 0.5; +v1_Kd @Const 'v1_Kd' { } = 11.147; +v1_h @Const 'v1_h' { } = 1; +v2_Kd @Const 'v2_Kd' { } = 1; +v2_h @Const 'v2_h' { } = 4; +v3_Kd @Const 'v3_Kd' { } = 20; +v3_h @Const 'v3_h' { } = 1; +v4_Kd @Const 'v4_Kd' { } = 0.2; +v4_h @Const 'v4_h' { } = 4; +v5_Kd @Const 'v5_Kd' { } = 0.2; +v5_h @Const 'v5_h' { } = 4; +v6_Kd @Const 'v6_Kd' { } = 0.04; +v6_h @Const 'v6_h' { } = 4; +v7_Kd @Const 'v7_Kd' { } = 0.02; +v7_h @Const 'v7_h' { } = 4; +v8_Kd @Const 'v8_Kd' { } = 0.04; +v8_h @Const 'v8_h' { } = 4; +v9_Kd @Const 'v9_Kd' { } = 0.2; +v9_h @Const 'v9_h' { } = 4; +pp1_mrna_degradation_rate @Const 'pp1_mrna_degradation_rate' { } = 1; +pp2_mrna_degradation_rate @Const 'pp2_mrna_degradation_rate' { } = 1; +pro1_strength @Const 'pro1_strength' { } = 2; +pro2_strength @Const 'pro2_strength' { } = 4.5077; +pro3_strength @Const 'pro3_strength' { } = 5; +pro4_strength @Const 'pro4_strength' { } = 5; +pro5_strength @Const 'pro5_strength' { } = 5; +pro6_strength @Const 'pro6_strength' { } = 1.31; +pro7_strength @Const 'pro7_strength' { } = 1.31; +pro8_strength @Const 'pro8_strength' { } = 5; +pro9_strength @Const 'pro9_strength' { } = 5; +pp3_mrna_degradation_rate @Const 'pp3_mrna_degradation_rate' { } = 1; +v10_Kd @Const 'v10_Kd' { } = 0.02; +v10_h @Const 'v10_h' { } = 4; +v11_Kd @Const 'v11_Kd' { } = 0.1; +v11_h @Const 'v11_h' { } = 2; +v12_Kd @Const 'v12_Kd' { } = 0.1; +v12_h @Const 'v12_h' { } = 2; +v13_Kd @Const 'v13_Kd' { } = 0.01; +v13_h @Const 'v13_h' { } = 2; +pp4_mrna_degradation_rate @Const 'pp4_mrna_degradation_rate' { } = 1; +v14_Kd @Const 'v14_Kd' { } = 1; +v14_h @Const 'v14_h' { } = 4; +v15_Kd @Const 'v15_Kd' { } = 20; +v15_h @Const 'v15_h' { } = 1; +pp5_mrna_degradation_rate @Const 'pp5_mrna_degradation_rate' { } = 1; +rbs1_strength @Const 'rbs1_strength' { } = 0.3668; +rbs2_strength @Const 'rbs2_strength' { } = 1.4102; +rbs3_strength @Const 'rbs3_strength' { } = 0.8; +rbs4_strength @Const 'rbs4_strength' { } = 2.21; +rbs5_strength @Const 'rbs5_strength' { } = 0.5; +rbs6_strength @Const 'rbs6_strength' { } = 2; +rbs7_strength @Const 'rbs7_strength' { } = 5; +rbs8_strength @Const 'rbs8_strength' { } = 3.6377; +rbs9_strength @Const 'rbs9_strength' { } = 8; +pp6_mrna_degradation_rate @Const 'pp6_mrna_degradation_rate' { } = 1; +pp7_mrna_degradation_rate @Const 'pp7_mrna_degradation_rate' { } = 1; + diff --git a/latest/cases/01395/l3v2/index.heta b/latest/cases/01395/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01395/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01395/l3v2/json/output.json b/latest/cases/01395/l3v2/json/output.json new file mode 100644 index 000000000..27807a586 --- /dev/null +++ b/latest/cases/01395/l3v2/json/output.json @@ -0,0 +1,1418 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "DefaultCompartment", + "title": "DefaultCompartment", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "pp9_mrna", + "title": "pp9_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p9", + "title": "p9", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp8_mrna", + "title": "pp8_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p8", + "title": "p8", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp7_mrna", + "title": "pp7_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p7", + "title": "p7", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp6_mrna", + "title": "pp6_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p6", + "title": "p6", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp5_mrna", + "title": "pp5_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p5", + "title": "p5", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp4_mrna", + "title": "pp4_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p4", + "title": "p4", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp3_mrna", + "title": "pp3_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p3", + "title": "p3", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp2_mrna", + "title": "pp2_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p2", + "title": "p2", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "pp1_mrna", + "title": "pp1_mrna", + "assignments": { + "start_": "0 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Species", + "id": "p1", + "title": "p1", + "assignments": { + "start_": "5 / DefaultCompartment" + }, + "compartment": "DefaultCompartment" + }, + { + "class": "Reaction", + "id": "pp9_v1", + "title": "pp9_v1", + "assignments": { + "ode_": "cod9" + }, + "actors": [ + { + "target": "pp9_mrna", + "stoichiometry": 1 + } + ], + "reversible": false + }, + { + "class": "Reaction", + "id": "pp9_v2", + "title": "pp9_v2", + "assignments": { + "ode_": "pp9_mrna_degradation_rate * pp9_mrna" + }, + "actors": [ + { + "target": "pp9_mrna", + "stoichiometry": -1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "p9" + } + ] + }, + { + "class": "Reaction", + "id": "pp9_v3", + "title": "pp9_v3", + "assignments": { + "ode_": "rbs9_strength * pp9_mrna" + }, + "actors": [ + { + "target": "p9", + "stoichiometry": 1 + } + ], + "reversible": false, + "modifiers": [ + { + "target": "pp9_mrna" + } + ] + }, + { + "class": "Reaction", + 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"pp6_mrna_degradation_rate", + "title": "pp6_mrna_degradation_rate", + "num": 1 + }, + { + "class": "Const", + "id": "pp7_mrna_degradation_rate", + "title": "pp7_mrna_degradation_rate", + "num": 1 + }, + { + "class": "Record", + "id": "as8", + "title": "as8", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p5 / v9_Kd, v9_h) - 1) / (1 + pow(p5 / v9_Kd, v9_h))" + } + }, + { + "class": "Record", + "id": "cod1", + "title": "cod1", + "assignments": { + "start_": "1", + "ode_": "pro1_strength" + } + }, + { + "class": "Record", + "id": "cod2", + "title": "cod2", + "assignments": { + "start_": "1", + "ode_": "pro2_strength * as1 * rs1" + } + }, + { + "class": "Record", + "id": "cod3", + "title": "cod3", + "assignments": { + "start_": "1", + "ode_": "pro3_strength * rs2 * rs3" + } + }, + { + "class": "Record", + "id": "cod4", + "title": "cod4", + "assignments": { + "start_": "1", + "ode_": "pro4_strength * rs7 * rs6" + } + }, + { + "class": "Record", + "id": "cod5", + "title": "cod5", + "assignments": { + "start_": "1", + "ode_": "pro5_strength * as2" + } + }, + { + "class": "Record", + "id": "cod6", + "title": "cod6", + "assignments": { + "start_": "1", + "ode_": "pro6_strength * (as3 + as4)" + } + }, + { + "class": "Record", + "id": "cod7", + "title": "cod7", + "assignments": { + "start_": "1", + "ode_": "pro7_strength * (as7 + as8)" + } + }, + { + "class": "Record", + "id": "cod8", + "title": "cod8", + "assignments": { + "start_": "1", + "ode_": "pro8_strength * as5 * rs4" + } + }, + { + "class": "Record", + "id": "cod9", + "title": "cod9", + "assignments": { + "start_": "1", + "ode_": "pro9_strength * as6 * rs5" + } + }, + { + "class": "Record", + "id": "rs1", + "title": "rs1", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p9 / v13_Kd, v13_h))" + } + }, + { + "class": "Record", + "id": "rs2", + "title": "rs2", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p2 / v2_Kd, v2_h))" + } + }, + { + "class": "Record", + "id": "rs3", + "title": "rs3", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p3 / v3_Kd, v3_h))" + } + }, + { + "class": "Record", + "id": "rs4", + "title": "rs4", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p8 / v11_Kd, v11_h))" + } + }, + { + "class": "Record", + "id": "rs5", + "title": "rs5", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p8 / v12_Kd, v12_h))" + } + }, + { + "class": "Record", + "id": "rs6", + "title": "rs6", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p2 / v14_Kd, v14_h))" + } + }, + { + "class": "Record", + "id": "rs7", + "title": "rs7", + "assignments": { + "start_": "1", + "ode_": "1 / (1 + pow(p3 / v15_Kd, v15_h))" + } + }, + { + "class": "Record", + "id": "as1", + "title": "as1", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p1 / v1_Kd, v1_h) - 1) / (1 + pow(p1 / v1_Kd, v1_h))" + } + }, + { + "class": "Record", + "id": "as2", + "title": "as2", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p4 / v4_Kd, v4_h) - 1) / (1 + pow(p4 / v4_Kd, v4_h))" + } + }, + { + "class": "Record", + "id": "as3", + "title": "as3", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p5 / v5_Kd, v5_h) - 1) / (1 + pow(p5 / v5_Kd, v5_h))" + } + }, + { + "class": "Record", + "id": "as4", + "title": "as4", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p6 / v6_Kd, v6_h) - 1) / (1 + pow(p6 / v6_Kd, v6_h))" + } + }, + { + "class": "Record", + "id": "as5", + "title": "as5", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p7 / v7_Kd, v7_h) - 1) / (1 + pow(p7 / v7_Kd, v7_h))" + } + }, + { + "class": "Record", + "id": "as6", + "title": "as6", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p7 / v10_Kd, v10_h) - 1) / (1 + pow(p7 / v10_Kd, v10_h))" + } + }, + { + "class": "Record", + "id": "as7", + "title": "as7", + "assignments": { + "start_": "1", + "ode_": "(1 + pow(p6 / v8_Kd, v8_h) - 1) / (1 + pow(p6 / v8_Kd, v8_h))" + } + } +] \ No newline at end of file diff --git a/latest/cases/01395/model-sbml-l2v5.xml b/latest/cases/01395/model-sbml-l2v5.xml new file mode 100644 index 000000000..ec61790de --- /dev/null +++ b/latest/cases/01395/model-sbml-l2v5.xml @@ -0,0 +1,1179 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + p5 + v9_Kd + + v9_h + + + 1 + + + + 1 + + + + + p5 + v9_Kd + + v9_h + + + + + + + + pro1_strength + + + + + + + pro2_strength + as1 + rs1 + + + + + + + + pro3_strength + rs2 + rs3 + + + + + + + + pro4_strength + rs7 + rs6 + + + + + + + + pro5_strength + as2 + + + + + + + + pro6_strength + + + as3 + as4 + + + + + + + + + pro7_strength + + + as7 + as8 + + + + + + + + + pro8_strength + as5 + rs4 + + + + + + + + pro9_strength + as6 + rs5 + + + + + + + + 1 + + + 1 + + + + + p9 + v13_Kd + + v13_h + + + + + + + + + + 1 + + + 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pp5_mrna + + + + + + + + + + + + + + + + rbs5_strength + pp5_mrna + + + + + + + + + + + + + p5_degradation_rate + p5 + + + + + + + + + + + cod4 + + + + + + + + + + + + + + + pp4_mrna_degradation_rate + pp4_mrna + + + + + + + + + + + + + + + + rbs4_strength + pp4_mrna + + + + + + + + + + + + + p4_degradation_rate + p4 + + + + + + + + + + + cod3 + + + + + + + + + + + + + + + pp3_mrna_degradation_rate + pp3_mrna + + + + + + + + + + + + + + + + rbs3_strength + pp3_mrna + + + + + + + + + + + + + p3_degradation_rate + p3 + + + + + + + + + + + cod2 + + + + + + + + + + + + + + + pp2_mrna_degradation_rate + pp2_mrna + + + + + + + + + + + + + + + + rbs2_strength + pp2_mrna + + + + + + + + + + + + + p2_degradation_rate + p2 + + + + + + + + + + + cod1 + + + + + + + + + + + + + + + pp1_mrna_degradation_rate + pp1_mrna + + + + + + + + + + + + + + + + rbs1_strength + pp1_mrna + + + + + + + + + + + + + p1_degradation_rate + p1 + + + + + + + diff --git a/latest/cases/01395/model-sbml-l3v2.xml b/latest/cases/01395/model-sbml-l3v2.xml new file mode 100644 index 000000000..3c9e36677 --- /dev/null +++ b/latest/cases/01395/model-sbml-l3v2.xml @@ -0,0 +1,1179 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + p5 + v9_Kd + + v9_h + + + 1 + + + + 1 + + + + + p5 + v9_Kd + + v9_h + + + + + + + + pro1_strength + + + + + + + pro2_strength + as1 + rs1 + + + + + + + + pro3_strength + rs2 + rs3 + + + + + + + + pro4_strength + rs7 + rs6 + + + + + + + + pro5_strength + as2 + + + + + + + + pro6_strength + + + as3 + as4 + + + + + + + + + pro7_strength + + + as7 + as8 + + + + + + + + + pro8_strength + as5 + rs4 + + + + + + + + pro9_strength + as6 + rs5 + + + + + + + + 1 + + + 1 + + + + + p9 + v13_Kd + + v13_h + + + + + + + + + + 1 + + + 1 + + + + + p2 + v2_Kd + + v2_h + + + + + 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rbs5_strength + pp5_mrna + + + + + + + + + + + + + p5_degradation_rate + p5 + + + + + + + + + + + cod4 + + + + + + + + + + + + + + + pp4_mrna_degradation_rate + pp4_mrna + + + + + + + + + + + + + + + + rbs4_strength + pp4_mrna + + + + + + + + + + + + + p4_degradation_rate + p4 + + + + + + + + + + + cod3 + + + + + + + + + + + + + + + pp3_mrna_degradation_rate + pp3_mrna + + + + + + + + + + + + + + + + rbs3_strength + pp3_mrna + + + + + + + + + + + + + p3_degradation_rate + p3 + + + + + + + + + + + cod2 + + + + + + + + + + + + + + + pp2_mrna_degradation_rate + pp2_mrna + + + + + + + + + + + + + + + + rbs2_strength + pp2_mrna + + + + + + + + + + + + + p2_degradation_rate + p2 + + + + + + + + + + + cod1 + + + + + + + + + + + + + + + pp1_mrna_degradation_rate + pp1_mrna + + + + + + + + + + + + + + + + rbs1_strength + pp1_mrna + + + + + + + + + + + + + p1_degradation_rate + p1 + + + + + + + diff --git a/latest/cases/01395/output.heta b/latest/cases/01395/output.heta new file mode 100644 index 000000000..cd86cf7ff --- /dev/null +++ b/latest/cases/01395/output.heta @@ -0,0 +1,420 @@ +/* +category: Test +synopsis: A larger model where the order of assignment rules is important. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this real model of a reaction system, the order of the assignment rules makes a difference in how the simulation proceeds: it is important to carry out the assignments such that the independent assignments are performed first, with the dependent assignments carried out after the assignments to variables they each depend on. This has been seen to make an appreciable difference when using large timesteps and the Euler method. + +The model contains: +* 18 species (pp9_mrna, p9, pp8_mrna, p8, pp7_mrna, p7, pp6_mrna, p6, pp5_mrna, p5, pp4_mrna, p4, pp3_mrna, p3, pp2_mrna, p2, pp1_mrna, p1) +* 90 parameters (pp8_mrna_degradation_rate, pp9_mrna_degradation_rate, p1_degradation_rate, p2_degradation_rate, p3_degradation_rate, p4_degradation_rate, p5_degradation_rate, p6_degradation_rate, p7_degradation_rate, p8_degradation_rate, p9_degradation_rate, v1_Kd, v1_h, v2_Kd, v2_h, v3_Kd, v3_h, v4_Kd, v4_h, v5_Kd, v5_h, v6_Kd, v6_h, v7_Kd, v7_h, v8_Kd, v8_h, v9_Kd, v9_h, pp1_mrna_degradation_rate, pp2_mrna_degradation_rate, pro1_strength, pro2_strength, pro3_strength, pro4_strength, pro5_strength, pro6_strength, pro7_strength, pro8_strength, pro9_strength, pp3_mrna_degradation_rate, v10_Kd, v10_h, v11_Kd, v11_h, v12_Kd, v12_h, v13_Kd, v13_h, pp4_mrna_degradation_rate, v14_Kd, v14_h, v15_Kd, v15_h, pp5_mrna_degradation_rate, rbs1_strength, rbs2_strength, rbs3_strength, rbs4_strength, rbs5_strength, rbs6_strength, rbs7_strength, rbs8_strength, rbs9_strength, pp6_mrna_degradation_rate, pp7_mrna_degradation_rate, as8, cod1, cod2, cod3, cod4, cod5, cod6, cod7, cod8, cod9, rs1, rs2, rs3, rs4, rs5, rs6, rs7, as1, as2, as3, as4, as5, as6, as7) +* 1 compartment (DefaultCompartment) + +There are 36 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| pp9_v1: -> pp9_mrna | $cod9$ | +| pp9_v2: pp9_mrna -> | $pp9_mrna_degradation_rate * pp9_mrna$ | +| pp9_v3: -> p9 | $rbs9_strength * pp9_mrna$ | +| pp9_v4: p9 -> | $p9_degradation_rate * p9$ | +| pp8_v1: -> pp8_mrna | $cod8$ | +| pp8_v2: pp8_mrna -> | $pp8_mrna_degradation_rate * pp8_mrna$ | +| pp8_v3: -> p8 | $rbs8_strength * pp8_mrna$ | +| pp8_v4: p8 -> | $p8_degradation_rate * p8$ | +| pp7_v1: -> pp7_mrna | $cod7$ | +| pp7_v2: pp7_mrna -> | $pp7_mrna_degradation_rate * pp7_mrna$ | +| pp7_v3: -> p7 | $rbs7_strength * pp7_mrna$ | +| pp7_v4: p7 -> | $p7_degradation_rate * p7$ | +| pp6_v1: -> pp6_mrna | $cod6$ | +| pp6_v2: pp6_mrna -> | $pp6_mrna_degradation_rate * pp6_mrna$ | +| pp6_v3: -> p6 | $rbs6_strength * pp6_mrna$ | +| pp6_v4: p6 -> | $p6_degradation_rate * p6$ | +| pp5_v1: -> pp5_mrna | $cod5$ | +| pp5_v2: pp5_mrna -> | $pp5_mrna_degradation_rate * pp5_mrna$ | +| pp5_v3: -> p5 | $rbs5_strength * pp5_mrna$ | +| pp5_v4: p5 -> | $p5_degradation_rate * p5$ | +| pp4_v1: -> pp4_mrna | $cod4$ | +| pp4_v2: pp4_mrna -> | $pp4_mrna_degradation_rate * pp4_mrna$ | +| pp4_v3: -> p4 | $rbs4_strength * pp4_mrna$ | +| pp4_v4: p4 -> | $p4_degradation_rate * p4$ | +| pp3_v1: -> pp3_mrna | $cod3$ | +| pp3_v2: pp3_mrna -> | $pp3_mrna_degradation_rate * pp3_mrna$ | +| pp3_v3: -> p3 | $rbs3_strength * pp3_mrna$ | +| pp3_v4: p3 -> | $p3_degradation_rate * p3$ | +| pp2_v1: -> pp2_mrna | $cod2$ | +| pp2_v2: pp2_mrna -> | $pp2_mrna_degradation_rate * pp2_mrna$ | +| pp2_v3: -> p2 | $rbs2_strength * pp2_mrna$ | +| pp2_v4: p2 -> | $p2_degradation_rate * p2$ | +| pp1_v1: -> pp1_mrna | $cod1$ | +| pp1_v2: pp1_mrna -> | $pp1_mrna_degradation_rate * pp1_mrna$ | +| pp1_v3: -> p1 | $rbs1_strength * pp1_mrna$ | +| pp1_v4: p1 -> | $p1_degradation_rate * p1$ |] + + +There are 24 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | as8 | $(1 + (p5 / v9_Kd)^v9_h - 1) / (1 + (p5 / v9_Kd)^v9_h)$ | +| Assignment | cod1 | $pro1_strength$ | +| Assignment | cod2 | $pro2_strength * as1 * rs1$ | +| Assignment | cod3 | $pro3_strength * rs2 * rs3$ | +| Assignment | cod4 | $pro4_strength * rs7 * rs6$ | +| Assignment | cod5 | $pro5_strength * as2$ | +| Assignment | cod6 | $pro6_strength * (as3 + as4)$ | +| Assignment | cod7 | $pro7_strength * (as7 + as8)$ | +| Assignment | cod8 | $pro8_strength * as5 * rs4$ | +| Assignment | cod9 | $pro9_strength * as6 * rs5$ | +| Assignment | rs1 | $1 / (1 + (p9 / v13_Kd)^v13_h)$ | +| Assignment | rs2 | $1 / (1 + (p2 / v2_Kd)^v2_h)$ | +| Assignment | rs3 | $1 / (1 + (p3 / v3_Kd)^v3_h)$ | +| Assignment | rs4 | $1 / (1 + (p8 / v11_Kd)^v11_h)$ | +| Assignment | rs5 | $1 / (1 + (p8 / v12_Kd)^v12_h)$ | +| Assignment | rs6 | $1 / (1 + (p2 / v14_Kd)^v14_h)$ | +| Assignment | rs7 | $1 / (1 + (p3 / v15_Kd)^v15_h)$ | +| Assignment | as1 | $(1 + (p1 / v1_Kd)^v1_h - 1) / (1 + (p1 / v1_Kd)^v1_h)$ | +| Assignment | as2 | $(1 + (p4 / v4_Kd)^v4_h - 1) / (1 + (p4 / v4_Kd)^v4_h)$ | +| Assignment | as3 | $(1 + (p5 / v5_Kd)^v5_h - 1) / (1 + (p5 / v5_Kd)^v5_h)$ | +| Assignment | as4 | $(1 + (p6 / v6_Kd)^v6_h - 1) / (1 + (p6 / v6_Kd)^v6_h)$ | +| Assignment | as5 | $(1 + (p7 / v7_Kd)^v7_h - 1) / (1 + (p7 / v7_Kd)^v7_h)$ | +| Assignment | as6 | $(1 + (p7 / v10_Kd)^v10_h - 1) / (1 + (p7 / v10_Kd)^v10_h)$ | +| Assignment | as7 | $(1 + (p6 / v8_Kd)^v8_h - 1) / (1 + (p6 / v8_Kd)^v8_h)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species pp9_mrna | $0$ | variable | +| Initial amount of species p9 | $0$ | variable | +| Initial amount of species pp8_mrna | $0$ | variable | +| Initial amount of species p8 | $0$ | variable | +| Initial amount of species pp7_mrna | $0$ | variable | +| Initial amount of species p7 | $0$ | variable | +| Initial amount of species pp6_mrna | $0$ | variable | +| Initial amount of species p6 | $0$ | variable | +| Initial amount of species pp5_mrna | $0$ | variable | +| Initial amount of species p5 | $0$ | variable | +| Initial amount of species pp4_mrna | $0$ | variable | +| Initial amount of species p4 | $0$ | variable | +| Initial amount of species pp3_mrna | $0$ | variable | +| Initial amount of species p3 | $0$ | variable | +| Initial amount of species pp2_mrna | $0$ | variable | +| Initial amount of species p2 | $0$ | variable | +| Initial amount of species pp1_mrna | $0$ | variable | +| Initial amount of species p1 | $5$ | variable | +| Initial value of parameter pp8_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter pp9_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter p1_degradation_rate | $0.5$ | constant | +| Initial value of parameter p2_degradation_rate | $0.5$ | constant | +| Initial value of parameter p3_degradation_rate | $0.5$ | constant | +| Initial value of parameter p4_degradation_rate | $0.5$ | constant | +| Initial value of parameter p5_degradation_rate | $0.5$ | constant | +| Initial value of parameter p6_degradation_rate | $0.5$ | constant | +| Initial value of parameter p7_degradation_rate | $0.5$ | constant | +| Initial value of parameter p8_degradation_rate | $0.5$ | constant | +| Initial value of parameter p9_degradation_rate | $0.5$ | constant | +| Initial value of parameter v1_Kd | $11.147$ | constant | +| Initial value of parameter v1_h | $1$ | constant | +| Initial value of parameter v2_Kd | $1$ | constant | +| Initial value of parameter v2_h | $4$ | constant | +| Initial value of parameter v3_Kd | $20$ | constant | +| Initial value of parameter v3_h | $1$ | constant | +| Initial value of parameter v4_Kd | $0.2$ | constant | +| Initial value of parameter v4_h | $4$ | constant | +| Initial value of parameter v5_Kd | $0.2$ | constant | +| Initial value of parameter v5_h | $4$ | constant | +| Initial value of parameter v6_Kd | $0.04$ | constant | +| Initial value of parameter v6_h | $4$ | constant | +| Initial value of parameter v7_Kd | $0.02$ | constant | +| Initial value of parameter v7_h | $4$ | constant | +| Initial value of parameter v8_Kd | $0.04$ | constant | +| Initial value of parameter v8_h | $4$ | constant | +| Initial value of parameter v9_Kd | $0.2$ | constant | +| Initial value of parameter v9_h | $4$ | constant | +| Initial value of parameter pp1_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter pp2_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter pro1_strength | $2$ | constant | +| Initial value of parameter pro2_strength | $4.5077$ | constant | +| Initial value of parameter pro3_strength | $5$ | constant | +| Initial value of parameter pro4_strength | $5$ | constant | +| Initial value of parameter pro5_strength | $5$ | constant | +| Initial value of parameter pro6_strength | $1.31$ | constant | +| Initial value of parameter pro7_strength | $1.31$ | constant | +| Initial value of parameter pro8_strength | $5$ | constant | +| Initial value of parameter pro9_strength | $5$ | constant | +| Initial value of parameter pp3_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter v10_Kd | $0.02$ | constant | +| Initial value of parameter v10_h | $4$ | constant | +| Initial value of parameter v11_Kd | $0.1$ | constant | +| Initial value of parameter v11_h | $2$ | constant | +| Initial value of parameter v12_Kd | $0.1$ | constant | +| Initial value of parameter v12_h | $2$ | constant | +| Initial value of parameter v13_Kd | $0.01$ | constant | +| Initial value of parameter v13_h | $2$ | constant | +| Initial value of parameter pp4_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter v14_Kd | $1$ | constant | +| Initial value of parameter v14_h | $4$ | constant | +| Initial value of parameter v15_Kd | $20$ | constant | +| Initial value of parameter v15_h | $1$ | constant | +| Initial value of parameter pp5_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter rbs1_strength | $0.3668$ | constant | +| Initial value of parameter rbs2_strength | $1.4102$ | constant | +| Initial value of parameter rbs3_strength | $0.8$ | constant | +| Initial value of parameter rbs4_strength | $2.21$ | constant | +| Initial value of parameter rbs5_strength | $0.5$ | constant | +| Initial value of parameter rbs6_strength | $2$ | constant | +| Initial value of parameter rbs7_strength | $5$ | constant | +| Initial value of parameter rbs8_strength | $3.6377$ | constant | +| Initial value of parameter rbs9_strength | $8$ | constant | +| Initial value of parameter pp6_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter pp7_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter as8 | $(1 + (p5 / v9_Kd)^v9_h - 1) / (1 + (p5 / v9_Kd)^v9_h)$ | variable | +| Initial value of parameter cod1 | $pro1_strength$ | variable | +| Initial value of parameter cod2 | $pro2_strength * as1 * rs1$ | variable | +| Initial value of parameter cod3 | $pro3_strength * rs2 * rs3$ | variable | +| Initial value of parameter cod4 | $pro4_strength * rs7 * rs6$ | variable | +| Initial value of parameter cod5 | $pro5_strength * as2$ | variable | +| Initial value of parameter cod6 | $pro6_strength * (as3 + as4)$ | variable | +| Initial value of parameter cod7 | $pro7_strength * (as7 + as8)$ | variable | +| Initial value of parameter cod8 | $pro8_strength * as5 * rs4$ | variable | +| Initial value of parameter cod9 | $pro9_strength * as6 * rs5$ | variable | +| Initial value of parameter rs1 | $1 / (1 + (p9 / v13_Kd)^v13_h)$ | variable | +| Initial value of parameter rs2 | $1 / (1 + (p2 / v2_Kd)^v2_h)$ | variable | +| Initial value of parameter rs3 | $1 / (1 + (p3 / v3_Kd)^v3_h)$ | variable | +| Initial value of parameter rs4 | $1 / (1 + (p8 / v11_Kd)^v11_h)$ | variable | +| Initial value of parameter rs5 | $1 / (1 + (p8 / v12_Kd)^v12_h)$ | variable | +| Initial value of parameter rs6 | $1 / (1 + (p2 / v14_Kd)^v14_h)$ | variable | +| Initial value of parameter rs7 | $1 / (1 + (p3 / v15_Kd)^v15_h)$ | variable | +| Initial value of parameter as1 | $(1 + (p1 / v1_Kd)^v1_h - 1) / (1 + (p1 / v1_Kd)^v1_h)$ | variable | +| Initial value of parameter as2 | $(1 + (p4 / v4_Kd)^v4_h - 1) / (1 + (p4 / v4_Kd)^v4_h)$ | variable | +| Initial value of parameter as3 | $(1 + (p5 / v5_Kd)^v5_h - 1) / (1 + (p5 / v5_Kd)^v5_h)$ | variable | +| Initial value of parameter as4 | $(1 + (p6 / v6_Kd)^v6_h - 1) / (1 + (p6 / v6_Kd)^v6_h)$ | variable | +| Initial value of parameter as5 | $(1 + (p7 / v7_Kd)^v7_h - 1) / (1 + (p7 / v7_Kd)^v7_h)$ | variable | +| Initial value of parameter as6 | $(1 + (p7 / v10_Kd)^v10_h - 1) / (1 + (p7 / v10_Kd)^v10_h)$ | variable | +| Initial value of parameter as7 | $(1 + (p6 / v8_Kd)^v8_h - 1) / (1 + (p6 / v8_Kd)^v8_h)$ | variable | +| Initial volume of compartment 'DefaultCompartment' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +DefaultCompartment @Compartment 'DefaultCompartment' { boundary: true, } .= 1; + +pp9_mrna @Species 'pp9_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p9 @Species 'p9' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp8_mrna @Species 'pp8_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p8 @Species 'p8' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp7_mrna @Species 'pp7_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p7 @Species 'p7' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp6_mrna @Species 'pp6_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p6 @Species 'p6' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp5_mrna @Species 'pp5_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p5 @Species 'p5' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp4_mrna @Species 'pp4_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p4 @Species 'p4' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp3_mrna @Species 'pp3_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p3 @Species 'p3' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp2_mrna @Species 'pp2_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p2 @Species 'p2' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +pp1_mrna @Species 'pp1_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment; +p1 @Species 'p1' { compartment: DefaultCompartment, } .= 5 / DefaultCompartment; + +pp9_v1 @Reaction 'pp9_v1' { actors: = pp9_mrna, reversible: false, }; +pp9_v1 := cod9; +pp9_v2 @Reaction 'pp9_v2' { actors: pp9_mrna = , modifiers: [p9], reversible: false, }; +pp9_v2 := pp9_mrna_degradation_rate * pp9_mrna; +pp9_v3 @Reaction 'pp9_v3' { actors: = p9, modifiers: [pp9_mrna], reversible: false, }; +pp9_v3 := rbs9_strength * pp9_mrna; +pp9_v4 @Reaction 'pp9_v4' { actors: p9 = , reversible: false, }; +pp9_v4 := p9_degradation_rate * p9; +pp8_v1 @Reaction 'pp8_v1' { actors: = pp8_mrna, reversible: false, }; +pp8_v1 := cod8; +pp8_v2 @Reaction 'pp8_v2' { actors: pp8_mrna = , modifiers: [p8], reversible: false, }; +pp8_v2 := pp8_mrna_degradation_rate * pp8_mrna; +pp8_v3 @Reaction 'pp8_v3' { actors: = p8, modifiers: [pp8_mrna], reversible: false, }; +pp8_v3 := rbs8_strength * pp8_mrna; +pp8_v4 @Reaction 'pp8_v4' { actors: p8 = , reversible: false, }; +pp8_v4 := p8_degradation_rate * p8; +pp7_v1 @Reaction 'pp7_v1' { actors: = pp7_mrna, reversible: false, }; +pp7_v1 := cod7; +pp7_v2 @Reaction 'pp7_v2' { actors: pp7_mrna = , modifiers: [p7], reversible: false, }; +pp7_v2 := pp7_mrna_degradation_rate * pp7_mrna; +pp7_v3 @Reaction 'pp7_v3' { actors: = p7, modifiers: [pp7_mrna], reversible: false, }; +pp7_v3 := rbs7_strength * pp7_mrna; +pp7_v4 @Reaction 'pp7_v4' { actors: p7 = , reversible: false, }; +pp7_v4 := p7_degradation_rate * p7; +pp6_v1 @Reaction 'pp6_v1' { actors: = pp6_mrna, reversible: false, }; +pp6_v1 := cod6; +pp6_v2 @Reaction 'pp6_v2' { actors: pp6_mrna = , modifiers: [p6], reversible: false, }; +pp6_v2 := pp6_mrna_degradation_rate * pp6_mrna; +pp6_v3 @Reaction 'pp6_v3' { actors: = p6, modifiers: [pp6_mrna], reversible: false, }; +pp6_v3 := rbs6_strength * pp6_mrna; +pp6_v4 @Reaction 'pp6_v4' { actors: p6 = , reversible: false, }; +pp6_v4 := p6_degradation_rate * p6; +pp5_v1 @Reaction 'pp5_v1' { actors: = pp5_mrna, reversible: false, }; +pp5_v1 := cod5; +pp5_v2 @Reaction 'pp5_v2' { actors: pp5_mrna = , modifiers: [p5], reversible: false, }; +pp5_v2 := pp5_mrna_degradation_rate * pp5_mrna; +pp5_v3 @Reaction 'pp5_v3' { actors: = p5, modifiers: [pp5_mrna], reversible: false, }; +pp5_v3 := rbs5_strength * pp5_mrna; +pp5_v4 @Reaction 'pp5_v4' { actors: p5 = , reversible: false, }; +pp5_v4 := p5_degradation_rate * p5; +pp4_v1 @Reaction 'pp4_v1' { actors: = pp4_mrna, reversible: false, }; +pp4_v1 := cod4; +pp4_v2 @Reaction 'pp4_v2' { actors: pp4_mrna = , modifiers: [p4], reversible: false, }; +pp4_v2 := pp4_mrna_degradation_rate * pp4_mrna; +pp4_v3 @Reaction 'pp4_v3' { actors: = p4, modifiers: [pp4_mrna], reversible: false, }; +pp4_v3 := rbs4_strength * pp4_mrna; +pp4_v4 @Reaction 'pp4_v4' { actors: p4 = , reversible: false, }; +pp4_v4 := p4_degradation_rate * p4; +pp3_v1 @Reaction 'pp3_v1' { actors: = pp3_mrna, reversible: false, }; +pp3_v1 := cod3; +pp3_v2 @Reaction 'pp3_v2' { actors: pp3_mrna = , modifiers: [p3], reversible: false, }; +pp3_v2 := pp3_mrna_degradation_rate * pp3_mrna; +pp3_v3 @Reaction 'pp3_v3' { actors: = p3, modifiers: [pp3_mrna], reversible: false, }; +pp3_v3 := rbs3_strength * pp3_mrna; +pp3_v4 @Reaction 'pp3_v4' { actors: p3 = , reversible: false, }; +pp3_v4 := p3_degradation_rate * p3; +pp2_v1 @Reaction 'pp2_v1' { actors: = pp2_mrna, reversible: false, }; +pp2_v1 := cod2; +pp2_v2 @Reaction 'pp2_v2' { actors: pp2_mrna = , modifiers: [p2], reversible: false, }; +pp2_v2 := pp2_mrna_degradation_rate * pp2_mrna; +pp2_v3 @Reaction 'pp2_v3' { actors: = p2, modifiers: [pp2_mrna], reversible: false, }; +pp2_v3 := rbs2_strength * pp2_mrna; +pp2_v4 @Reaction 'pp2_v4' { actors: p2 = , reversible: false, }; +pp2_v4 := p2_degradation_rate * p2; +pp1_v1 @Reaction 'pp1_v1' { actors: = pp1_mrna, reversible: false, }; +pp1_v1 := cod1; +pp1_v2 @Reaction 'pp1_v2' { actors: pp1_mrna = , modifiers: [p1], reversible: false, }; +pp1_v2 := pp1_mrna_degradation_rate * pp1_mrna; +pp1_v3 @Reaction 'pp1_v3' { actors: = p1, modifiers: [pp1_mrna], reversible: false, }; +pp1_v3 := rbs1_strength * pp1_mrna; +pp1_v4 @Reaction 'pp1_v4' { actors: p1 = , reversible: false, }; +pp1_v4 := p1_degradation_rate * p1; + +as8 @Record 'as8' { } .= 1; +as8 := (1 + pow(p5 / v9_Kd, v9_h) - 1) / (1 + pow(p5 / v9_Kd, v9_h)); +cod1 @Record 'cod1' { } .= 1; +cod1 := pro1_strength; +cod2 @Record 'cod2' { } .= 1; +cod2 := pro2_strength * as1 * rs1; +cod3 @Record 'cod3' { } .= 1; +cod3 := pro3_strength * rs2 * rs3; +cod4 @Record 'cod4' { } .= 1; +cod4 := pro4_strength * rs7 * rs6; +cod5 @Record 'cod5' { } .= 1; +cod5 := pro5_strength * as2; +cod6 @Record 'cod6' { } .= 1; +cod6 := pro6_strength * (as3 + as4); +cod7 @Record 'cod7' { } .= 1; +cod7 := pro7_strength * (as7 + as8); +cod8 @Record 'cod8' { } .= 1; +cod8 := pro8_strength * as5 * rs4; +cod9 @Record 'cod9' { } .= 1; +cod9 := pro9_strength * as6 * rs5; +rs1 @Record 'rs1' { } .= 1; +rs1 := 1 / (1 + pow(p9 / v13_Kd, v13_h)); +rs2 @Record 'rs2' { } .= 1; +rs2 := 1 / (1 + pow(p2 / v2_Kd, v2_h)); +rs3 @Record 'rs3' { } .= 1; +rs3 := 1 / (1 + pow(p3 / v3_Kd, v3_h)); +rs4 @Record 'rs4' { } .= 1; +rs4 := 1 / (1 + pow(p8 / v11_Kd, v11_h)); +rs5 @Record 'rs5' { } .= 1; +rs5 := 1 / (1 + pow(p8 / v12_Kd, v12_h)); +rs6 @Record 'rs6' { } .= 1; +rs6 := 1 / (1 + pow(p2 / v14_Kd, v14_h)); +rs7 @Record 'rs7' { } .= 1; +rs7 := 1 / (1 + pow(p3 / v15_Kd, v15_h)); +as1 @Record 'as1' { } .= 1; +as1 := (1 + pow(p1 / v1_Kd, v1_h) - 1) / (1 + pow(p1 / v1_Kd, v1_h)); +as2 @Record 'as2' { } .= 1; +as2 := (1 + pow(p4 / v4_Kd, v4_h) - 1) / (1 + pow(p4 / v4_Kd, v4_h)); +as3 @Record 'as3' { } .= 1; +as3 := (1 + pow(p5 / v5_Kd, v5_h) - 1) / (1 + pow(p5 / v5_Kd, v5_h)); +as4 @Record 'as4' { } .= 1; +as4 := (1 + pow(p6 / v6_Kd, v6_h) - 1) / (1 + pow(p6 / v6_Kd, v6_h)); +as5 @Record 'as5' { } .= 1; +as5 := (1 + pow(p7 / v7_Kd, v7_h) - 1) / (1 + pow(p7 / v7_Kd, v7_h)); +as6 @Record 'as6' { } .= 1; +as6 := (1 + pow(p7 / v10_Kd, v10_h) - 1) / (1 + pow(p7 / v10_Kd, v10_h)); +as7 @Record 'as7' { } .= 1; +as7 := (1 + pow(p6 / v8_Kd, v8_h) - 1) / (1 + pow(p6 / v8_Kd, v8_h)); + +pp8_mrna_degradation_rate @Const 'pp8_mrna_degradation_rate' { } = 1; +pp9_mrna_degradation_rate @Const 'pp9_mrna_degradation_rate' { } = 1; +p1_degradation_rate @Const 'p1_degradation_rate' { } = 0.5; +p2_degradation_rate @Const 'p2_degradation_rate' { } = 0.5; +p3_degradation_rate @Const 'p3_degradation_rate' { } = 0.5; +p4_degradation_rate @Const 'p4_degradation_rate' { } = 0.5; +p5_degradation_rate @Const 'p5_degradation_rate' { } = 0.5; +p6_degradation_rate @Const 'p6_degradation_rate' { } = 0.5; +p7_degradation_rate @Const 'p7_degradation_rate' { } = 0.5; +p8_degradation_rate @Const 'p8_degradation_rate' { } = 0.5; +p9_degradation_rate @Const 'p9_degradation_rate' { } = 0.5; +v1_Kd @Const 'v1_Kd' { } = 11.147; +v1_h @Const 'v1_h' { } = 1; +v2_Kd @Const 'v2_Kd' { } = 1; +v2_h @Const 'v2_h' { } = 4; +v3_Kd @Const 'v3_Kd' { } = 20; +v3_h @Const 'v3_h' { } = 1; +v4_Kd @Const 'v4_Kd' { } = 0.2; +v4_h @Const 'v4_h' { } = 4; +v5_Kd @Const 'v5_Kd' { } = 0.2; +v5_h @Const 'v5_h' { } = 4; +v6_Kd @Const 'v6_Kd' { } = 0.04; +v6_h @Const 'v6_h' { } = 4; +v7_Kd @Const 'v7_Kd' { } = 0.02; +v7_h @Const 'v7_h' { } = 4; +v8_Kd @Const 'v8_Kd' { } = 0.04; +v8_h @Const 'v8_h' { } = 4; +v9_Kd @Const 'v9_Kd' { } = 0.2; +v9_h @Const 'v9_h' { } = 4; +pp1_mrna_degradation_rate @Const 'pp1_mrna_degradation_rate' { } = 1; +pp2_mrna_degradation_rate @Const 'pp2_mrna_degradation_rate' { } = 1; +pro1_strength @Const 'pro1_strength' { } = 2; +pro2_strength @Const 'pro2_strength' { } = 4.5077; +pro3_strength @Const 'pro3_strength' { } = 5; +pro4_strength @Const 'pro4_strength' { } = 5; +pro5_strength @Const 'pro5_strength' { } = 5; +pro6_strength @Const 'pro6_strength' { } = 1.31; +pro7_strength @Const 'pro7_strength' { } = 1.31; +pro8_strength @Const 'pro8_strength' { } = 5; +pro9_strength @Const 'pro9_strength' { } = 5; +pp3_mrna_degradation_rate @Const 'pp3_mrna_degradation_rate' { } = 1; +v10_Kd @Const 'v10_Kd' { } = 0.02; +v10_h @Const 'v10_h' { } = 4; +v11_Kd @Const 'v11_Kd' { } = 0.1; +v11_h @Const 'v11_h' { } = 2; +v12_Kd @Const 'v12_Kd' { } = 0.1; +v12_h @Const 'v12_h' { } = 2; +v13_Kd @Const 'v13_Kd' { } = 0.01; +v13_h @Const 'v13_h' { } = 2; +pp4_mrna_degradation_rate @Const 'pp4_mrna_degradation_rate' { } = 1; +v14_Kd @Const 'v14_Kd' { } = 1; +v14_h @Const 'v14_h' { } = 4; +v15_Kd @Const 'v15_Kd' { } = 20; +v15_h @Const 'v15_h' { } = 1; +pp5_mrna_degradation_rate @Const 'pp5_mrna_degradation_rate' { } = 1; +rbs1_strength @Const 'rbs1_strength' { } = 0.3668; +rbs2_strength @Const 'rbs2_strength' { } = 1.4102; +rbs3_strength @Const 'rbs3_strength' { } = 0.8; +rbs4_strength @Const 'rbs4_strength' { } = 2.21; +rbs5_strength @Const 'rbs5_strength' { } = 0.5; +rbs6_strength @Const 'rbs6_strength' { } = 2; +rbs7_strength @Const 'rbs7_strength' { } = 5; +rbs8_strength @Const 'rbs8_strength' { } = 3.6377; +rbs9_strength @Const 'rbs9_strength' { } = 8; +pp6_mrna_degradation_rate @Const 'pp6_mrna_degradation_rate' { } = 1; +pp7_mrna_degradation_rate @Const 'pp7_mrna_degradation_rate' { } = 1; + diff --git a/latest/cases/01395/synopsis.txt b/latest/cases/01395/synopsis.txt new file mode 100644 index 000000000..967d0dc73 --- /dev/null +++ b/latest/cases/01395/synopsis.txt @@ -0,0 +1,204 @@ + +category: Test +synopsis: A larger model where the order of assignment rules is important. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this real model of a reaction system, the order of the assignment rules makes a difference in how the simulation proceeds: it is important to carry out the assignments such that the independent assignments are performed first, with the dependent assignments carried out after the assignments to variables they each depend on. This has been seen to make an appreciable difference when using large timesteps and the Euler method. + +The model contains: +* 18 species (pp9_mrna, p9, pp8_mrna, p8, pp7_mrna, p7, pp6_mrna, p6, pp5_mrna, p5, pp4_mrna, p4, pp3_mrna, p3, pp2_mrna, p2, pp1_mrna, p1) +* 90 parameters (pp8_mrna_degradation_rate, pp9_mrna_degradation_rate, p1_degradation_rate, p2_degradation_rate, p3_degradation_rate, p4_degradation_rate, p5_degradation_rate, p6_degradation_rate, p7_degradation_rate, p8_degradation_rate, p9_degradation_rate, v1_Kd, v1_h, v2_Kd, v2_h, v3_Kd, v3_h, v4_Kd, v4_h, v5_Kd, v5_h, v6_Kd, v6_h, v7_Kd, v7_h, v8_Kd, v8_h, v9_Kd, v9_h, pp1_mrna_degradation_rate, pp2_mrna_degradation_rate, pro1_strength, pro2_strength, pro3_strength, pro4_strength, pro5_strength, pro6_strength, pro7_strength, pro8_strength, pro9_strength, pp3_mrna_degradation_rate, v10_Kd, v10_h, v11_Kd, v11_h, v12_Kd, v12_h, v13_Kd, v13_h, pp4_mrna_degradation_rate, v14_Kd, v14_h, v15_Kd, v15_h, pp5_mrna_degradation_rate, rbs1_strength, rbs2_strength, rbs3_strength, rbs4_strength, rbs5_strength, rbs6_strength, rbs7_strength, rbs8_strength, rbs9_strength, pp6_mrna_degradation_rate, pp7_mrna_degradation_rate, as8, cod1, cod2, cod3, cod4, cod5, cod6, cod7, cod8, cod9, rs1, rs2, rs3, rs4, rs5, rs6, rs7, as1, as2, as3, as4, as5, as6, as7) +* 1 compartment (DefaultCompartment) + +There are 36 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| pp9_v1: -> pp9_mrna | $cod9$ | +| pp9_v2: pp9_mrna -> | $pp9_mrna_degradation_rate * pp9_mrna$ | +| pp9_v3: -> p9 | $rbs9_strength * pp9_mrna$ | +| pp9_v4: p9 -> | $p9_degradation_rate * p9$ | +| pp8_v1: -> pp8_mrna | $cod8$ | +| pp8_v2: pp8_mrna -> | $pp8_mrna_degradation_rate * pp8_mrna$ | +| pp8_v3: -> p8 | $rbs8_strength * pp8_mrna$ | +| pp8_v4: p8 -> | $p8_degradation_rate * p8$ | +| pp7_v1: -> pp7_mrna | $cod7$ | +| pp7_v2: pp7_mrna -> | $pp7_mrna_degradation_rate * pp7_mrna$ | +| pp7_v3: -> p7 | $rbs7_strength * pp7_mrna$ | +| pp7_v4: p7 -> | $p7_degradation_rate * p7$ | +| pp6_v1: -> pp6_mrna | $cod6$ | +| pp6_v2: pp6_mrna -> | $pp6_mrna_degradation_rate * pp6_mrna$ | +| pp6_v3: -> p6 | $rbs6_strength * pp6_mrna$ | +| pp6_v4: p6 -> | $p6_degradation_rate * p6$ | +| pp5_v1: -> pp5_mrna | $cod5$ | +| pp5_v2: pp5_mrna -> | $pp5_mrna_degradation_rate * pp5_mrna$ | +| pp5_v3: -> p5 | $rbs5_strength * pp5_mrna$ | +| pp5_v4: p5 -> | $p5_degradation_rate * p5$ | +| pp4_v1: -> pp4_mrna | $cod4$ | +| pp4_v2: pp4_mrna -> | $pp4_mrna_degradation_rate * pp4_mrna$ | +| pp4_v3: -> p4 | $rbs4_strength * pp4_mrna$ | +| pp4_v4: p4 -> | $p4_degradation_rate * p4$ | +| pp3_v1: -> pp3_mrna | $cod3$ | +| pp3_v2: pp3_mrna -> | $pp3_mrna_degradation_rate * pp3_mrna$ | +| pp3_v3: -> p3 | $rbs3_strength * pp3_mrna$ | +| pp3_v4: p3 -> | $p3_degradation_rate * p3$ | +| pp2_v1: -> pp2_mrna | $cod2$ | +| pp2_v2: pp2_mrna -> | $pp2_mrna_degradation_rate * pp2_mrna$ | +| pp2_v3: -> p2 | $rbs2_strength * pp2_mrna$ | +| pp2_v4: p2 -> | $p2_degradation_rate * p2$ | +| pp1_v1: -> pp1_mrna | $cod1$ | +| pp1_v2: pp1_mrna -> | $pp1_mrna_degradation_rate * pp1_mrna$ | +| pp1_v3: -> p1 | $rbs1_strength * pp1_mrna$ | +| pp1_v4: p1 -> | $p1_degradation_rate * p1$ |] + + +There are 24 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | as8 | $(1 + (p5 / v9_Kd)^v9_h - 1) / (1 + (p5 / v9_Kd)^v9_h)$ | +| Assignment | cod1 | $pro1_strength$ | +| Assignment | cod2 | $pro2_strength * as1 * rs1$ | +| Assignment | cod3 | $pro3_strength * rs2 * rs3$ | +| Assignment | cod4 | $pro4_strength * rs7 * rs6$ | +| Assignment | cod5 | $pro5_strength * as2$ | +| Assignment | cod6 | $pro6_strength * (as3 + as4)$ | +| Assignment | cod7 | $pro7_strength * (as7 + as8)$ | +| Assignment | cod8 | $pro8_strength * as5 * rs4$ | +| Assignment | cod9 | $pro9_strength * as6 * rs5$ | +| Assignment | rs1 | $1 / (1 + (p9 / v13_Kd)^v13_h)$ | +| Assignment | rs2 | $1 / (1 + (p2 / v2_Kd)^v2_h)$ | +| Assignment | rs3 | $1 / (1 + (p3 / v3_Kd)^v3_h)$ | +| Assignment | rs4 | $1 / (1 + (p8 / v11_Kd)^v11_h)$ | +| Assignment | rs5 | $1 / (1 + (p8 / v12_Kd)^v12_h)$ | +| Assignment | rs6 | $1 / (1 + (p2 / v14_Kd)^v14_h)$ | +| Assignment | rs7 | $1 / (1 + (p3 / v15_Kd)^v15_h)$ | +| Assignment | as1 | $(1 + (p1 / v1_Kd)^v1_h - 1) / (1 + (p1 / v1_Kd)^v1_h)$ | +| Assignment | as2 | $(1 + (p4 / v4_Kd)^v4_h - 1) / (1 + (p4 / v4_Kd)^v4_h)$ | +| Assignment | as3 | $(1 + (p5 / v5_Kd)^v5_h - 1) / (1 + (p5 / v5_Kd)^v5_h)$ | +| Assignment | as4 | $(1 + (p6 / v6_Kd)^v6_h - 1) / (1 + (p6 / v6_Kd)^v6_h)$ | +| Assignment | as5 | $(1 + (p7 / v7_Kd)^v7_h - 1) / (1 + (p7 / v7_Kd)^v7_h)$ | +| Assignment | as6 | $(1 + (p7 / v10_Kd)^v10_h - 1) / (1 + (p7 / v10_Kd)^v10_h)$ | +| Assignment | as7 | $(1 + (p6 / v8_Kd)^v8_h - 1) / (1 + (p6 / v8_Kd)^v8_h)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species pp9_mrna | $0$ | variable | +| Initial amount of species p9 | $0$ | variable | +| Initial amount of species pp8_mrna | $0$ | variable | +| Initial amount of species p8 | $0$ | variable | +| Initial amount of species pp7_mrna | $0$ | variable | +| Initial amount of species p7 | $0$ | variable | +| Initial amount of species pp6_mrna | $0$ | variable | +| Initial amount of species p6 | $0$ | variable | +| Initial amount of species pp5_mrna | $0$ | variable | +| Initial amount of species p5 | $0$ | variable | +| Initial amount of species pp4_mrna | $0$ | variable | +| Initial amount of species p4 | $0$ | variable | +| Initial amount of species pp3_mrna | $0$ | variable | +| Initial amount of species p3 | $0$ | variable | +| Initial amount of species pp2_mrna | $0$ | variable | +| Initial amount of species p2 | $0$ | variable | +| Initial amount of species pp1_mrna | $0$ | variable | +| Initial amount of species p1 | $5$ | variable | +| Initial value of parameter pp8_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter pp9_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter p1_degradation_rate | $0.5$ | constant | +| Initial value of parameter p2_degradation_rate | $0.5$ | constant | +| Initial value of parameter p3_degradation_rate | $0.5$ | constant | +| Initial value of parameter p4_degradation_rate | $0.5$ | constant | +| Initial value of parameter p5_degradation_rate | $0.5$ | constant | +| Initial value of parameter p6_degradation_rate | $0.5$ | constant | +| Initial value of parameter p7_degradation_rate | $0.5$ | constant | +| Initial value of parameter p8_degradation_rate | $0.5$ | constant | +| Initial value of parameter p9_degradation_rate | $0.5$ | constant | +| Initial value of parameter v1_Kd | $11.147$ | constant | +| Initial value of parameter v1_h | $1$ | constant | +| Initial value of parameter v2_Kd | $1$ | constant | +| Initial value of parameter v2_h | $4$ | constant | +| Initial value of parameter v3_Kd | $20$ | constant | +| Initial value of parameter v3_h | $1$ | constant | +| Initial value of parameter v4_Kd | $0.2$ | constant | +| Initial value of parameter v4_h | $4$ | constant | +| Initial value of parameter v5_Kd | $0.2$ | constant | +| Initial value of parameter v5_h | $4$ | constant | +| Initial value of parameter v6_Kd | $0.04$ | constant | +| Initial value of parameter v6_h | $4$ | constant | +| Initial value of parameter v7_Kd | $0.02$ | constant | +| Initial value of parameter v7_h | $4$ | constant | +| Initial value of parameter v8_Kd | $0.04$ | constant | +| Initial value of parameter v8_h | $4$ | constant | +| Initial value of parameter v9_Kd | $0.2$ | constant | +| Initial value of parameter v9_h | $4$ | constant | +| Initial value of parameter pp1_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter pp2_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter pro1_strength | $2$ | constant | +| Initial value of parameter pro2_strength | $4.5077$ | constant | +| Initial value of parameter pro3_strength | $5$ | constant | +| Initial value of parameter pro4_strength | $5$ | constant | +| Initial value of parameter pro5_strength | $5$ | constant | +| Initial value of parameter pro6_strength | $1.31$ | constant | +| Initial value of parameter pro7_strength | $1.31$ | constant | +| Initial value of parameter pro8_strength | $5$ | constant | +| Initial value of parameter pro9_strength | $5$ | constant | +| Initial value of parameter pp3_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter v10_Kd | $0.02$ | constant | +| Initial value of parameter v10_h | $4$ | constant | +| Initial value of parameter v11_Kd | $0.1$ | constant | +| Initial value of parameter v11_h | $2$ | constant | +| Initial value of parameter v12_Kd | $0.1$ | constant | +| Initial value of parameter v12_h | $2$ | constant | +| Initial value of parameter v13_Kd | $0.01$ | constant | +| Initial value of parameter v13_h | $2$ | constant | +| Initial value of parameter pp4_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter v14_Kd | $1$ | constant | +| Initial value of parameter v14_h | $4$ | constant | +| Initial value of parameter v15_Kd | $20$ | constant | +| Initial value of parameter v15_h | $1$ | constant | +| Initial value of parameter pp5_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter rbs1_strength | $0.3668$ | constant | +| Initial value of parameter rbs2_strength | $1.4102$ | constant | +| Initial value of parameter rbs3_strength | $0.8$ | constant | +| Initial value of parameter rbs4_strength | $2.21$ | constant | +| Initial value of parameter rbs5_strength | $0.5$ | constant | +| Initial value of parameter rbs6_strength | $2$ | constant | +| Initial value of parameter rbs7_strength | $5$ | constant | +| Initial value of parameter rbs8_strength | $3.6377$ | constant | +| Initial value of parameter rbs9_strength | $8$ | constant | +| Initial value of parameter pp6_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter pp7_mrna_degradation_rate | $1$ | constant | +| Initial value of parameter as8 | $(1 + (p5 / v9_Kd)^v9_h - 1) / (1 + (p5 / v9_Kd)^v9_h)$ | variable | +| Initial value of parameter cod1 | $pro1_strength$ | variable | +| Initial value of parameter cod2 | $pro2_strength * as1 * rs1$ | variable | +| Initial value of parameter cod3 | $pro3_strength * rs2 * rs3$ | variable | +| Initial value of parameter cod4 | $pro4_strength * rs7 * rs6$ | variable | +| Initial value of parameter cod5 | $pro5_strength * as2$ | variable | +| Initial value of parameter cod6 | $pro6_strength * (as3 + as4)$ | variable | +| Initial value of parameter cod7 | $pro7_strength * (as7 + as8)$ | variable | +| Initial value of parameter cod8 | $pro8_strength * as5 * rs4$ | variable | +| Initial value of parameter cod9 | $pro9_strength * as6 * rs5$ | variable | +| Initial value of parameter rs1 | $1 / (1 + (p9 / v13_Kd)^v13_h)$ | variable | +| Initial value of parameter rs2 | $1 / (1 + (p2 / v2_Kd)^v2_h)$ | variable | +| Initial value of parameter rs3 | $1 / (1 + (p3 / v3_Kd)^v3_h)$ | variable | +| Initial value of parameter rs4 | $1 / (1 + (p8 / v11_Kd)^v11_h)$ | variable | +| Initial value of parameter rs5 | $1 / (1 + (p8 / v12_Kd)^v12_h)$ | variable | +| Initial value of parameter rs6 | $1 / (1 + (p2 / v14_Kd)^v14_h)$ | variable | +| Initial value of parameter rs7 | $1 / (1 + (p3 / v15_Kd)^v15_h)$ | variable | +| Initial value of parameter as1 | $(1 + (p1 / v1_Kd)^v1_h - 1) / (1 + (p1 / v1_Kd)^v1_h)$ | variable | +| Initial value of parameter as2 | $(1 + (p4 / v4_Kd)^v4_h - 1) / (1 + (p4 / v4_Kd)^v4_h)$ | variable | +| Initial value of parameter as3 | $(1 + (p5 / v5_Kd)^v5_h - 1) / (1 + (p5 / v5_Kd)^v5_h)$ | variable | +| Initial value of parameter as4 | $(1 + (p6 / v6_Kd)^v6_h - 1) / (1 + (p6 / v6_Kd)^v6_h)$ | variable | +| Initial value of parameter as5 | $(1 + (p7 / v7_Kd)^v7_h - 1) / (1 + (p7 / v7_Kd)^v7_h)$ | variable | +| Initial value of parameter as6 | $(1 + (p7 / v10_Kd)^v10_h - 1) / (1 + (p7 / v10_Kd)^v10_h)$ | variable | +| Initial value of parameter as7 | $(1 + (p6 / v8_Kd)^v8_h - 1) / (1 + (p6 / v8_Kd)^v8_h)$ | variable | +| Initial volume of compartment 'DefaultCompartment' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01396/l2v5/index.heta b/latest/cases/01396/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01396/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01396/l3v2/index.heta b/latest/cases/01396/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01396/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01396/synopsis.txt b/latest/cases/01396/synopsis.txt new file mode 100644 index 000000000..a3337440e --- /dev/null +++ b/latest/cases/01396/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A fast reaction with an assigned stoichiometry +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, FastReaction, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a fast reaction has a stoichiometry assigned by an initial assignment. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (default_compartment) +* 1 species reference (S1_stoichiometry) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1_stoichiometry S1 -> S2 | $1 * S1$ | fast |] +Note: the following stoichiometries are set separately: S1_stoichiometry + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant | +| Initial value of species reference 'S1_stoichiometry' | $2 + 3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01397/l2v5/build.log b/latest/cases/01397/l2v5/build.log new file mode 100644 index 000000000..4fe062f18 --- /dev/null +++ b/latest/cases/01397/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01397/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01397/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01397/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01397/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01397/l2v5/index.heta b/latest/cases/01397/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01397/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01397/l3v2/index.heta b/latest/cases/01397/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01397/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01397/model-sbml-l2v5.xml b/latest/cases/01397/model-sbml-l2v5.xml new file mode 100644 index 000000000..563be716b --- /dev/null +++ b/latest/cases/01397/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + 2 + 3 + + + + + + + + + + + + + 1 + S1 + + + + + + + diff --git a/latest/cases/01397/synopsis.txt b/latest/cases/01397/synopsis.txt new file mode 100644 index 000000000..94c74dc43 --- /dev/null +++ b/latest/cases/01397/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A fast reaction with an assigned stoichiometry +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, FastReaction, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In this model, a fast reaction has a stoichiometry assigned with StoichiometryMath. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (default_compartment) +* 1 species reference (S1_stoichiometry) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1_stoichiometry S1 -> S2 | $1 * S1$ | fast |] +Note: the following stoichiometries are set separately: S1_stoichiometry + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01398/l2v5/index.heta b/latest/cases/01398/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01398/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01398/l3v2/index.heta b/latest/cases/01398/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01398/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01398/synopsis.txt b/latest/cases/01398/synopsis.txt new file mode 100644 index 000000000..5d87f66ba --- /dev/null +++ b/latest/cases/01398/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A fast reaction with an assigned stoichiometry from an event +componentTags: CSymbolTime, Compartment, EventNoDelay, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, FastReaction, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a fast reaction has a stoichiometry assigned by an event. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (default_compartment) +* 1 species reference (S1_stoichiometry) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1_stoichiometry S1 -> S2 | $1 * S1$ | fast |] +Note: the following stoichiometries are set separately: S1_stoichiometry + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 4.5$ | $S1 = 5$ | +| | | $S1_stoichiometry = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial volume of compartment 'default_compartment' | $1$ | constant | +| Initial value of species reference 'S1_stoichiometry' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01399/l2v5/heta-code/output.heta b/latest/cases/01399/l2v5/heta-code/output.heta new file mode 100644 index 000000000..7c146f10e --- /dev/null +++ b/latest/cases/01399/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +default_compartment @Compartment { boundary: true, aux: {{"sboTerm":"SBO:0000410"}}, } .= 1; + +S1 @Species { compartment: default_compartment, } .= 5; +S2 @Species { compartment: default_compartment, } .= 5; + +J0 @Reaction { actors: S1 = S2, }; +J0 := k1__J0_local * S1 * S2; + +k1__J0_local @Const { } = -1; + diff --git a/latest/cases/01399/l2v5/index.heta b/latest/cases/01399/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01399/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01399/l2v5/json/output.json b/latest/cases/01399/l2v5/json/output.json new file mode 100644 index 000000000..a333989b5 --- /dev/null +++ b/latest/cases/01399/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "default_compartment", + "aux": { + "sboTerm": "SBO:0000410" + }, + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "5" + }, + "compartment": "default_compartment" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "5" + }, + "compartment": "default_compartment" + }, + { + "class": "Const", + "id": "k1__J0_local", + "num": -1 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1__J0_local * S1 * S2" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01399/l3v2/index.heta b/latest/cases/01399/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01399/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01399/model-sbml-l2v5.xml b/latest/cases/01399/model-sbml-l2v5.xml new file mode 100644 index 000000000..bb5ec637a --- /dev/null +++ b/latest/cases/01399/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + k1 + S1 + S2 + + + + + + + + + + diff --git a/latest/cases/01399/output.heta b/latest/cases/01399/output.heta new file mode 100644 index 000000000..4dfed9535 --- /dev/null +++ b/latest/cases/01399/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: A fast reaction with a local parameter. +componentTags: Compartment, Reaction, Species +testTags: Amount, FastReaction, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + +In this model, a fast reaction has a local parameter that ensures that the reaction proceeds in reverse. + +The model contains: +* 2 species (S1, S2) +* 1 local parameter (J0.k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $k1 * S1 * S2$ | fast |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $5$ | variable | +| Initial value of local parameter 'J0.k1' | $-1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +default_compartment @Compartment { boundary: true, aux: {{"sboTerm":"SBO:0000410"}}, } .= 1; + +S1 @Species { compartment: default_compartment, } .= 5; +S2 @Species { compartment: default_compartment, } .= 5; + +J0 @Reaction { actors: S1 = S2, }; +J0 := k1__J0_local * S1 * S2; + +k1__J0_local @Const { } = -1; + diff --git a/latest/cases/01399/synopsis.txt b/latest/cases/01399/synopsis.txt new file mode 100644 index 000000000..e987211a3 --- /dev/null +++ b/latest/cases/01399/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A fast reaction with a local parameter. +componentTags: Compartment, Reaction, Species +testTags: Amount, FastReaction, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + +In this model, a fast reaction has a local parameter that ensures that the reaction proceeds in reverse. + +The model contains: +* 2 species (S1, S2) +* 1 local parameter (J0.k1) +* 1 compartment (default_compartment) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $k1 * S1 * S2$ | fast |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $5$ | variable | +| Initial value of local parameter 'J0.k1' | $-1$ | constant | +| Initial volume of compartment 'default_compartment' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01400/l2v5/index.heta b/latest/cases/01400/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01400/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01400/l3v2/build.log b/latest/cases/01400/l3v2/build.log new file mode 100644 index 000000000..e95af3d9f --- /dev/null +++ b/latest/cases/01400/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01400/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01400/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01400/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01400/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01400/l3v2/index.heta b/latest/cases/01400/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01400/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01400/model-sbml-l3v2.xml b/latest/cases/01400/model-sbml-l3v2.xml new file mode 100644 index 000000000..2d2636c6e --- /dev/null +++ b/latest/cases/01400/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + delay + + rateOf + S1 + + 1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01400/synopsis.txt b/latest/cases/01400/synopsis.txt new file mode 100644 index 000000000..d416a1bc1 --- /dev/null +++ b/latest/cases/01400/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A delay of a rateOf. +componentTags: AssignmentRule, CSymbolDelay, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +In this model, we test the calculation of the delay of the result of a 'rateOf' csymbol. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P0, P1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ | +| Assignment | P1 | $delay(rateOf(S1), 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial value of parameter P1 | $delay(rateOf(S1), 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01401/l2v5/index.heta b/latest/cases/01401/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01401/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01401/l3v2/build.log b/latest/cases/01401/l3v2/build.log new file mode 100644 index 000000000..ece5d45fd --- /dev/null +++ b/latest/cases/01401/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01401/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01401/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01401/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01401/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01401/l3v2/index.heta b/latest/cases/01401/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01401/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01401/model-sbml-l3v2.xml b/latest/cases/01401/model-sbml-l3v2.xml new file mode 100644 index 000000000..7104fe5d2 --- /dev/null +++ b/latest/cases/01401/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + -0.1 + S1 + + + + + + + delay + + rateOf + S1 + + 1 + + + + + + diff --git a/latest/cases/01401/synopsis.txt b/latest/cases/01401/synopsis.txt new file mode 100644 index 000000000..fe92460b6 --- /dev/null +++ b/latest/cases/01401/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A delay of a rateOf. +componentTags: AssignmentRule, CSymbolDelay, CSymbolRateOf, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +In this model, we test the calculation of the delay of the result of a 'rateOf' csymbol. + +The model contains: +* 3 parameters (P0, S1, P1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ | +| Rate | S1 | $-0.1 * S1$ | +| Assignment | P1 | $delay(rateOf(S1), 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial value of parameter S1 | $5$ | variable | +| Initial value of parameter P1 | $delay(rateOf(S1), 1)$ | variable |] + diff --git a/latest/cases/01402/l2v5/index.heta b/latest/cases/01402/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01402/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01402/l3v2/build.log b/latest/cases/01402/l3v2/build.log new file mode 100644 index 000000000..e07594d21 --- /dev/null +++ b/latest/cases/01402/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01402/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01402/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01402/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01402/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01402/l3v2/index.heta b/latest/cases/01402/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01402/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01402/model-sbml-l3v2.xml b/latest/cases/01402/model-sbml-l3v2.xml new file mode 100644 index 000000000..0631c7387 --- /dev/null +++ b/latest/cases/01402/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01402/synopsis.txt b/latest/cases/01402/synopsis.txt new file mode 100644 index 000000000..754c03568 --- /dev/null +++ b/latest/cases/01402/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A combination of a model converstion factor and the rateOf function. +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the species are affected by a reaction, which is itself affected by a model-wide conversion factor. The parameter P0 ensures that the rateOf function incorporates the conversion factor into its own return value. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P0, conversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the model is 'conversion' + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter conversion | $2$ | constant | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01403/l2v5/index.heta b/latest/cases/01403/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01403/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01403/l3v2/build.log b/latest/cases/01403/l3v2/build.log new file mode 100644 index 000000000..e7a9123c1 --- /dev/null +++ b/latest/cases/01403/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01403/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01403/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01403/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01403/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01403/l3v2/index.heta b/latest/cases/01403/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01403/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01403/model-sbml-l3v2.xml b/latest/cases/01403/model-sbml-l3v2.xml new file mode 100644 index 000000000..e8e660470 --- /dev/null +++ b/latest/cases/01403/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + delay + + rateOf + S1 + + 1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01403/synopsis.txt b/latest/cases/01403/synopsis.txt new file mode 100644 index 000000000..0ea6212f5 --- /dev/null +++ b/latest/cases/01403/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A model with a rateOf, delay, and model conversion factor. +componentTags: AssignmentRule, CSymbolDelay, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, a reaction affects the level of two species, modified by a conversion factor. This affects the 'rateOf' function, which in turn is used in a delay function. + +The model contains: +* 2 species (S1, S2) +* 3 parameters (P0, P1, conversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the model is 'conversion' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ | +| Assignment | P1 | $delay(rateOf(S1), 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter conversion | $2$ | constant | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial value of parameter P1 | $delay(rateOf(S1), 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01404/l2v5/index.heta b/latest/cases/01404/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01404/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01404/l3v2/build.log b/latest/cases/01404/l3v2/build.log new file mode 100644 index 000000000..1d95dbbd2 --- /dev/null +++ b/latest/cases/01404/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01404/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01404/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01404/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01404/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01404/l3v2/index.heta b/latest/cases/01404/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01404/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01404/model-sbml-l3v2.xml b/latest/cases/01404/model-sbml-l3v2.xml new file mode 100644 index 000000000..7a81552c3 --- /dev/null +++ b/latest/cases/01404/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + delay + S1 + 1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01404/synopsis.txt b/latest/cases/01404/synopsis.txt new file mode 100644 index 000000000..dc7678817 --- /dev/null +++ b/latest/cases/01404/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A combination of a model converstion factor and the delay function. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the species are affected by a reaction, which is itself affected by a model-wide conversion factor. The parameter P0 ensures that the delay function incorporates the conversion factor into its own return value. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P0, conversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the model is 'conversion' + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $delay(S1, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter conversion | $2$ | constant | +| Initial value of parameter P0 | $delay(S1, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01405/l2v5/index.heta b/latest/cases/01405/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01405/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01405/l3v2/build.log b/latest/cases/01405/l3v2/build.log new file mode 100644 index 000000000..e0362bcd6 --- /dev/null +++ b/latest/cases/01405/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01405/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01405/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01405/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01405/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01405/l3v2/index.heta b/latest/cases/01405/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01405/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01405/model-sbml-l3v2.xml b/latest/cases/01405/model-sbml-l3v2.xml new file mode 100644 index 000000000..6b2ce41d2 --- /dev/null +++ b/latest/cases/01405/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01405/synopsis.txt b/latest/cases/01405/synopsis.txt new file mode 100644 index 000000000..ee1412047 --- /dev/null +++ b/latest/cases/01405/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A combination of a species converstion factor and the rateOf function. +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the species are affected by a reaction, one of which is affected by a species conversion factor. The parameter P0 ensures that the rateOf function incorporates the conversion factor into its own return value. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P0, conversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the species 'S1' is '' + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter conversion | $2$ | constant | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01406/l2v5/index.heta b/latest/cases/01406/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01406/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01406/l3v2/build.log b/latest/cases/01406/l3v2/build.log new file mode 100644 index 000000000..f52f66b53 --- /dev/null +++ b/latest/cases/01406/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01406/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01406/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01406/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01406/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01406/l3v2/index.heta b/latest/cases/01406/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01406/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01406/model-sbml-l3v2.xml b/latest/cases/01406/model-sbml-l3v2.xml new file mode 100644 index 000000000..5b75f0506 --- /dev/null +++ b/latest/cases/01406/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + delay + + rateOf + S1 + + 1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01406/synopsis.txt b/latest/cases/01406/synopsis.txt new file mode 100644 index 000000000..5b5cf8d99 --- /dev/null +++ b/latest/cases/01406/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A model with a rateOf, delay, and model conversion factor. +componentTags: AssignmentRule, CSymbolDelay, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, a reaction affects the level of two species, modified by a conversion factor. This affects the 'rateOf' function, which in turn is used in a delay function. + +The model contains: +* 2 species (S1, S2) +* 3 parameters (P0, P1, conversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the species 'S1' is 'conversion' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ | +| Assignment | P1 | $delay(rateOf(S1), 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter conversion | $2$ | constant | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial value of parameter P1 | $delay(rateOf(S1), 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01407/l2v5/index.heta b/latest/cases/01407/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01407/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01407/l3v2/build.log b/latest/cases/01407/l3v2/build.log new file mode 100644 index 000000000..04cb74cb0 --- /dev/null +++ b/latest/cases/01407/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01407/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01407/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01407/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01407/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01407/l3v2/index.heta b/latest/cases/01407/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01407/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01407/model-sbml-l3v2.xml b/latest/cases/01407/model-sbml-l3v2.xml new file mode 100644 index 000000000..4aa07f760 --- /dev/null +++ b/latest/cases/01407/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + delay + S1 + 1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01407/synopsis.txt b/latest/cases/01407/synopsis.txt new file mode 100644 index 000000000..124b47c39 --- /dev/null +++ b/latest/cases/01407/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A combination of a species conversion factor and the delay function. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the species are affected by a reaction, and one of them is further affected by a species conversion factor. The parameter P0 ensures that the delay function incorporates the conversion factor into its own return value. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P0, conversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the species 'S1' is 'conversion' + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $delay(S1, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter conversion | $2$ | constant | +| Initial value of parameter P0 | $delay(S1, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01408/l2v5/index.heta b/latest/cases/01408/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01408/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01408/l3v2/build.log b/latest/cases/01408/l3v2/build.log new file mode 100644 index 000000000..6435b872d --- /dev/null +++ b/latest/cases/01408/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01408/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01408/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01408/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01408/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01408/l3v2/index.heta b/latest/cases/01408/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01408/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01408/model-sbml-l3v2.xml b/latest/cases/01408/model-sbml-l3v2.xml new file mode 100644 index 000000000..8e76096e3 --- /dev/null +++ b/latest/cases/01408/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + rateOf + S2 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01408/synopsis.txt b/latest/cases/01408/synopsis.txt new file mode 100644 index 000000000..fe1ee3202 --- /dev/null +++ b/latest/cases/01408/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A combination of a species and model conversion factors and the rateOf function. +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the species are affected by a reaction, one of which is affected by a species conversion factor, and the other of which is affected by the model conversion factor. The parameters P0 and P1 ensure that the rateOf function incorporates the conversion factors into their own return values. + +The model contains: +* 2 species (S1, S2) +* 4 parameters (P0, P1, mconversion, sconversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the model is 'mconversion' +The conversion factor for the species 'S1' is 'sconversion' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ | +| Assignment | P1 | $rateOf(S2)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter mconversion | $3$ | constant | +| Initial value of parameter sconversion | $2$ | constant | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial value of parameter P1 | $rateOf(S2)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01409/l2v5/index.heta b/latest/cases/01409/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01409/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01409/l3v2/build.log b/latest/cases/01409/l3v2/build.log new file mode 100644 index 000000000..824c8054a --- /dev/null +++ b/latest/cases/01409/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01409/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01409/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01409/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01409/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01409/l3v2/index.heta b/latest/cases/01409/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01409/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01409/model-sbml-l3v2.xml b/latest/cases/01409/model-sbml-l3v2.xml new file mode 100644 index 000000000..0117f1bad --- /dev/null +++ b/latest/cases/01409/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + delay + + rateOf + S1 + + 1 + + + + + + + rateOf + S2 + + + + + + + delay + + rateOf + S2 + + 1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01409/synopsis.txt b/latest/cases/01409/synopsis.txt new file mode 100644 index 000000000..e2958857f --- /dev/null +++ b/latest/cases/01409/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: A model with a rateOf, delay, and model and species conversion factors. +componentTags: AssignmentRule, CSymbolDelay, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, a reaction affects the level of two species, one modified by a model conversion factor and the other by a species conversion factor. This affects the 'rateOf' functions, which in turn are used in delay functions. + +The model contains: +* 2 species (S1, S2) +* 6 parameters (P0, P1, P2, P3, sconversion, mconversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the model is 'mconversion' +The conversion factor for the species 'S1' is 'sconversion' + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ | +| Assignment | P1 | $delay(rateOf(S1), 1)$ | +| Assignment | P2 | $rateOf(S2)$ | +| Assignment | P3 | $delay(rateOf(S2), 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter sconversion | $2$ | constant | +| Initial value of parameter mconversion | $3$ | constant | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial value of parameter P1 | $delay(rateOf(S1), 1)$ | variable | +| Initial value of parameter P2 | $rateOf(S2)$ | variable | +| Initial value of parameter P3 | $delay(rateOf(S2), 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01410/l2v5/index.heta b/latest/cases/01410/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01410/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01410/l3v2/build.log b/latest/cases/01410/l3v2/build.log new file mode 100644 index 000000000..a1ac743ca --- /dev/null +++ b/latest/cases/01410/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01410/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01410/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01410/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01410/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01410/l3v2/index.heta b/latest/cases/01410/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01410/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01410/model-sbml-l3v2.xml b/latest/cases/01410/model-sbml-l3v2.xml new file mode 100644 index 000000000..0c042bc65 --- /dev/null +++ b/latest/cases/01410/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + delay + S1 + 1 + + + + + + + delay + S2 + 1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01410/synopsis.txt b/latest/cases/01410/synopsis.txt new file mode 100644 index 000000000..f4d043c01 --- /dev/null +++ b/latest/cases/01410/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A combination of model and species conversion factors and the delay function. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the species are affected by a reaction, and one of them is further affected by a model conversion factor, while the other by a species conversion factor. The parameters P0 and P1 ensure that the delay functions incorporate the conversion factors into their own return value. + +The model contains: +* 2 species (S1, S2) +* 4 parameters (P0, P1, sconversion, mconversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the model is 'mconversion' +The conversion factor for the species 'S1' is 'sconversion' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $delay(S1, 1)$ | +| Assignment | P1 | $delay(S2, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter sconversion | $2$ | constant | +| Initial value of parameter mconversion | $3$ | constant | +| Initial value of parameter P0 | $delay(S1, 1)$ | variable | +| Initial value of parameter P1 | $delay(S2, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01411/l2v5/build.log b/latest/cases/01411/l2v5/build.log new file mode 100644 index 000000000..8fa64c75a --- /dev/null +++ b/latest/cases/01411/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01411/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01411/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01411/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01411/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01411/l2v5/index.heta b/latest/cases/01411/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01411/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01411/l3v2/build.log b/latest/cases/01411/l3v2/build.log new file mode 100644 index 000000000..15fcc0cdd --- /dev/null +++ b/latest/cases/01411/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01411/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01411/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01411/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01411/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01411/l3v2/index.heta b/latest/cases/01411/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01411/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01411/model-sbml-l2v5.xml b/latest/cases/01411/model-sbml-l2v5.xml new file mode 100644 index 000000000..d892f14e8 --- /dev/null +++ b/latest/cases/01411/model-sbml-l2v5.xml @@ -0,0 +1,68 @@ + + + + + + + + + a + + + b + + + + a + b + + + + + + + + + + + + + + + + + + + + delay + + addtwo + S1 + S2 + + 1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01411/model-sbml-l3v2.xml b/latest/cases/01411/model-sbml-l3v2.xml new file mode 100644 index 000000000..2806f2012 --- /dev/null +++ b/latest/cases/01411/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + a + + + b + + + + a + b + + + + + + + + + + + + + + + + + + + + delay + + addtwo + S1 + S2 + + 1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01411/synopsis.txt b/latest/cases/01411/synopsis.txt new file mode 100644 index 000000000..b040f34d3 --- /dev/null +++ b/latest/cases/01411/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A delay with a function definition as an argument +componentTags: AssignmentRule, CSymbolDelay, Compartment, FunctionDefinition, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, a delay function takes a function definition as an argument. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (P1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> 2S2 | $0.1 * S1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $delay(addtwo(S1, S2), 1)$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addtwo | a, b | $a + b$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter P1 | $delay(addtwo(S1, S2), 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01412/l2v5/build.log b/latest/cases/01412/l2v5/build.log new file mode 100644 index 000000000..72ce4e2e8 --- /dev/null +++ b/latest/cases/01412/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01412/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01412/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01412/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01412/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01412/l2v5/index.heta b/latest/cases/01412/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01412/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01412/l3v2/build.log b/latest/cases/01412/l3v2/build.log new file mode 100644 index 000000000..7315f04e1 --- /dev/null +++ b/latest/cases/01412/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01412/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01412/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01412/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01412/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01412/l3v2/index.heta b/latest/cases/01412/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01412/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01412/model-sbml-l2v5.xml b/latest/cases/01412/model-sbml-l2v5.xml new file mode 100644 index 000000000..89b599650 --- /dev/null +++ b/latest/cases/01412/model-sbml-l2v5.xml @@ -0,0 +1,62 @@ + + + + + + + + + a + + + b + + + + a + b + + + + + + + + + + + + + + + delay + + addtwo + S1 + S2 + + 1 + + + + + + + + -0.1 + S1 + + + + + + + + 0.2 + S1 + + + + + + diff --git a/latest/cases/01412/model-sbml-l3v2.xml b/latest/cases/01412/model-sbml-l3v2.xml new file mode 100644 index 000000000..7b8617a78 --- /dev/null +++ b/latest/cases/01412/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + + + + + + a + + + b + + + + a + b + + + + + + + + + + + + + + + delay + + addtwo + S1 + S2 + + 1 + + + + + + + + -0.1 + S1 + + + + + + + + 0.2 + S1 + + + + + + diff --git a/latest/cases/01412/synopsis.txt b/latest/cases/01412/synopsis.txt new file mode 100644 index 000000000..f9d77a2bf --- /dev/null +++ b/latest/cases/01412/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A delay with a function definition as an argument +componentTags: AssignmentRule, CSymbolDelay, FunctionDefinition, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, a delay function takes a function definition as an argument. + +The model contains: +* 3 parameters (P1, S1, S2) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $delay(addtwo(S1, S2), 1)$ | +| Rate | S1 | $-0.1 * S1$ | +| Rate | S2 | $0.2 * S1$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addtwo | a, b | $a + b$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $delay(addtwo(S1, S2), 1)$ | variable | +| Initial value of parameter S1 | $5$ | variable | +| Initial value of parameter S2 | $1$ | variable |] + diff --git a/latest/cases/01413/l2v5/build.log b/latest/cases/01413/l2v5/build.log new file mode 100644 index 000000000..094bf5da4 --- /dev/null +++ b/latest/cases/01413/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01413/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01413/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01413/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01413/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01413/l2v5/index.heta b/latest/cases/01413/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01413/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01413/l3v2/build.log b/latest/cases/01413/l3v2/build.log new file mode 100644 index 000000000..25a399820 --- /dev/null +++ b/latest/cases/01413/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01413/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01413/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01413/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01413/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01413/l3v2/index.heta b/latest/cases/01413/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01413/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01413/model-sbml-l2v5.xml b/latest/cases/01413/model-sbml-l2v5.xml new file mode 100644 index 000000000..0bdb96eb9 --- /dev/null +++ b/latest/cases/01413/model-sbml-l2v5.xml @@ -0,0 +1,52 @@ + + + + + + + + + a + + + b + + + + a + b + + + + + + + + + + + + + + delay + S1 + + addtwo + 0.5 + 0.5 + + + + + + + + + -0.1 + S1 + + + + + + diff --git a/latest/cases/01413/model-sbml-l3v2.xml b/latest/cases/01413/model-sbml-l3v2.xml new file mode 100644 index 000000000..700a1b336 --- /dev/null +++ b/latest/cases/01413/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + a + + + b + + + + a + b + + + + + + + + + + + + + + delay + S1 + + addtwo + 0.5 + 0.5 + + + + + + + + + -0.1 + S1 + + + + + + diff --git a/latest/cases/01413/synopsis.txt b/latest/cases/01413/synopsis.txt new file mode 100644 index 000000000..7e8349123 --- /dev/null +++ b/latest/cases/01413/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A delay with a function definition as an argument +componentTags: AssignmentRule, CSymbolDelay, FunctionDefinition, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, a delay function takes a function definition as an argument. + +The model contains: +* 2 parameters (P1, S1) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $delay(S1, addtwo(0.5, 0.5))$ | +| Rate | S1 | $-0.1 * S1$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addtwo | a, b | $a + b$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $delay(S1, addtwo(0.5, 0.5))$ | variable | +| Initial value of parameter S1 | $5$ | variable |] + diff --git a/latest/cases/01414/l2v5/build.log b/latest/cases/01414/l2v5/build.log new file mode 100644 index 000000000..fd6ca72df --- /dev/null +++ b/latest/cases/01414/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01414/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01414/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01414/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01414/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01414/l2v5/index.heta b/latest/cases/01414/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01414/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01414/l3v2/build.log b/latest/cases/01414/l3v2/build.log new file mode 100644 index 000000000..4c6d3a120 --- /dev/null +++ b/latest/cases/01414/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01414/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01414/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01414/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01414/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01414/l3v2/index.heta b/latest/cases/01414/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01414/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01414/model-sbml-l2v5.xml b/latest/cases/01414/model-sbml-l2v5.xml new file mode 100644 index 000000000..28c930550 --- /dev/null +++ b/latest/cases/01414/model-sbml-l2v5.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + 0.1 + + delay + P1 + k + + + + + + + + + + + diff --git a/latest/cases/01414/model-sbml-l3v2.xml b/latest/cases/01414/model-sbml-l3v2.xml new file mode 100644 index 000000000..5180e2657 --- /dev/null +++ b/latest/cases/01414/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + 0.1 + + delay + P1 + k + + + + + + + + + + + diff --git a/latest/cases/01414/synopsis.txt b/latest/cases/01414/synopsis.txt new file mode 100644 index 000000000..ee78f96c8 --- /dev/null +++ b/latest/cases/01414/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A delay function in a kinetic law that uses a local parameter as an argument. +componentTags: CSymbolDelay, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, kinetic law uses a delay function with a local parameter as an argument for the delay length. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 local parameter (J0.k) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> | $0.1 * delay(P1, k)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial value of parameter P1 | $3$ | variable | +| Initial value of local parameter 'J0.k' | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01415/l2v5/build.log b/latest/cases/01415/l2v5/build.log new file mode 100644 index 000000000..8ca134941 --- /dev/null +++ b/latest/cases/01415/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01415/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01415/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01415/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01415/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01415/l2v5/index.heta b/latest/cases/01415/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01415/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01415/l3v2/build.log b/latest/cases/01415/l3v2/build.log new file mode 100644 index 000000000..48a847a4e --- /dev/null +++ b/latest/cases/01415/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01415/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01415/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01415/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01415/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01415/l3v2/index.heta b/latest/cases/01415/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01415/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01415/model-sbml-l2v5.xml b/latest/cases/01415/model-sbml-l2v5.xml new file mode 100644 index 000000000..d04fbdd1b --- /dev/null +++ b/latest/cases/01415/model-sbml-l2v5.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + 0.1 + + delay + P1 + k + + + + + + + + + + + diff --git a/latest/cases/01415/model-sbml-l3v2.xml b/latest/cases/01415/model-sbml-l3v2.xml new file mode 100644 index 000000000..c3281d93d --- /dev/null +++ b/latest/cases/01415/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + 0.1 + + delay + P1 + k + + + + + + + + + + + diff --git a/latest/cases/01415/synopsis.txt b/latest/cases/01415/synopsis.txt new file mode 100644 index 000000000..27aa1d4d5 --- /dev/null +++ b/latest/cases/01415/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A delay function in a kinetic law that uses a local parameter as an argument. +componentTags: CSymbolDelay, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, kinetic law uses a delay function with a local parameter as an argument for the delay length. It shadows a global parameter with the same ID but a different value. + +The model contains: +* 1 species (S1) +* 2 parameters (P1, k) +* 1 local parameter (J0.k) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> | $0.1 * delay(P1, k)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial value of parameter P1 | $3$ | variable | +| Initial value of parameter k | $0$ | variable | +| Initial value of local parameter 'J0.k' | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01416/l2v5/index.heta b/latest/cases/01416/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01416/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01416/l3v2/build.log b/latest/cases/01416/l3v2/build.log new file mode 100644 index 000000000..f39ec81bd --- /dev/null +++ b/latest/cases/01416/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01416/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01416/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01416/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01416/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01416/l3v2/index.heta b/latest/cases/01416/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01416/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01416/model-sbml-l3v2.xml b/latest/cases/01416/model-sbml-l3v2.xml new file mode 100644 index 000000000..c16b78aba --- /dev/null +++ b/latest/cases/01416/model-sbml-l3v2.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + delay + S1 + 1 + + + + + + diff --git a/latest/cases/01416/synopsis.txt b/latest/cases/01416/synopsis.txt new file mode 100644 index 000000000..e74d2fd19 --- /dev/null +++ b/latest/cases/01416/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: A delay function for a variable with a rate rule with no MathML. +componentTags: AssignmentRule, CSymbolDelay, Parameter, RateRule +testTags: InitialValueReassigned, NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, one parameter shadows another parameter via a delay, but the other parameter's rate rule is empty, meaning it does not change. + +The model contains: +* 2 parameters (S1, P1) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $$ | +| Assignment | P1 | $delay(S1, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S1 | $3$ | variable | +| Initial value of parameter P1 | $delay(S1, 1)$ | variable |] + diff --git a/latest/cases/01417/l2v5/index.heta b/latest/cases/01417/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01417/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01417/l3v2/build.log b/latest/cases/01417/l3v2/build.log new file mode 100644 index 000000000..0a391ba20 --- /dev/null +++ b/latest/cases/01417/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01417/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01417/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01417/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01417/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01417/l3v2/index.heta b/latest/cases/01417/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01417/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01417/model-sbml-l3v2.xml b/latest/cases/01417/model-sbml-l3v2.xml new file mode 100644 index 000000000..52b151f1f --- /dev/null +++ b/latest/cases/01417/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + delay + S1 + S1_stoich + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01417/synopsis.txt b/latest/cases/01417/synopsis.txt new file mode 100644 index 000000000..c21756734 --- /dev/null +++ b/latest/cases/01417/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A delay function that uses a species reference as an argument. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, a delay function takes a species reference as the amount it is supposed to delay. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> | $0.1 * S1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $delay(S1, S1_stoich)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial value of parameter P1 | $delay(S1, S1_stoich)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01418/l2v5/index.heta b/latest/cases/01418/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01418/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01418/l3v2/build.log b/latest/cases/01418/l3v2/build.log new file mode 100644 index 000000000..947c43924 --- /dev/null +++ b/latest/cases/01418/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01418/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01418/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01418/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01418/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01418/l3v2/index.heta b/latest/cases/01418/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01418/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01418/model-sbml-l3v2.xml b/latest/cases/01418/model-sbml-l3v2.xml new file mode 100644 index 000000000..ec92a882d --- /dev/null +++ b/latest/cases/01418/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + delay + S1_stoich + 1 + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01418/synopsis.txt b/latest/cases/01418/synopsis.txt new file mode 100644 index 000000000..a8d9e020d --- /dev/null +++ b/latest/cases/01418/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A delay function of a species reference. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, a delay function references a (constant) species reference. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> | $0.1 * S1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $delay(S1_stoich, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial value of parameter P1 | $delay(S1_stoich, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01419/l2v5/index.heta b/latest/cases/01419/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01419/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01419/l3v2/build.log b/latest/cases/01419/l3v2/build.log new file mode 100644 index 000000000..f1ab5a9c2 --- /dev/null +++ b/latest/cases/01419/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01419/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01419/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01419/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01419/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01419/l3v2/index.heta b/latest/cases/01419/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01419/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01419/model-sbml-l3v2.xml b/latest/cases/01419/model-sbml-l3v2.xml new file mode 100644 index 000000000..5e43f3ce2 --- /dev/null +++ b/latest/cases/01419/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + delay + S1_stoich + 1 + + + + + + 1 + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01419/synopsis.txt b/latest/cases/01419/synopsis.txt new file mode 100644 index 000000000..1a28042eb --- /dev/null +++ b/latest/cases/01419/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A delay function of a species reference. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, a delay function references a (non-constant) species reference. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> | $0.1 * S1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $delay(S1_stoich, 1)$ | +| Rate | S1_stoich | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial value of parameter P1 | $delay(S1_stoich, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01420/l2v5/heta-code/output.heta b/latest/cases/01420/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8cb4d4936 --- /dev/null +++ b/latest/cases/01420/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + A = , }; +J0 := (-1); + diff --git a/latest/cases/01420/l2v5/index.heta b/latest/cases/01420/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01420/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01420/l2v5/json/output.json b/latest/cases/01420/l2v5/json/output.json new file mode 100644 index 000000000..667ad1340 --- /dev/null +++ b/latest/cases/01420/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01420/l3v2/heta-code/output.heta b/latest/cases/01420/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2b21d1dc0 --- /dev/null +++ b/latest/cases/01420/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + A = , }; +J0 := (-1); + diff --git a/latest/cases/01420/l3v2/index.heta b/latest/cases/01420/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01420/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01420/l3v2/json/output.json b/latest/cases/01420/l3v2/json/output.json new file mode 100644 index 000000000..b9efd4908 --- /dev/null +++ b/latest/cases/01420/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01420/model-sbml-l2v5.xml b/latest/cases/01420/model-sbml-l2v5.xml new file mode 100644 index 000000000..e48c79857 --- /dev/null +++ b/latest/cases/01420/model-sbml-l2v5.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01420/model-sbml-l3v2.xml b/latest/cases/01420/model-sbml-l3v2.xml new file mode 100644 index 000000000..fe410bc2e --- /dev/null +++ b/latest/cases/01420/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01420/output.heta b/latest/cases/01420/output.heta new file mode 100644 index 000000000..bed311df4 --- /dev/null +++ b/latest/cases/01420/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two reactants that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled reactants. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + A -> | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + A = , }; +J0 := (-1); + diff --git a/latest/cases/01420/synopsis.txt b/latest/cases/01420/synopsis.txt new file mode 100644 index 000000000..161263c53 --- /dev/null +++ b/latest/cases/01420/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two reactants that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled reactants. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + A -> | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01421/l2v5/heta-code/output.heta b/latest/cases/01421/l2v5/heta-code/output.heta new file mode 100644 index 000000000..db492c9ea --- /dev/null +++ b/latest/cases/01421/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + 2*A = , }; +J0 := (-1); + diff --git a/latest/cases/01421/l2v5/index.heta b/latest/cases/01421/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01421/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01421/l2v5/json/output.json b/latest/cases/01421/l2v5/json/output.json new file mode 100644 index 000000000..853216d2f --- /dev/null +++ b/latest/cases/01421/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -2 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01421/l3v2/heta-code/output.heta b/latest/cases/01421/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9448de402 --- /dev/null +++ b/latest/cases/01421/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + 2*A = , }; +J0 := (-1); + diff --git a/latest/cases/01421/l3v2/index.heta b/latest/cases/01421/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01421/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01421/l3v2/json/output.json b/latest/cases/01421/l3v2/json/output.json new file mode 100644 index 000000000..eecf9e4e5 --- /dev/null +++ b/latest/cases/01421/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -2 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01421/model-sbml-l2v5.xml b/latest/cases/01421/model-sbml-l2v5.xml new file mode 100644 index 000000000..34e8ef1da --- /dev/null +++ b/latest/cases/01421/model-sbml-l2v5.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01421/model-sbml-l3v2.xml b/latest/cases/01421/model-sbml-l3v2.xml new file mode 100644 index 000000000..8b8140c77 --- /dev/null +++ b/latest/cases/01421/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01421/output.heta b/latest/cases/01421/output.heta new file mode 100644 index 000000000..9f607173d --- /dev/null +++ b/latest/cases/01421/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two reactants that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled reactants. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + 2A -> | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + 2*A = , }; +J0 := (-1); + diff --git a/latest/cases/01421/synopsis.txt b/latest/cases/01421/synopsis.txt new file mode 100644 index 000000000..387da47d2 --- /dev/null +++ b/latest/cases/01421/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two reactants that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled reactants. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + 2A -> | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01422/l2v5/heta-code/output.heta b/latest/cases/01422/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0170099e6 --- /dev/null +++ b/latest/cases/01422/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A = A, }; +J0 := (-1); + diff --git a/latest/cases/01422/l2v5/index.heta b/latest/cases/01422/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01422/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01422/l2v5/json/output.json b/latest/cases/01422/l2v5/json/output.json new file mode 100644 index 000000000..2f43ffd1e --- /dev/null +++ b/latest/cases/01422/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01422/l3v2/heta-code/output.heta b/latest/cases/01422/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e57f1cb06 --- /dev/null +++ b/latest/cases/01422/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A = A, }; +J0 := (-1); + diff --git a/latest/cases/01422/l3v2/index.heta b/latest/cases/01422/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01422/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01422/l3v2/json/output.json b/latest/cases/01422/l3v2/json/output.json new file mode 100644 index 000000000..e404bc998 --- /dev/null +++ b/latest/cases/01422/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01422/model-sbml-l2v5.xml b/latest/cases/01422/model-sbml-l2v5.xml new file mode 100644 index 000000000..7f08aa2b0 --- /dev/null +++ b/latest/cases/01422/model-sbml-l2v5.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01422/model-sbml-l3v2.xml b/latest/cases/01422/model-sbml-l3v2.xml new file mode 100644 index 000000000..15ba5affa --- /dev/null +++ b/latest/cases/01422/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01422/output.heta b/latest/cases/01422/output.heta new file mode 100644 index 000000000..59ceb946f --- /dev/null +++ b/latest/cases/01422/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two reactants that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled reactants. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + -1A -> | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A = A, }; +J0 := (-1); + diff --git a/latest/cases/01422/synopsis.txt b/latest/cases/01422/synopsis.txt new file mode 100644 index 000000000..d2d69beaa --- /dev/null +++ b/latest/cases/01422/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two reactants that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled reactants. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + -1A -> | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01423/l2v5/heta-code/output.heta b/latest/cases/01423/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0170099e6 --- /dev/null +++ b/latest/cases/01423/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A = A, }; +J0 := (-1); + diff --git a/latest/cases/01423/l2v5/index.heta b/latest/cases/01423/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01423/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01423/l2v5/json/output.json b/latest/cases/01423/l2v5/json/output.json new file mode 100644 index 000000000..7e5248fd0 --- /dev/null +++ b/latest/cases/01423/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01423/l3v2/heta-code/output.heta b/latest/cases/01423/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e57f1cb06 --- /dev/null +++ b/latest/cases/01423/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A = A, }; +J0 := (-1); + diff --git a/latest/cases/01423/l3v2/index.heta b/latest/cases/01423/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01423/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01423/l3v2/json/output.json b/latest/cases/01423/l3v2/json/output.json new file mode 100644 index 000000000..c220bd1aa --- /dev/null +++ b/latest/cases/01423/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01423/model-sbml-l2v5.xml b/latest/cases/01423/model-sbml-l2v5.xml new file mode 100644 index 000000000..6bd900cf8 --- /dev/null +++ b/latest/cases/01423/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01423/model-sbml-l3v2.xml b/latest/cases/01423/model-sbml-l3v2.xml new file mode 100644 index 000000000..e503f1e95 --- /dev/null +++ b/latest/cases/01423/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01423/output.heta b/latest/cases/01423/output.heta new file mode 100644 index 000000000..cd1032ea0 --- /dev/null +++ b/latest/cases/01423/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references--in this case, zero. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A -> A | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A = A, }; +J0 := (-1); + diff --git a/latest/cases/01423/synopsis.txt b/latest/cases/01423/synopsis.txt new file mode 100644 index 000000000..5836bc423 --- /dev/null +++ b/latest/cases/01423/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references--in this case, zero. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A -> A | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01424/l2v5/heta-code/output.heta b/latest/cases/01424/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c505764b5 --- /dev/null +++ b/latest/cases/01424/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A = 2*A, }; +J0 := 1; + diff --git a/latest/cases/01424/l2v5/index.heta b/latest/cases/01424/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01424/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01424/l2v5/json/output.json b/latest/cases/01424/l2v5/json/output.json new file mode 100644 index 000000000..46e1d7994 --- /dev/null +++ b/latest/cases/01424/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 2 + }, + { + "target": "A", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01424/l3v2/heta-code/output.heta b/latest/cases/01424/l3v2/heta-code/output.heta new file mode 100644 index 000000000..aa8d6088f --- /dev/null +++ b/latest/cases/01424/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A = 2*A, }; +J0 := 1; + diff --git a/latest/cases/01424/l3v2/index.heta b/latest/cases/01424/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01424/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01424/l3v2/json/output.json b/latest/cases/01424/l3v2/json/output.json new file mode 100644 index 000000000..3e33a9ae0 --- /dev/null +++ b/latest/cases/01424/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 2 + }, + { + "target": "A", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01424/model-sbml-l2v5.xml b/latest/cases/01424/model-sbml-l2v5.xml new file mode 100644 index 000000000..cde9f398a --- /dev/null +++ b/latest/cases/01424/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01424/model-sbml-l3v2.xml b/latest/cases/01424/model-sbml-l3v2.xml new file mode 100644 index 000000000..5640f5b82 --- /dev/null +++ b/latest/cases/01424/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01424/output.heta b/latest/cases/01424/output.heta new file mode 100644 index 000000000..7ab342e0b --- /dev/null +++ b/latest/cases/01424/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A -> 2A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A = 2*A, }; +J0 := 1; + diff --git a/latest/cases/01424/synopsis.txt b/latest/cases/01424/synopsis.txt new file mode 100644 index 000000000..7b91e5a87 --- /dev/null +++ b/latest/cases/01424/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A -> 2A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01425/l2v5/heta-code/output.heta b/latest/cases/01425/l2v5/heta-code/output.heta new file mode 100644 index 000000000..4d08de694 --- /dev/null +++ b/latest/cases/01425/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: 2*A = A, }; +J0 := (-1); + diff --git a/latest/cases/01425/l2v5/index.heta b/latest/cases/01425/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01425/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01425/l2v5/json/output.json b/latest/cases/01425/l2v5/json/output.json new file mode 100644 index 000000000..eed6543dd --- /dev/null +++ b/latest/cases/01425/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -2 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01425/l3v2/heta-code/output.heta b/latest/cases/01425/l3v2/heta-code/output.heta new file mode 100644 index 000000000..30fff9410 --- /dev/null +++ b/latest/cases/01425/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: 2*A = A, }; +J0 := (-1); + diff --git a/latest/cases/01425/l3v2/index.heta b/latest/cases/01425/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01425/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01425/l3v2/json/output.json b/latest/cases/01425/l3v2/json/output.json new file mode 100644 index 000000000..cb71e7c1a --- /dev/null +++ b/latest/cases/01425/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -2 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01425/model-sbml-l2v5.xml b/latest/cases/01425/model-sbml-l2v5.xml new file mode 100644 index 000000000..23b087caa --- /dev/null +++ b/latest/cases/01425/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01425/model-sbml-l3v2.xml b/latest/cases/01425/model-sbml-l3v2.xml new file mode 100644 index 000000000..61fa6d8e4 --- /dev/null +++ b/latest/cases/01425/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01425/output.heta b/latest/cases/01425/output.heta new file mode 100644 index 000000000..2ff1b720a --- /dev/null +++ b/latest/cases/01425/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2A -> A | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: 2*A = A, }; +J0 := (-1); + diff --git a/latest/cases/01425/synopsis.txt b/latest/cases/01425/synopsis.txt new file mode 100644 index 000000000..a17813080 --- /dev/null +++ b/latest/cases/01425/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2A -> A | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01426/l2v5/heta-code/output.heta b/latest/cases/01426/l2v5/heta-code/output.heta new file mode 100644 index 000000000..dd3ad933f --- /dev/null +++ b/latest/cases/01426/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: 3*A + 2*A = , }; +J0 := (-1); + diff --git a/latest/cases/01426/l2v5/index.heta b/latest/cases/01426/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01426/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01426/l2v5/json/output.json b/latest/cases/01426/l2v5/json/output.json new file mode 100644 index 000000000..963022442 --- /dev/null +++ b/latest/cases/01426/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -3 + }, + { + "target": "A", + "stoichiometry": -2 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01426/l3v2/heta-code/output.heta b/latest/cases/01426/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e4f1d51dd --- /dev/null +++ b/latest/cases/01426/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: 3*A + 2*A = , }; +J0 := (-1); + diff --git a/latest/cases/01426/l3v2/index.heta b/latest/cases/01426/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01426/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01426/l3v2/json/output.json b/latest/cases/01426/l3v2/json/output.json new file mode 100644 index 000000000..e42342023 --- /dev/null +++ b/latest/cases/01426/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -3 + }, + { + "target": "A", + "stoichiometry": -2 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01426/model-sbml-l2v5.xml b/latest/cases/01426/model-sbml-l2v5.xml new file mode 100644 index 000000000..f2f1410b0 --- /dev/null +++ b/latest/cases/01426/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01426/model-sbml-l3v2.xml b/latest/cases/01426/model-sbml-l3v2.xml new file mode 100644 index 000000000..650e4d0b8 --- /dev/null +++ b/latest/cases/01426/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01426/output.heta b/latest/cases/01426/output.heta new file mode 100644 index 000000000..ff994b594 --- /dev/null +++ b/latest/cases/01426/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2A -> -3A | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: 3*A + 2*A = , }; +J0 := (-1); + diff --git a/latest/cases/01426/synopsis.txt b/latest/cases/01426/synopsis.txt new file mode 100644 index 000000000..9ea1c99b5 --- /dev/null +++ b/latest/cases/01426/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2A -> -3A | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01427/l2v5/heta-code/output.heta b/latest/cases/01427/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0bf393731 --- /dev/null +++ b/latest/cases/01427/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = 3*A + 2*A, }; +J0 := 1; + diff --git a/latest/cases/01427/l2v5/index.heta b/latest/cases/01427/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01427/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01427/l2v5/json/output.json b/latest/cases/01427/l2v5/json/output.json new file mode 100644 index 000000000..e81e3979e --- /dev/null +++ b/latest/cases/01427/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 3 + }, + { + "target": "A", + "stoichiometry": 2 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01427/l3v2/heta-code/output.heta b/latest/cases/01427/l3v2/heta-code/output.heta new file mode 100644 index 000000000..055602256 --- /dev/null +++ b/latest/cases/01427/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = 3*A + 2*A, }; +J0 := 1; + diff --git a/latest/cases/01427/l3v2/index.heta b/latest/cases/01427/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01427/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01427/l3v2/json/output.json b/latest/cases/01427/l3v2/json/output.json new file mode 100644 index 000000000..280e29676 --- /dev/null +++ b/latest/cases/01427/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 3 + }, + { + "target": "A", + "stoichiometry": 2 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01427/model-sbml-l2v5.xml b/latest/cases/01427/model-sbml-l2v5.xml new file mode 100644 index 000000000..1e8353983 --- /dev/null +++ b/latest/cases/01427/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01427/model-sbml-l3v2.xml b/latest/cases/01427/model-sbml-l3v2.xml new file mode 100644 index 000000000..2a4a4ee29 --- /dev/null +++ b/latest/cases/01427/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01427/output.heta b/latest/cases/01427/output.heta new file mode 100644 index 000000000..ca5f44eff --- /dev/null +++ b/latest/cases/01427/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -2A -> 3A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = 3*A + 2*A, }; +J0 := 1; + diff --git a/latest/cases/01427/synopsis.txt b/latest/cases/01427/synopsis.txt new file mode 100644 index 000000000..b0e44adce --- /dev/null +++ b/latest/cases/01427/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -2A -> 3A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01428/l2v5/heta-code/output.heta b/latest/cases/01428/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f10aa0c73 --- /dev/null +++ b/latest/cases/01428/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = A + A, }; +J0 := 1; + diff --git a/latest/cases/01428/l2v5/index.heta b/latest/cases/01428/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01428/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01428/l2v5/json/output.json b/latest/cases/01428/l2v5/json/output.json new file mode 100644 index 000000000..6fd369bab --- /dev/null +++ b/latest/cases/01428/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01428/l3v2/heta-code/output.heta b/latest/cases/01428/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4230f118a --- /dev/null +++ b/latest/cases/01428/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = A + A, }; +J0 := 1; + diff --git a/latest/cases/01428/l3v2/index.heta b/latest/cases/01428/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01428/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01428/l3v2/json/output.json b/latest/cases/01428/l3v2/json/output.json new file mode 100644 index 000000000..6e01a6b4b --- /dev/null +++ b/latest/cases/01428/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01428/model-sbml-l2v5.xml b/latest/cases/01428/model-sbml-l2v5.xml new file mode 100644 index 000000000..462156620 --- /dev/null +++ b/latest/cases/01428/model-sbml-l2v5.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01428/model-sbml-l3v2.xml b/latest/cases/01428/model-sbml-l3v2.xml new file mode 100644 index 000000000..1807ff071 --- /dev/null +++ b/latest/cases/01428/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01428/output.heta b/latest/cases/01428/output.heta new file mode 100644 index 000000000..919d35316 --- /dev/null +++ b/latest/cases/01428/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two products that both point to the same species. This is equivalent to a reaction with a single product whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> A + A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = A + A, }; +J0 := 1; + diff --git a/latest/cases/01428/synopsis.txt b/latest/cases/01428/synopsis.txt new file mode 100644 index 000000000..52951031b --- /dev/null +++ b/latest/cases/01428/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two products that both point to the same species. This is equivalent to a reaction with a single product whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> A + A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01429/l2v5/heta-code/output.heta b/latest/cases/01429/l2v5/heta-code/output.heta new file mode 100644 index 000000000..a2e48c7fb --- /dev/null +++ b/latest/cases/01429/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = A + 2*A, }; +J0 := 1; + diff --git a/latest/cases/01429/l2v5/index.heta b/latest/cases/01429/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01429/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01429/l2v5/json/output.json b/latest/cases/01429/l2v5/json/output.json new file mode 100644 index 000000000..afea8e1ed --- /dev/null +++ b/latest/cases/01429/l2v5/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": 2 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01429/l3v2/heta-code/output.heta b/latest/cases/01429/l3v2/heta-code/output.heta new file mode 100644 index 000000000..61716034f --- /dev/null +++ b/latest/cases/01429/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = A + 2*A, }; +J0 := 1; + diff --git a/latest/cases/01429/l3v2/index.heta b/latest/cases/01429/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01429/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01429/l3v2/json/output.json b/latest/cases/01429/l3v2/json/output.json new file mode 100644 index 000000000..db32b3648 --- /dev/null +++ b/latest/cases/01429/l3v2/json/output.json @@ -0,0 +1,38 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": 2 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01429/model-sbml-l2v5.xml b/latest/cases/01429/model-sbml-l2v5.xml new file mode 100644 index 000000000..ec67858d3 --- /dev/null +++ b/latest/cases/01429/model-sbml-l2v5.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01429/model-sbml-l3v2.xml b/latest/cases/01429/model-sbml-l3v2.xml new file mode 100644 index 000000000..1f7bd2200 --- /dev/null +++ b/latest/cases/01429/model-sbml-l3v2.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01429/output.heta b/latest/cases/01429/output.heta new file mode 100644 index 000000000..05b561918 --- /dev/null +++ b/latest/cases/01429/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two products that both point to the same species. This is equivalent to a reaction with a single product whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> A + 2A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = A + 2*A, }; +J0 := 1; + diff --git a/latest/cases/01429/synopsis.txt b/latest/cases/01429/synopsis.txt new file mode 100644 index 000000000..92c363c85 --- /dev/null +++ b/latest/cases/01429/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has two products that both point to the same species. This is equivalent to a reaction with a single product whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> A + 2A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01430/l2v5/heta-code/output.heta b/latest/cases/01430/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ff69b6825 --- /dev/null +++ b/latest/cases/01430/l2v5/heta-code/output.heta @@ -0,0 +1,17 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 20; +B @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + A = B + B, }; +J0 := 1; + diff --git a/latest/cases/01430/l2v5/index.heta b/latest/cases/01430/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01430/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01430/l2v5/json/output.json b/latest/cases/01430/l2v5/json/output.json new file mode 100644 index 000000000..e651fec04 --- /dev/null +++ b/latest/cases/01430/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "20" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "B", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "B", + "stoichiometry": 1 + }, + { + "target": "B", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01430/l3v2/heta-code/output.heta b/latest/cases/01430/l3v2/heta-code/output.heta new file mode 100644 index 000000000..467417813 --- /dev/null +++ b/latest/cases/01430/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 20; +B @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + A = B + B, }; +J0 := 1; + diff --git a/latest/cases/01430/l3v2/index.heta b/latest/cases/01430/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01430/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01430/l3v2/json/output.json b/latest/cases/01430/l3v2/json/output.json new file mode 100644 index 000000000..01951c844 --- /dev/null +++ b/latest/cases/01430/l3v2/json/output.json @@ -0,0 +1,54 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "20" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "B", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "B", + "stoichiometry": 1 + }, + { + "target": "B", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01430/model-sbml-l2v5.xml b/latest/cases/01430/model-sbml-l2v5.xml new file mode 100644 index 000000000..615f3e28f --- /dev/null +++ b/latest/cases/01430/model-sbml-l2v5.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01430/model-sbml-l3v2.xml b/latest/cases/01430/model-sbml-l3v2.xml new file mode 100644 index 000000000..d035020d9 --- /dev/null +++ b/latest/cases/01430/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01430/output.heta b/latest/cases/01430/output.heta new file mode 100644 index 000000000..f2c11cd73 --- /dev/null +++ b/latest/cases/01430/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that both point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + A -> B + B | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $20$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 20; +B @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + A = B + B, }; +J0 := 1; + diff --git a/latest/cases/01430/synopsis.txt b/latest/cases/01430/synopsis.txt new file mode 100644 index 000000000..438f67ca0 --- /dev/null +++ b/latest/cases/01430/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that both point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + A -> B + B | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $20$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01431/l2v5/heta-code/output.heta b/latest/cases/01431/l2v5/heta-code/output.heta new file mode 100644 index 000000000..1c71794d7 --- /dev/null +++ b/latest/cases/01431/l2v5/heta-code/output.heta @@ -0,0 +1,17 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; +B @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + B = A + B, }; +J0 := 1; + diff --git a/latest/cases/01431/l2v5/index.heta b/latest/cases/01431/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01431/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01431/l2v5/json/output.json b/latest/cases/01431/l2v5/json/output.json new file mode 100644 index 000000000..f0df5e7b0 --- /dev/null +++ b/latest/cases/01431/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "B", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "B", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "B", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01431/l3v2/heta-code/output.heta b/latest/cases/01431/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1738cd24d --- /dev/null +++ b/latest/cases/01431/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; +B @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + B = A + B, }; +J0 := 1; + diff --git a/latest/cases/01431/l3v2/index.heta b/latest/cases/01431/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01431/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01431/l3v2/json/output.json b/latest/cases/01431/l3v2/json/output.json new file mode 100644 index 000000000..c79c2bc74 --- /dev/null +++ b/latest/cases/01431/l3v2/json/output.json @@ -0,0 +1,54 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "B", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "B", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "B", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01431/model-sbml-l2v5.xml b/latest/cases/01431/model-sbml-l2v5.xml new file mode 100644 index 000000000..83185cd2e --- /dev/null +++ b/latest/cases/01431/model-sbml-l2v5.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01431/model-sbml-l3v2.xml b/latest/cases/01431/model-sbml-l3v2.xml new file mode 100644 index 000000000..69f00d7ec --- /dev/null +++ b/latest/cases/01431/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01431/output.heta b/latest/cases/01431/output.heta new file mode 100644 index 000000000..c91ad88cd --- /dev/null +++ b/latest/cases/01431/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + B -> A + B | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; +B @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + B = A + B, }; +J0 := 1; + diff --git a/latest/cases/01431/synopsis.txt b/latest/cases/01431/synopsis.txt new file mode 100644 index 000000000..ec93c3ffe --- /dev/null +++ b/latest/cases/01431/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + B -> A + B | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01432/l2v5/heta-code/output.heta b/latest/cases/01432/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ac7a0ee7d --- /dev/null +++ b/latest/cases/01432/l2v5/heta-code/output.heta @@ -0,0 +1,17 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 30; +B @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + 2*A = 2*B + B, }; +J0 := 1; + diff --git a/latest/cases/01432/l2v5/index.heta b/latest/cases/01432/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01432/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01432/l2v5/json/output.json b/latest/cases/01432/l2v5/json/output.json new file mode 100644 index 000000000..af1b91470 --- /dev/null +++ b/latest/cases/01432/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "30" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "B", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "B", + "stoichiometry": 2 + }, + { + "target": "A", + "stoichiometry": -2 + }, + { + "target": "B", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01432/l3v2/heta-code/output.heta b/latest/cases/01432/l3v2/heta-code/output.heta new file mode 100644 index 000000000..49ae59976 --- /dev/null +++ b/latest/cases/01432/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 30; +B @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + 2*A = 2*B + B, }; +J0 := 1; + diff --git a/latest/cases/01432/l3v2/index.heta b/latest/cases/01432/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01432/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01432/l3v2/json/output.json b/latest/cases/01432/l3v2/json/output.json new file mode 100644 index 000000000..f19a1835c --- /dev/null +++ b/latest/cases/01432/l3v2/json/output.json @@ -0,0 +1,54 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "30" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "B", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "B", + "stoichiometry": 2 + }, + { + "target": "A", + "stoichiometry": -2 + }, + { + "target": "B", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01432/model-sbml-l2v5.xml b/latest/cases/01432/model-sbml-l2v5.xml new file mode 100644 index 000000000..707524f90 --- /dev/null +++ b/latest/cases/01432/model-sbml-l2v5.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01432/model-sbml-l3v2.xml b/latest/cases/01432/model-sbml-l3v2.xml new file mode 100644 index 000000000..0c5959782 --- /dev/null +++ b/latest/cases/01432/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01432/output.heta b/latest/cases/01432/output.heta new file mode 100644 index 000000000..93eca38f6 --- /dev/null +++ b/latest/cases/01432/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2A + -1B -> -1A + 2B | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $30$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 30; +B @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: A + 2*A = 2*B + B, }; +J0 := 1; + diff --git a/latest/cases/01432/synopsis.txt b/latest/cases/01432/synopsis.txt new file mode 100644 index 000000000..030889e9c --- /dev/null +++ b/latest/cases/01432/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2A + -1B -> -1A + 2B | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $30$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01433/l2v5/heta-code/output.heta b/latest/cases/01433/l2v5/heta-code/output.heta new file mode 100644 index 000000000..9b633c0dd --- /dev/null +++ b/latest/cases/01433/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: 2*A + A + A + 2*A = 5*A + A + 4*A, }; +J0 := 1; + diff --git a/latest/cases/01433/l2v5/index.heta b/latest/cases/01433/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01433/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01433/l2v5/json/output.json b/latest/cases/01433/l2v5/json/output.json new file mode 100644 index 000000000..da28c1204 --- /dev/null +++ b/latest/cases/01433/l2v5/json/output.json @@ -0,0 +1,83 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 5 + }, + { + "target": "A", + "stoichiometry": -2 + }, + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -2 + }, + { + "target": "A", + "stoichiometry": 4 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01433/l3v2/heta-code/output.heta b/latest/cases/01433/l3v2/heta-code/output.heta new file mode 100644 index 000000000..de9d1b917 --- /dev/null +++ b/latest/cases/01433/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: 2*A + A + A + 2*A = 5*A + A + 4*A, }; +J0 := 1; + diff --git a/latest/cases/01433/l3v2/index.heta b/latest/cases/01433/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01433/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01433/l3v2/json/output.json b/latest/cases/01433/l3v2/json/output.json new file mode 100644 index 000000000..95327084e --- /dev/null +++ b/latest/cases/01433/l3v2/json/output.json @@ -0,0 +1,58 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "A", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "A", + "stoichiometry": 5 + }, + { + "target": "A", + "stoichiometry": -2 + }, + { + "target": "A", + "stoichiometry": 1 + }, + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -1 + }, + { + "target": "A", + "stoichiometry": -2 + }, + { + "target": "A", + "stoichiometry": 4 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01433/model-sbml-l2v5.xml b/latest/cases/01433/model-sbml-l2v5.xml new file mode 100644 index 000000000..88bc20b74 --- /dev/null +++ b/latest/cases/01433/model-sbml-l2v5.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01433/model-sbml-l3v2.xml b/latest/cases/01433/model-sbml-l3v2.xml new file mode 100644 index 000000000..437c654ab --- /dev/null +++ b/latest/cases/01433/model-sbml-l3v2.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01433/output.heta b/latest/cases/01433/output.heta new file mode 100644 index 000000000..40f72e37d --- /dev/null +++ b/latest/cases/01433/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + 2A + -4A -> 5A + -2A + A + -1A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +A @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: 2*A + A + A + 2*A = 5*A + A + 4*A, }; +J0 := 1; + diff --git a/latest/cases/01433/synopsis.txt b/latest/cases/01433/synopsis.txt new file mode 100644 index 000000000..dc957949e --- /dev/null +++ b/latest/cases/01433/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species +testTags: Amount, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A + 2A + -4A -> 5A + -2A + A + -1A | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01434/l2v5/index.heta b/latest/cases/01434/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01434/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01434/l3v2/build.log b/latest/cases/01434/l3v2/build.log new file mode 100644 index 000000000..9ccdef4dc --- /dev/null +++ b/latest/cases/01434/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01434/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01434/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01434/model-sbml-l3v2.xml"... +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 82 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01434/l3v2/index.heta b/latest/cases/01434/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01434/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01434/model-sbml-l3v2.xml b/latest/cases/01434/model-sbml-l3v2.xml new file mode 100644 index 000000000..2cd358471 --- /dev/null +++ b/latest/cases/01434/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01434/synopsis.txt b/latest/cases/01434/synopsis.txt new file mode 100644 index 000000000..0180891ff --- /dev/null +++ b/latest/cases/01434/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned stoichiometries +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants that all point to the same species, each of which has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A1_sr A + A1_sr2 A -> | $-1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | constant | +| Initial value of species reference 'A1_sr2' | $1$ | constant |] + diff --git a/latest/cases/01435/l2v5/build.log b/latest/cases/01435/l2v5/build.log new file mode 100644 index 000000000..1bdb3a77f --- /dev/null +++ b/latest/cases/01435/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01435/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01435/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01435/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01435/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01435/l2v5/index.heta b/latest/cases/01435/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01435/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01435/l3v2/index.heta b/latest/cases/01435/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01435/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01435/model-sbml-l2v5.xml b/latest/cases/01435/model-sbml-l2v5.xml new file mode 100644 index 000000000..dfa284fca --- /dev/null +++ b/latest/cases/01435/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + 2 + + + + + + + 1 + + + + + + + -1 + + + + + + diff --git a/latest/cases/01435/synopsis.txt b/latest/cases/01435/synopsis.txt new file mode 100644 index 000000000..d702d0bd1 --- /dev/null +++ b/latest/cases/01435/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Multiple species references to the same species +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species, each of which has an assigned value with stoichiometryMath. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A1_sr A + A1_sr2 A -> | $-1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | variable | +| Initial value of species reference 'A1_sr2' | $1$ | variable |] + diff --git a/latest/cases/01436/l2v5/index.heta b/latest/cases/01436/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01436/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01436/l3v2/build.log b/latest/cases/01436/l3v2/build.log new file mode 100644 index 000000000..7f07ec322 --- /dev/null +++ b/latest/cases/01436/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01436/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01436/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01436/model-sbml-l3v2.xml"... +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 82 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01436/l3v2/index.heta b/latest/cases/01436/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01436/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01436/model-sbml-l3v2.xml b/latest/cases/01436/model-sbml-l3v2.xml new file mode 100644 index 000000000..8ed3501d6 --- /dev/null +++ b/latest/cases/01436/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01436/synopsis.txt b/latest/cases/01436/synopsis.txt new file mode 100644 index 000000000..5e7f59275 --- /dev/null +++ b/latest/cases/01436/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned stoichiometries +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species, each of which has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A1_sr A -> A1_sr2 A | $-1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | constant | +| Initial value of species reference 'A1_sr2' | $1$ | constant |] + diff --git a/latest/cases/01437/l2v5/build.log b/latest/cases/01437/l2v5/build.log new file mode 100644 index 000000000..4f06b818a --- /dev/null +++ b/latest/cases/01437/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01437/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01437/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01437/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01437/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01437/l2v5/index.heta b/latest/cases/01437/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01437/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01437/l3v2/index.heta b/latest/cases/01437/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01437/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01437/model-sbml-l2v5.xml b/latest/cases/01437/model-sbml-l2v5.xml new file mode 100644 index 000000000..915ceca80 --- /dev/null +++ b/latest/cases/01437/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + 2 + + + + + + + + + 1 + + + + + + + -1 + + + + + + diff --git a/latest/cases/01437/synopsis.txt b/latest/cases/01437/synopsis.txt new file mode 100644 index 000000000..797655a09 --- /dev/null +++ b/latest/cases/01437/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned stoichiometries +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants that all point to the same species, each of which has a stoichiometryMath. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A1_sr A -> A1_sr2 A | $-1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | variable | +| Initial value of species reference 'A1_sr2' | $1$ | variable |] + diff --git a/latest/cases/01438/l2v5/index.heta b/latest/cases/01438/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01438/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01438/l3v2/build.log b/latest/cases/01438/l3v2/build.log new file mode 100644 index 000000000..c0de2b5d5 --- /dev/null +++ b/latest/cases/01438/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01438/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01438/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01438/model-sbml-l3v2.xml"... +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 82 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01438/l3v2/index.heta b/latest/cases/01438/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01438/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01438/model-sbml-l3v2.xml b/latest/cases/01438/model-sbml-l3v2.xml new file mode 100644 index 000000000..af922e088 --- /dev/null +++ b/latest/cases/01438/model-sbml-l3v2.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + 2 + + + + + 1 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01438/synopsis.txt b/latest/cases/01438/synopsis.txt new file mode 100644 index 000000000..80af310ef --- /dev/null +++ b/latest/cases/01438/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned stoichiometries +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species, each of which has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> A1_sr A + A1_sr2 A | $1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | constant | +| Initial value of species reference 'A1_sr2' | $1$ | constant |] + diff --git a/latest/cases/01439/l2v5/build.log b/latest/cases/01439/l2v5/build.log new file mode 100644 index 000000000..7b46a4803 --- /dev/null +++ b/latest/cases/01439/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01439/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01439/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01439/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01439/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01439/l2v5/index.heta b/latest/cases/01439/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01439/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01439/l3v2/index.heta b/latest/cases/01439/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01439/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01439/model-sbml-l2v5.xml b/latest/cases/01439/model-sbml-l2v5.xml new file mode 100644 index 000000000..80c05109a --- /dev/null +++ b/latest/cases/01439/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + 2 + + + + + + + 1 + + + + + + + 1 + + + + + + diff --git a/latest/cases/01439/synopsis.txt b/latest/cases/01439/synopsis.txt new file mode 100644 index 000000000..cc3929af1 --- /dev/null +++ b/latest/cases/01439/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned stoichiometries +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species, each of which has a stoichiometry math. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> A1_sr A + A1_sr2 A | $1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | variable | +| Initial value of species reference 'A1_sr2' | $1$ | variable |] + diff --git a/latest/cases/01440/l2v5/index.heta b/latest/cases/01440/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01440/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01440/l3v2/build.log b/latest/cases/01440/l3v2/build.log new file mode 100644 index 000000000..563e70e3c --- /dev/null +++ b/latest/cases/01440/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01440/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01440/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01440/model-sbml-l3v2.xml"... +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01440/l3v2/index.heta b/latest/cases/01440/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01440/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01440/model-sbml-l3v2.xml b/latest/cases/01440/model-sbml-l3v2.xml new file mode 100644 index 000000000..25cbe47c6 --- /dev/null +++ b/latest/cases/01440/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + 2 + + + + + 1 + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01440/synopsis.txt b/latest/cases/01440/synopsis.txt new file mode 100644 index 000000000..747ab5834 --- /dev/null +++ b/latest/cases/01440/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned stoichiometries +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple products that all point to two species, and each has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) +* 4 species references (A_sr1, A_sr2, B_sr1, B_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A_sr1 A + A_sr2 A -> B_sr1 B + B_sr2 B | $1$ |] +Note: the following stoichiometries are set separately: A_sr1, A_sr2, B_sr1, B_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $30$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A_sr1' | $2$ | constant | +| Initial value of species reference 'A_sr2' | $1$ | constant | +| Initial value of species reference 'B_sr1' | $2$ | constant | +| Initial value of species reference 'B_sr2' | $1$ | constant |] + diff --git a/latest/cases/01441/l2v5/build.log b/latest/cases/01441/l2v5/build.log new file mode 100644 index 000000000..df8164f3b --- /dev/null +++ b/latest/cases/01441/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01441/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01441/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01441/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01441/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01441/l2v5/index.heta b/latest/cases/01441/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01441/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01441/l3v2/index.heta b/latest/cases/01441/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01441/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01441/model-sbml-l2v5.xml b/latest/cases/01441/model-sbml-l2v5.xml new file mode 100644 index 000000000..378ec1c7c --- /dev/null +++ b/latest/cases/01441/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + 2 + + + + + + + 1 + + + + + + + + + 2 + + + + + + + 1 + + + + + + + 1 + + + + + + diff --git a/latest/cases/01441/synopsis.txt b/latest/cases/01441/synopsis.txt new file mode 100644 index 000000000..e8e56286c --- /dev/null +++ b/latest/cases/01441/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned stoichiometries +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple products that all point to the same species, each of which has a stoichiometry math. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) +* 4 species references (A_sr1, A_sr2, B_sr1, B_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A_sr1 A + A_sr2 A -> B_sr1 B + B_sr2 B | $1$ |] +Note: the following stoichiometries are set separately: A_sr1, A_sr2, B_sr1, B_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $30$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A_sr1' | $2$ | variable | +| Initial value of species reference 'A_sr2' | $1$ | variable | +| Initial value of species reference 'B_sr1' | $2$ | variable | +| Initial value of species reference 'B_sr2' | $1$ | variable |] + diff --git a/latest/cases/01442/l2v5/index.heta b/latest/cases/01442/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01442/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01442/l3v2/build.log b/latest/cases/01442/l3v2/build.log new file mode 100644 index 000000000..3edf630f7 --- /dev/null +++ b/latest/cases/01442/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01442/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01442/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01442/model-sbml-l3v2.xml"... +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01442/l3v2/index.heta b/latest/cases/01442/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01442/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01442/model-sbml-l3v2.xml b/latest/cases/01442/model-sbml-l3v2.xml new file mode 100644 index 000000000..eea02bfbc --- /dev/null +++ b/latest/cases/01442/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + 2 + + + + + 1 + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01442/synopsis.txt b/latest/cases/01442/synopsis.txt new file mode 100644 index 000000000..b8dfd7db1 --- /dev/null +++ b/latest/cases/01442/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned stoichiometries +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactions and products that all point to two species, and each has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) +* 4 species references (A_sr1, B_sr1, A_sr2, B_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A_sr1 A + B_sr1 B -> A_sr2 A + B_sr2 B | $-1$ |] +Note: the following stoichiometries are set separately: A_sr1, B_sr1, A_sr2, B_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A_sr1' | $2$ | constant | +| Initial value of species reference 'B_sr1' | $2$ | constant | +| Initial value of species reference 'A_sr2' | $1$ | constant | +| Initial value of species reference 'B_sr2' | $1$ | constant |] + diff --git a/latest/cases/01443/l2v5/build.log b/latest/cases/01443/l2v5/build.log new file mode 100644 index 000000000..f851b8e1b --- /dev/null +++ b/latest/cases/01443/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01443/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01443/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01443/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01443/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01443/l2v5/index.heta b/latest/cases/01443/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01443/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01443/l3v2/index.heta b/latest/cases/01443/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01443/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01443/model-sbml-l2v5.xml b/latest/cases/01443/model-sbml-l2v5.xml new file mode 100644 index 000000000..cecea7a5a --- /dev/null +++ b/latest/cases/01443/model-sbml-l2v5.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + 2 + + + + + + + 2 + + + + + + + + + 1 + + + + + + + 1 + + + + + + + -1 + + + + + + diff --git a/latest/cases/01443/synopsis.txt b/latest/cases/01443/synopsis.txt new file mode 100644 index 000000000..6bd78ce1f --- /dev/null +++ b/latest/cases/01443/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned stoichiometries +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple products that all point to two species, and each has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) +* 4 species references (A_sr1, B_sr1, A_sr2, B_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A_sr1 A + B_sr1 B -> A_sr2 A + B_sr2 B | $-1$ |] +Note: the following stoichiometries are set separately: A_sr1, B_sr1, A_sr2, B_sr2 + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A_sr1' | $2$ | variable | +| Initial value of species reference 'B_sr1' | $2$ | variable | +| Initial value of species reference 'A_sr2' | $1$ | variable | +| Initial value of species reference 'B_sr2' | $1$ | variable |] + diff --git a/latest/cases/01444/l2v5/index.heta b/latest/cases/01444/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01444/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01444/l3v2/build.log b/latest/cases/01444/l3v2/build.log new file mode 100644 index 000000000..c90a88aa1 --- /dev/null +++ b/latest/cases/01444/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01444/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01444/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01444/model-sbml-l3v2.xml"... +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01444/l3v2/index.heta b/latest/cases/01444/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01444/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01444/model-sbml-l3v2.xml b/latest/cases/01444/model-sbml-l3v2.xml new file mode 100644 index 000000000..99486c387 --- /dev/null +++ b/latest/cases/01444/model-sbml-l3v2.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + + + + + + time + 5 + + + + + + + 1 + + + + + 1 + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01444/synopsis.txt b/latest/cases/01444/synopsis.txt new file mode 100644 index 000000000..4d7d4f118 --- /dev/null +++ b/latest/cases/01444/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: CSymbolTime, Compartment, EventNoDelay, InitialAssignment, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants that all point to the same species, each of which has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. Partway through the simulation, the stoichiometries change due to an event. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A1_sr A + A1_sr2 A -> | $-1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time >= 5$ | $A1_sr = 1$ | +| | | $A1_sr2 = 1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | constant | +| Initial value of species reference 'A1_sr2' | $1$ | constant |] + diff --git a/latest/cases/01445/l2v5/index.heta b/latest/cases/01445/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01445/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01445/l3v2/build.log b/latest/cases/01445/l3v2/build.log new file mode 100644 index 000000000..66d82e666 --- /dev/null +++ b/latest/cases/01445/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01445/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01445/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01445/model-sbml-l3v2.xml"... +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01445/l3v2/index.heta b/latest/cases/01445/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01445/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01445/model-sbml-l3v2.xml b/latest/cases/01445/model-sbml-l3v2.xml new file mode 100644 index 000000000..7929459ea --- /dev/null +++ b/latest/cases/01445/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + + + + + + time + 5 + + + + + + + 1 + + + + + 2 + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01445/synopsis.txt b/latest/cases/01445/synopsis.txt new file mode 100644 index 000000000..7e6cb2502 --- /dev/null +++ b/latest/cases/01445/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: CSymbolTime, Compartment, EventNoDelay, InitialAssignment, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species, each of which has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. Partway through the simulation, the stoichiometries change due to an event. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A1_sr A -> A1_sr2 A | $-1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time >= 5$ | $A1_sr = 1$ | +| | | $A1_sr2 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | variable | +| Initial value of species reference 'A1_sr2' | $1$ | variable |] + diff --git a/latest/cases/01446/l2v5/index.heta b/latest/cases/01446/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01446/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01446/l3v2/build.log b/latest/cases/01446/l3v2/build.log new file mode 100644 index 000000000..644ce9216 --- /dev/null +++ b/latest/cases/01446/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01446/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01446/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01446/model-sbml-l3v2.xml"... +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01446/l3v2/index.heta b/latest/cases/01446/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01446/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01446/model-sbml-l3v2.xml b/latest/cases/01446/model-sbml-l3v2.xml new file mode 100644 index 000000000..65ebc03c0 --- /dev/null +++ b/latest/cases/01446/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + 2 + + + + + 1 + + + + + + + + + + time + 5 + + + + + + + 1 + + + + + 3 + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01446/synopsis.txt b/latest/cases/01446/synopsis.txt new file mode 100644 index 000000000..3cf31e758 --- /dev/null +++ b/latest/cases/01446/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: CSymbolTime, Compartment, EventNoDelay, InitialAssignment, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species, each of which has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. Partway through the simulation, the stoichiometries change due to an event. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> A1_sr A + A1_sr2 A | $1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time >= 5$ | $A1_sr = 1$ | +| | | $A1_sr2 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | variable | +| Initial value of species reference 'A1_sr2' | $1$ | variable |] + diff --git a/latest/cases/01447/l2v5/index.heta b/latest/cases/01447/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01447/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01447/l3v2/build.log b/latest/cases/01447/l3v2/build.log new file mode 100644 index 000000000..14760975a --- /dev/null +++ b/latest/cases/01447/l3v2/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01447/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01447/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01447/model-sbml-l3v2.xml"... +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01447/l3v2/index.heta b/latest/cases/01447/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01447/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01447/model-sbml-l3v2.xml b/latest/cases/01447/model-sbml-l3v2.xml new file mode 100644 index 000000000..c5143009b --- /dev/null +++ b/latest/cases/01447/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + 2 + + + + + 1 + + + + + + + + + + time + 5 + + + + + + + 1 + + + + + 3 + + + + + 1 + + + + + 3 + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01447/synopsis.txt b/latest/cases/01447/synopsis.txt new file mode 100644 index 000000000..71e8c9eb1 --- /dev/null +++ b/latest/cases/01447/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: CSymbolTime, Compartment, EventNoDelay, InitialAssignment, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple products that all point to two species, and each has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. Partway through the simulation, the stoichiometries change due to an event. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) +* 4 species references (A_sr1, A_sr2, B_sr1, B_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A_sr1 A + A_sr2 A -> B_sr1 B + B_sr2 B | $1$ |] +Note: the following stoichiometries are set separately: A_sr1, A_sr2, B_sr1, B_sr2 + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time >= 5$ | $A_sr1 = 1$ | +| | | $A_sr2 = 3$ | +| | | $B_sr1 = 1$ | +| | | $B_sr2 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $50$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A_sr1' | $2$ | variable | +| Initial value of species reference 'A_sr2' | $1$ | variable | +| Initial value of species reference 'B_sr1' | $2$ | variable | +| Initial value of species reference 'B_sr2' | $1$ | variable |] + diff --git a/latest/cases/01448/l2v5/index.heta b/latest/cases/01448/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01448/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01448/l3v2/build.log b/latest/cases/01448/l3v2/build.log new file mode 100644 index 000000000..157954476 --- /dev/null +++ b/latest/cases/01448/l3v2/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01448/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01448/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01448/model-sbml-l3v2.xml"... +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01448/l3v2/index.heta b/latest/cases/01448/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01448/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01448/model-sbml-l3v2.xml b/latest/cases/01448/model-sbml-l3v2.xml new file mode 100644 index 000000000..bfd30e195 --- /dev/null +++ b/latest/cases/01448/model-sbml-l3v2.xml @@ -0,0 +1,87 @@ + + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + 2 + + + + + 1 + + + + + + + + + + time + 5 + + + + + + + 1 + + + + + 2 + + + + + 1 + + + + + 2 + + + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01448/synopsis.txt b/latest/cases/01448/synopsis.txt new file mode 100644 index 000000000..7442631ff --- /dev/null +++ b/latest/cases/01448/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: CSymbolTime, Compartment, EventNoDelay, InitialAssignment, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactions and products that all point to two species, and each has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. Partway through the simulation, the stoichiometries change due to an event. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) +* 4 species references (A_sr1, B_sr1, A_sr2, B_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A_sr1 A + B_sr1 B -> A_sr2 A + B_sr2 B | $-1$ |] +Note: the following stoichiometries are set separately: A_sr1, B_sr1, A_sr2, B_sr2 + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time >= 5$ | $A_sr1 = 1$ | +| | | $A_sr2 = 2$ | +| | | $B_sr1 = 1$ | +| | | $B_sr2 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A_sr1' | $2$ | variable | +| Initial value of species reference 'B_sr1' | $2$ | variable | +| Initial value of species reference 'A_sr2' | $1$ | variable | +| Initial value of species reference 'B_sr2' | $1$ | variable |] + diff --git a/latest/cases/01449/l2v5/index.heta b/latest/cases/01449/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01449/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01449/l3v2/build.log b/latest/cases/01449/l3v2/build.log new file mode 100644 index 000000000..074468bbb --- /dev/null +++ b/latest/cases/01449/l3v2/build.log @@ -0,0 +1,14 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01449/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01449/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01449/model-sbml-l3v2.xml"... +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[error] A1_sr component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] A1_sr2_proc Property "actors[0].target" has lost reference "A1_sr2". +[error] A1_sr_proc Property "actors[0].target" has lost reference "A1_sr". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01449/l3v2/index.heta b/latest/cases/01449/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01449/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01449/model-sbml-l3v2.xml b/latest/cases/01449/model-sbml-l3v2.xml new file mode 100644 index 000000000..d55ae7adf --- /dev/null +++ b/latest/cases/01449/model-sbml-l3v2.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + + + -1 + + + + + 1 + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01449/synopsis.txt b/latest/cases/01449/synopsis.txt new file mode 100644 index 000000000..9c9d6aeb8 --- /dev/null +++ b/latest/cases/01449/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: Compartment, InitialAssignment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants that all point to the same species, each of which has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. The species references change due to rate rules, which end up cancelling each other out. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A1_sr A + A1_sr2 A -> | $-1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A1_sr2 | $-1$ | +| Rate | A1_sr | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | variable | +| Initial value of species reference 'A1_sr2' | $1$ | variable |] + diff --git a/latest/cases/01450/l2v5/index.heta b/latest/cases/01450/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01450/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01450/l3v2/build.log b/latest/cases/01450/l3v2/build.log new file mode 100644 index 000000000..a6380b2b6 --- /dev/null +++ b/latest/cases/01450/l3v2/build.log @@ -0,0 +1,14 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01450/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01450/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01450/model-sbml-l3v2.xml"... +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[error] A1_sr component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] A1_sr2_proc Property "actors[0].target" has lost reference "A1_sr2". +[error] A1_sr_proc Property "actors[0].target" has lost reference "A1_sr". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01450/l3v2/index.heta b/latest/cases/01450/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01450/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01450/model-sbml-l3v2.xml b/latest/cases/01450/model-sbml-l3v2.xml new file mode 100644 index 000000000..a112937cd --- /dev/null +++ b/latest/cases/01450/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + + + 1 + + + + + 1 + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01450/synopsis.txt b/latest/cases/01450/synopsis.txt new file mode 100644 index 000000000..fd3745eba --- /dev/null +++ b/latest/cases/01450/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: Compartment, InitialAssignment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species, each of which has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. The species references change due to rate rules, which end up cancelling each other out. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A1_sr A -> A1_sr2 A | $-1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A1_sr2 | $1$ | +| Rate | A1_sr | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | variable | +| Initial value of species reference 'A1_sr2' | $1$ | variable |] + diff --git a/latest/cases/01451/l2v5/index.heta b/latest/cases/01451/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01451/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01451/l3v2/build.log b/latest/cases/01451/l3v2/build.log new file mode 100644 index 000000000..2d45a3298 --- /dev/null +++ b/latest/cases/01451/l3v2/build.log @@ -0,0 +1,14 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01451/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01451/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01451/model-sbml-l3v2.xml"... +[error] A1_sr component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[error] A1_sr2 component does not exist which is not allowed for the "update" action. +[error] A1_sr component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] A1_sr2_proc Property "actors[0].target" has lost reference "A1_sr2". +[error] A1_sr_proc Property "actors[0].target" has lost reference "A1_sr". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01451/l3v2/index.heta b/latest/cases/01451/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01451/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01451/model-sbml-l3v2.xml b/latest/cases/01451/model-sbml-l3v2.xml new file mode 100644 index 000000000..45575377c --- /dev/null +++ b/latest/cases/01451/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + 2 + + + + + 1 + + + + + + + -1 + + + + + 1 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01451/synopsis.txt b/latest/cases/01451/synopsis.txt new file mode 100644 index 000000000..953c09f13 --- /dev/null +++ b/latest/cases/01451/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: Compartment, InitialAssignment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactants and products that all point to the same species, each of which has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. The species references change due to rate rules, which end up cancelling each other out. + +The model contains: +* 1 species (A) +* 1 compartment (C) +* 2 species references (A1_sr, A1_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> A1_sr A + A1_sr2 A | $1$ |] +Note: the following stoichiometries are set separately: A1_sr, A1_sr2 + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A1_sr2 | $-1$ | +| Rate | A1_sr | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A1_sr' | $2$ | variable | +| Initial value of species reference 'A1_sr2' | $1$ | variable |] + diff --git a/latest/cases/01452/l2v5/index.heta b/latest/cases/01452/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01452/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01452/l3v2/build.log b/latest/cases/01452/l3v2/build.log new file mode 100644 index 000000000..e4c8961b9 --- /dev/null +++ b/latest/cases/01452/l3v2/build.log @@ -0,0 +1,20 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01452/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01452/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01452/model-sbml-l3v2.xml"... +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 87 +[error] A_sr1_proc Property "actors[0].target" has lost reference "A_sr1". +[error] A_sr2_proc Property "actors[0].target" has lost reference "A_sr2". +[error] B_sr1_proc Property "actors[0].target" has lost reference "B_sr1". +[error] B_sr2_proc Property "actors[0].target" has lost reference "B_sr2". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01452/l3v2/index.heta b/latest/cases/01452/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01452/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01452/model-sbml-l3v2.xml b/latest/cases/01452/model-sbml-l3v2.xml new file mode 100644 index 000000000..36cd700de --- /dev/null +++ b/latest/cases/01452/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + 2 + + + + + 1 + + + + + + + -1 + + + + + 1 + + + + + -1 + + + + + 1 + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01452/synopsis.txt b/latest/cases/01452/synopsis.txt new file mode 100644 index 000000000..1d187399b --- /dev/null +++ b/latest/cases/01452/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: Compartment, InitialAssignment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple products that all point to two species, and each has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. The species references change due to rate rules, which end up cancelling each other out. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) +* 4 species references (A_sr1, A_sr2, B_sr1, B_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A_sr1 A + A_sr2 A -> B_sr1 B + B_sr2 B | $1$ |] +Note: the following stoichiometries are set separately: A_sr1, A_sr2, B_sr1, B_sr2 + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A_sr1 | $-1$ | +| Rate | A_sr2 | $1$ | +| Rate | B_sr1 | $-1$ | +| Rate | B_sr2 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $50$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A_sr1' | $2$ | variable | +| Initial value of species reference 'A_sr2' | $1$ | variable | +| Initial value of species reference 'B_sr1' | $2$ | variable | +| Initial value of species reference 'B_sr2' | $1$ | variable |] + diff --git a/latest/cases/01453/l2v5/index.heta b/latest/cases/01453/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01453/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01453/l3v2/build.log b/latest/cases/01453/l3v2/build.log new file mode 100644 index 000000000..fade06480 --- /dev/null +++ b/latest/cases/01453/l3v2/build.log @@ -0,0 +1,20 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01453/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01453/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01453/model-sbml-l3v2.xml"... +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[error] A_sr1 component does not exist which is not allowed for the "update" action. +[error] A_sr2 component does not exist which is not allowed for the "update" action. +[error] B_sr1 component does not exist which is not allowed for the "update" action. +[error] B_sr2 component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 87 +[error] A_sr1_proc Property "actors[0].target" has lost reference "A_sr1". +[error] A_sr2_proc Property "actors[0].target" has lost reference "A_sr2". +[error] B_sr1_proc Property "actors[0].target" has lost reference "B_sr1". +[error] B_sr2_proc Property "actors[0].target" has lost reference "B_sr2". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01453/l3v2/index.heta b/latest/cases/01453/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01453/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01453/model-sbml-l3v2.xml b/latest/cases/01453/model-sbml-l3v2.xml new file mode 100644 index 000000000..b59a83f9f --- /dev/null +++ b/latest/cases/01453/model-sbml-l3v2.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + 2 + + + + + 1 + + + + + 2 + + + + + 1 + + + + + + + 1 + + + + + 1 + + + + + 1 + + + + + 1 + + + + + + + + + + + + + + + + -1 + + + + + + diff --git a/latest/cases/01453/synopsis.txt b/latest/cases/01453/synopsis.txt new file mode 100644 index 000000000..7cbe6c84c --- /dev/null +++ b/latest/cases/01453/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Multiple species references to the same species with assigned variable stoichiometries +componentTags: Compartment, InitialAssignment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this test, a single reaction has multiple reactions and products that all point to two species, and each has an assigned value. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references. The species references change due to rate rules, which end up cancelling each other out. + +The model contains: +* 2 species (A, B) +* 1 compartment (C) +* 4 species references (A_sr1, B_sr1, A_sr2, B_sr2) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: A_sr1 A + B_sr1 B -> A_sr2 A + B_sr2 B | $-1$ |] +Note: the following stoichiometries are set separately: A_sr1, B_sr1, A_sr2, B_sr2 + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | A_sr1 | $1$ | +| Rate | A_sr2 | $1$ | +| Rate | B_sr1 | $1$ | +| Rate | B_sr2 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species A | $1$ | variable | +| Initial concentration of species B | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'A_sr1' | $2$ | variable | +| Initial value of species reference 'B_sr1' | $2$ | variable | +| Initial value of species reference 'A_sr2' | $1$ | variable | +| Initial value of species reference 'B_sr2' | $1$ | variable |] + diff --git a/latest/cases/01454/l2v5/build.log b/latest/cases/01454/l2v5/build.log new file mode 100644 index 000000000..945bd72ed --- /dev/null +++ b/latest/cases/01454/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01454/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01454/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01454/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01454/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01454/l2v5/index.heta b/latest/cases/01454/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01454/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01454/l3v2/build.log b/latest/cases/01454/l3v2/build.log new file mode 100644 index 000000000..3ca2150c1 --- /dev/null +++ b/latest/cases/01454/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01454/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01454/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01454/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01454/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01454/l3v2/index.heta b/latest/cases/01454/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01454/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01454/model-sbml-l2v5.xml b/latest/cases/01454/model-sbml-l2v5.xml new file mode 100644 index 000000000..5b30862af --- /dev/null +++ b/latest/cases/01454/model-sbml-l2v5.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + + delay + S1 + 0.1 + + + + + + diff --git a/latest/cases/01454/model-sbml-l3v2.xml b/latest/cases/01454/model-sbml-l3v2.xml new file mode 100644 index 000000000..5db84bcbb --- /dev/null +++ b/latest/cases/01454/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + + delay + S1 + 0.1 + + + + + + diff --git a/latest/cases/01454/synopsis.txt b/latest/cases/01454/synopsis.txt new file mode 100644 index 000000000..0840af20a --- /dev/null +++ b/latest/cases/01454/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + This test is the same basic test as 01198: a species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That difference is that this value then gets assigned to the parameter 'x' via a delay of 0.1, ensuring that the delay function also takes this into consideration. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $delay(S1, 0.1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $delay(S1, 0.1)$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01455/l2v5/index.heta b/latest/cases/01455/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01455/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01455/l3v2/build.log b/latest/cases/01455/l3v2/build.log new file mode 100644 index 000000000..6fe764a88 --- /dev/null +++ b/latest/cases/01455/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01455/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01455/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01455/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01455/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01455/l3v2/index.heta b/latest/cases/01455/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01455/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01455/model-sbml-l3v2.xml b/latest/cases/01455/model-sbml-l3v2.xml new file mode 100644 index 000000000..96a05a4ad --- /dev/null +++ b/latest/cases/01455/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + + + + + 2 + + + + + + diff --git a/latest/cases/01455/synopsis.txt b/latest/cases/01455/synopsis.txt new file mode 100644 index 000000000..ddbbabace --- /dev/null +++ b/latest/cases/01455/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Testing the rateOf csymbol together with the hasOnlySubstanceUnits attribute +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, species S1 in non-unity compartment C is affected by a reaction, which affects how its amount changes. Because it is set hasOnlySubstanceUnits=true, the rateOf csymbol tracks how the amount of S1 changes in time (i.e. the reaction rate), instead of how its concentration changes in time. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter x | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01456/l2v5/index.heta b/latest/cases/01456/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01456/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01456/l3v2/build.log b/latest/cases/01456/l3v2/build.log new file mode 100644 index 000000000..a25c1bad3 --- /dev/null +++ b/latest/cases/01456/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01456/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01456/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01456/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01456/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01456/l3v2/index.heta b/latest/cases/01456/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01456/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01456/model-sbml-l3v2.xml b/latest/cases/01456/model-sbml-l3v2.xml new file mode 100644 index 000000000..a3367b06f --- /dev/null +++ b/latest/cases/01456/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + + + + + + 2 + + + + + + diff --git a/latest/cases/01456/synopsis.txt b/latest/cases/01456/synopsis.txt new file mode 100644 index 000000000..1f52c0b11 --- /dev/null +++ b/latest/cases/01456/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Testing the rateOf csymbol together with a non-unity compartment +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species in a non-unity compartment is affected by a reaction, but is set hasOnlySubstanceUnits=false, meaning that outside of reactions, it is to be treated as a concentration. This includes the 'rateOf' csymbol, meaning that 'rateOf(S1)' means the rate of change of the concentration of S1, not the rate of change of the amount of S1. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter x | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01457/l2v5/index.heta b/latest/cases/01457/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01457/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01457/l3v2/build.log b/latest/cases/01457/l3v2/build.log new file mode 100644 index 000000000..bcf623f58 --- /dev/null +++ b/latest/cases/01457/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01457/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01457/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01457/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01457/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01457/l3v2/index.heta b/latest/cases/01457/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01457/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01457/model-sbml-l3v2.xml b/latest/cases/01457/model-sbml-l3v2.xml new file mode 100644 index 000000000..274093e10 --- /dev/null +++ b/latest/cases/01457/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + 2 + + + + + + rateOf + S1 + + + + + + diff --git a/latest/cases/01457/synopsis.txt b/latest/cases/01457/synopsis.txt new file mode 100644 index 000000000..8f9bb4105 --- /dev/null +++ b/latest/cases/01457/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: Testing the rateOf csymbol together with the hasOnlySubstanceUnits attribute +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, RateRule, Species +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, species S1 in non-unity compartment C is affected by a rate rule, which affects how its amount changes, because it is set hasOnlySubstanceUnits=true. Similarly, the rateOf csymbol tracks how the amount of S1 changes in time instead of how its concentration changes in time. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $2$ | +| Assignment | x | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter x | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01458/l2v5/index.heta b/latest/cases/01458/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01458/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01458/l3v2/build.log b/latest/cases/01458/l3v2/build.log new file mode 100644 index 000000000..5d490e4e6 --- /dev/null +++ b/latest/cases/01458/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01458/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01458/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01458/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01458/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01458/l3v2/index.heta b/latest/cases/01458/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01458/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01458/model-sbml-l3v2.xml b/latest/cases/01458/model-sbml-l3v2.xml new file mode 100644 index 000000000..e4a15ea65 --- /dev/null +++ b/latest/cases/01458/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + 2 + + + + + + rateOf + S1 + + + + + + diff --git a/latest/cases/01458/synopsis.txt b/latest/cases/01458/synopsis.txt new file mode 100644 index 000000000..f0998d1db --- /dev/null +++ b/latest/cases/01458/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Testing the rateOf csymbol together with a non-unity compartment +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, RateRule, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species in a non-unity compartment is affected by a reaction, but is set hasOnlySubstanceUnits=false, meaning that outside of reactions, it is to be treated as a concentration. This includes the 'rateOf' csymbol, meaning that 'rateOf(S1)' means the rate of change of the concentration of S1, not the rate of change of the amount of S1. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $2$ | +| Assignment | x | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter x | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01459/l2v5/index.heta b/latest/cases/01459/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01459/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01459/l3v2/build.log b/latest/cases/01459/l3v2/build.log new file mode 100644 index 000000000..b1e9ed8c3 --- /dev/null +++ b/latest/cases/01459/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01459/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01459/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01459/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01459/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01459/l3v2/index.heta b/latest/cases/01459/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01459/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01459/model-sbml-l3v2.xml b/latest/cases/01459/model-sbml-l3v2.xml new file mode 100644 index 000000000..adc13003d --- /dev/null +++ b/latest/cases/01459/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + rateOf + k1 + + + + + + + + + + diff --git a/latest/cases/01459/synopsis.txt b/latest/cases/01459/synopsis.txt new file mode 100644 index 000000000..138a1ebfc --- /dev/null +++ b/latest/cases/01459/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: The rateOf csymbol applied to a local parameter. +componentTags: CSymbolRateOf, Compartment, Reaction, Species +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The kinetic law in this test takes the rateOf csymbol of a local parameter, which, by definition, must be zero, since local parameters may not change. + +The model contains: +* 1 species (S1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $rateOf(k1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01460/l2v5/index.heta b/latest/cases/01460/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01460/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01460/l3v2/build.log b/latest/cases/01460/l3v2/build.log new file mode 100644 index 000000000..8261c4fc5 --- /dev/null +++ b/latest/cases/01460/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01460/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01460/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01460/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01460/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01460/l3v2/index.heta b/latest/cases/01460/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01460/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01460/model-sbml-l3v2.xml b/latest/cases/01460/model-sbml-l3v2.xml new file mode 100644 index 000000000..7956712ad --- /dev/null +++ b/latest/cases/01460/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + rateOf + k1 + + + + + + + + + + diff --git a/latest/cases/01460/synopsis.txt b/latest/cases/01460/synopsis.txt new file mode 100644 index 000000000..206fed90b --- /dev/null +++ b/latest/cases/01460/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: The rateOf csymbol applied to a local parameter. +componentTags: CSymbolRateOf, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + The kinetic law in this test takes the rateOf csymbol of a local parameter, which, by definition, must be zero, since local parameters may not change. There is an additional global parameter with the same ID that *does* change in time,which must not be used by the rateOf function. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $rateOf(k1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial value of parameter k1 | $1$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01461/l2v5/index.heta b/latest/cases/01461/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01461/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01461/l3v2/build.log b/latest/cases/01461/l3v2/build.log new file mode 100644 index 000000000..b2e7d1a73 --- /dev/null +++ b/latest/cases/01461/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01461/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01461/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01461/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01461/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01461/l3v2/index.heta b/latest/cases/01461/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01461/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01461/model-sbml-l3v2.xml b/latest/cases/01461/model-sbml-l3v2.xml new file mode 100644 index 000000000..9a0df0bb0 --- /dev/null +++ b/latest/cases/01461/model-sbml-l3v2.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + rateOf + p + + + + + + + + diff --git a/latest/cases/01461/synopsis.txt b/latest/cases/01461/synopsis.txt new file mode 100644 index 000000000..139ab43ff --- /dev/null +++ b/latest/cases/01461/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: The rateOf csymbol of a parameter with a rate rule with no MathML. +componentTags: AssignmentRule, CSymbolRateOf, Parameter, RateRule +testTags: InitialValueReassigned, NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this test, the parameter p has a rate rule with no MathML, meaning it does not change in time. The rateOf csymbol for that parameter therefore equals zero. + +The model contains: +* 2 parameters (x, p) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $rateOf(p)$ | +| Rate | p | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $rateOf(p)$ | variable | +| Initial value of parameter p | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01462/l2v5/index.heta b/latest/cases/01462/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01462/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01462/l3v2/build.log b/latest/cases/01462/l3v2/build.log new file mode 100644 index 000000000..486466de4 --- /dev/null +++ b/latest/cases/01462/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01462/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01462/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01462/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01462/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01462/l3v2/index.heta b/latest/cases/01462/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01462/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01462/model-sbml-l3v2.xml b/latest/cases/01462/model-sbml-l3v2.xml new file mode 100644 index 000000000..234a72b88 --- /dev/null +++ b/latest/cases/01462/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + + rateOf + S1 + + + + + + diff --git a/latest/cases/01462/synopsis.txt b/latest/cases/01462/synopsis.txt new file mode 100644 index 000000000..c08b1e698 --- /dev/null +++ b/latest/cases/01462/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule. +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + This test is the same basic test as 01198: a species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. This test additionally checks to ensure that the rateOf S1 is correctly reported. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01463/l2v5/index.heta b/latest/cases/01463/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01463/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01463/l3v2/build.log b/latest/cases/01463/l3v2/build.log new file mode 100644 index 000000000..2eb69a950 --- /dev/null +++ b/latest/cases/01463/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01463/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01463/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01463/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01463/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01463/l3v2/index.heta b/latest/cases/01463/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01463/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01463/model-sbml-l3v2.xml b/latest/cases/01463/model-sbml-l3v2.xml new file mode 100644 index 000000000..d6214d0b9 --- /dev/null +++ b/latest/cases/01463/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + + rateOf + S1 + + + + + + diff --git a/latest/cases/01463/synopsis.txt b/latest/cases/01463/synopsis.txt new file mode 100644 index 000000000..3c8ccae92 --- /dev/null +++ b/latest/cases/01463/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule. +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + This test modifies test 1462 slightly so that the species is set 'hasOnlySubstanceUnits=true', meaning that the species concentration is affected more straightforwardly by the two rates of change. This test checks to ensure that the rateOf S1 continues to be correctly reported (this time as the rate of change of its amount). + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01464/l2v5/index.heta b/latest/cases/01464/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01464/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01464/l3v2/build.log b/latest/cases/01464/l3v2/build.log new file mode 100644 index 000000000..be154e8fc --- /dev/null +++ b/latest/cases/01464/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01464/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01464/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01464/model-sbml-l3v2.xml"... +[error] S1_sr component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[error] S1_sr_proc Property "actors[0].target" has lost reference "S1_sr". +[error] Record "S1_sr_proc" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01464/l3v2/index.heta b/latest/cases/01464/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01464/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01464/model-sbml-l3v2.xml b/latest/cases/01464/model-sbml-l3v2.xml new file mode 100644 index 000000000..3e1ed2f03 --- /dev/null +++ b/latest/cases/01464/model-sbml-l3v2.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01464/synopsis.txt b/latest/cases/01464/synopsis.txt new file mode 100644 index 000000000..a860f2c03 --- /dev/null +++ b/latest/cases/01464/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A rate rule with no math to a species reference. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this test, a rate rule with no child MathML points to a species reference, which does not end up changing. + +The model contains: +* 1 species (S1) +* 1 compartment (C1) +* 1 species reference (S1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_sr S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_sr + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_sr | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial volume of compartment 'C1' | $1$ | constant | +| Initial value of species reference 'S1_sr' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01465/l2v5/index.heta b/latest/cases/01465/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01465/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01465/l3v2/build.log b/latest/cases/01465/l3v2/build.log new file mode 100644 index 000000000..774b2f65a --- /dev/null +++ b/latest/cases/01465/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01465/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01465/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01465/model-sbml-l3v2.xml"... +[error] S1_sr component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 82 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01465/l3v2/index.heta b/latest/cases/01465/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01465/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01465/model-sbml-l3v2.xml b/latest/cases/01465/model-sbml-l3v2.xml new file mode 100644 index 000000000..09987910a --- /dev/null +++ b/latest/cases/01465/model-sbml-l3v2.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01465/synopsis.txt b/latest/cases/01465/synopsis.txt new file mode 100644 index 000000000..6f3db76c7 --- /dev/null +++ b/latest/cases/01465/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: An assignment rule with no math to a species reference. +componentTags: AssignmentRule, Compartment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this test, an assignment rule with no child MathML points to a species reference, which does not end up changing. + +The model contains: +* 1 species (S1) +* 1 compartment (C1) +* 1 species reference (S1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_sr S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_sr + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1_sr | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial volume of compartment 'C1' | $1$ | constant | +| Initial value of species reference 'S1_sr' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01466/l2v5/index.heta b/latest/cases/01466/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01466/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01466/l3v2/heta-code/output.heta b/latest/cases/01466/l3v2/heta-code/output.heta new file mode 100644 index 000000000..867b7ba68 --- /dev/null +++ b/latest/cases/01466/l3v2/heta-code/output.heta @@ -0,0 +1,617 @@ + + +t @TimeScale { }; + +A0 @Record { } .= 0; +A0 [Eb0]= 2; +A1 @Record { } .= 0; +A1 [Eb1]= 2; +A2 @Record { } .= 0; +A2 [Eb2]= 2; +A3 @Record { } .= 0; +A3 [Eb3]= 2; +A4 @Record { } .= 0; +A4 [Eb4]= 2; +A5 @Record { } .= 0; +A5 [Eb5]= 2; +A6 @Record { } .= 0; +A6 [Eb6]= 2; +A7 @Record { } .= 0; +A7 [Eb7]= 2; +A8 @Record { } .= 0; +A8 [Eb8]= 2; +A9 @Record { } .= 0; +A9 [Eb9]= 2; +A10 @Record { } .= 0; +A10 [Eb10]= 2; +A11 @Record { } .= 0; +A11 [Eb11]= 2; +A12 @Record { } .= 0; +A12 [Eb12]= 2; +A13 @Record { } .= 0; +A13 [Eb13]= 2; +A14 @Record { } .= 0; +A14 [Eb14]= 2; +A15 @Record { } .= 0; +A15 [Eb15]= 2; +A16 @Record { } .= 0; +A16 [Eb16]= 2; +A17 @Record { } .= 0; +A17 [Eb17]= 2; +A18 @Record { } .= 0; +A18 [Eb18]= 2; +A19 @Record { } .= 0; +A19 [Eb19]= 2; +A20 @Record { } .= 0; +A20 [Eb20]= 2; +A21 @Record { } .= 0; +A21 [Eb21]= 2; +A22 @Record { } .= 0; +A22 [Eb22]= 2; +A23 @Record { } .= 0; +A23 [Eb23]= 2; +A24 @Record { } .= 0; +A24 [Eb24]= 2; +A25 @Record { } .= 0; +A25 [Eb25]= 2; +A26 @Record { } .= 0; +A26 [Eb26]= 2; +A27 @Record { } .= 0; +A27 [Eb27]= 2; +A28 @Record { } .= 0; +A28 [Eb28]= 2; +A29 @Record { } .= 0; +A29 [Eb29]= 2; +A30 @Record { } .= 0; +A30 [Eb30]= 2; +A31 @Record { } .= 0; +A31 [Eb31]= 2; +A32 @Record { } .= 0; +A32 [Eb32]= 2; +A33 @Record { } .= 0; +A33 [Eb33]= 2; +A34 @Record { } .= 0; +A34 [Eb34]= 2; +A35 @Record { } .= 0; +A35 [Eb35]= 2; +A36 @Record { } .= 0; +A36 [Eb36]= 2; +A37 @Record { } .= 0; +A37 [Eb37]= 2; +A38 @Record { } .= 0; +A38 [Eb38]= 2; +A39 @Record { } .= 0; +A39 [Eb39]= 2; +A40 @Record { } .= 0; +A40 [Eb40]= 2; +A41 @Record { } .= 0; +A41 [Eb41]= 2; +A42 @Record { } .= 0; +A42 [Eb42]= 2; +A43 @Record { } .= 0; +A43 [Eb43]= 2; +A44 @Record { } .= 0; +A44 [Eb44]= 2; +A45 @Record { } .= 0; +A45 [Eb45]= 2; +A46 @Record { } .= 0; +A46 [Eb46]= 2; +A47 @Record { } .= 0; +A47 [Eb47]= 2; +A48 @Record { } .= 0; +A48 [Eb48]= 2; +A49 @Record { } .= 0; +A49 [Eb49]= 2; +A50 @Record { } .= 0; +A50 [Eb50]= 2; +A51 @Record { } .= 0; +A51 [Eb51]= 2; +A52 @Record { } .= 0; +A52 [Eb52]= 2; +A53 @Record { } .= 0; +A53 [Eb53]= 2; +A54 @Record { } .= 0; +A54 [Eb54]= 2; +A55 @Record { } .= 0; +A55 [Eb55]= 2; +A56 @Record { } .= 0; +A56 [Eb56]= 2; +A57 @Record { } .= 0; +A57 [Eb57]= 2; +A58 @Record { } .= 0; +A58 [Eb58]= 2; +A59 @Record { } .= 0; +A59 [Eb59]= 2; +A60 @Record { } .= 0; +A60 [Eb60]= 2; +A61 @Record { } .= 0; +A61 [Eb61]= 2; +A62 @Record { } .= 0; +A62 [Eb62]= 2; +A63 @Record { } .= 0; +A63 [Eb63]= 2; +A64 @Record { } .= 0; +A64 [Eb64]= 2; +A65 @Record { } .= 0; +A65 [Eb65]= 2; +A66 @Record { } .= 0; +A66 [Eb66]= 2; +A67 @Record { } .= 0; +A67 [Eb67]= 2; +A68 @Record { } .= 0; +A68 [Eb68]= 2; +A69 @Record { } .= 0; +A69 [Eb69]= 2; +A70 @Record { } .= 0; +A70 [Eb70]= 2; +A71 @Record { } .= 0; +A71 [Eb71]= 2; +A72 @Record { } .= 0; +A72 [Eb72]= 2; +A73 @Record { } .= 0; +A73 [Eb73]= 2; +A74 @Record { } .= 0; +A74 [Eb74]= 2; +A75 @Record { } .= 0; +A75 [Eb75]= 2; +A76 @Record { } .= 0; +A76 [Eb76]= 2; +A77 @Record { } .= 0; +A77 [Eb77]= 2; +A78 @Record { } .= 0; +A78 [Eb78]= 2; +A79 @Record { } .= 0; +A79 [Eb79]= 2; +A80 @Record { } .= 0; +A80 [Eb80]= 2; +A81 @Record { } .= 0; +A81 [Eb81]= 2; +A82 @Record { } .= 0; +A82 [Eb82]= 2; +A83 @Record { } .= 0; +A83 [Eb83]= 2; +A84 @Record { } .= 0; +A84 [Eb84]= 2; +A85 @Record { } .= 0; +A85 [Eb85]= 2; +A86 @Record { } .= 0; +A86 [Eb86]= 2; +A87 @Record { } .= 0; +A87 [Eb87]= 2; +A88 @Record { } .= 0; +A88 [Eb88]= 2; +A89 @Record { } .= 0; +A89 [Eb89]= 2; +A90 @Record { } .= 0; +A90 [Eb90]= 2; +A91 @Record { } .= 0; +A91 [Eb91]= 2; +A92 @Record { } .= 0; +A92 [Eb92]= 2; +A93 @Record { } .= 0; +A93 [Eb93]= 2; +A94 @Record { } .= 0; +A94 [Eb94]= 2; +A95 @Record { } .= 0; +A95 [Eb95]= 2; +A96 @Record { } .= 0; +A96 [Eb96]= 2; +A97 @Record { } .= 0; +A97 [Eb97]= 2; +A98 @Record { } .= 0; +A98 [Eb98]= 2; +A99 @Record { } .= 0; +A99 [Eb99]= 2; +B0 @Record { } .= 0; +B0 [E0]= 2; +B1 @Record { } .= 0; +B1 [E1]= 2; +B2 @Record { } .= 0; +B2 [E2]= 2; +B3 @Record { } .= 0; +B3 [E3]= 2; +B4 @Record { } .= 0; +B4 [E4]= 2; +B5 @Record { } .= 0; +B5 [E5]= 2; +B6 @Record { } .= 0; +B6 [E6]= 2; +B7 @Record { } .= 0; +B7 [E7]= 2; +B8 @Record { } .= 0; +B8 [E8]= 2; +B9 @Record { } .= 0; +B9 [E9]= 2; +B10 @Record { } .= 0; +B10 [E10]= 2; +B11 @Record { } .= 0; +B11 [E11]= 2; +B12 @Record { } .= 0; +B12 [E12]= 2; +B13 @Record { } .= 0; +B13 [E13]= 2; +B14 @Record { } .= 0; +B14 [E14]= 2; +B15 @Record { } .= 0; +B15 [E15]= 2; +B16 @Record { } .= 0; +B16 [E16]= 2; +B17 @Record { } .= 0; +B17 [E17]= 2; +B18 @Record { } .= 0; +B18 [E18]= 2; +B19 @Record { } .= 0; +B19 [E19]= 2; +B20 @Record { } .= 0; +B20 [E20]= 2; +B21 @Record { } .= 0; +B21 [E21]= 2; +B22 @Record { } .= 0; +B22 [E22]= 2; +B23 @Record { } .= 0; +B23 [E23]= 2; +B24 @Record { } .= 0; +B24 [E24]= 2; +B25 @Record { } .= 0; +B25 [E25]= 2; +B26 @Record { } .= 0; +B26 [E26]= 2; +B27 @Record { } .= 0; +B27 [E27]= 2; +B28 @Record { } .= 0; +B28 [E28]= 2; +B29 @Record { } .= 0; +B29 [E29]= 2; +B30 @Record { } .= 0; +B30 [E30]= 2; +B31 @Record { } .= 0; +B31 [E31]= 2; +B32 @Record { } .= 0; +B32 [E32]= 2; +B33 @Record { } .= 0; +B33 [E33]= 2; +B34 @Record { } .= 0; +B34 [E34]= 2; +B35 @Record { } .= 0; +B35 [E35]= 2; +B36 @Record { } .= 0; +B36 [E36]= 2; +B37 @Record { } .= 0; +B37 [E37]= 2; +B38 @Record { } .= 0; +B38 [E38]= 2; +B39 @Record { } .= 0; +B39 [E39]= 2; +B40 @Record { } .= 0; +B40 [E40]= 2; +B41 @Record { } .= 0; +B41 [E41]= 2; +B42 @Record { } .= 0; +B42 [E42]= 2; +B43 @Record { } .= 0; +B43 [E43]= 2; +B44 @Record { } .= 0; +B44 [E44]= 2; +B45 @Record { } .= 0; +B45 [E45]= 2; +B46 @Record { } .= 0; +B46 [E46]= 2; +B47 @Record { } .= 0; +B47 [E47]= 2; +B48 @Record { } .= 0; +B48 [E48]= 2; +B49 @Record { } .= 0; +B49 [E49]= 2; +B50 @Record { } .= 0; +B50 [E50]= 2; +B51 @Record { } .= 0; +B51 [E51]= 2; +B52 @Record { } .= 0; +B52 [E52]= 2; +B53 @Record { } .= 0; +B53 [E53]= 2; +B54 @Record { } .= 0; +B54 [E54]= 2; +B55 @Record { } .= 0; +B55 [E55]= 2; +B56 @Record { } .= 0; +B56 [E56]= 2; +B57 @Record { } .= 0; +B57 [E57]= 2; +B58 @Record { } .= 0; +B58 [E58]= 2; +B59 @Record { } .= 0; +B59 [E59]= 2; +B60 @Record { } .= 0; +B60 [E60]= 2; +B61 @Record { } .= 0; +B61 [E61]= 2; +B62 @Record { } .= 0; +B62 [E62]= 2; +B63 @Record { } .= 0; +B63 [E63]= 2; +B64 @Record { } .= 0; +B64 [E64]= 2; +B65 @Record { } .= 0; +B65 [E65]= 2; +B66 @Record { } .= 0; +B66 [E66]= 2; +B67 @Record { } .= 0; +B67 [E67]= 2; +B68 @Record { } .= 0; +B68 [E68]= 2; +B69 @Record { } .= 0; +B69 [E69]= 2; +B70 @Record { } .= 0; +B70 [E70]= 2; +B71 @Record { } .= 0; +B71 [E71]= 2; +B72 @Record { } .= 0; +B72 [E72]= 2; +B73 @Record { } .= 0; +B73 [E73]= 2; +B74 @Record { } .= 0; +B74 [E74]= 2; +B75 @Record { } .= 0; +B75 [E75]= 2; +B76 @Record { } .= 0; +B76 [E76]= 2; +B77 @Record { } .= 0; +B77 [E77]= 2; +B78 @Record { } .= 0; +B78 [E78]= 2; +B79 @Record { } .= 0; +B79 [E79]= 2; +B80 @Record { } .= 0; +B80 [E80]= 2; +B81 @Record { } .= 0; +B81 [E81]= 2; +B82 @Record { } .= 0; +B82 [E82]= 2; +B83 @Record { } .= 0; +B83 [E83]= 2; +B84 @Record { } .= 0; +B84 [E84]= 2; +B85 @Record { } .= 0; +B85 [E85]= 2; +B86 @Record { } .= 0; +B86 [E86]= 2; +B87 @Record { } .= 0; +B87 [E87]= 2; +B88 @Record { } .= 0; +B88 [E88]= 2; +B89 @Record { } .= 0; +B89 [E89]= 2; +B90 @Record { } .= 0; +B90 [E90]= 2; +B91 @Record { } .= 0; +B91 [E91]= 2; +B92 @Record { } .= 0; +B92 [E92]= 2; +B93 @Record { } .= 0; +B93 [E93]= 2; +B94 @Record { } .= 0; +B94 [E94]= 2; +B95 @Record { } .= 0; +B95 [E95]= 2; +B96 @Record { } .= 0; +B96 [E96]= 2; +B97 @Record { } .= 0; +B97 [E97]= 2; +B98 @Record { } .= 0; +B98 [E98]= 2; +B99 @Record { } .= 0; +B99 [E99]= 2; +Asum @Record { }; +Asum := A0 + A1 + A2 + A3 + A4 + A5 + A6 + A7 + A8 + A9 + A10 + A11 + A12 + A13 + A14 + A15 + A16 + A17 + A18 + A19 + A20 + A21 + A22 + A23 + A24 + A25 + A26 + A27 + A28 + A29 + A30 + A31 + A32 + A33 + A34 + A35 + A36 + A37 + A38 + A39 + A40 + A41 + A42 + A43 + A44 + A45 + A46 + A47 + A48 + A49 + A50 + A51 + A52 + A53 + A54 + A55 + A56 + A57 + A58 + A59 + A60 + A61 + A62 + A63 + A64 + A65 + A66 + A67 + A68 + A69 + A70 + A71 + A72 + A73 + A74 + A75 + A76 + A77 + A78 + A79 + A80 + A81 + A82 + A83 + A84 + A85 + A86 + A87 + A88 + A89 + A90 + A91 + A92 + A93 + A94 + A95 + A96 + A97 + A98 + A99; +Bsum @Record { }; +Bsum := B0 + B1 + B2 + B3 + B4 + B5 + B6 + B7 + B8 + B9 + B10 + B11 + B12 + B13 + B14 + B15 + B16 + B17 + B18 + B19 + B20 + B21 + B22 + B23 + B24 + B25 + B26 + B27 + B28 + B29 + B30 + B31 + B32 + B33 + B34 + B35 + B36 + B37 + B38 + B39 + B40 + B41 + B42 + B43 + B44 + B45 + B46 + B47 + B48 + B49 + B50 + B51 + B52 + B53 + B54 + B55 + B56 + B57 + B58 + B59 + B60 + B61 + B62 + B63 + B64 + B65 + B66 + B67 + B68 + B69 + B70 + B71 + B72 + B73 + B74 + B75 + B76 + B77 + B78 + B79 + B80 + B81 + B82 + B83 + B84 + B85 + B86 + B87 + B88 + B89 + B90 + B91 + B92 + B93 + B94 + B95 + B96 + B97 + B98 + B99; +Allsum @Record { }; +Allsum := Asum + Bsum; +toodiverged @Record { } .= 0; +toodiverged [_E0]= 1; + +trig @Const { } = 1; + +E0 @DSwitcher { trigger: trig > 0 and A0 < 1, }; +E1 @DSwitcher { trigger: trig > 0 and A1 < 1, }; +E2 @DSwitcher { trigger: trig > 0 and A2 < 1, }; +E3 @DSwitcher { trigger: trig > 0 and A3 < 1, }; +E4 @DSwitcher { trigger: trig > 0 and A4 < 1, }; +E5 @DSwitcher { trigger: trig > 0 and A5 < 1, }; +E6 @DSwitcher { trigger: trig > 0 and A6 < 1, }; +E7 @DSwitcher { trigger: trig > 0 and A7 < 1, }; +E8 @DSwitcher { trigger: trig > 0 and A8 < 1, }; +E9 @DSwitcher { trigger: trig > 0 and A9 < 1, }; +E10 @DSwitcher { trigger: trig > 0 and A10 < 1, }; +E11 @DSwitcher { trigger: trig > 0 and A11 < 1, }; +E12 @DSwitcher { trigger: trig > 0 and A12 < 1, }; +E13 @DSwitcher { trigger: trig > 0 and A13 < 1, }; +E14 @DSwitcher { trigger: trig > 0 and A14 < 1, }; +E15 @DSwitcher { trigger: trig > 0 and A15 < 1, }; +E16 @DSwitcher { trigger: trig > 0 and A16 < 1, }; +E17 @DSwitcher { trigger: trig > 0 and A17 < 1, }; +E18 @DSwitcher { trigger: trig > 0 and A18 < 1, }; +E19 @DSwitcher { trigger: trig > 0 and A19 < 1, }; +E20 @DSwitcher { trigger: trig > 0 and A20 < 1, }; +E21 @DSwitcher { trigger: trig > 0 and A21 < 1, }; +E22 @DSwitcher { trigger: trig > 0 and A22 < 1, }; +E23 @DSwitcher { trigger: trig > 0 and A23 < 1, }; +E24 @DSwitcher { trigger: trig > 0 and A24 < 1, }; +E25 @DSwitcher { trigger: trig > 0 and A25 < 1, }; +E26 @DSwitcher { trigger: trig > 0 and A26 < 1, }; +E27 @DSwitcher { trigger: trig > 0 and A27 < 1, }; +E28 @DSwitcher { trigger: trig > 0 and A28 < 1, }; +E29 @DSwitcher { trigger: trig > 0 and A29 < 1, }; +E30 @DSwitcher { trigger: trig > 0 and A30 < 1, }; +E31 @DSwitcher { trigger: trig > 0 and A31 < 1, }; +E32 @DSwitcher { trigger: trig > 0 and A32 < 1, }; +E33 @DSwitcher { trigger: trig > 0 and A33 < 1, }; +E34 @DSwitcher { trigger: trig > 0 and A34 < 1, }; +E35 @DSwitcher { trigger: trig > 0 and A35 < 1, }; +E36 @DSwitcher { trigger: trig > 0 and A36 < 1, }; +E37 @DSwitcher { trigger: trig > 0 and A37 < 1, }; +E38 @DSwitcher { trigger: trig > 0 and A38 < 1, }; +E39 @DSwitcher { trigger: trig > 0 and A39 < 1, }; +E40 @DSwitcher { trigger: trig > 0 and A40 < 1, }; +E41 @DSwitcher { trigger: trig > 0 and A41 < 1, }; +E42 @DSwitcher { trigger: trig > 0 and A42 < 1, }; +E43 @DSwitcher { trigger: trig > 0 and A43 < 1, }; +E44 @DSwitcher { trigger: trig > 0 and A44 < 1, }; +E45 @DSwitcher { trigger: trig > 0 and A45 < 1, }; +E46 @DSwitcher { trigger: trig > 0 and A46 < 1, }; +E47 @DSwitcher { trigger: trig > 0 and A47 < 1, }; +E48 @DSwitcher { trigger: trig > 0 and A48 < 1, }; +E49 @DSwitcher { trigger: trig > 0 and A49 < 1, }; +E50 @DSwitcher { trigger: trig > 0 and A50 < 1, }; +E51 @DSwitcher { trigger: trig > 0 and A51 < 1, }; +E52 @DSwitcher { trigger: trig > 0 and A52 < 1, }; +E53 @DSwitcher { trigger: trig > 0 and A53 < 1, }; +E54 @DSwitcher { trigger: trig > 0 and A54 < 1, }; +E55 @DSwitcher { trigger: trig > 0 and A55 < 1, }; +E56 @DSwitcher { trigger: trig > 0 and A56 < 1, }; +E57 @DSwitcher { trigger: trig > 0 and A57 < 1, }; +E58 @DSwitcher { trigger: trig > 0 and A58 < 1, }; +E59 @DSwitcher { trigger: trig > 0 and A59 < 1, }; +E60 @DSwitcher { trigger: trig > 0 and A60 < 1, }; +E61 @DSwitcher { trigger: trig > 0 and A61 < 1, }; +E62 @DSwitcher { trigger: trig > 0 and A62 < 1, }; +E63 @DSwitcher { trigger: trig > 0 and A63 < 1, }; +E64 @DSwitcher { trigger: trig > 0 and A64 < 1, }; +E65 @DSwitcher { trigger: trig > 0 and A65 < 1, }; +E66 @DSwitcher { trigger: trig > 0 and A66 < 1, }; +E67 @DSwitcher { trigger: trig > 0 and A67 < 1, }; +E68 @DSwitcher { trigger: trig > 0 and A68 < 1, }; +E69 @DSwitcher { trigger: trig > 0 and A69 < 1, }; +E70 @DSwitcher { trigger: trig > 0 and A70 < 1, }; +E71 @DSwitcher { trigger: trig > 0 and A71 < 1, }; +E72 @DSwitcher { trigger: trig > 0 and A72 < 1, }; +E73 @DSwitcher { trigger: trig > 0 and A73 < 1, }; +E74 @DSwitcher { trigger: trig > 0 and A74 < 1, }; +E75 @DSwitcher { trigger: trig > 0 and A75 < 1, }; +E76 @DSwitcher { trigger: trig > 0 and A76 < 1, }; +E77 @DSwitcher { trigger: trig > 0 and A77 < 1, }; +E78 @DSwitcher { trigger: trig > 0 and A78 < 1, }; +E79 @DSwitcher { trigger: trig > 0 and A79 < 1, }; +E80 @DSwitcher { trigger: trig > 0 and A80 < 1, }; +E81 @DSwitcher { trigger: trig > 0 and A81 < 1, }; +E82 @DSwitcher { trigger: trig > 0 and A82 < 1, }; +E83 @DSwitcher { trigger: trig > 0 and A83 < 1, }; +E84 @DSwitcher { trigger: trig > 0 and A84 < 1, }; +E85 @DSwitcher { trigger: trig > 0 and A85 < 1, }; +E86 @DSwitcher { trigger: trig > 0 and A86 < 1, }; +E87 @DSwitcher { trigger: trig > 0 and A87 < 1, }; +E88 @DSwitcher { trigger: trig > 0 and A88 < 1, }; +E89 @DSwitcher { trigger: trig > 0 and A89 < 1, }; +E90 @DSwitcher { trigger: trig > 0 and A90 < 1, }; +E91 @DSwitcher { trigger: trig > 0 and A91 < 1, }; +E92 @DSwitcher { trigger: trig > 0 and A92 < 1, }; +E93 @DSwitcher { trigger: trig > 0 and A93 < 1, }; +E94 @DSwitcher { trigger: trig > 0 and A94 < 1, }; +E95 @DSwitcher { trigger: trig > 0 and A95 < 1, }; +E96 @DSwitcher { trigger: trig > 0 and A96 < 1, }; +E97 @DSwitcher { trigger: trig > 0 and A97 < 1, }; +E98 @DSwitcher { trigger: trig > 0 and A98 < 1, }; +E99 @DSwitcher { trigger: trig > 0 and A99 < 1, }; +Eb0 @DSwitcher { trigger: trig > 0 and B0 < 1, }; +Eb1 @DSwitcher { trigger: trig > 0 and B1 < 1, }; +Eb2 @DSwitcher { trigger: trig > 0 and B2 < 1, }; +Eb3 @DSwitcher { trigger: trig > 0 and B3 < 1, }; +Eb4 @DSwitcher { trigger: trig > 0 and B4 < 1, }; +Eb5 @DSwitcher { trigger: trig > 0 and B5 < 1, }; +Eb6 @DSwitcher { trigger: trig > 0 and B6 < 1, }; +Eb7 @DSwitcher { trigger: trig > 0 and B7 < 1, }; +Eb8 @DSwitcher { trigger: trig > 0 and B8 < 1, }; +Eb9 @DSwitcher { trigger: trig > 0 and B9 < 1, }; +Eb10 @DSwitcher { trigger: trig > 0 and B10 < 1, }; +Eb11 @DSwitcher { trigger: trig > 0 and B11 < 1, }; +Eb12 @DSwitcher { trigger: trig > 0 and B12 < 1, }; +Eb13 @DSwitcher { trigger: trig > 0 and B13 < 1, }; +Eb14 @DSwitcher { trigger: trig > 0 and B14 < 1, }; +Eb15 @DSwitcher { trigger: trig > 0 and B15 < 1, }; +Eb16 @DSwitcher { trigger: trig > 0 and B16 < 1, }; +Eb17 @DSwitcher { trigger: trig > 0 and B17 < 1, }; +Eb18 @DSwitcher { trigger: trig > 0 and B18 < 1, }; +Eb19 @DSwitcher { trigger: trig > 0 and B19 < 1, }; +Eb20 @DSwitcher { trigger: trig > 0 and B20 < 1, }; +Eb21 @DSwitcher { trigger: trig > 0 and B21 < 1, }; +Eb22 @DSwitcher { trigger: trig > 0 and B22 < 1, }; +Eb23 @DSwitcher { trigger: trig > 0 and B23 < 1, }; +Eb24 @DSwitcher { trigger: trig > 0 and B24 < 1, }; +Eb25 @DSwitcher { trigger: trig > 0 and B25 < 1, }; +Eb26 @DSwitcher { trigger: trig > 0 and B26 < 1, }; +Eb27 @DSwitcher { trigger: trig > 0 and B27 < 1, }; +Eb28 @DSwitcher { trigger: trig > 0 and B28 < 1, }; +Eb29 @DSwitcher { trigger: trig > 0 and B29 < 1, }; +Eb30 @DSwitcher { trigger: trig > 0 and B30 < 1, }; +Eb31 @DSwitcher { trigger: trig > 0 and B31 < 1, }; +Eb32 @DSwitcher { trigger: trig > 0 and B32 < 1, }; +Eb33 @DSwitcher { trigger: trig > 0 and B33 < 1, }; +Eb34 @DSwitcher { trigger: trig > 0 and B34 < 1, }; +Eb35 @DSwitcher { trigger: trig > 0 and B35 < 1, }; +Eb36 @DSwitcher { trigger: trig > 0 and B36 < 1, }; +Eb37 @DSwitcher { trigger: trig > 0 and B37 < 1, }; +Eb38 @DSwitcher { trigger: trig > 0 and B38 < 1, }; +Eb39 @DSwitcher { trigger: trig > 0 and B39 < 1, }; +Eb40 @DSwitcher { trigger: trig > 0 and B40 < 1, }; +Eb41 @DSwitcher { trigger: trig > 0 and B41 < 1, }; +Eb42 @DSwitcher { trigger: trig > 0 and B42 < 1, }; +Eb43 @DSwitcher { trigger: trig > 0 and B43 < 1, }; +Eb44 @DSwitcher { trigger: trig > 0 and B44 < 1, }; +Eb45 @DSwitcher { trigger: trig > 0 and B45 < 1, }; +Eb46 @DSwitcher { trigger: trig > 0 and B46 < 1, }; +Eb47 @DSwitcher { trigger: trig > 0 and B47 < 1, }; +Eb48 @DSwitcher { trigger: trig > 0 and B48 < 1, }; +Eb49 @DSwitcher { trigger: trig > 0 and B49 < 1, }; +Eb50 @DSwitcher { trigger: trig > 0 and B50 < 1, }; +Eb51 @DSwitcher { trigger: trig > 0 and B51 < 1, }; +Eb52 @DSwitcher { trigger: trig > 0 and B52 < 1, }; +Eb53 @DSwitcher { trigger: trig > 0 and B53 < 1, }; +Eb54 @DSwitcher { trigger: trig > 0 and B54 < 1, }; +Eb55 @DSwitcher { trigger: trig > 0 and B55 < 1, }; +Eb56 @DSwitcher { trigger: trig > 0 and B56 < 1, }; +Eb57 @DSwitcher { trigger: trig > 0 and B57 < 1, }; +Eb58 @DSwitcher { trigger: trig > 0 and B58 < 1, }; +Eb59 @DSwitcher { trigger: trig > 0 and B59 < 1, }; +Eb60 @DSwitcher { trigger: trig > 0 and B60 < 1, }; +Eb61 @DSwitcher { trigger: trig > 0 and B61 < 1, }; +Eb62 @DSwitcher { trigger: trig > 0 and B62 < 1, }; +Eb63 @DSwitcher { trigger: trig > 0 and B63 < 1, }; +Eb64 @DSwitcher { trigger: trig > 0 and B64 < 1, }; +Eb65 @DSwitcher { trigger: trig > 0 and B65 < 1, }; +Eb66 @DSwitcher { trigger: trig > 0 and B66 < 1, }; +Eb67 @DSwitcher { trigger: trig > 0 and B67 < 1, }; +Eb68 @DSwitcher { trigger: trig > 0 and B68 < 1, }; +Eb69 @DSwitcher { trigger: trig > 0 and B69 < 1, }; +Eb70 @DSwitcher { trigger: trig > 0 and B70 < 1, }; +Eb71 @DSwitcher { trigger: trig > 0 and B71 < 1, }; +Eb72 @DSwitcher { trigger: trig > 0 and B72 < 1, }; +Eb73 @DSwitcher { trigger: trig > 0 and B73 < 1, }; +Eb74 @DSwitcher { trigger: trig > 0 and B74 < 1, }; +Eb75 @DSwitcher { trigger: trig > 0 and B75 < 1, }; +Eb76 @DSwitcher { trigger: trig > 0 and B76 < 1, }; +Eb77 @DSwitcher { trigger: trig > 0 and B77 < 1, }; +Eb78 @DSwitcher { trigger: trig > 0 and B78 < 1, }; +Eb79 @DSwitcher { trigger: trig > 0 and B79 < 1, }; +Eb80 @DSwitcher { trigger: trig > 0 and B80 < 1, }; +Eb81 @DSwitcher { trigger: trig > 0 and B81 < 1, }; +Eb82 @DSwitcher { trigger: trig > 0 and B82 < 1, }; +Eb83 @DSwitcher { trigger: trig > 0 and B83 < 1, }; +Eb84 @DSwitcher { trigger: trig > 0 and B84 < 1, }; +Eb85 @DSwitcher { trigger: trig > 0 and B85 < 1, }; +Eb86 @DSwitcher { trigger: trig > 0 and B86 < 1, }; +Eb87 @DSwitcher { trigger: trig > 0 and B87 < 1, }; +Eb88 @DSwitcher { trigger: trig > 0 and B88 < 1, }; +Eb89 @DSwitcher { trigger: trig > 0 and B89 < 1, }; +Eb90 @DSwitcher { trigger: trig > 0 and B90 < 1, }; +Eb91 @DSwitcher { trigger: trig > 0 and B91 < 1, }; +Eb92 @DSwitcher { trigger: trig > 0 and B92 < 1, }; +Eb93 @DSwitcher { trigger: trig > 0 and B93 < 1, }; +Eb94 @DSwitcher { trigger: trig > 0 and B94 < 1, }; +Eb95 @DSwitcher { trigger: trig > 0 and B95 < 1, }; +Eb96 @DSwitcher { trigger: trig > 0 and B96 < 1, }; +Eb97 @DSwitcher { trigger: trig > 0 and B97 < 1, }; +Eb98 @DSwitcher { trigger: trig > 0 and B98 < 1, }; +Eb99 @DSwitcher { trigger: trig > 0 and B99 < 1, }; +_E0 @DSwitcher { trigger: abs(Asum - Bsum) > 100, }; + diff --git a/latest/cases/01466/l3v2/index.heta b/latest/cases/01466/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01466/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01466/l3v2/json/output.json b/latest/cases/01466/l3v2/json/output.json new file mode 100644 index 000000000..b277bb743 --- /dev/null +++ b/latest/cases/01466/l3v2/json/output.json @@ -0,0 +1,2644 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "trig", + "num": 1 + }, + { + "class": "Record", + "id": "A0", + "assignments": { + "start_": "0", + "Eb0": "2" + } + }, + { + "class": "Record", + "id": "A1", + "assignments": { + "start_": "0", + "Eb1": "2" + } + }, + { + "class": "Record", + "id": "A2", + "assignments": { + "start_": "0", + "Eb2": "2" + } + }, + { + "class": "Record", + "id": "A3", + "assignments": { + "start_": "0", + "Eb3": "2" + } + }, + { + "class": "Record", + "id": "A4", + "assignments": { + "start_": "0", + "Eb4": "2" + } + }, + { + "class": "Record", + "id": "A5", + "assignments": { + "start_": "0", + "Eb5": "2" + } + }, + { + "class": "Record", + "id": "A6", + "assignments": { + "start_": "0", + "Eb6": "2" + } + }, + { + "class": "Record", + "id": "A7", + "assignments": { + "start_": "0", + "Eb7": "2" + } + }, + { + "class": "Record", + "id": "A8", + "assignments": { + "start_": "0", + "Eb8": "2" + } + }, + { + "class": "Record", + "id": "A9", + "assignments": { + "start_": "0", + "Eb9": "2" + } + }, + { + "class": "Record", + "id": "A10", + "assignments": { + "start_": "0", + "Eb10": "2" + } + }, + { + "class": "Record", + "id": "A11", + "assignments": { + "start_": "0", + "Eb11": "2" + } + }, + { + "class": "Record", + "id": "A12", + "assignments": { + "start_": "0", + "Eb12": "2" + } + }, + { + "class": "Record", + "id": "A13", + "assignments": { + "start_": "0", + "Eb13": "2" + } + }, + { + "class": "Record", + "id": "A14", + "assignments": { + "start_": "0", + "Eb14": "2" + } + }, + { + "class": "Record", + "id": "A15", + "assignments": { + "start_": "0", + "Eb15": "2" + } + }, + { + "class": "Record", + "id": "A16", + "assignments": { + "start_": "0", + "Eb16": "2" + } + }, + { + "class": "Record", + "id": "A17", + "assignments": { + "start_": "0", + "Eb17": "2" + } + }, + { + "class": "Record", + "id": "A18", + "assignments": { + "start_": "0", + "Eb18": "2" + } + }, + { + "class": "Record", + "id": "A19", + "assignments": { + "start_": "0", + "Eb19": "2" + } + }, + { + "class": "Record", + "id": "A20", + "assignments": { + "start_": "0", + "Eb20": "2" + } + }, + { + "class": "Record", + "id": "A21", + "assignments": { + "start_": "0", + "Eb21": "2" + } + }, + { + "class": "Record", + "id": "A22", + "assignments": { + "start_": "0", + "Eb22": "2" + } + }, + { + "class": "Record", + "id": "A23", + "assignments": { + "start_": "0", + "Eb23": "2" + } + }, + { + "class": "Record", + "id": "A24", + "assignments": { + "start_": "0", + "Eb24": "2" + } + }, + { + "class": "Record", + "id": "A25", + "assignments": { + "start_": "0", + "Eb25": "2" + } + }, + { + "class": "Record", + "id": "A26", + "assignments": { + "start_": "0", + "Eb26": "2" + } + }, + { + "class": "Record", + "id": "A27", + "assignments": { + "start_": "0", + "Eb27": "2" + } + }, + { + "class": "Record", + "id": "A28", + "assignments": { + "start_": "0", + "Eb28": "2" + } + }, + { + "class": "Record", + "id": "A29", + "assignments": { + "start_": "0", + "Eb29": "2" + } + }, + { + "class": "Record", + "id": "A30", + "assignments": { + "start_": "0", + "Eb30": "2" + } + }, + { + "class": "Record", + "id": "A31", + "assignments": { + "start_": "0", + "Eb31": "2" + } + }, + { + "class": "Record", + "id": "A32", + "assignments": { + "start_": "0", + "Eb32": "2" + } + }, + { + "class": "Record", + "id": "A33", + "assignments": { + "start_": "0", + "Eb33": "2" + } + }, + { + "class": "Record", + "id": "A34", + "assignments": { + "start_": "0", + "Eb34": "2" + } + }, + { + "class": "Record", + "id": "A35", + "assignments": { + "start_": "0", + "Eb35": "2" + } + }, + { + "class": "Record", + "id": "A36", + "assignments": { + "start_": "0", + "Eb36": "2" + } + }, + { + "class": "Record", + "id": "A37", + "assignments": { + "start_": "0", + "Eb37": "2" + } + }, + { + "class": "Record", + "id": "A38", + "assignments": { + "start_": "0", + "Eb38": "2" + } + }, + { + "class": "Record", + "id": "A39", + "assignments": { + "start_": "0", + "Eb39": "2" + } + }, + { + "class": "Record", + "id": "A40", + "assignments": { + "start_": "0", + "Eb40": "2" + } + }, + { + "class": "Record", + "id": "A41", + "assignments": { + "start_": "0", + "Eb41": "2" + } + }, + { + "class": "Record", + "id": "A42", + 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+ "start_": "0", + "E2": "2" + } + }, + { + "class": "Record", + "id": "B3", + "assignments": { + "start_": "0", + "E3": "2" + } + }, + { + "class": "Record", + "id": "B4", + "assignments": { + "start_": "0", + "E4": "2" + } + }, + { + "class": "Record", + "id": "B5", + "assignments": { + "start_": "0", + "E5": "2" + } + }, + { + "class": "Record", + "id": "B6", + "assignments": { + "start_": "0", + "E6": "2" + } + }, + { + "class": "Record", + "id": "B7", + "assignments": { + "start_": "0", + "E7": "2" + } + }, + { + "class": "Record", + "id": "B8", + "assignments": { + "start_": "0", + "E8": "2" + } + }, + { + "class": "Record", + "id": "B9", + "assignments": { + "start_": "0", + "E9": "2" + } + }, + { + "class": "Record", + "id": "B10", + "assignments": { + "start_": "0", + "E10": "2" + } + }, + { + "class": "Record", + "id": "B11", + "assignments": { + "start_": "0", + "E11": "2" + } + }, + { + "class": "Record", + "id": "B12", + "assignments": { + "start_": "0", + "E12": "2" + } + }, + { + "class": "Record", + "id": "B13", + "assignments": { + "start_": "0", + "E13": "2" + } + }, + { + "class": "Record", + "id": "B14", + "assignments": { + "start_": "0", + "E14": "2" + } + }, + { + "class": "Record", + "id": "B15", + "assignments": { + "start_": "0", + "E15": "2" + } + }, + { + "class": "Record", + "id": "B16", + "assignments": { + "start_": "0", + "E16": "2" + } + }, + { + "class": "Record", + "id": "B17", + "assignments": { + "start_": "0", + "E17": "2" + } + }, + { + "class": "Record", + "id": "B18", + "assignments": { + "start_": "0", + "E18": "2" + } + }, + { + "class": "Record", + "id": "B19", + "assignments": { + "start_": "0", + "E19": "2" + } + }, + { + "class": "Record", + "id": "B20", + "assignments": { + "start_": "0", + "E20": "2" + } + }, + { + "class": "Record", + "id": "B21", + "assignments": { + "start_": "0", + "E21": "2" + } + }, + { + "class": "Record", + "id": "B22", + "assignments": { + "start_": "0", + "E22": "2" + } + }, + { + "class": "Record", + "id": "B23", + "assignments": { + "start_": "0", + "E23": "2" + } + }, + { + "class": "Record", + "id": "B24", + "assignments": { + "start_": "0", + "E24": "2" + } + }, + { + "class": "Record", + "id": "B25", + "assignments": { + "start_": "0", + "E25": "2" + } + }, + { + "class": "Record", + "id": "B26", + "assignments": { + "start_": "0", + "E26": "2" + } + }, + { + "class": "Record", + "id": "B27", + "assignments": { + "start_": "0", + "E27": "2" + } + }, + { + "class": "Record", + "id": "B28", + "assignments": { + "start_": "0", + "E28": "2" + } + }, + { + "class": "Record", + "id": "B29", + "assignments": { + "start_": "0", + "E29": "2" + } + }, + { + "class": "Record", + "id": "B30", + "assignments": { + "start_": "0", + "E30": "2" + } + }, + { + "class": "Record", + "id": "B31", + "assignments": { + "start_": "0", + "E31": "2" + } + }, + { + "class": "Record", + "id": "B32", + "assignments": { + "start_": "0", + "E32": "2" + } + }, + { + "class": "Record", + "id": 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@@ -0,0 +1,1061 @@ +/* +category: Test +synopsis: A test of random event execution at t0. +componentTags: AssignmentRule, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, EventT0Firing, InitialValueReassigned, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, 200 events 'compete' in pairs to assing values to variables: if E0 fires, Eb0 will not, and visa versa, for all events E0-E99, Eb0-Eb99. Because all events have the same priority, the E# set should win about half the time (assigning a value to the corresponding 'A' variable), and the Eb# set should win the other half, assigning values to the corresponding 'B' variables. + + 'toodiverged' will only equal 1 if (Asum-Bsum)>100. Since the standard deviation of 100 coin flips is 5, which would correspond to a difference of 20, 'toodiverged' will only equal 1 if the observed distribution of choices is more than five standard deviations away from expected (0), which will happen approximately one time in 1.7 million. + +The model contains: +* 205 parameters (trig, A0, A1, A2, A3, A4, A5, A6, A7, A8, A9, A10, A11, A12, A13, A14, A15, A16, A17, A18, A19, A20, A21, A22, A23, A24, A25, A26, A27, A28, A29, A30, A31, A32, A33, A34, A35, A36, A37, A38, A39, A40, A41, A42, A43, A44, A45, A46, A47, A48, A49, A50, A51, A52, A53, A54, A55, A56, A57, A58, A59, A60, A61, A62, A63, A64, A65, A66, A67, A68, A69, A70, A71, A72, A73, A74, A75, A76, A77, A78, A79, A80, A81, A82, A83, A84, A85, A86, A87, A88, A89, A90, A91, A92, A93, A94, A95, A96, A97, A98, A99, B0, B1, B2, B3, B4, B5, B6, B7, B8, B9, B10, B11, B12, B13, B14, B15, B16, B17, B18, B19, B20, B21, B22, B23, B24, B25, B26, B27, B28, B29, B30, B31, B32, B33, B34, B35, B36, B37, B38, B39, B40, B41, B42, B43, B44, B45, B46, B47, B48, B49, B50, B51, B52, B53, B54, B55, B56, B57, B58, B59, B60, B61, B62, B63, B64, B65, B66, B67, B68, B69, B70, B71, B72, B73, B74, B75, B76, B77, B78, B79, B80, B81, B82, B83, B84, B85, B86, B87, B88, B89, B90, B91, B92, B93, B94, B95, B96, B97, B98, B99, Asum, Bsum, Allsum, toodiverged) + +There are 201 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *initialValue* | *Event Assignments* | +| E0 | $(trig > 0) && (A0 < 1)$ | $5$ | false | false | $B0 = 2$ | +| E1 | $(trig > 0) && (A1 < 1)$ | $5$ | false | false | $B1 = 2$ | +| E2 | $(trig > 0) && (A2 < 1)$ | $5$ | false | false | $B2 = 2$ | +| E3 | $(trig > 0) && (A3 < 1)$ | $5$ | false | false | $B3 = 2$ | +| E4 | $(trig > 0) && (A4 < 1)$ | $5$ | false | false | $B4 = 2$ | +| E5 | $(trig > 0) && (A5 < 1)$ | $5$ | false | false | $B5 = 2$ | +| E6 | $(trig > 0) && (A6 < 1)$ | $5$ | false | false | $B6 = 2$ | +| E7 | $(trig > 0) && (A7 < 1)$ | $5$ | false | false | $B7 = 2$ | +| E8 | $(trig > 0) && (A8 < 1)$ | $5$ | false | false | $B8 = 2$ | +| E9 | $(trig > 0) && (A9 < 1)$ | $5$ | false | false | $B9 = 2$ | +| E10 | $(trig > 0) && (A10 < 1)$ | $5$ | false | false | $B10 = 2$ | +| E11 | $(trig > 0) && (A11 < 1)$ | $5$ | false | false | $B11 = 2$ | +| E12 | $(trig > 0) && (A12 < 1)$ | $5$ | false | false | $B12 = 2$ | +| E13 | $(trig > 0) && (A13 < 1)$ | $5$ | false | false | $B13 = 2$ | +| E14 | $(trig > 0) && (A14 < 1)$ | $5$ | false | false | $B14 = 2$ | +| E15 | $(trig > 0) && (A15 < 1)$ | $5$ | false | false | $B15 = 2$ | +| E16 | $(trig > 0) && (A16 < 1)$ | $5$ | false | false | $B16 = 2$ | +| E17 | $(trig > 0) && (A17 < 1)$ | $5$ | false | false | $B17 = 2$ | +| E18 | $(trig > 0) && (A18 < 1)$ | $5$ | false | false | $B18 = 2$ | +| E19 | $(trig > 0) && (A19 < 1)$ | $5$ | false | false | $B19 = 2$ | +| E20 | $(trig > 0) && (A20 < 1)$ | $5$ | false | false | $B20 = 2$ | +| E21 | $(trig > 0) && (A21 < 1)$ | $5$ | false | false | $B21 = 2$ | +| E22 | $(trig > 0) && (A22 < 1)$ | $5$ | false | false | $B22 = 2$ | +| E23 | $(trig > 0) && (A23 < 1)$ | $5$ | false | false | $B23 = 2$ | +| E24 | $(trig > 0) && (A24 < 1)$ | $5$ | false | false | $B24 = 2$ | +| E25 | $(trig > 0) && (A25 < 1)$ | $5$ | false | false | $B25 = 2$ | +| E26 | $(trig > 0) && (A26 < 1)$ | $5$ | false | false | $B26 = 2$ | +| E27 | $(trig > 0) && (A27 < 1)$ | $5$ | false | false | $B27 = 2$ | +| E28 | $(trig > 0) && (A28 < 1)$ | $5$ | false | false | $B28 = 2$ | +| E29 | $(trig > 0) && (A29 < 1)$ | $5$ | false | false | $B29 = 2$ | +| E30 | $(trig > 0) && (A30 < 1)$ | $5$ | false | false | $B30 = 2$ | +| E31 | $(trig > 0) && (A31 < 1)$ | $5$ | false | false | $B31 = 2$ | +| E32 | $(trig > 0) && (A32 < 1)$ | $5$ | false | false | $B32 = 2$ | +| E33 | $(trig > 0) && (A33 < 1)$ | $5$ | false | false | $B33 = 2$ | +| E34 | $(trig > 0) && (A34 < 1)$ | $5$ | false | false | $B34 = 2$ | +| E35 | $(trig > 0) && (A35 < 1)$ | $5$ | false | false | $B35 = 2$ | +| E36 | $(trig > 0) && (A36 < 1)$ | $5$ | false | false | $B36 = 2$ | +| E37 | $(trig > 0) && (A37 < 1)$ | $5$ | false | false | $B37 = 2$ | +| E38 | $(trig > 0) && (A38 < 1)$ | $5$ | false | false | $B38 = 2$ | +| E39 | $(trig > 0) && (A39 < 1)$ | $5$ | false | false | $B39 = 2$ | +| E40 | $(trig > 0) && (A40 < 1)$ | $5$ | false | false | $B40 = 2$ | +| E41 | $(trig > 0) && (A41 < 1)$ | $5$ | false | false | $B41 = 2$ | +| E42 | $(trig > 0) && (A42 < 1)$ | $5$ | false | false | $B42 = 2$ | +| E43 | $(trig > 0) && (A43 < 1)$ | $5$ | false | false | $B43 = 2$ | +| E44 | $(trig > 0) && (A44 < 1)$ | $5$ | false | false | $B44 = 2$ | +| E45 | $(trig > 0) && (A45 < 1)$ | $5$ | false | false | $B45 = 2$ | +| E46 | $(trig > 0) && (A46 < 1)$ | $5$ | false | false | $B46 = 2$ | +| E47 | $(trig > 0) && (A47 < 1)$ | $5$ | false | false | $B47 = 2$ | +| E48 | $(trig > 0) && (A48 < 1)$ | $5$ | false | false | $B48 = 2$ | +| E49 | $(trig > 0) && (A49 < 1)$ | $5$ | false | false | $B49 = 2$ | +| E50 | $(trig > 0) && (A50 < 1)$ | $5$ | false | false | $B50 = 2$ | +| E51 | $(trig > 0) && (A51 < 1)$ | $5$ | false | false | $B51 = 2$ | +| E52 | $(trig > 0) && (A52 < 1)$ | $5$ | false | false | $B52 = 2$ | +| E53 | $(trig > 0) && (A53 < 1)$ | $5$ | false | false | $B53 = 2$ | +| E54 | $(trig > 0) && (A54 < 1)$ | $5$ | false | false | $B54 = 2$ | +| E55 | $(trig > 0) && (A55 < 1)$ | $5$ | false | false | $B55 = 2$ | +| E56 | $(trig > 0) && (A56 < 1)$ | $5$ | false | false | $B56 = 2$ | +| E57 | $(trig > 0) && (A57 < 1)$ | $5$ | false | false | $B57 = 2$ | +| E58 | $(trig > 0) && (A58 < 1)$ | $5$ | false | false | $B58 = 2$ | +| E59 | $(trig > 0) && (A59 < 1)$ | $5$ | false | false | $B59 = 2$ | +| E60 | $(trig > 0) && (A60 < 1)$ | $5$ | false | false | $B60 = 2$ | +| E61 | $(trig > 0) && (A61 < 1)$ | $5$ | false | false | $B61 = 2$ | +| E62 | $(trig > 0) && (A62 < 1)$ | $5$ | false | false | $B62 = 2$ | +| E63 | $(trig > 0) && (A63 < 1)$ | $5$ | false | false | $B63 = 2$ | +| E64 | $(trig > 0) && (A64 < 1)$ | $5$ | false | false | $B64 = 2$ | +| E65 | $(trig > 0) && (A65 < 1)$ | $5$ | false | false | $B65 = 2$ | +| E66 | $(trig > 0) && (A66 < 1)$ | $5$ | false | false | $B66 = 2$ | +| E67 | $(trig > 0) && (A67 < 1)$ | $5$ | false | false | $B67 = 2$ | +| E68 | $(trig > 0) && (A68 < 1)$ | $5$ | false | false | $B68 = 2$ | +| E69 | $(trig > 0) && (A69 < 1)$ | $5$ | false | false | $B69 = 2$ | +| E70 | $(trig > 0) && (A70 < 1)$ | $5$ | false | false | $B70 = 2$ | +| E71 | $(trig > 0) && (A71 < 1)$ | $5$ | false | false | $B71 = 2$ | +| E72 | $(trig > 0) && (A72 < 1)$ | $5$ | false | false | $B72 = 2$ | +| E73 | $(trig > 0) && (A73 < 1)$ | $5$ | false | false | $B73 = 2$ | +| E74 | $(trig > 0) && (A74 < 1)$ | $5$ | false | false | $B74 = 2$ | +| E75 | $(trig > 0) && (A75 < 1)$ | $5$ | false | false | $B75 = 2$ | +| E76 | $(trig > 0) && (A76 < 1)$ | $5$ | false | false | $B76 = 2$ | +| E77 | $(trig > 0) && (A77 < 1)$ | $5$ | false | false | $B77 = 2$ | +| E78 | $(trig > 0) && (A78 < 1)$ | $5$ | false | false | $B78 = 2$ | +| E79 | $(trig > 0) && (A79 < 1)$ | $5$ | false | false | $B79 = 2$ | +| E80 | $(trig > 0) && (A80 < 1)$ | $5$ | false | false | $B80 = 2$ | +| E81 | $(trig > 0) && (A81 < 1)$ | $5$ | false | false | $B81 = 2$ | +| E82 | $(trig > 0) && (A82 < 1)$ | $5$ | false | false | $B82 = 2$ | +| E83 | $(trig > 0) && (A83 < 1)$ | $5$ | false | false | $B83 = 2$ | +| E84 | $(trig > 0) && (A84 < 1)$ | $5$ | false | false | $B84 = 2$ | +| E85 | $(trig > 0) && (A85 < 1)$ | $5$ | false | false | $B85 = 2$ | +| E86 | $(trig > 0) && (A86 < 1)$ | $5$ | false | false | $B86 = 2$ | +| E87 | $(trig > 0) && (A87 < 1)$ | $5$ | false | false | $B87 = 2$ | +| E88 | $(trig > 0) && (A88 < 1)$ | $5$ | false | false | $B88 = 2$ | +| E89 | $(trig > 0) && (A89 < 1)$ | $5$ | false | false | $B89 = 2$ | +| E90 | $(trig > 0) && (A90 < 1)$ | $5$ | false | false | $B90 = 2$ | +| E91 | $(trig > 0) && (A91 < 1)$ | $5$ | false | false | $B91 = 2$ | +| E92 | $(trig > 0) && (A92 < 1)$ | $5$ | false | false | $B92 = 2$ | +| E93 | $(trig > 0) && (A93 < 1)$ | $5$ | false | false | $B93 = 2$ | +| E94 | $(trig > 0) && (A94 < 1)$ | $5$ | false | false | $B94 = 2$ | +| E95 | $(trig > 0) && (A95 < 1)$ | $5$ | false | false | $B95 = 2$ | +| E96 | $(trig > 0) && (A96 < 1)$ | $5$ | false | false | $B96 = 2$ | +| E97 | $(trig > 0) && (A97 < 1)$ | $5$ | false | false | $B97 = 2$ | +| E98 | $(trig > 0) && (A98 < 1)$ | $5$ | false | false | $B98 = 2$ | +| E99 | $(trig > 0) && (A99 < 1)$ | $5$ | false | false | $B99 = 2$ | +| Eb0 | $(trig > 0) && (B0 < 1)$ | $5$ | false | false | $A0 = 2$ | +| Eb1 | $(trig > 0) && (B1 < 1)$ | $5$ | false | false | $A1 = 2$ | +| Eb2 | $(trig > 0) && (B2 < 1)$ | $5$ | false | false | $A2 = 2$ | +| Eb3 | $(trig > 0) && (B3 < 1)$ | $5$ | false | false | $A3 = 2$ | +| Eb4 | $(trig > 0) && (B4 < 1)$ | $5$ | false | false | $A4 = 2$ | +| Eb5 | $(trig > 0) && (B5 < 1)$ | $5$ | false | false | $A5 = 2$ | +| Eb6 | $(trig > 0) && (B6 < 1)$ | $5$ | false | false | $A6 = 2$ | +| Eb7 | $(trig > 0) && (B7 < 1)$ | $5$ | false | false | $A7 = 2$ | +| Eb8 | $(trig > 0) && (B8 < 1)$ | $5$ | false | false | $A8 = 2$ | +| Eb9 | $(trig > 0) && (B9 < 1)$ | $5$ | false | false | $A9 = 2$ | +| Eb10 | $(trig > 0) && (B10 < 1)$ | $5$ | false | false | $A10 = 2$ | +| Eb11 | $(trig > 0) && (B11 < 1)$ | $5$ | false | false | $A11 = 2$ | +| Eb12 | $(trig > 0) && (B12 < 1)$ | $5$ | false | false | $A12 = 2$ | +| Eb13 | $(trig > 0) && (B13 < 1)$ | $5$ | false | false | $A13 = 2$ | +| Eb14 | $(trig > 0) && (B14 < 1)$ | $5$ | false | false | $A14 = 2$ | +| Eb15 | $(trig > 0) && (B15 < 1)$ | $5$ | false | false | $A15 = 2$ | +| Eb16 | $(trig > 0) && (B16 < 1)$ | $5$ | false | false | $A16 = 2$ | +| Eb17 | $(trig > 0) && (B17 < 1)$ | $5$ | false | false | $A17 = 2$ | +| Eb18 | $(trig > 0) && (B18 < 1)$ | $5$ | false | false | $A18 = 2$ | +| Eb19 | $(trig > 0) && (B19 < 1)$ | $5$ | false | false | $A19 = 2$ | +| Eb20 | $(trig > 0) && (B20 < 1)$ | $5$ | false | false | $A20 = 2$ | +| Eb21 | $(trig > 0) && (B21 < 1)$ | $5$ | false | false | $A21 = 2$ | +| Eb22 | $(trig > 0) && (B22 < 1)$ | $5$ | false | false | $A22 = 2$ | +| Eb23 | $(trig > 0) && (B23 < 1)$ | $5$ | false | false | $A23 = 2$ | +| Eb24 | $(trig > 0) && (B24 < 1)$ | $5$ | false | false | $A24 = 2$ | +| Eb25 | $(trig > 0) && (B25 < 1)$ | $5$ | false | false | $A25 = 2$ | +| Eb26 | $(trig > 0) && (B26 < 1)$ | $5$ | false | false | $A26 = 2$ | +| Eb27 | $(trig > 0) && (B27 < 1)$ | $5$ | false | false | $A27 = 2$ | +| Eb28 | $(trig > 0) && (B28 < 1)$ | $5$ | false | false | $A28 = 2$ | +| Eb29 | $(trig > 0) && (B29 < 1)$ | $5$ | false | false | $A29 = 2$ | +| Eb30 | $(trig > 0) && (B30 < 1)$ | $5$ | false | false | $A30 = 2$ | +| Eb31 | $(trig > 0) && (B31 < 1)$ | $5$ | false | false | $A31 = 2$ | +| Eb32 | $(trig > 0) && (B32 < 1)$ | $5$ | false | false | $A32 = 2$ | +| Eb33 | $(trig > 0) && (B33 < 1)$ | $5$ | false | false | $A33 = 2$ | +| Eb34 | $(trig > 0) && (B34 < 1)$ | $5$ | false | false | $A34 = 2$ | +| Eb35 | $(trig > 0) && (B35 < 1)$ | $5$ | false | false | $A35 = 2$ | +| Eb36 | $(trig > 0) && (B36 < 1)$ | $5$ | false | false | $A36 = 2$ | +| Eb37 | $(trig > 0) && (B37 < 1)$ | $5$ | false | false | $A37 = 2$ | +| Eb38 | $(trig > 0) && (B38 < 1)$ | $5$ | false | false | $A38 = 2$ | +| Eb39 | $(trig > 0) && (B39 < 1)$ | $5$ | false | false | $A39 = 2$ | +| Eb40 | $(trig > 0) && (B40 < 1)$ | $5$ | false | false | $A40 = 2$ | +| Eb41 | $(trig > 0) && (B41 < 1)$ | $5$ | false | false | $A41 = 2$ | +| Eb42 | $(trig > 0) && (B42 < 1)$ | $5$ | false | false | $A42 = 2$ | +| Eb43 | $(trig > 0) && (B43 < 1)$ | $5$ | false | false | $A43 = 2$ | +| Eb44 | $(trig > 0) && (B44 < 1)$ | $5$ | false | false | $A44 = 2$ | +| Eb45 | $(trig > 0) && (B45 < 1)$ | $5$ | false | false | $A45 = 2$ | +| Eb46 | $(trig > 0) && (B46 < 1)$ | $5$ | false | false | $A46 = 2$ | +| Eb47 | $(trig > 0) && (B47 < 1)$ | $5$ | false | false | $A47 = 2$ | +| Eb48 | $(trig > 0) && (B48 < 1)$ | $5$ | false | false | $A48 = 2$ | +| Eb49 | $(trig > 0) && (B49 < 1)$ | $5$ | false | false | $A49 = 2$ | +| Eb50 | $(trig > 0) && (B50 < 1)$ | $5$ | false | false | $A50 = 2$ | +| Eb51 | $(trig > 0) && (B51 < 1)$ | $5$ | false | false | $A51 = 2$ | +| Eb52 | $(trig > 0) && (B52 < 1)$ | $5$ | false | false | $A52 = 2$ | +| Eb53 | $(trig > 0) && (B53 < 1)$ | $5$ | false | false | $A53 = 2$ | +| Eb54 | $(trig > 0) && (B54 < 1)$ | $5$ | false | false | $A54 = 2$ | +| Eb55 | $(trig > 0) && (B55 < 1)$ | $5$ | false | false | $A55 = 2$ | +| Eb56 | $(trig > 0) && (B56 < 1)$ | $5$ | false | false | $A56 = 2$ | +| Eb57 | $(trig > 0) && (B57 < 1)$ | $5$ | false | false | $A57 = 2$ | +| Eb58 | $(trig > 0) && (B58 < 1)$ | $5$ | false | false | $A58 = 2$ | +| Eb59 | $(trig > 0) && (B59 < 1)$ | $5$ | false | false | $A59 = 2$ | +| Eb60 | $(trig > 0) && (B60 < 1)$ | $5$ | false | false | $A60 = 2$ | +| Eb61 | $(trig > 0) && (B61 < 1)$ | $5$ | false | false | $A61 = 2$ | +| Eb62 | $(trig > 0) && (B62 < 1)$ | $5$ | false | false | $A62 = 2$ | +| Eb63 | $(trig > 0) && (B63 < 1)$ | $5$ | false | false | $A63 = 2$ | +| Eb64 | $(trig > 0) && (B64 < 1)$ | $5$ | false | false | $A64 = 2$ | +| Eb65 | $(trig > 0) && (B65 < 1)$ | $5$ | false | false | $A65 = 2$ | +| Eb66 | $(trig > 0) && (B66 < 1)$ | $5$ | false | false | $A66 = 2$ | +| Eb67 | $(trig > 0) && (B67 < 1)$ | $5$ | false | false | $A67 = 2$ | +| Eb68 | $(trig > 0) && (B68 < 1)$ | $5$ | false | false | $A68 = 2$ | +| Eb69 | $(trig > 0) && (B69 < 1)$ | $5$ | false | false | $A69 = 2$ | +| Eb70 | $(trig > 0) && (B70 < 1)$ | $5$ | false | false | $A70 = 2$ | +| Eb71 | $(trig > 0) && (B71 < 1)$ | $5$ | false | false | $A71 = 2$ | +| Eb72 | $(trig > 0) && (B72 < 1)$ | $5$ | false | false | $A72 = 2$ | +| Eb73 | $(trig > 0) && (B73 < 1)$ | $5$ | false | false | $A73 = 2$ | +| Eb74 | $(trig > 0) && (B74 < 1)$ | $5$ | false | false | $A74 = 2$ | +| Eb75 | $(trig > 0) && (B75 < 1)$ | $5$ | false | false | $A75 = 2$ | +| Eb76 | $(trig > 0) && (B76 < 1)$ | $5$ | false | false | $A76 = 2$ | +| Eb77 | $(trig > 0) && (B77 < 1)$ | $5$ | false | false | $A77 = 2$ | +| Eb78 | $(trig > 0) && (B78 < 1)$ | $5$ | false | false | $A78 = 2$ | +| Eb79 | $(trig > 0) && (B79 < 1)$ | $5$ | false | false | $A79 = 2$ | +| Eb80 | $(trig > 0) && (B80 < 1)$ | $5$ | false | false | $A80 = 2$ | +| Eb81 | $(trig > 0) && (B81 < 1)$ | $5$ | false | false | $A81 = 2$ | +| Eb82 | $(trig > 0) && (B82 < 1)$ | $5$ | false | false | $A82 = 2$ | +| Eb83 | $(trig > 0) && (B83 < 1)$ | $5$ | false | false | $A83 = 2$ | +| Eb84 | $(trig > 0) && (B84 < 1)$ | $5$ | false | false | $A84 = 2$ | +| Eb85 | $(trig > 0) && (B85 < 1)$ | $5$ | false | false | $A85 = 2$ | +| Eb86 | $(trig > 0) && (B86 < 1)$ | $5$ | false | false | $A86 = 2$ | +| Eb87 | $(trig > 0) && (B87 < 1)$ | $5$ | false | false | $A87 = 2$ | +| Eb88 | $(trig > 0) && (B88 < 1)$ | $5$ | false | false | $A88 = 2$ | +| Eb89 | $(trig > 0) && (B89 < 1)$ | $5$ | false | false | $A89 = 2$ | +| Eb90 | $(trig > 0) && (B90 < 1)$ | $5$ | false | false | $A90 = 2$ | +| Eb91 | $(trig > 0) && (B91 < 1)$ | $5$ | false | false | $A91 = 2$ | +| Eb92 | $(trig > 0) && (B92 < 1)$ | $5$ | false | false | $A92 = 2$ | +| Eb93 | $(trig > 0) && (B93 < 1)$ | $5$ | false | false | $A93 = 2$ | +| Eb94 | $(trig > 0) && (B94 < 1)$ | $5$ | false | false | $A94 = 2$ | +| Eb95 | $(trig > 0) && (B95 < 1)$ | $5$ | false | false | $A95 = 2$ | +| Eb96 | $(trig > 0) && (B96 < 1)$ | $5$ | false | false | $A96 = 2$ | +| Eb97 | $(trig > 0) && (B97 < 1)$ | $5$ | false | false | $A97 = 2$ | +| Eb98 | $(trig > 0) && (B98 < 1)$ | $5$ | false | false | $A98 = 2$ | +| Eb99 | $(trig > 0) && (B99 < 1)$ | $5$ | false | false | $A99 = 2$ | +| _E0 | $abs(Asum - Bsum) > 100$ | (unset) | true | true | $toodiverged = 1$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Asum | $A0 + A1 + A2 + A3 + A4 + A5 + A6 + A7 + A8 + A9 + A10 + A11 + A12 + A13 + A14 + A15 + A16 + A17 + A18 + A19 + A20 + A21 + A22 + A23 + A24 + A25 + A26 + A27 + A28 + A29 + A30 + A31 + A32 + A33 + A34 + A35 + A36 + A37 + A38 + A39 + A40 + A41 + A42 + A43 + A44 + A45 + A46 + A47 + A48 + A49 + A50 + A51 + A52 + A53 + A54 + A55 + A56 + A57 + A58 + A59 + A60 + A61 + A62 + A63 + A64 + A65 + A66 + A67 + A68 + A69 + A70 + A71 + A72 + A73 + A74 + A75 + A76 + A77 + A78 + A79 + A80 + A81 + A82 + A83 + A84 + A85 + A86 + A87 + A88 + A89 + A90 + A91 + A92 + A93 + A94 + A95 + A96 + A97 + A98 + A99$ | +| Assignment | Bsum | $B0 + B1 + B2 + B3 + B4 + B5 + B6 + B7 + B8 + B9 + B10 + B11 + B12 + B13 + B14 + B15 + B16 + B17 + B18 + B19 + B20 + B21 + B22 + B23 + B24 + B25 + B26 + B27 + B28 + B29 + B30 + B31 + B32 + B33 + B34 + B35 + B36 + B37 + B38 + B39 + B40 + B41 + B42 + B43 + B44 + B45 + B46 + B47 + B48 + B49 + B50 + B51 + B52 + B53 + B54 + B55 + B56 + B57 + B58 + B59 + B60 + B61 + B62 + B63 + B64 + B65 + B66 + B67 + B68 + B69 + B70 + B71 + B72 + B73 + B74 + B75 + B76 + B77 + B78 + B79 + B80 + B81 + B82 + B83 + B84 + B85 + B86 + B87 + B88 + B89 + B90 + B91 + B92 + B93 + B94 + B95 + B96 + B97 + B98 + B99$ | +| Assignment | Allsum | $Asum + Bsum$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter trig | $1$ | constant | +| Initial value of parameter A0 | $0$ | variable | +| Initial value of parameter A1 | $0$ | variable | +| Initial value of parameter A2 | $0$ | variable | +| Initial value of parameter A3 | $0$ | variable | +| Initial value of parameter A4 | $0$ | variable | +| Initial value of parameter A5 | $0$ | variable | +| Initial value of parameter A6 | $0$ | variable | +| Initial value of parameter A7 | $0$ | variable | +| Initial value of parameter A8 | $0$ | variable | +| Initial value of parameter A9 | $0$ | variable | +| Initial value of parameter A10 | $0$ | variable | +| Initial value of parameter A11 | $0$ | variable | +| Initial value of parameter A12 | $0$ | variable | +| Initial value of parameter A13 | $0$ | variable | +| Initial value of parameter A14 | $0$ | variable | +| Initial value of parameter A15 | $0$ | variable | +| Initial value of parameter A16 | $0$ | variable | +| Initial value of parameter A17 | $0$ | variable | +| Initial value of parameter A18 | $0$ | variable | +| Initial value of parameter A19 | $0$ | variable | +| Initial value of parameter A20 | $0$ | variable | +| Initial value of parameter A21 | $0$ | variable | +| Initial value of parameter A22 | $0$ | variable | +| Initial value of parameter A23 | $0$ | variable | +| Initial value of parameter A24 | $0$ | variable | +| Initial value of parameter A25 | $0$ | variable | +| Initial value of parameter A26 | $0$ | variable | +| Initial value of parameter A27 | $0$ | variable | +| Initial value of parameter A28 | $0$ | variable | +| Initial value of parameter A29 | $0$ | variable | +| Initial value of parameter A30 | $0$ | variable | +| Initial value of parameter A31 | $0$ | variable | +| Initial value of parameter A32 | $0$ | variable | +| Initial value of parameter A33 | $0$ | variable | +| Initial value of parameter A34 | $0$ | variable | +| Initial value of parameter A35 | $0$ | variable | +| Initial value of parameter A36 | $0$ | variable | +| Initial value of parameter A37 | $0$ | variable | +| Initial value of parameter A38 | $0$ | variable | +| Initial value of parameter A39 | $0$ | variable | +| Initial value of parameter A40 | $0$ | variable | +| Initial value of parameter A41 | $0$ | variable | +| Initial value of parameter A42 | $0$ | variable | +| Initial value of parameter A43 | $0$ | variable | +| Initial value of parameter A44 | $0$ | variable | +| Initial value of parameter A45 | $0$ | variable | +| Initial value of parameter A46 | $0$ | variable | +| Initial value of parameter A47 | $0$ | variable | +| Initial value of parameter A48 | $0$ | variable | +| Initial value of parameter A49 | $0$ | variable | +| Initial value of parameter A50 | $0$ | variable | +| Initial value of parameter A51 | $0$ | variable | +| Initial value of parameter A52 | $0$ | variable | +| Initial value of parameter A53 | $0$ | variable | +| Initial value of parameter A54 | $0$ | variable | +| Initial value of parameter A55 | $0$ | variable | +| Initial value of parameter A56 | $0$ | variable | +| Initial value of parameter A57 | $0$ | variable | +| Initial value of parameter A58 | $0$ | variable | +| Initial value of parameter A59 | $0$ | variable | +| Initial value of parameter A60 | $0$ | variable | +| Initial value of parameter A61 | $0$ | variable | +| Initial value of parameter A62 | $0$ | variable | +| Initial value of parameter A63 | $0$ | variable | +| Initial value of parameter A64 | $0$ | variable | +| Initial value of parameter A65 | $0$ | variable | +| Initial value of parameter A66 | $0$ | variable | +| Initial value of parameter A67 | $0$ | variable | +| Initial value of parameter A68 | $0$ | variable | +| Initial value of parameter A69 | $0$ | variable | +| Initial value of parameter A70 | $0$ | variable | +| Initial value of parameter A71 | $0$ | variable | +| Initial value of parameter A72 | $0$ | variable | +| Initial value of parameter A73 | $0$ | variable | +| Initial value of parameter A74 | $0$ | variable | +| Initial value of parameter A75 | $0$ | variable | +| Initial value of parameter A76 | $0$ | variable | +| Initial value of parameter A77 | $0$ | variable | +| Initial value of parameter A78 | $0$ | variable | +| Initial value of parameter A79 | $0$ | variable | +| Initial value of parameter A80 | $0$ | variable | +| Initial value of parameter A81 | $0$ | variable | +| Initial value of parameter A82 | $0$ | variable | +| Initial value of parameter A83 | $0$ | variable | +| Initial value of parameter A84 | $0$ | variable | +| Initial value of parameter A85 | $0$ | variable | +| Initial value of parameter A86 | $0$ | variable | +| Initial value of parameter A87 | $0$ | variable | +| Initial value of parameter A88 | $0$ | variable | +| Initial value of parameter A89 | $0$ | variable | +| Initial value of parameter A90 | $0$ | variable | +| Initial value of parameter A91 | $0$ | variable | +| Initial value of parameter A92 | $0$ | variable | +| Initial value of parameter A93 | $0$ | variable | +| Initial value of parameter A94 | $0$ | variable | +| Initial value of parameter A95 | $0$ | variable | +| Initial value of parameter A96 | $0$ | variable | +| Initial value of parameter A97 | $0$ | variable | +| Initial value of parameter A98 | $0$ | variable | +| Initial value of parameter A99 | $0$ | variable | +| Initial value of parameter B0 | $0$ | variable | +| Initial value of parameter B1 | $0$ | variable | +| Initial value of parameter B2 | $0$ | variable | +| Initial value of parameter B3 | $0$ | variable | +| Initial value of parameter B4 | $0$ | variable | +| Initial value of parameter B5 | $0$ | variable | +| Initial value of parameter B6 | $0$ | variable | +| Initial value of parameter B7 | $0$ | variable | +| Initial value of parameter B8 | $0$ | variable | +| Initial value of parameter B9 | $0$ | variable | +| Initial value of parameter B10 | $0$ | variable | +| Initial value of parameter B11 | $0$ | variable | +| Initial value of parameter B12 | $0$ | variable | +| Initial value of parameter B13 | $0$ | variable | +| Initial value of parameter B14 | $0$ | variable | +| Initial value of parameter B15 | $0$ | variable | +| Initial value of parameter B16 | $0$ | variable | +| Initial value of parameter B17 | $0$ | variable | +| Initial value of parameter B18 | $0$ | variable | +| Initial value of parameter B19 | $0$ | variable | +| Initial value of parameter B20 | $0$ | variable | +| Initial value of parameter B21 | $0$ | variable | +| Initial value of parameter B22 | $0$ | variable | +| Initial value of parameter B23 | $0$ | variable | +| Initial value of parameter B24 | $0$ | variable | +| Initial value of parameter B25 | $0$ | variable | +| Initial value of parameter B26 | $0$ | variable | +| Initial value of parameter B27 | $0$ | variable | +| Initial value of parameter B28 | $0$ | variable | +| Initial value of parameter B29 | $0$ | variable | +| Initial value of parameter B30 | $0$ | variable | +| Initial value of parameter B31 | $0$ | variable | +| Initial value of parameter B32 | $0$ | variable | +| Initial value of parameter B33 | $0$ | variable | +| Initial value of parameter B34 | $0$ | variable | +| Initial value of parameter B35 | $0$ | variable | +| Initial value of parameter B36 | $0$ | variable | +| Initial value of parameter B37 | $0$ | variable | +| Initial value of parameter B38 | $0$ | variable | +| Initial value of parameter B39 | $0$ | variable | +| Initial value of parameter B40 | $0$ | variable | +| Initial value of parameter B41 | $0$ | variable | +| Initial value of parameter B42 | $0$ | variable | +| Initial value of parameter B43 | $0$ | variable | +| Initial value of parameter B44 | $0$ | variable | +| Initial value of parameter B45 | $0$ | variable | +| Initial value of parameter B46 | $0$ | variable | +| Initial value of parameter B47 | $0$ | variable | +| Initial value of parameter B48 | $0$ | variable | +| Initial value of parameter B49 | $0$ | variable | +| Initial value of parameter B50 | $0$ | variable | +| Initial value of parameter B51 | $0$ | variable | +| Initial value of parameter B52 | $0$ | variable | +| Initial value of parameter B53 | $0$ | variable | +| Initial value of parameter B54 | $0$ | variable | +| Initial value of parameter B55 | $0$ | variable | +| Initial value of parameter B56 | $0$ | variable | +| Initial value of parameter B57 | $0$ | variable | +| Initial value of parameter B58 | $0$ | variable | +| Initial value of parameter B59 | $0$ | variable | +| Initial value of parameter B60 | $0$ | variable | +| Initial value of parameter B61 | $0$ | variable | +| Initial value of parameter B62 | $0$ | variable | +| Initial value of parameter B63 | $0$ | variable | +| Initial value of parameter B64 | $0$ | variable | +| Initial value of parameter B65 | $0$ | variable | +| Initial value of parameter B66 | $0$ | variable | +| Initial value of parameter B67 | $0$ | variable | +| Initial value of parameter B68 | $0$ | variable | +| Initial value of parameter B69 | $0$ | variable | +| Initial value of parameter B70 | $0$ | variable | +| Initial value of parameter B71 | $0$ | variable | +| Initial value of parameter B72 | $0$ | variable | +| Initial value of parameter B73 | $0$ | variable | +| Initial value of parameter B74 | $0$ | variable | +| Initial value of parameter B75 | $0$ | variable | +| Initial value of parameter B76 | $0$ | variable | +| Initial value of parameter B77 | $0$ | variable | +| Initial value of parameter B78 | $0$ | variable | +| Initial value of parameter B79 | $0$ | variable | +| Initial value of parameter B80 | $0$ | variable | +| Initial value of parameter B81 | $0$ | variable | +| Initial value of parameter B82 | $0$ | variable | +| Initial value of parameter B83 | $0$ | variable | +| Initial value of parameter B84 | $0$ | variable | +| Initial value of parameter B85 | $0$ | variable | +| Initial value of parameter B86 | $0$ | variable | +| Initial value of parameter B87 | $0$ | variable | +| Initial value of parameter B88 | $0$ | variable | +| Initial value of parameter B89 | $0$ | variable | +| Initial value of parameter B90 | $0$ | variable | +| Initial value of parameter B91 | $0$ | variable | +| Initial value of parameter B92 | $0$ | variable | +| Initial value of parameter B93 | $0$ | variable | +| Initial value of parameter B94 | $0$ | variable | +| Initial value of parameter B95 | $0$ | variable | +| Initial value of parameter B96 | $0$ | variable | +| Initial value of parameter B97 | $0$ | variable | +| Initial value of parameter B98 | $0$ | variable | +| Initial value of parameter B99 | $0$ | variable | +| Initial value of parameter Asum | $A0 + A1 + A2 + A3 + A4 + A5 + A6 + A7 + A8 + A9 + A10 + A11 + A12 + A13 + A14 + A15 + A16 + A17 + A18 + A19 + A20 + A21 + A22 + A23 + A24 + A25 + A26 + A27 + A28 + A29 + A30 + A31 + A32 + A33 + A34 + A35 + A36 + A37 + A38 + A39 + A40 + A41 + A42 + A43 + A44 + A45 + A46 + A47 + A48 + A49 + A50 + A51 + A52 + A53 + A54 + A55 + A56 + A57 + A58 + A59 + A60 + A61 + A62 + A63 + A64 + A65 + A66 + A67 + A68 + A69 + A70 + A71 + A72 + A73 + A74 + A75 + A76 + A77 + A78 + A79 + A80 + A81 + A82 + A83 + A84 + A85 + A86 + A87 + A88 + A89 + A90 + A91 + A92 + A93 + A94 + A95 + A96 + A97 + A98 + A99$ | variable | +| Initial value of parameter Bsum | $B0 + B1 + B2 + B3 + B4 + B5 + B6 + B7 + B8 + B9 + B10 + B11 + B12 + B13 + B14 + B15 + B16 + B17 + B18 + B19 + B20 + B21 + B22 + B23 + B24 + B25 + B26 + B27 + B28 + B29 + B30 + B31 + B32 + B33 + B34 + B35 + B36 + B37 + B38 + B39 + B40 + B41 + B42 + B43 + B44 + B45 + B46 + B47 + B48 + B49 + B50 + B51 + B52 + B53 + B54 + B55 + B56 + B57 + B58 + B59 + B60 + B61 + B62 + B63 + B64 + B65 + B66 + B67 + B68 + B69 + B70 + B71 + B72 + B73 + B74 + B75 + B76 + B77 + B78 + B79 + B80 + B81 + B82 + B83 + B84 + B85 + B86 + B87 + B88 + B89 + B90 + B91 + B92 + B93 + B94 + B95 + B96 + B97 + B98 + B99$ | variable | +| Initial value of parameter Allsum | $Asum + Bsum$ | variable | +| Initial value of parameter toodiverged | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +A0 @Record { } .= 0; +A0 [Eb0]= 2; +A1 @Record { } .= 0; +A1 [Eb1]= 2; +A2 @Record { } .= 0; +A2 [Eb2]= 2; +A3 @Record { } .= 0; +A3 [Eb3]= 2; +A4 @Record { } .= 0; +A4 [Eb4]= 2; +A5 @Record { } .= 0; +A5 [Eb5]= 2; +A6 @Record { } .= 0; +A6 [Eb6]= 2; +A7 @Record { } .= 0; +A7 [Eb7]= 2; +A8 @Record { } .= 0; +A8 [Eb8]= 2; +A9 @Record { } .= 0; +A9 [Eb9]= 2; +A10 @Record { } .= 0; +A10 [Eb10]= 2; +A11 @Record { } .= 0; +A11 [Eb11]= 2; +A12 @Record { } .= 0; +A12 [Eb12]= 2; +A13 @Record { } .= 0; +A13 [Eb13]= 2; +A14 @Record { } .= 0; +A14 [Eb14]= 2; +A15 @Record { } .= 0; +A15 [Eb15]= 2; +A16 @Record { } .= 0; +A16 [Eb16]= 2; +A17 @Record { } .= 0; +A17 [Eb17]= 2; +A18 @Record { } .= 0; +A18 [Eb18]= 2; +A19 @Record { } .= 0; +A19 [Eb19]= 2; +A20 @Record { } .= 0; +A20 [Eb20]= 2; +A21 @Record { } .= 0; +A21 [Eb21]= 2; +A22 @Record { } .= 0; +A22 [Eb22]= 2; +A23 @Record { } .= 0; +A23 [Eb23]= 2; +A24 @Record { } .= 0; +A24 [Eb24]= 2; +A25 @Record { } .= 0; +A25 [Eb25]= 2; +A26 @Record { } .= 0; +A26 [Eb26]= 2; +A27 @Record { } .= 0; +A27 [Eb27]= 2; +A28 @Record { } .= 0; +A28 [Eb28]= 2; +A29 @Record { } .= 0; +A29 [Eb29]= 2; +A30 @Record { } .= 0; +A30 [Eb30]= 2; +A31 @Record { } .= 0; +A31 [Eb31]= 2; +A32 @Record { } .= 0; +A32 [Eb32]= 2; +A33 @Record { } .= 0; +A33 [Eb33]= 2; +A34 @Record { } .= 0; +A34 [Eb34]= 2; +A35 @Record { } .= 0; +A35 [Eb35]= 2; +A36 @Record { } .= 0; +A36 [Eb36]= 2; +A37 @Record { } .= 0; +A37 [Eb37]= 2; +A38 @Record { } .= 0; +A38 [Eb38]= 2; +A39 @Record { } .= 0; +A39 [Eb39]= 2; +A40 @Record { } .= 0; +A40 [Eb40]= 2; +A41 @Record { } .= 0; +A41 [Eb41]= 2; +A42 @Record { } .= 0; +A42 [Eb42]= 2; +A43 @Record { } .= 0; +A43 [Eb43]= 2; +A44 @Record { } .= 0; +A44 [Eb44]= 2; +A45 @Record { } .= 0; +A45 [Eb45]= 2; +A46 @Record { } .= 0; +A46 [Eb46]= 2; +A47 @Record { } .= 0; +A47 [Eb47]= 2; +A48 @Record { } .= 0; +A48 [Eb48]= 2; +A49 @Record { } .= 0; +A49 [Eb49]= 2; +A50 @Record { } .= 0; +A50 [Eb50]= 2; +A51 @Record { } .= 0; +A51 [Eb51]= 2; +A52 @Record { } .= 0; +A52 [Eb52]= 2; +A53 @Record { } .= 0; +A53 [Eb53]= 2; +A54 @Record { } .= 0; +A54 [Eb54]= 2; +A55 @Record { } .= 0; +A55 [Eb55]= 2; +A56 @Record { } .= 0; +A56 [Eb56]= 2; +A57 @Record { } .= 0; +A57 [Eb57]= 2; +A58 @Record { } .= 0; +A58 [Eb58]= 2; +A59 @Record { } .= 0; +A59 [Eb59]= 2; +A60 @Record { } .= 0; +A60 [Eb60]= 2; +A61 @Record { } .= 0; +A61 [Eb61]= 2; +A62 @Record { } .= 0; +A62 [Eb62]= 2; +A63 @Record { } .= 0; +A63 [Eb63]= 2; +A64 @Record { } .= 0; +A64 [Eb64]= 2; +A65 @Record { } .= 0; +A65 [Eb65]= 2; +A66 @Record { } .= 0; +A66 [Eb66]= 2; +A67 @Record { } .= 0; +A67 [Eb67]= 2; +A68 @Record { } .= 0; +A68 [Eb68]= 2; +A69 @Record { } .= 0; +A69 [Eb69]= 2; +A70 @Record { } .= 0; +A70 [Eb70]= 2; +A71 @Record { } .= 0; +A71 [Eb71]= 2; +A72 @Record { } .= 0; +A72 [Eb72]= 2; +A73 @Record { } .= 0; +A73 [Eb73]= 2; +A74 @Record { } .= 0; +A74 [Eb74]= 2; +A75 @Record { } .= 0; +A75 [Eb75]= 2; +A76 @Record { } .= 0; +A76 [Eb76]= 2; +A77 @Record { } .= 0; +A77 [Eb77]= 2; +A78 @Record { } .= 0; +A78 [Eb78]= 2; +A79 @Record { } .= 0; +A79 [Eb79]= 2; +A80 @Record { } .= 0; +A80 [Eb80]= 2; +A81 @Record { } .= 0; +A81 [Eb81]= 2; +A82 @Record { } .= 0; +A82 [Eb82]= 2; +A83 @Record { } .= 0; +A83 [Eb83]= 2; +A84 @Record { } .= 0; +A84 [Eb84]= 2; +A85 @Record { } .= 0; +A85 [Eb85]= 2; +A86 @Record { } .= 0; +A86 [Eb86]= 2; +A87 @Record { } .= 0; +A87 [Eb87]= 2; +A88 @Record { } .= 0; +A88 [Eb88]= 2; +A89 @Record { } .= 0; +A89 [Eb89]= 2; +A90 @Record { } .= 0; +A90 [Eb90]= 2; +A91 @Record { } .= 0; +A91 [Eb91]= 2; +A92 @Record { } .= 0; +A92 [Eb92]= 2; +A93 @Record { } .= 0; +A93 [Eb93]= 2; +A94 @Record { } .= 0; +A94 [Eb94]= 2; +A95 @Record { } .= 0; +A95 [Eb95]= 2; +A96 @Record { } .= 0; +A96 [Eb96]= 2; +A97 @Record { } .= 0; +A97 [Eb97]= 2; +A98 @Record { } .= 0; +A98 [Eb98]= 2; +A99 @Record { } .= 0; +A99 [Eb99]= 2; +B0 @Record { } .= 0; +B0 [E0]= 2; +B1 @Record { } .= 0; +B1 [E1]= 2; +B2 @Record { } .= 0; +B2 [E2]= 2; +B3 @Record { } .= 0; +B3 [E3]= 2; +B4 @Record { } .= 0; +B4 [E4]= 2; +B5 @Record { } .= 0; +B5 [E5]= 2; +B6 @Record { } .= 0; +B6 [E6]= 2; +B7 @Record { } .= 0; +B7 [E7]= 2; +B8 @Record { } .= 0; +B8 [E8]= 2; +B9 @Record { } .= 0; +B9 [E9]= 2; +B10 @Record { } .= 0; +B10 [E10]= 2; +B11 @Record { } .= 0; +B11 [E11]= 2; +B12 @Record { } .= 0; +B12 [E12]= 2; +B13 @Record { } .= 0; +B13 [E13]= 2; +B14 @Record { } .= 0; +B14 [E14]= 2; +B15 @Record { } .= 0; +B15 [E15]= 2; +B16 @Record { } .= 0; +B16 [E16]= 2; +B17 @Record { } .= 0; +B17 [E17]= 2; +B18 @Record { } .= 0; +B18 [E18]= 2; +B19 @Record { } .= 0; +B19 [E19]= 2; +B20 @Record { } .= 0; +B20 [E20]= 2; +B21 @Record { } .= 0; +B21 [E21]= 2; +B22 @Record { } .= 0; +B22 [E22]= 2; +B23 @Record { } .= 0; +B23 [E23]= 2; +B24 @Record { } .= 0; +B24 [E24]= 2; +B25 @Record { } .= 0; +B25 [E25]= 2; +B26 @Record { } .= 0; +B26 [E26]= 2; +B27 @Record { } .= 0; +B27 [E27]= 2; +B28 @Record { } .= 0; +B28 [E28]= 2; +B29 @Record { } .= 0; +B29 [E29]= 2; +B30 @Record { } .= 0; +B30 [E30]= 2; +B31 @Record { } .= 0; +B31 [E31]= 2; +B32 @Record { } .= 0; +B32 [E32]= 2; +B33 @Record { } .= 0; +B33 [E33]= 2; +B34 @Record { } .= 0; +B34 [E34]= 2; +B35 @Record { } .= 0; +B35 [E35]= 2; +B36 @Record { } .= 0; +B36 [E36]= 2; +B37 @Record { } .= 0; +B37 [E37]= 2; +B38 @Record { } .= 0; +B38 [E38]= 2; +B39 @Record { } .= 0; +B39 [E39]= 2; +B40 @Record { } .= 0; +B40 [E40]= 2; +B41 @Record { } .= 0; +B41 [E41]= 2; +B42 @Record { } .= 0; +B42 [E42]= 2; +B43 @Record { } .= 0; +B43 [E43]= 2; +B44 @Record { } .= 0; +B44 [E44]= 2; +B45 @Record { } .= 0; +B45 [E45]= 2; +B46 @Record { } .= 0; +B46 [E46]= 2; +B47 @Record { } .= 0; +B47 [E47]= 2; +B48 @Record { } .= 0; +B48 [E48]= 2; +B49 @Record { } .= 0; +B49 [E49]= 2; +B50 @Record { } .= 0; +B50 [E50]= 2; +B51 @Record { } .= 0; +B51 [E51]= 2; +B52 @Record { } .= 0; +B52 [E52]= 2; +B53 @Record { } .= 0; +B53 [E53]= 2; +B54 @Record { } .= 0; +B54 [E54]= 2; +B55 @Record { } .= 0; +B55 [E55]= 2; +B56 @Record { } .= 0; +B56 [E56]= 2; +B57 @Record { } .= 0; +B57 [E57]= 2; +B58 @Record { } .= 0; +B58 [E58]= 2; +B59 @Record { } .= 0; +B59 [E59]= 2; +B60 @Record { } .= 0; +B60 [E60]= 2; +B61 @Record { } .= 0; +B61 [E61]= 2; +B62 @Record { } .= 0; +B62 [E62]= 2; +B63 @Record { } .= 0; +B63 [E63]= 2; +B64 @Record { } .= 0; +B64 [E64]= 2; +B65 @Record { } .= 0; +B65 [E65]= 2; +B66 @Record { } .= 0; +B66 [E66]= 2; +B67 @Record { } .= 0; +B67 [E67]= 2; +B68 @Record { } .= 0; +B68 [E68]= 2; +B69 @Record { } .= 0; +B69 [E69]= 2; +B70 @Record { } .= 0; +B70 [E70]= 2; +B71 @Record { } .= 0; +B71 [E71]= 2; +B72 @Record { } .= 0; +B72 [E72]= 2; +B73 @Record { } .= 0; +B73 [E73]= 2; +B74 @Record { } .= 0; +B74 [E74]= 2; +B75 @Record { } .= 0; +B75 [E75]= 2; +B76 @Record { } .= 0; +B76 [E76]= 2; +B77 @Record { } .= 0; +B77 [E77]= 2; +B78 @Record { } .= 0; +B78 [E78]= 2; +B79 @Record { } .= 0; +B79 [E79]= 2; +B80 @Record { } .= 0; +B80 [E80]= 2; +B81 @Record { } .= 0; +B81 [E81]= 2; +B82 @Record { } .= 0; +B82 [E82]= 2; +B83 @Record { } .= 0; +B83 [E83]= 2; +B84 @Record { } .= 0; +B84 [E84]= 2; +B85 @Record { } .= 0; +B85 [E85]= 2; +B86 @Record { } .= 0; +B86 [E86]= 2; +B87 @Record { } .= 0; +B87 [E87]= 2; +B88 @Record { } .= 0; +B88 [E88]= 2; +B89 @Record { } .= 0; +B89 [E89]= 2; +B90 @Record { } .= 0; +B90 [E90]= 2; +B91 @Record { } .= 0; +B91 [E91]= 2; +B92 @Record { } .= 0; +B92 [E92]= 2; +B93 @Record { } .= 0; +B93 [E93]= 2; +B94 @Record { } .= 0; +B94 [E94]= 2; +B95 @Record { } .= 0; +B95 [E95]= 2; +B96 @Record { } .= 0; +B96 [E96]= 2; +B97 @Record { } .= 0; +B97 [E97]= 2; +B98 @Record { } .= 0; +B98 [E98]= 2; +B99 @Record { } .= 0; +B99 [E99]= 2; +Asum @Record { }; +Asum := A0 + A1 + A2 + A3 + A4 + A5 + A6 + A7 + A8 + A9 + A10 + A11 + A12 + A13 + A14 + A15 + A16 + A17 + A18 + A19 + A20 + A21 + A22 + A23 + A24 + A25 + A26 + A27 + A28 + A29 + A30 + A31 + A32 + A33 + A34 + A35 + A36 + A37 + A38 + A39 + A40 + A41 + A42 + A43 + A44 + A45 + A46 + A47 + A48 + A49 + A50 + A51 + A52 + A53 + A54 + A55 + A56 + A57 + A58 + A59 + A60 + A61 + A62 + A63 + A64 + A65 + A66 + A67 + A68 + A69 + A70 + A71 + A72 + A73 + A74 + A75 + A76 + A77 + A78 + A79 + A80 + A81 + A82 + A83 + A84 + A85 + A86 + A87 + A88 + A89 + A90 + A91 + A92 + A93 + A94 + A95 + A96 + A97 + A98 + A99; +Bsum @Record { }; +Bsum := B0 + B1 + B2 + B3 + B4 + B5 + B6 + B7 + B8 + B9 + B10 + B11 + B12 + B13 + B14 + B15 + B16 + B17 + B18 + B19 + B20 + B21 + B22 + B23 + B24 + B25 + B26 + B27 + B28 + B29 + B30 + B31 + B32 + B33 + B34 + B35 + B36 + B37 + B38 + B39 + B40 + B41 + B42 + B43 + B44 + B45 + B46 + B47 + B48 + B49 + B50 + B51 + B52 + B53 + B54 + B55 + B56 + B57 + B58 + B59 + B60 + B61 + B62 + B63 + B64 + B65 + B66 + B67 + B68 + B69 + B70 + B71 + B72 + B73 + B74 + B75 + B76 + B77 + B78 + B79 + B80 + B81 + B82 + B83 + B84 + B85 + B86 + B87 + B88 + B89 + B90 + B91 + B92 + B93 + B94 + B95 + B96 + B97 + B98 + B99; +Allsum @Record { }; +Allsum := Asum + Bsum; +toodiverged @Record { } .= 0; +toodiverged [_E0]= 1; + +trig @Const { } = 1; + +E0 @DSwitcher { trigger: trig > 0 and A0 < 1, }; +E1 @DSwitcher { trigger: trig > 0 and A1 < 1, }; +E2 @DSwitcher { trigger: trig > 0 and A2 < 1, }; +E3 @DSwitcher { trigger: trig > 0 and A3 < 1, }; +E4 @DSwitcher { trigger: trig > 0 and A4 < 1, }; +E5 @DSwitcher { trigger: trig > 0 and A5 < 1, }; +E6 @DSwitcher { trigger: trig > 0 and A6 < 1, }; +E7 @DSwitcher { trigger: trig > 0 and A7 < 1, }; +E8 @DSwitcher { trigger: trig > 0 and A8 < 1, }; +E9 @DSwitcher { trigger: trig > 0 and A9 < 1, }; +E10 @DSwitcher { trigger: trig > 0 and A10 < 1, }; +E11 @DSwitcher { trigger: trig > 0 and A11 < 1, }; +E12 @DSwitcher { trigger: trig > 0 and A12 < 1, }; +E13 @DSwitcher { trigger: trig > 0 and A13 < 1, }; +E14 @DSwitcher { trigger: trig > 0 and A14 < 1, }; +E15 @DSwitcher { trigger: trig > 0 and A15 < 1, }; +E16 @DSwitcher { trigger: trig > 0 and A16 < 1, }; +E17 @DSwitcher { trigger: trig > 0 and A17 < 1, }; +E18 @DSwitcher { trigger: trig > 0 and A18 < 1, }; +E19 @DSwitcher { trigger: trig > 0 and A19 < 1, }; +E20 @DSwitcher { trigger: trig > 0 and A20 < 1, }; +E21 @DSwitcher { trigger: trig > 0 and A21 < 1, }; +E22 @DSwitcher { trigger: trig > 0 and A22 < 1, }; +E23 @DSwitcher { trigger: trig > 0 and A23 < 1, }; +E24 @DSwitcher { trigger: trig > 0 and A24 < 1, }; +E25 @DSwitcher { trigger: trig > 0 and A25 < 1, }; +E26 @DSwitcher { trigger: trig > 0 and A26 < 1, }; +E27 @DSwitcher { trigger: trig > 0 and A27 < 1, }; +E28 @DSwitcher { trigger: trig > 0 and A28 < 1, }; +E29 @DSwitcher { trigger: trig > 0 and A29 < 1, }; +E30 @DSwitcher { trigger: trig > 0 and A30 < 1, }; +E31 @DSwitcher { trigger: trig > 0 and A31 < 1, }; +E32 @DSwitcher { trigger: trig > 0 and A32 < 1, }; +E33 @DSwitcher { trigger: trig > 0 and A33 < 1, }; +E34 @DSwitcher { trigger: trig > 0 and A34 < 1, }; +E35 @DSwitcher { trigger: trig > 0 and A35 < 1, }; +E36 @DSwitcher { trigger: trig > 0 and A36 < 1, }; +E37 @DSwitcher { trigger: trig > 0 and A37 < 1, }; +E38 @DSwitcher { trigger: trig > 0 and A38 < 1, }; +E39 @DSwitcher { trigger: trig > 0 and A39 < 1, }; +E40 @DSwitcher { trigger: trig > 0 and A40 < 1, }; +E41 @DSwitcher { trigger: trig > 0 and A41 < 1, }; +E42 @DSwitcher { trigger: trig > 0 and A42 < 1, }; +E43 @DSwitcher { trigger: trig > 0 and A43 < 1, }; +E44 @DSwitcher { trigger: trig > 0 and A44 < 1, }; +E45 @DSwitcher { trigger: trig > 0 and A45 < 1, }; +E46 @DSwitcher { trigger: trig > 0 and A46 < 1, }; +E47 @DSwitcher { trigger: trig > 0 and A47 < 1, }; +E48 @DSwitcher { trigger: trig > 0 and A48 < 1, }; +E49 @DSwitcher { trigger: trig > 0 and A49 < 1, }; +E50 @DSwitcher { trigger: trig > 0 and A50 < 1, }; +E51 @DSwitcher { trigger: trig > 0 and A51 < 1, }; +E52 @DSwitcher { trigger: trig > 0 and A52 < 1, }; +E53 @DSwitcher { trigger: trig > 0 and A53 < 1, }; +E54 @DSwitcher { trigger: trig > 0 and A54 < 1, }; +E55 @DSwitcher { trigger: trig > 0 and A55 < 1, }; +E56 @DSwitcher { trigger: trig > 0 and A56 < 1, }; +E57 @DSwitcher { trigger: trig > 0 and A57 < 1, }; +E58 @DSwitcher { trigger: trig > 0 and A58 < 1, }; +E59 @DSwitcher { trigger: trig > 0 and A59 < 1, }; +E60 @DSwitcher { trigger: trig > 0 and A60 < 1, }; +E61 @DSwitcher { trigger: trig > 0 and A61 < 1, }; +E62 @DSwitcher { trigger: trig > 0 and A62 < 1, }; +E63 @DSwitcher { trigger: trig > 0 and A63 < 1, }; +E64 @DSwitcher { trigger: trig > 0 and A64 < 1, }; +E65 @DSwitcher { trigger: trig > 0 and A65 < 1, }; +E66 @DSwitcher { trigger: trig > 0 and A66 < 1, }; +E67 @DSwitcher { trigger: trig > 0 and A67 < 1, }; +E68 @DSwitcher { trigger: trig > 0 and A68 < 1, }; +E69 @DSwitcher { trigger: trig > 0 and A69 < 1, }; +E70 @DSwitcher { trigger: trig > 0 and A70 < 1, }; +E71 @DSwitcher { trigger: trig > 0 and A71 < 1, }; +E72 @DSwitcher { trigger: trig > 0 and A72 < 1, }; +E73 @DSwitcher { trigger: trig > 0 and A73 < 1, }; +E74 @DSwitcher { trigger: trig > 0 and A74 < 1, }; +E75 @DSwitcher { trigger: trig > 0 and A75 < 1, }; +E76 @DSwitcher { trigger: trig > 0 and A76 < 1, }; +E77 @DSwitcher { trigger: trig > 0 and A77 < 1, }; +E78 @DSwitcher { trigger: trig > 0 and A78 < 1, }; +E79 @DSwitcher { trigger: trig > 0 and A79 < 1, }; +E80 @DSwitcher { trigger: trig > 0 and A80 < 1, }; +E81 @DSwitcher { trigger: trig > 0 and A81 < 1, }; +E82 @DSwitcher { trigger: trig > 0 and A82 < 1, }; +E83 @DSwitcher { trigger: trig > 0 and A83 < 1, }; +E84 @DSwitcher { trigger: trig > 0 and A84 < 1, }; +E85 @DSwitcher { trigger: trig > 0 and A85 < 1, }; +E86 @DSwitcher { trigger: trig > 0 and A86 < 1, }; +E87 @DSwitcher { trigger: trig > 0 and A87 < 1, }; +E88 @DSwitcher { trigger: trig > 0 and A88 < 1, }; +E89 @DSwitcher { trigger: trig > 0 and A89 < 1, }; +E90 @DSwitcher { trigger: trig > 0 and A90 < 1, }; +E91 @DSwitcher { trigger: trig > 0 and A91 < 1, }; +E92 @DSwitcher { trigger: trig > 0 and A92 < 1, }; +E93 @DSwitcher { trigger: trig > 0 and A93 < 1, }; +E94 @DSwitcher { trigger: trig > 0 and A94 < 1, }; +E95 @DSwitcher { trigger: trig > 0 and A95 < 1, }; +E96 @DSwitcher { trigger: trig > 0 and A96 < 1, }; +E97 @DSwitcher { trigger: trig > 0 and A97 < 1, }; +E98 @DSwitcher { trigger: trig > 0 and A98 < 1, }; +E99 @DSwitcher { trigger: trig > 0 and A99 < 1, }; +Eb0 @DSwitcher { trigger: trig > 0 and B0 < 1, }; +Eb1 @DSwitcher { trigger: trig > 0 and B1 < 1, }; +Eb2 @DSwitcher { trigger: trig > 0 and B2 < 1, }; +Eb3 @DSwitcher { trigger: trig > 0 and B3 < 1, }; +Eb4 @DSwitcher { trigger: trig > 0 and B4 < 1, }; +Eb5 @DSwitcher { trigger: trig > 0 and B5 < 1, }; +Eb6 @DSwitcher { trigger: trig > 0 and B6 < 1, }; +Eb7 @DSwitcher { trigger: trig > 0 and B7 < 1, }; +Eb8 @DSwitcher { trigger: trig > 0 and B8 < 1, }; +Eb9 @DSwitcher { trigger: trig > 0 and B9 < 1, }; +Eb10 @DSwitcher { trigger: trig > 0 and B10 < 1, }; +Eb11 @DSwitcher { trigger: trig > 0 and B11 < 1, }; +Eb12 @DSwitcher { trigger: trig > 0 and B12 < 1, }; +Eb13 @DSwitcher { trigger: trig > 0 and B13 < 1, }; +Eb14 @DSwitcher { trigger: trig > 0 and B14 < 1, }; +Eb15 @DSwitcher { trigger: trig > 0 and B15 < 1, }; +Eb16 @DSwitcher { trigger: trig > 0 and B16 < 1, }; +Eb17 @DSwitcher { trigger: trig > 0 and B17 < 1, }; +Eb18 @DSwitcher { trigger: trig > 0 and B18 < 1, }; +Eb19 @DSwitcher { trigger: trig > 0 and B19 < 1, }; +Eb20 @DSwitcher { trigger: trig > 0 and B20 < 1, }; +Eb21 @DSwitcher { trigger: trig > 0 and B21 < 1, }; +Eb22 @DSwitcher { trigger: trig > 0 and B22 < 1, }; +Eb23 @DSwitcher { trigger: trig > 0 and B23 < 1, }; +Eb24 @DSwitcher { trigger: trig > 0 and B24 < 1, }; +Eb25 @DSwitcher { trigger: trig > 0 and B25 < 1, }; +Eb26 @DSwitcher { trigger: trig > 0 and B26 < 1, }; +Eb27 @DSwitcher { trigger: trig > 0 and B27 < 1, }; +Eb28 @DSwitcher { trigger: trig > 0 and B28 < 1, }; +Eb29 @DSwitcher { trigger: trig > 0 and B29 < 1, }; +Eb30 @DSwitcher { trigger: trig > 0 and B30 < 1, }; +Eb31 @DSwitcher { trigger: trig > 0 and B31 < 1, }; +Eb32 @DSwitcher { trigger: trig > 0 and B32 < 1, }; +Eb33 @DSwitcher { trigger: trig > 0 and B33 < 1, }; +Eb34 @DSwitcher { trigger: trig > 0 and B34 < 1, }; +Eb35 @DSwitcher { trigger: trig > 0 and B35 < 1, }; +Eb36 @DSwitcher { trigger: trig > 0 and B36 < 1, }; +Eb37 @DSwitcher { trigger: trig > 0 and B37 < 1, }; +Eb38 @DSwitcher { trigger: trig > 0 and B38 < 1, }; +Eb39 @DSwitcher { trigger: trig > 0 and B39 < 1, }; +Eb40 @DSwitcher { trigger: trig > 0 and B40 < 1, }; +Eb41 @DSwitcher { trigger: trig > 0 and B41 < 1, }; +Eb42 @DSwitcher { trigger: trig > 0 and B42 < 1, }; +Eb43 @DSwitcher { trigger: trig > 0 and B43 < 1, }; +Eb44 @DSwitcher { trigger: trig > 0 and B44 < 1, }; +Eb45 @DSwitcher { trigger: trig > 0 and B45 < 1, }; +Eb46 @DSwitcher { trigger: trig > 0 and B46 < 1, }; +Eb47 @DSwitcher { trigger: trig > 0 and B47 < 1, }; +Eb48 @DSwitcher { trigger: trig > 0 and B48 < 1, }; +Eb49 @DSwitcher { trigger: trig > 0 and B49 < 1, }; +Eb50 @DSwitcher { trigger: trig > 0 and B50 < 1, }; +Eb51 @DSwitcher { trigger: trig > 0 and B51 < 1, }; +Eb52 @DSwitcher { trigger: trig > 0 and B52 < 1, }; +Eb53 @DSwitcher { trigger: trig > 0 and B53 < 1, }; +Eb54 @DSwitcher { trigger: trig > 0 and B54 < 1, }; +Eb55 @DSwitcher { trigger: trig > 0 and B55 < 1, }; +Eb56 @DSwitcher { trigger: trig > 0 and B56 < 1, }; +Eb57 @DSwitcher { trigger: trig > 0 and B57 < 1, }; +Eb58 @DSwitcher { trigger: trig > 0 and B58 < 1, }; +Eb59 @DSwitcher { trigger: trig > 0 and B59 < 1, }; +Eb60 @DSwitcher { trigger: trig > 0 and B60 < 1, }; +Eb61 @DSwitcher { trigger: trig > 0 and B61 < 1, }; +Eb62 @DSwitcher { trigger: trig > 0 and B62 < 1, }; +Eb63 @DSwitcher { trigger: trig > 0 and B63 < 1, }; +Eb64 @DSwitcher { trigger: trig > 0 and B64 < 1, }; +Eb65 @DSwitcher { trigger: trig > 0 and B65 < 1, }; +Eb66 @DSwitcher { trigger: trig > 0 and B66 < 1, }; +Eb67 @DSwitcher { trigger: trig > 0 and B67 < 1, }; +Eb68 @DSwitcher { trigger: trig > 0 and B68 < 1, }; +Eb69 @DSwitcher { trigger: trig > 0 and B69 < 1, }; +Eb70 @DSwitcher { trigger: trig > 0 and B70 < 1, }; +Eb71 @DSwitcher { trigger: trig > 0 and B71 < 1, }; +Eb72 @DSwitcher { trigger: trig > 0 and B72 < 1, }; +Eb73 @DSwitcher { trigger: trig > 0 and B73 < 1, }; +Eb74 @DSwitcher { trigger: trig > 0 and B74 < 1, }; +Eb75 @DSwitcher { trigger: trig > 0 and B75 < 1, }; +Eb76 @DSwitcher { trigger: trig > 0 and B76 < 1, }; +Eb77 @DSwitcher { trigger: trig > 0 and B77 < 1, }; +Eb78 @DSwitcher { trigger: trig > 0 and B78 < 1, }; +Eb79 @DSwitcher { trigger: trig > 0 and B79 < 1, }; +Eb80 @DSwitcher { trigger: trig > 0 and B80 < 1, }; +Eb81 @DSwitcher { trigger: trig > 0 and B81 < 1, }; +Eb82 @DSwitcher { trigger: trig > 0 and B82 < 1, }; +Eb83 @DSwitcher { trigger: trig > 0 and B83 < 1, }; +Eb84 @DSwitcher { trigger: trig > 0 and B84 < 1, }; +Eb85 @DSwitcher { trigger: trig > 0 and B85 < 1, }; +Eb86 @DSwitcher { trigger: trig > 0 and B86 < 1, }; +Eb87 @DSwitcher { trigger: trig > 0 and B87 < 1, }; +Eb88 @DSwitcher { trigger: trig > 0 and B88 < 1, }; +Eb89 @DSwitcher { trigger: trig > 0 and B89 < 1, }; +Eb90 @DSwitcher { trigger: trig > 0 and B90 < 1, }; +Eb91 @DSwitcher { trigger: trig > 0 and B91 < 1, }; +Eb92 @DSwitcher { trigger: trig > 0 and B92 < 1, }; +Eb93 @DSwitcher { trigger: trig > 0 and B93 < 1, }; +Eb94 @DSwitcher { trigger: trig > 0 and B94 < 1, }; +Eb95 @DSwitcher { trigger: trig > 0 and B95 < 1, }; +Eb96 @DSwitcher { trigger: trig > 0 and B96 < 1, }; +Eb97 @DSwitcher { trigger: trig > 0 and B97 < 1, }; +Eb98 @DSwitcher { trigger: trig > 0 and B98 < 1, }; +Eb99 @DSwitcher { trigger: trig > 0 and B99 < 1, }; +_E0 @DSwitcher { trigger: abs(Asum - Bsum) > 100, }; + diff --git a/latest/cases/01466/synopsis.txt b/latest/cases/01466/synopsis.txt new file mode 100644 index 000000000..0a51a40ae --- /dev/null +++ b/latest/cases/01466/synopsis.txt @@ -0,0 +1,442 @@ + +category: Test +synopsis: A test of random event execution at t0. +componentTags: AssignmentRule, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, EventT0Firing, InitialValueReassigned, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, 200 events 'compete' in pairs to assing values to variables: if E0 fires, Eb0 will not, and visa versa, for all events E0-E99, Eb0-Eb99. Because all events have the same priority, the E# set should win about half the time (assigning a value to the corresponding 'A' variable), and the Eb# set should win the other half, assigning values to the corresponding 'B' variables. + + 'toodiverged' will only equal 1 if (Asum-Bsum)>100. Since the standard deviation of 100 coin flips is 5, which would correspond to a difference of 20, 'toodiverged' will only equal 1 if the observed distribution of choices is more than five standard deviations away from expected (0), which will happen approximately one time in 1.7 million. + +The model contains: +* 205 parameters (trig, A0, A1, A2, A3, A4, A5, A6, A7, A8, A9, A10, A11, A12, A13, A14, A15, A16, A17, A18, A19, A20, A21, A22, A23, A24, A25, A26, A27, A28, A29, A30, A31, A32, A33, A34, A35, A36, A37, A38, A39, A40, A41, A42, A43, A44, A45, A46, A47, A48, A49, A50, A51, A52, A53, A54, A55, A56, A57, A58, A59, A60, A61, A62, A63, A64, A65, A66, A67, A68, A69, A70, A71, A72, A73, A74, A75, A76, A77, A78, A79, A80, A81, A82, A83, A84, A85, A86, A87, A88, A89, A90, A91, A92, A93, A94, A95, A96, A97, A98, A99, B0, B1, B2, B3, B4, B5, B6, B7, B8, B9, B10, B11, B12, B13, B14, B15, B16, B17, B18, B19, B20, B21, B22, B23, B24, B25, B26, B27, B28, B29, B30, B31, B32, B33, B34, B35, B36, B37, B38, B39, B40, B41, B42, B43, B44, B45, B46, B47, B48, B49, B50, B51, B52, B53, B54, B55, B56, B57, B58, B59, B60, B61, B62, B63, B64, B65, B66, B67, B68, B69, B70, B71, B72, B73, B74, B75, B76, B77, B78, B79, B80, B81, B82, B83, B84, B85, B86, B87, B88, B89, B90, B91, B92, B93, B94, B95, B96, B97, B98, B99, Asum, Bsum, Allsum, toodiverged) + +There are 201 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *initialValue* | *Event Assignments* | +| E0 | $(trig > 0) && (A0 < 1)$ | $5$ | false | false | $B0 = 2$ | +| E1 | $(trig > 0) && (A1 < 1)$ | $5$ | false | false | $B1 = 2$ | +| E2 | $(trig > 0) && (A2 < 1)$ | $5$ | false | false | $B2 = 2$ | +| E3 | $(trig > 0) && (A3 < 1)$ | $5$ | false | false | $B3 = 2$ | +| E4 | $(trig > 0) && (A4 < 1)$ | $5$ | false | false | $B4 = 2$ | +| E5 | $(trig > 0) && (A5 < 1)$ | $5$ | false | false | $B5 = 2$ | +| E6 | $(trig > 0) && (A6 < 1)$ | $5$ | false | false | $B6 = 2$ | +| E7 | $(trig > 0) && (A7 < 1)$ | $5$ | false | false | $B7 = 2$ | +| E8 | $(trig > 0) && (A8 < 1)$ | $5$ | false | false | $B8 = 2$ | +| E9 | $(trig > 0) && (A9 < 1)$ | $5$ | false | false | $B9 = 2$ | +| E10 | $(trig > 0) && (A10 < 1)$ | $5$ | false | false | $B10 = 2$ | +| E11 | $(trig > 0) && (A11 < 1)$ | $5$ | false | false | $B11 = 2$ | +| E12 | $(trig > 0) && (A12 < 1)$ | $5$ | false | false | $B12 = 2$ | +| E13 | $(trig > 0) && (A13 < 1)$ | $5$ | false | false | $B13 = 2$ | +| E14 | $(trig > 0) && (A14 < 1)$ | $5$ | false | false | $B14 = 2$ | +| E15 | $(trig > 0) && (A15 < 1)$ | $5$ | false | false | $B15 = 2$ | +| E16 | $(trig > 0) && (A16 < 1)$ | $5$ | false | false | $B16 = 2$ | +| E17 | $(trig > 0) && (A17 < 1)$ | $5$ | false | false | $B17 = 2$ | +| E18 | $(trig > 0) && (A18 < 1)$ | $5$ | false | false | $B18 = 2$ | +| E19 | $(trig > 0) && (A19 < 1)$ | $5$ | false | false | $B19 = 2$ | +| E20 | $(trig > 0) && (A20 < 1)$ | $5$ | false | false | $B20 = 2$ | +| E21 | $(trig > 0) && (A21 < 1)$ | $5$ | false | false | $B21 = 2$ | +| E22 | $(trig > 0) && (A22 < 1)$ | $5$ | false | false | $B22 = 2$ | +| E23 | $(trig > 0) && (A23 < 1)$ | $5$ | false | false | $B23 = 2$ | +| E24 | $(trig > 0) && (A24 < 1)$ | $5$ | false | false | $B24 = 2$ | +| E25 | $(trig > 0) && (A25 < 1)$ | $5$ | false | false | $B25 = 2$ | +| E26 | $(trig > 0) && (A26 < 1)$ | $5$ | false | false | $B26 = 2$ | +| E27 | $(trig > 0) && (A27 < 1)$ | $5$ | false | false | $B27 = 2$ | +| E28 | $(trig > 0) && (A28 < 1)$ | $5$ | false | false | $B28 = 2$ | +| E29 | $(trig > 0) && (A29 < 1)$ | $5$ | false | false | $B29 = 2$ | +| E30 | $(trig > 0) && (A30 < 1)$ | $5$ | false | false | $B30 = 2$ | +| E31 | $(trig > 0) && (A31 < 1)$ | $5$ | false | false | $B31 = 2$ | +| E32 | $(trig > 0) && (A32 < 1)$ | $5$ | false | false | $B32 = 2$ | +| E33 | $(trig > 0) && (A33 < 1)$ | $5$ | false | false | $B33 = 2$ | +| E34 | $(trig > 0) && (A34 < 1)$ | $5$ | false | false | $B34 = 2$ | +| E35 | $(trig > 0) && (A35 < 1)$ | $5$ | false | false | $B35 = 2$ | +| E36 | $(trig > 0) && (A36 < 1)$ | $5$ | false | false | $B36 = 2$ | +| E37 | $(trig > 0) && (A37 < 1)$ | $5$ | false | false | $B37 = 2$ | +| E38 | $(trig > 0) && (A38 < 1)$ | $5$ | false | false | $B38 = 2$ | +| E39 | $(trig > 0) && (A39 < 1)$ | $5$ | false | false | $B39 = 2$ | +| E40 | $(trig > 0) && (A40 < 1)$ | $5$ | false | false | $B40 = 2$ | +| E41 | $(trig > 0) && (A41 < 1)$ | $5$ | false | false | $B41 = 2$ | +| E42 | $(trig > 0) && (A42 < 1)$ | $5$ | false | false | $B42 = 2$ | +| E43 | $(trig > 0) && (A43 < 1)$ | $5$ | false | false | $B43 = 2$ | +| E44 | $(trig > 0) && (A44 < 1)$ | $5$ | false | false | $B44 = 2$ | +| E45 | $(trig > 0) && (A45 < 1)$ | $5$ | false | false | $B45 = 2$ | +| E46 | $(trig > 0) && (A46 < 1)$ | $5$ | false | false | $B46 = 2$ | +| E47 | $(trig > 0) && (A47 < 1)$ | $5$ | false | false | $B47 = 2$ | +| E48 | $(trig > 0) && (A48 < 1)$ | $5$ | false | false | $B48 = 2$ | +| E49 | $(trig > 0) && (A49 < 1)$ | $5$ | false | false | $B49 = 2$ | +| E50 | $(trig > 0) && (A50 < 1)$ | $5$ | false | false | $B50 = 2$ | +| E51 | $(trig > 0) && (A51 < 1)$ | $5$ | false | false | $B51 = 2$ | +| E52 | $(trig > 0) && (A52 < 1)$ | $5$ | false | false | $B52 = 2$ | +| E53 | $(trig > 0) && (A53 < 1)$ | $5$ | false | false | $B53 = 2$ | +| E54 | $(trig > 0) && (A54 < 1)$ | $5$ | false | false | $B54 = 2$ | +| E55 | $(trig > 0) && (A55 < 1)$ | $5$ | false | false | $B55 = 2$ | +| E56 | $(trig > 0) && (A56 < 1)$ | $5$ | false | false | $B56 = 2$ | +| E57 | $(trig > 0) && (A57 < 1)$ | $5$ | false | false | $B57 = 2$ | +| E58 | $(trig > 0) && (A58 < 1)$ | $5$ | false | false | $B58 = 2$ | +| E59 | $(trig > 0) && (A59 < 1)$ | $5$ | false | false | $B59 = 2$ | +| E60 | $(trig > 0) && (A60 < 1)$ | $5$ | false | false | $B60 = 2$ | +| E61 | $(trig > 0) && (A61 < 1)$ | $5$ | false | false | $B61 = 2$ | +| E62 | $(trig > 0) && (A62 < 1)$ | $5$ | false | false | $B62 = 2$ | +| E63 | $(trig > 0) && (A63 < 1)$ | $5$ | false | false | $B63 = 2$ | +| E64 | $(trig > 0) && (A64 < 1)$ | $5$ | false | false | $B64 = 2$ | +| E65 | $(trig > 0) && (A65 < 1)$ | $5$ | false | false | $B65 = 2$ | +| E66 | $(trig > 0) && (A66 < 1)$ | $5$ | false | false | $B66 = 2$ | +| E67 | $(trig > 0) && (A67 < 1)$ | $5$ | false | false | $B67 = 2$ | +| E68 | $(trig > 0) && (A68 < 1)$ | $5$ | false | false | $B68 = 2$ | +| E69 | $(trig > 0) && (A69 < 1)$ | $5$ | false | false | $B69 = 2$ | +| E70 | $(trig > 0) && (A70 < 1)$ | $5$ | false | false | $B70 = 2$ | +| E71 | $(trig > 0) && (A71 < 1)$ | $5$ | false | false | $B71 = 2$ | +| E72 | $(trig > 0) && (A72 < 1)$ | $5$ | false | false | $B72 = 2$ | +| E73 | $(trig > 0) && (A73 < 1)$ | $5$ | false | false | $B73 = 2$ | +| E74 | $(trig > 0) && (A74 < 1)$ | $5$ | false | false | $B74 = 2$ | +| E75 | $(trig > 0) && (A75 < 1)$ | $5$ | false | false | $B75 = 2$ | +| E76 | $(trig > 0) && (A76 < 1)$ | $5$ | false | false | $B76 = 2$ | +| E77 | $(trig > 0) && (A77 < 1)$ | $5$ | false | false | $B77 = 2$ | +| E78 | $(trig > 0) && (A78 < 1)$ | $5$ | false | false | $B78 = 2$ | +| E79 | $(trig > 0) && (A79 < 1)$ | $5$ | false | false | $B79 = 2$ | +| E80 | $(trig > 0) && (A80 < 1)$ | $5$ | false | false | $B80 = 2$ | +| E81 | $(trig > 0) && (A81 < 1)$ | $5$ | false | false | $B81 = 2$ | +| E82 | $(trig > 0) && (A82 < 1)$ | $5$ | false | false | $B82 = 2$ | +| E83 | $(trig > 0) && (A83 < 1)$ | $5$ | false | false | $B83 = 2$ | +| E84 | $(trig > 0) && (A84 < 1)$ | $5$ | false | false | $B84 = 2$ | +| E85 | $(trig > 0) && (A85 < 1)$ | $5$ | false | false | $B85 = 2$ | +| E86 | $(trig > 0) && (A86 < 1)$ | $5$ | false | false | $B86 = 2$ | +| E87 | $(trig > 0) && (A87 < 1)$ | $5$ | false | false | $B87 = 2$ | +| E88 | $(trig > 0) && (A88 < 1)$ | $5$ | false | false | $B88 = 2$ | +| E89 | $(trig > 0) && (A89 < 1)$ | $5$ | false | false | $B89 = 2$ | +| E90 | $(trig > 0) && (A90 < 1)$ | $5$ | false | false | $B90 = 2$ | +| E91 | $(trig > 0) && (A91 < 1)$ | $5$ | false | false | $B91 = 2$ | +| E92 | $(trig > 0) && (A92 < 1)$ | $5$ | false | false | $B92 = 2$ | +| E93 | $(trig > 0) && (A93 < 1)$ | $5$ | false | false | $B93 = 2$ | +| E94 | $(trig > 0) && (A94 < 1)$ | $5$ | false | false | $B94 = 2$ | +| E95 | $(trig > 0) && (A95 < 1)$ | $5$ | false | false | $B95 = 2$ | +| E96 | $(trig > 0) && (A96 < 1)$ | $5$ | false | false | $B96 = 2$ | +| E97 | $(trig > 0) && (A97 < 1)$ | $5$ | false | false | $B97 = 2$ | +| E98 | $(trig > 0) && (A98 < 1)$ | $5$ | false | false | $B98 = 2$ | +| E99 | $(trig > 0) && (A99 < 1)$ | $5$ | false | false | $B99 = 2$ | +| Eb0 | $(trig > 0) && (B0 < 1)$ | $5$ | false | false | $A0 = 2$ | +| Eb1 | $(trig > 0) && (B1 < 1)$ | $5$ | false | false | $A1 = 2$ | +| Eb2 | $(trig > 0) && (B2 < 1)$ | $5$ | false | false | $A2 = 2$ | +| Eb3 | $(trig > 0) && (B3 < 1)$ | $5$ | false | false | $A3 = 2$ | +| Eb4 | $(trig > 0) && (B4 < 1)$ | $5$ | false | false | $A4 = 2$ | +| Eb5 | $(trig > 0) && (B5 < 1)$ | $5$ | false | false | $A5 = 2$ | +| Eb6 | $(trig > 0) && (B6 < 1)$ | $5$ | false | false | $A6 = 2$ | +| Eb7 | $(trig > 0) && (B7 < 1)$ | $5$ | false | false | $A7 = 2$ | +| Eb8 | $(trig > 0) && (B8 < 1)$ | $5$ | false | false | $A8 = 2$ | +| Eb9 | $(trig > 0) && (B9 < 1)$ | $5$ | false | false | $A9 = 2$ | +| Eb10 | $(trig > 0) && (B10 < 1)$ | $5$ | false | false | $A10 = 2$ | +| Eb11 | $(trig > 0) && (B11 < 1)$ | $5$ | false | false | $A11 = 2$ | +| Eb12 | $(trig > 0) && (B12 < 1)$ | $5$ | false | false | $A12 = 2$ | +| Eb13 | $(trig > 0) && (B13 < 1)$ | $5$ | false | false | $A13 = 2$ | +| Eb14 | $(trig > 0) && (B14 < 1)$ | $5$ | false | false | $A14 = 2$ | +| Eb15 | $(trig > 0) && (B15 < 1)$ | $5$ | false | false | $A15 = 2$ | +| Eb16 | $(trig > 0) && (B16 < 1)$ | $5$ | false | false | $A16 = 2$ | +| Eb17 | $(trig > 0) && (B17 < 1)$ | $5$ | false | false | $A17 = 2$ | +| Eb18 | $(trig > 0) && (B18 < 1)$ | $5$ | false | false | $A18 = 2$ | +| Eb19 | $(trig > 0) && (B19 < 1)$ | $5$ | false | false | $A19 = 2$ | +| Eb20 | $(trig > 0) && (B20 < 1)$ | $5$ | false | false | $A20 = 2$ | +| Eb21 | $(trig > 0) && (B21 < 1)$ | $5$ | false | false | $A21 = 2$ | +| Eb22 | $(trig > 0) && (B22 < 1)$ | $5$ | false | false | $A22 = 2$ | +| Eb23 | $(trig > 0) && (B23 < 1)$ | $5$ | false | false | $A23 = 2$ | +| Eb24 | $(trig > 0) && (B24 < 1)$ | $5$ | false | false | $A24 = 2$ | +| Eb25 | $(trig > 0) && (B25 < 1)$ | $5$ | false | false | $A25 = 2$ | +| Eb26 | $(trig > 0) && (B26 < 1)$ | $5$ | false | false | $A26 = 2$ | +| Eb27 | $(trig > 0) && (B27 < 1)$ | $5$ | false | false | $A27 = 2$ | +| Eb28 | $(trig > 0) && (B28 < 1)$ | $5$ | false | false | $A28 = 2$ | +| Eb29 | $(trig > 0) && (B29 < 1)$ | $5$ | false | false | $A29 = 2$ | +| Eb30 | $(trig > 0) && (B30 < 1)$ | $5$ | false | false | $A30 = 2$ | +| Eb31 | $(trig > 0) && (B31 < 1)$ | $5$ | false | false | $A31 = 2$ | +| Eb32 | $(trig > 0) && (B32 < 1)$ | $5$ | false | false | $A32 = 2$ | +| Eb33 | $(trig > 0) && (B33 < 1)$ | $5$ | false | false | $A33 = 2$ | +| Eb34 | $(trig > 0) && (B34 < 1)$ | $5$ | false | false | $A34 = 2$ | +| Eb35 | $(trig > 0) && (B35 < 1)$ | $5$ | false | false | $A35 = 2$ | +| Eb36 | $(trig > 0) && (B36 < 1)$ | $5$ | false | false | $A36 = 2$ | +| Eb37 | $(trig > 0) && (B37 < 1)$ | $5$ | false | false | $A37 = 2$ | +| Eb38 | $(trig > 0) && (B38 < 1)$ | $5$ | false | false | $A38 = 2$ | +| Eb39 | $(trig > 0) && (B39 < 1)$ | $5$ | false | false | $A39 = 2$ | +| Eb40 | $(trig > 0) && (B40 < 1)$ | $5$ | false | false | $A40 = 2$ | +| Eb41 | $(trig > 0) && (B41 < 1)$ | $5$ | false | false | $A41 = 2$ | +| Eb42 | $(trig > 0) && (B42 < 1)$ | $5$ | false | false | $A42 = 2$ | +| Eb43 | $(trig > 0) && (B43 < 1)$ | $5$ | false | false | $A43 = 2$ | +| Eb44 | $(trig > 0) && (B44 < 1)$ | $5$ | false | false | $A44 = 2$ | +| Eb45 | $(trig > 0) && (B45 < 1)$ | $5$ | false | false | $A45 = 2$ | +| Eb46 | $(trig > 0) && (B46 < 1)$ | $5$ | false | false | $A46 = 2$ | +| Eb47 | $(trig > 0) && (B47 < 1)$ | $5$ | false | false | $A47 = 2$ | +| Eb48 | $(trig > 0) && (B48 < 1)$ | $5$ | false | false | $A48 = 2$ | +| Eb49 | $(trig > 0) && (B49 < 1)$ | $5$ | false | false | $A49 = 2$ | +| Eb50 | $(trig > 0) && (B50 < 1)$ | $5$ | false | false | $A50 = 2$ | +| Eb51 | $(trig > 0) && (B51 < 1)$ | $5$ | false | false | $A51 = 2$ | +| Eb52 | $(trig > 0) && (B52 < 1)$ | $5$ | false | false | $A52 = 2$ | +| Eb53 | $(trig > 0) && (B53 < 1)$ | $5$ | false | false | $A53 = 2$ | +| Eb54 | $(trig > 0) && (B54 < 1)$ | $5$ | false | false | $A54 = 2$ | +| Eb55 | $(trig > 0) && (B55 < 1)$ | $5$ | false | false | $A55 = 2$ | +| Eb56 | $(trig > 0) && (B56 < 1)$ | $5$ | false | false | $A56 = 2$ | +| Eb57 | $(trig > 0) && (B57 < 1)$ | $5$ | false | false | $A57 = 2$ | +| Eb58 | $(trig > 0) && (B58 < 1)$ | $5$ | false | false | $A58 = 2$ | +| Eb59 | $(trig > 0) && (B59 < 1)$ | $5$ | false | false | $A59 = 2$ | +| Eb60 | $(trig > 0) && (B60 < 1)$ | $5$ | false | false | $A60 = 2$ | +| Eb61 | $(trig > 0) && (B61 < 1)$ | $5$ | false | false | $A61 = 2$ | +| Eb62 | $(trig > 0) && (B62 < 1)$ | $5$ | false | false | $A62 = 2$ | +| Eb63 | $(trig > 0) && (B63 < 1)$ | $5$ | false | false | $A63 = 2$ | +| Eb64 | $(trig > 0) && (B64 < 1)$ | $5$ | false | false | $A64 = 2$ | +| Eb65 | $(trig > 0) && (B65 < 1)$ | $5$ | false | false | $A65 = 2$ | +| Eb66 | $(trig > 0) && (B66 < 1)$ | $5$ | false | false | $A66 = 2$ | +| Eb67 | $(trig > 0) && (B67 < 1)$ | $5$ | false | false | $A67 = 2$ | +| Eb68 | $(trig > 0) && (B68 < 1)$ | $5$ | false | false | $A68 = 2$ | +| Eb69 | $(trig > 0) && (B69 < 1)$ | $5$ | false | false | $A69 = 2$ | +| Eb70 | $(trig > 0) && (B70 < 1)$ | $5$ | false | false | $A70 = 2$ | +| Eb71 | $(trig > 0) && (B71 < 1)$ | $5$ | false | false | $A71 = 2$ | +| Eb72 | $(trig > 0) && (B72 < 1)$ | $5$ | false | false | $A72 = 2$ | +| Eb73 | $(trig > 0) && (B73 < 1)$ | $5$ | false | false | $A73 = 2$ | +| Eb74 | $(trig > 0) && (B74 < 1)$ | $5$ | false | false | $A74 = 2$ | +| Eb75 | $(trig > 0) && (B75 < 1)$ | $5$ | false | false | $A75 = 2$ | +| Eb76 | $(trig > 0) && (B76 < 1)$ | $5$ | false | false | $A76 = 2$ | +| Eb77 | $(trig > 0) && (B77 < 1)$ | $5$ | false | false | $A77 = 2$ | +| Eb78 | $(trig > 0) && (B78 < 1)$ | $5$ | false | false | $A78 = 2$ | +| Eb79 | $(trig > 0) && (B79 < 1)$ | $5$ | false | false | $A79 = 2$ | +| Eb80 | $(trig > 0) && (B80 < 1)$ | $5$ | false | false | $A80 = 2$ | +| Eb81 | $(trig > 0) && (B81 < 1)$ | $5$ | false | false | $A81 = 2$ | +| Eb82 | $(trig > 0) && (B82 < 1)$ | $5$ | false | false | $A82 = 2$ | +| Eb83 | $(trig > 0) && (B83 < 1)$ | $5$ | false | false | $A83 = 2$ | +| Eb84 | $(trig > 0) && (B84 < 1)$ | $5$ | false | false | $A84 = 2$ | +| Eb85 | $(trig > 0) && (B85 < 1)$ | $5$ | false | false | $A85 = 2$ | +| Eb86 | $(trig > 0) && (B86 < 1)$ | $5$ | false | false | $A86 = 2$ | +| Eb87 | $(trig > 0) && (B87 < 1)$ | $5$ | false | false | $A87 = 2$ | +| Eb88 | $(trig > 0) && (B88 < 1)$ | $5$ | false | false | $A88 = 2$ | +| Eb89 | $(trig > 0) && (B89 < 1)$ | $5$ | false | false | $A89 = 2$ | +| Eb90 | $(trig > 0) && (B90 < 1)$ | $5$ | false | false | $A90 = 2$ | +| Eb91 | $(trig > 0) && (B91 < 1)$ | $5$ | false | false | $A91 = 2$ | +| Eb92 | $(trig > 0) && (B92 < 1)$ | $5$ | false | false | $A92 = 2$ | +| Eb93 | $(trig > 0) && (B93 < 1)$ | $5$ | false | false | $A93 = 2$ | +| Eb94 | $(trig > 0) && (B94 < 1)$ | $5$ | false | false | $A94 = 2$ | +| Eb95 | $(trig > 0) && (B95 < 1)$ | $5$ | false | false | $A95 = 2$ | +| Eb96 | $(trig > 0) && (B96 < 1)$ | $5$ | false | false | $A96 = 2$ | +| Eb97 | $(trig > 0) && (B97 < 1)$ | $5$ | false | false | $A97 = 2$ | +| Eb98 | $(trig > 0) && (B98 < 1)$ | $5$ | false | false | $A98 = 2$ | +| Eb99 | $(trig > 0) && (B99 < 1)$ | $5$ | false | false | $A99 = 2$ | +| _E0 | $abs(Asum - Bsum) > 100$ | (unset) | true | true | $toodiverged = 1$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | Asum | $A0 + A1 + A2 + A3 + A4 + A5 + A6 + A7 + A8 + A9 + A10 + A11 + A12 + A13 + A14 + A15 + A16 + A17 + A18 + A19 + A20 + A21 + A22 + A23 + A24 + A25 + A26 + A27 + A28 + A29 + A30 + A31 + A32 + A33 + A34 + A35 + A36 + A37 + A38 + A39 + A40 + A41 + A42 + A43 + A44 + A45 + A46 + A47 + A48 + A49 + A50 + A51 + A52 + A53 + A54 + A55 + A56 + A57 + A58 + A59 + A60 + A61 + A62 + A63 + A64 + A65 + A66 + A67 + A68 + A69 + A70 + A71 + A72 + A73 + A74 + A75 + A76 + A77 + A78 + A79 + A80 + A81 + A82 + A83 + A84 + A85 + A86 + A87 + A88 + A89 + A90 + A91 + A92 + A93 + A94 + A95 + A96 + A97 + A98 + A99$ | +| Assignment | Bsum | $B0 + B1 + B2 + B3 + B4 + B5 + B6 + B7 + B8 + B9 + B10 + B11 + B12 + B13 + B14 + B15 + B16 + B17 + B18 + B19 + B20 + B21 + B22 + B23 + B24 + B25 + B26 + B27 + B28 + B29 + B30 + B31 + B32 + B33 + B34 + B35 + B36 + B37 + B38 + B39 + B40 + B41 + B42 + B43 + B44 + B45 + B46 + B47 + B48 + B49 + B50 + B51 + B52 + B53 + B54 + B55 + B56 + B57 + B58 + B59 + B60 + B61 + B62 + B63 + B64 + B65 + B66 + B67 + B68 + B69 + B70 + B71 + B72 + B73 + B74 + B75 + B76 + B77 + B78 + B79 + B80 + B81 + B82 + B83 + B84 + B85 + B86 + B87 + B88 + B89 + B90 + B91 + B92 + B93 + B94 + B95 + B96 + B97 + B98 + B99$ | +| Assignment | Allsum | $Asum + Bsum$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter trig | $1$ | constant | +| Initial value of parameter A0 | $0$ | variable | +| Initial value of parameter A1 | $0$ | variable | +| Initial value of parameter A2 | $0$ | variable | +| Initial value of parameter A3 | $0$ | variable | +| Initial value of parameter A4 | $0$ | variable | +| Initial value of parameter A5 | $0$ | variable | +| Initial value of parameter A6 | $0$ | variable | +| Initial value of parameter A7 | $0$ | variable | +| Initial value of parameter A8 | $0$ | variable | +| Initial value of parameter A9 | $0$ | variable | +| Initial value of parameter A10 | $0$ | variable | +| Initial value of parameter A11 | $0$ | variable | +| Initial value of parameter A12 | $0$ | variable | +| Initial value of parameter A13 | $0$ | variable | +| Initial value of parameter A14 | $0$ | variable | +| Initial value of parameter A15 | $0$ | variable | +| Initial value of parameter A16 | $0$ | variable | +| Initial value of parameter A17 | $0$ | variable | +| Initial value of parameter A18 | $0$ | variable | +| Initial value of parameter A19 | $0$ | variable | +| Initial value of parameter A20 | $0$ | variable | +| Initial value of parameter A21 | $0$ | variable | +| Initial value of parameter A22 | $0$ | variable | +| Initial value of parameter A23 | $0$ | variable | +| Initial value of parameter A24 | $0$ | variable | +| Initial value of parameter A25 | $0$ | variable | +| Initial value of parameter A26 | $0$ | variable | +| Initial value of parameter A27 | $0$ | variable | +| Initial value of parameter A28 | $0$ | variable | +| Initial value of parameter A29 | $0$ | variable | +| Initial value of parameter A30 | $0$ | variable | +| Initial value of parameter A31 | $0$ | variable | +| Initial value of parameter A32 | $0$ | variable | +| Initial value of parameter A33 | $0$ | variable | +| Initial value of parameter A34 | $0$ | variable | +| Initial value of parameter A35 | $0$ | variable | +| Initial value of parameter A36 | $0$ | variable | +| Initial value of parameter A37 | $0$ | variable | +| Initial value of parameter A38 | $0$ | variable | +| Initial value of parameter A39 | $0$ | variable | +| Initial value of parameter A40 | $0$ | variable | +| Initial value of parameter A41 | $0$ | variable | +| Initial value of parameter A42 | $0$ | variable | +| Initial value of parameter A43 | $0$ | variable | +| Initial value of parameter A44 | $0$ | variable | +| Initial value of parameter A45 | $0$ | variable | +| Initial value of parameter A46 | $0$ | variable | +| Initial value of parameter A47 | $0$ | variable | +| Initial value of parameter A48 | $0$ | variable | +| Initial value of parameter A49 | $0$ | variable | +| Initial value of parameter A50 | $0$ | variable | +| Initial value of parameter A51 | $0$ | variable | +| Initial value of parameter A52 | $0$ | variable | +| Initial value of parameter A53 | $0$ | variable | +| Initial value of parameter A54 | $0$ | variable | +| Initial value of parameter A55 | $0$ | variable | +| Initial value of parameter A56 | $0$ | variable | +| Initial value of parameter A57 | $0$ | variable | +| Initial value of parameter A58 | $0$ | variable | +| Initial value of parameter A59 | $0$ | variable | +| Initial value of parameter A60 | $0$ | variable | +| Initial value of parameter A61 | $0$ | variable | +| Initial value of parameter A62 | $0$ | variable | +| Initial value of parameter A63 | $0$ | variable | +| Initial value of parameter A64 | $0$ | variable | +| Initial value of parameter A65 | $0$ | variable | +| Initial value of parameter A66 | $0$ | variable | +| Initial value of parameter A67 | $0$ | variable | +| Initial value of parameter A68 | $0$ | variable | +| Initial value of parameter A69 | $0$ | variable | +| Initial value of parameter A70 | $0$ | variable | +| Initial value of parameter A71 | $0$ | variable | +| Initial value of parameter A72 | $0$ | variable | +| Initial value of parameter A73 | $0$ | variable | +| Initial value of parameter A74 | $0$ | variable | +| Initial value of parameter A75 | $0$ | variable | +| Initial value of parameter A76 | $0$ | variable | +| Initial value of parameter A77 | $0$ | variable | +| Initial value of parameter A78 | $0$ | variable | +| Initial value of parameter A79 | $0$ | variable | +| Initial value of parameter A80 | $0$ | variable | +| Initial value of parameter A81 | $0$ | variable | +| Initial value of parameter A82 | $0$ | variable | +| Initial value of parameter A83 | $0$ | variable | +| Initial value of parameter A84 | $0$ | variable | +| Initial value of parameter A85 | $0$ | variable | +| Initial value of parameter A86 | $0$ | variable | +| Initial value of parameter A87 | $0$ | variable | +| Initial value of parameter A88 | $0$ | variable | +| Initial value of parameter A89 | $0$ | variable | +| Initial value of parameter A90 | $0$ | variable | +| Initial value of parameter A91 | $0$ | variable | +| Initial value of parameter A92 | $0$ | variable | +| Initial value of parameter A93 | $0$ | variable | +| Initial value of parameter A94 | $0$ | variable | +| Initial value of parameter A95 | $0$ | variable | +| Initial value of parameter A96 | $0$ | variable | +| Initial value of parameter A97 | $0$ | variable | +| Initial value of parameter A98 | $0$ | variable | +| Initial value of parameter A99 | $0$ | variable | +| Initial value of parameter B0 | $0$ | variable | +| Initial value of parameter B1 | $0$ | variable | +| Initial value of parameter B2 | $0$ | variable | +| Initial value of parameter B3 | $0$ | variable | +| Initial value of parameter B4 | $0$ | variable | +| Initial value of parameter B5 | $0$ | variable | +| Initial value of parameter B6 | $0$ | variable | +| Initial value of parameter B7 | $0$ | variable | +| Initial value of parameter B8 | $0$ | variable | +| Initial value of parameter B9 | $0$ | variable | +| Initial value of parameter B10 | $0$ | variable | +| Initial value of parameter B11 | $0$ | variable | +| Initial value of parameter B12 | $0$ | variable | +| Initial value of parameter B13 | $0$ | variable | +| Initial value of parameter B14 | $0$ | variable | +| Initial value of parameter B15 | $0$ | variable | +| Initial value of parameter B16 | $0$ | variable | +| Initial value of parameter B17 | $0$ | variable | +| Initial value of parameter B18 | $0$ | variable | +| Initial value of parameter B19 | $0$ | variable | +| Initial value of parameter B20 | $0$ | variable | +| Initial value of parameter B21 | $0$ | variable | +| Initial value of parameter B22 | $0$ | variable | +| Initial value of parameter B23 | $0$ | variable | +| Initial value of parameter B24 | $0$ | variable | +| Initial value of parameter B25 | $0$ | variable | +| Initial value of parameter B26 | $0$ | variable | +| Initial value of parameter B27 | $0$ | variable | +| Initial value of parameter B28 | $0$ | variable | +| Initial value of parameter B29 | $0$ | variable | +| Initial value of parameter B30 | $0$ | variable | +| Initial value of parameter B31 | $0$ | variable | +| Initial value of parameter B32 | $0$ | variable | +| Initial value of parameter B33 | $0$ | variable | +| Initial value of parameter B34 | $0$ | variable | +| Initial value of parameter B35 | $0$ | variable | +| Initial value of parameter B36 | $0$ | variable | +| Initial value of parameter B37 | $0$ | variable | +| Initial value of parameter B38 | $0$ | variable | +| Initial value of parameter B39 | $0$ | variable | +| Initial value of parameter B40 | $0$ | variable | +| Initial value of parameter B41 | $0$ | variable | +| Initial value of parameter B42 | $0$ | variable | +| Initial value of parameter B43 | $0$ | variable | +| Initial value of parameter B44 | $0$ | variable | +| Initial value of parameter B45 | $0$ | variable | +| Initial value of parameter B46 | $0$ | variable | +| Initial value of parameter B47 | $0$ | variable | +| Initial value of parameter B48 | $0$ | variable | +| Initial value of parameter B49 | $0$ | variable | +| Initial value of parameter B50 | $0$ | variable | +| Initial value of parameter B51 | $0$ | variable | +| Initial value of parameter B52 | $0$ | variable | +| Initial value of parameter B53 | $0$ | variable | +| Initial value of parameter B54 | $0$ | variable | +| Initial value of parameter B55 | $0$ | variable | +| Initial value of parameter B56 | $0$ | variable | +| Initial value of parameter B57 | $0$ | variable | +| Initial value of parameter B58 | $0$ | variable | +| Initial value of parameter B59 | $0$ | variable | +| Initial value of parameter B60 | $0$ | variable | +| Initial value of parameter B61 | $0$ | variable | +| Initial value of parameter B62 | $0$ | variable | +| Initial value of parameter B63 | $0$ | variable | +| Initial value of parameter B64 | $0$ | variable | +| Initial value of parameter B65 | $0$ | variable | +| Initial value of parameter B66 | $0$ | variable | +| Initial value of parameter B67 | $0$ | variable | +| Initial value of parameter B68 | $0$ | variable | +| Initial value of parameter B69 | $0$ | variable | +| Initial value of parameter B70 | $0$ | variable | +| Initial value of parameter B71 | $0$ | variable | +| Initial value of parameter B72 | $0$ | variable | +| Initial value of parameter B73 | $0$ | variable | +| Initial value of parameter B74 | $0$ | variable | +| Initial value of parameter B75 | $0$ | variable | +| Initial value of parameter B76 | $0$ | variable | +| Initial value of parameter B77 | $0$ | variable | +| Initial value of parameter B78 | $0$ | variable | +| Initial value of parameter B79 | $0$ | variable | +| Initial value of parameter B80 | $0$ | variable | +| Initial value of parameter B81 | $0$ | variable | +| Initial value of parameter B82 | $0$ | variable | +| Initial value of parameter B83 | $0$ | variable | +| Initial value of parameter B84 | $0$ | variable | +| Initial value of parameter B85 | $0$ | variable | +| Initial value of parameter B86 | $0$ | variable | +| Initial value of parameter B87 | $0$ | variable | +| Initial value of parameter B88 | $0$ | variable | +| Initial value of parameter B89 | $0$ | variable | +| Initial value of parameter B90 | $0$ | variable | +| Initial value of parameter B91 | $0$ | variable | +| Initial value of parameter B92 | $0$ | variable | +| Initial value of parameter B93 | $0$ | variable | +| Initial value of parameter B94 | $0$ | variable | +| Initial value of parameter B95 | $0$ | variable | +| Initial value of parameter B96 | $0$ | variable | +| Initial value of parameter B97 | $0$ | variable | +| Initial value of parameter B98 | $0$ | variable | +| Initial value of parameter B99 | $0$ | variable | +| Initial value of parameter Asum | $A0 + A1 + A2 + A3 + A4 + A5 + A6 + A7 + A8 + A9 + A10 + A11 + A12 + A13 + A14 + A15 + A16 + A17 + A18 + A19 + A20 + A21 + A22 + A23 + A24 + A25 + A26 + A27 + A28 + A29 + A30 + A31 + A32 + A33 + A34 + A35 + A36 + A37 + A38 + A39 + A40 + A41 + A42 + A43 + A44 + A45 + A46 + A47 + A48 + A49 + A50 + A51 + A52 + A53 + A54 + A55 + A56 + A57 + A58 + A59 + A60 + A61 + A62 + A63 + A64 + A65 + A66 + A67 + A68 + A69 + A70 + A71 + A72 + A73 + A74 + A75 + A76 + A77 + A78 + A79 + A80 + A81 + A82 + A83 + A84 + A85 + A86 + A87 + A88 + A89 + A90 + A91 + A92 + A93 + A94 + A95 + A96 + A97 + A98 + A99$ | variable | +| Initial value of parameter Bsum | $B0 + B1 + B2 + B3 + B4 + B5 + B6 + B7 + B8 + B9 + B10 + B11 + B12 + B13 + B14 + B15 + B16 + B17 + B18 + B19 + B20 + B21 + B22 + B23 + B24 + B25 + B26 + B27 + B28 + B29 + B30 + B31 + B32 + B33 + B34 + B35 + B36 + B37 + B38 + B39 + B40 + B41 + B42 + B43 + B44 + B45 + B46 + B47 + B48 + B49 + B50 + B51 + B52 + B53 + B54 + B55 + B56 + B57 + B58 + B59 + B60 + B61 + B62 + B63 + B64 + B65 + B66 + B67 + B68 + B69 + B70 + B71 + B72 + B73 + B74 + B75 + B76 + B77 + B78 + B79 + B80 + B81 + B82 + B83 + B84 + B85 + B86 + B87 + B88 + B89 + B90 + B91 + B92 + B93 + B94 + B95 + B96 + B97 + B98 + B99$ | variable | +| Initial value of parameter Allsum | $Asum + Bsum$ | variable | +| Initial value of parameter toodiverged | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01467/l2v5/index.heta b/latest/cases/01467/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01467/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01467/l3v2/build.log b/latest/cases/01467/l3v2/build.log new file mode 100644 index 000000000..b12c58407 --- /dev/null +++ b/latest/cases/01467/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01467/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01467/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01467/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] Record "p8" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01467/l3v2/index.heta b/latest/cases/01467/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01467/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01467/model-sbml-l3v2.xml b/latest/cases/01467/model-sbml-l3v2.xml new file mode 100644 index 000000000..1f54557da --- /dev/null +++ b/latest/cases/01467/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + 80 + + + + + + + + + + + diff --git a/latest/cases/01467/synopsis.txt b/latest/cases/01467/synopsis.txt new file mode 100644 index 000000000..8dde279e8 --- /dev/null +++ b/latest/cases/01467/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: Hierarchical model with conversion factor test. +componentTags: AssignmentRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: InitialValueReassigned, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: comp + + This model repeats model 01137, testing a replacement with a conversion factor that affects the assignment rule of the replaced parameter, except that in this test, the conversion factor affects a sub-submodel variable, instead of a submodel variable directly. + +The 'flattened' version of this hierarchical model contains: +* 2 parameters (conv, p8) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p8 | $80 * conv$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter conv | $0.1$ | constant | +| Initial value of parameter p8 | $80 * conv$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01468/l2v5/index.heta b/latest/cases/01468/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01468/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01468/l3v2/heta-code/output.heta b/latest/cases/01468/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2a4369a14 --- /dev/null +++ b/latest/cases/01468/l3v2/heta-code/output.heta @@ -0,0 +1,6 @@ + + +t @TimeScale { }; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01468/l3v2/index.heta b/latest/cases/01468/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01468/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01468/l3v2/json/output.json b/latest/cases/01468/l3v2/json/output.json new file mode 100644 index 000000000..679092c23 --- /dev/null +++ b/latest/cases/01468/l3v2/json/output.json @@ -0,0 +1,10 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + } +] \ No newline at end of file diff --git a/latest/cases/01468/model-sbml-l3v2.xml b/latest/cases/01468/model-sbml-l3v2.xml new file mode 100644 index 000000000..ab3afe795 --- /dev/null +++ b/latest/cases/01468/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + 10 + + + + + + + + + + + + diff --git a/latest/cases/01468/output.heta b/latest/cases/01468/output.heta new file mode 100644 index 000000000..1c59764f1 --- /dev/null +++ b/latest/cases/01468/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub2__sub1__s1) +* 1 parameter (extentconv) +* 1 compartment (sub2__sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> sub2__sub1__s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub2__sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'sub2__sub1__C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01468/synopsis.txt b/latest/cases/01468/synopsis.txt new file mode 100644 index 000000000..59daa3295 --- /dev/null +++ b/latest/cases/01468/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection. + +The 'flattened' version of this hierarchical model contains: +* 1 species (sub2__sub1__s1) +* 1 parameter (extentconv) +* 1 compartment (sub2__sub1__C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> sub2__sub1__s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species sub2__sub1__s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'sub2__sub1__C' | $1$ | constant |] + diff --git a/latest/cases/01469/l2v5/index.heta b/latest/cases/01469/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01469/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01469/l3v2/heta-code/output.heta b/latest/cases/01469/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e94ad6c1a --- /dev/null +++ b/latest/cases/01469/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 1 / C; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01469/l3v2/index.heta b/latest/cases/01469/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01469/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01469/l3v2/json/output.json b/latest/cases/01469/l3v2/json/output.json new file mode 100644 index 000000000..ab441a826 --- /dev/null +++ b/latest/cases/01469/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + } +] \ No newline at end of file diff --git a/latest/cases/01469/model-sbml-l3v2.xml b/latest/cases/01469/model-sbml-l3v2.xml new file mode 100644 index 000000000..3aaa12acb --- /dev/null +++ b/latest/cases/01469/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10 + + + + + + + + + + + + diff --git a/latest/cases/01469/output.heta b/latest/cases/01469/output.heta new file mode 100644 index 000000000..1f37eaeeb --- /dev/null +++ b/latest/cases/01469/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:ExtentConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (extentconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 1 / C; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01469/synopsis.txt b/latest/cases/01469/synopsis.txt new file mode 100644 index 000000000..bec6d0d19 --- /dev/null +++ b/latest/cases/01469/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:ExtentConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (extentconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01470/l2v5/index.heta b/latest/cases/01470/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01470/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01470/l3v2/heta-code/output.heta b/latest/cases/01470/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e94ad6c1a --- /dev/null +++ b/latest/cases/01470/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 1 / C; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01470/l3v2/index.heta b/latest/cases/01470/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01470/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01470/l3v2/json/output.json b/latest/cases/01470/l3v2/json/output.json new file mode 100644 index 000000000..ab441a826 --- /dev/null +++ b/latest/cases/01470/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "1 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + } +] \ No newline at end of file diff --git a/latest/cases/01470/model-sbml-l3v2.xml b/latest/cases/01470/model-sbml-l3v2.xml new file mode 100644 index 000000000..a54b5586e --- /dev/null +++ b/latest/cases/01470/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10 + + + + + + + + + + + + diff --git a/latest/cases/01470/output.heta b/latest/cases/01470/output.heta new file mode 100644 index 000000000..8bee7be50 --- /dev/null +++ b/latest/cases/01470/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection. The species and compartment from the top-level model are replaced by the submodel elements. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (extentconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 1 / C; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01470/synopsis.txt b/latest/cases/01470/synopsis.txt new file mode 100644 index 000000000..1d6830d01 --- /dev/null +++ b/latest/cases/01470/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:Submodel +testTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection. The species and compartment from the top-level model are replaced by the submodel elements. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (extentconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $1$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01471/l2v5/index.heta b/latest/cases/01471/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01471/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01471/l3v2/heta-code/output.heta b/latest/cases/01471/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5155a7fc1 --- /dev/null +++ b/latest/cases/01471/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 1; + +S @Species { compartment: comp, } .= 5; +D @Species { compartment: comp, } .= 10; + diff --git a/latest/cases/01471/l3v2/index.heta b/latest/cases/01471/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01471/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01471/l3v2/json/output.json b/latest/cases/01471/l3v2/json/output.json new file mode 100644 index 000000000..506f1f0f2 --- /dev/null +++ b/latest/cases/01471/l3v2/json/output.json @@ -0,0 +1,29 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S", + "assignments": { + "start_": "5" + }, + "compartment": "comp" + }, + { + "class": "Species", + "id": "D", + "assignments": { + "start_": "10" + }, + "compartment": "comp" + } +] \ No newline at end of file diff --git a/latest/cases/01471/model-sbml-l3v2.xml b/latest/cases/01471/model-sbml-l3v2.xml new file mode 100644 index 000000000..6cfebe38a --- /dev/null +++ b/latest/cases/01471/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01471/output.heta b/latest/cases/01471/output.heta new file mode 100644 index 000000000..353533eee --- /dev/null +++ b/latest/cases/01471/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: Replacements in external models +componentTags: Compartment, Reaction, Species, comp:Deletion, comp:ExternalModelDefinition, comp:ModelDefinition, comp:Port, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In this modified example from the specification, an external model is referenced by both a ReplacedBy and a ReplacedElement. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S, A__E, D, A__ES) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__J0: S + A__E -> A__ES | $(S + A__E) / A__ES$ | +| A__J1: A__ES -> A__E + D | $A__ES / (A__E + D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S | $1$ | variable | +| Initial concentration of species A__E | $1$ | variable | +| Initial concentration of species D | $1$ | variable | +| Initial concentration of species A__ES | $1$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 1; + +S @Species { compartment: comp, } .= 5; +D @Species { compartment: comp, } .= 10; + diff --git a/latest/cases/01471/synopsis.txt b/latest/cases/01471/synopsis.txt new file mode 100644 index 000000000..fe07ba98e --- /dev/null +++ b/latest/cases/01471/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: Replacements in external models +componentTags: Compartment, Reaction, Species, comp:Deletion, comp:ExternalModelDefinition, comp:ModelDefinition, comp:Port, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In this modified example from the specification, an external model is referenced by both a ReplacedBy and a ReplacedElement. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S, A__E, D, A__ES) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__J0: S + A__E -> A__ES | $(S + A__E) / A__ES$ | +| A__J1: A__ES -> A__E + D | $A__ES / (A__E + D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S | $1$ | variable | +| Initial concentration of species A__E | $1$ | variable | +| Initial concentration of species D | $1$ | variable | +| Initial concentration of species A__ES | $1$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + diff --git a/latest/cases/01472/l2v5/index.heta b/latest/cases/01472/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01472/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01472/l3v2/heta-code/output.heta b/latest/cases/01472/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5155a7fc1 --- /dev/null +++ b/latest/cases/01472/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 1; + +S @Species { compartment: comp, } .= 5; +D @Species { compartment: comp, } .= 10; + diff --git a/latest/cases/01472/l3v2/index.heta b/latest/cases/01472/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01472/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01472/l3v2/json/output.json b/latest/cases/01472/l3v2/json/output.json new file mode 100644 index 000000000..506f1f0f2 --- /dev/null +++ b/latest/cases/01472/l3v2/json/output.json @@ -0,0 +1,29 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S", + "assignments": { + "start_": "5" + }, + "compartment": "comp" + }, + { + "class": "Species", + "id": "D", + "assignments": { + "start_": "10" + }, + "compartment": "comp" + } +] \ No newline at end of file diff --git a/latest/cases/01472/model-sbml-l3v2.xml b/latest/cases/01472/model-sbml-l3v2.xml new file mode 100644 index 000000000..99222173e --- /dev/null +++ b/latest/cases/01472/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01472/output.heta b/latest/cases/01472/output.heta new file mode 100644 index 000000000..5d5aa5667 --- /dev/null +++ b/latest/cases/01472/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: An element in an external model submodel as the target of a replacedBy element. +componentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In this model, an element is replaced by an element in a submodel of an external model. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S, A__submod1__E, D, A__submod1__ES) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| A__submod1__J0: S + A__submod1__E -> A__submod1__ES | $(S + A__submod1__E) / A__submod1__ES$ | fast | +| A__submod1__J1: A__submod1__ES -> A__submod1__E + D | $A__submod1__ES / (A__submod1__E + D)$ | fast |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S | $10$ | variable | +| Initial concentration of species A__submod1__E | $1$ | variable | +| Initial concentration of species D | $15$ | variable | +| Initial concentration of species A__submod1__ES | $1$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 1; + +S @Species { compartment: comp, } .= 5; +D @Species { compartment: comp, } .= 10; + diff --git a/latest/cases/01472/synopsis.txt b/latest/cases/01472/synopsis.txt new file mode 100644 index 000000000..af721d71d --- /dev/null +++ b/latest/cases/01472/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: An element in an external model submodel as the target of a replacedBy element. +componentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In this model, an element is replaced by an element in a submodel of an external model. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S, A__submod1__E, D, A__submod1__ES) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| A__submod1__J0: S + A__submod1__E -> A__submod1__ES | $(S + A__submod1__E) / A__submod1__ES$ | fast | +| A__submod1__J1: A__submod1__ES -> A__submod1__E + D | $A__submod1__ES / (A__submod1__E + D)$ | fast |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S | $10$ | variable | +| Initial concentration of species A__submod1__E | $1$ | variable | +| Initial concentration of species D | $15$ | variable | +| Initial concentration of species A__submod1__ES | $1$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + diff --git a/latest/cases/01473/l2v5/index.heta b/latest/cases/01473/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01473/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01473/l3v2/heta-code/output.heta b/latest/cases/01473/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5155a7fc1 --- /dev/null +++ b/latest/cases/01473/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 1; + +S @Species { compartment: comp, } .= 5; +D @Species { compartment: comp, } .= 10; + diff --git a/latest/cases/01473/l3v2/index.heta b/latest/cases/01473/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01473/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01473/l3v2/json/output.json b/latest/cases/01473/l3v2/json/output.json new file mode 100644 index 000000000..506f1f0f2 --- /dev/null +++ b/latest/cases/01473/l3v2/json/output.json @@ -0,0 +1,29 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S", + "assignments": { + "start_": "5" + }, + "compartment": "comp" + }, + { + "class": "Species", + "id": "D", + "assignments": { + "start_": "10" + }, + "compartment": "comp" + } +] \ No newline at end of file diff --git a/latest/cases/01473/model-sbml-l3v2.xml b/latest/cases/01473/model-sbml-l3v2.xml new file mode 100644 index 000000000..717ef667c --- /dev/null +++ b/latest/cases/01473/model-sbml-l3v2.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01473/output.heta b/latest/cases/01473/output.heta new file mode 100644 index 000000000..41a8b7291 --- /dev/null +++ b/latest/cases/01473/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: External models with submodels with replaced elements. +componentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In this modification of a model from the specification, an external model has submodels referenced by replacedElements. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S, D, A__submod1__E, A__submod1__ES) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__submod1__J0: S + A__submod1__E -> A__submod1__ES | $(S + A__submod1__E) / A__submod1__ES$ | +| A__submod1__J1: A__submod1__ES -> A__submod1__E + D | $A__submod1__ES / (A__submod1__E + D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S | $5$ | variable | +| Initial concentration of species D | $10$ | variable | +| Initial concentration of species A__submod1__E | $1$ | variable | +| Initial concentration of species A__submod1__ES | $1$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 1; + +S @Species { compartment: comp, } .= 5; +D @Species { compartment: comp, } .= 10; + diff --git a/latest/cases/01473/synopsis.txt b/latest/cases/01473/synopsis.txt new file mode 100644 index 000000000..d4925455f --- /dev/null +++ b/latest/cases/01473/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: External models with submodels with replaced elements. +componentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:SubmodelOutput +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + In this modification of a model from the specification, an external model has submodels referenced by replacedElements. + +The 'flattened' version of this hierarchical model contains: +* 4 species (S, D, A__submod1__E, A__submod1__ES) +* 1 compartment (comp) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| A__submod1__J0: S + A__submod1__E -> A__submod1__ES | $(S + A__submod1__E) / A__submod1__ES$ | +| A__submod1__J1: A__submod1__ES -> A__submod1__E + D | $A__submod1__ES / (A__submod1__E + D)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S | $5$ | variable | +| Initial concentration of species D | $10$ | variable | +| Initial concentration of species A__submod1__E | $1$ | variable | +| Initial concentration of species A__submod1__ES | $1$ | variable | +| Initial volume of compartment 'comp' | $1$ | constant |] + diff --git a/latest/cases/01474/l2v5/index.heta b/latest/cases/01474/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01474/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01474/l3v2/heta-code/output.heta b/latest/cases/01474/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cab425afc --- /dev/null +++ b/latest/cases/01474/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 0 / C; + +timeconv @Const { } = 100; + diff --git a/latest/cases/01474/l3v2/index.heta b/latest/cases/01474/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01474/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01474/l3v2/json/output.json b/latest/cases/01474/l3v2/json/output.json new file mode 100644 index 000000000..49a2d211c --- /dev/null +++ b/latest/cases/01474/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "timeconv", + "num": 100 + } +] \ No newline at end of file diff --git a/latest/cases/01474/model-sbml-l3v2.xml b/latest/cases/01474/model-sbml-l3v2.xml new file mode 100644 index 000000000..81d82f39f --- /dev/null +++ b/latest/cases/01474/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10 + + + + + + + + + + + + diff --git a/latest/cases/01474/output.heta b/latest/cases/01474/output.heta new file mode 100644 index 000000000..dd53cad22 --- /dev/null +++ b/latest/cases/01474/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: A hierarchical model with a reaction modified by a time conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the time conversion factor, separated by a level of submodel indirection. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (timeconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $(1 / timeconv) * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0$ | variable | +| Initial value of parameter timeconv | $100$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 0 / C; + +timeconv @Const { } = 100; + diff --git a/latest/cases/01474/synopsis.txt b/latest/cases/01474/synopsis.txt new file mode 100644 index 000000000..0942a56ea --- /dev/null +++ b/latest/cases/01474/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A hierarchical model with a reaction modified by a time conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the time conversion factor, separated by a level of submodel indirection. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (timeconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $(1 / timeconv) * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0$ | variable | +| Initial value of parameter timeconv | $100$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01475/l2v5/index.heta b/latest/cases/01475/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01475/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01475/l3v2/heta-code/output.heta b/latest/cases/01475/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cab425afc --- /dev/null +++ b/latest/cases/01475/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 0 / C; + +timeconv @Const { } = 100; + diff --git a/latest/cases/01475/l3v2/index.heta b/latest/cases/01475/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01475/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01475/l3v2/json/output.json b/latest/cases/01475/l3v2/json/output.json new file mode 100644 index 000000000..49a2d211c --- /dev/null +++ b/latest/cases/01475/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "timeconv", + "num": 100 + } +] \ No newline at end of file diff --git a/latest/cases/01475/model-sbml-l3v2.xml b/latest/cases/01475/model-sbml-l3v2.xml new file mode 100644 index 000000000..a3be48085 --- /dev/null +++ b/latest/cases/01475/model-sbml-l3v2.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01475/output.heta b/latest/cases/01475/output.heta new file mode 100644 index 000000000..0f957a143 --- /dev/null +++ b/latest/cases/01475/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: A hierarchical model with a reaction modified by a time conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the time conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (timeconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $(1 / timeconv) * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0$ | variable | +| Initial value of parameter timeconv | $100$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 0 / C; + +timeconv @Const { } = 100; + diff --git a/latest/cases/01475/synopsis.txt b/latest/cases/01475/synopsis.txt new file mode 100644 index 000000000..569ecad27 --- /dev/null +++ b/latest/cases/01475/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A hierarchical model with a reaction modified by a time conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:TimeConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the time conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (timeconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $(1 / timeconv) * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0$ | variable | +| Initial value of parameter timeconv | $100$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01476/l2v5/index.heta b/latest/cases/01476/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01476/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01476/l3v2/heta-code/output.heta b/latest/cases/01476/l3v2/heta-code/output.heta new file mode 100644 index 000000000..006dd51c8 --- /dev/null +++ b/latest/cases/01476/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 0 / C; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01476/l3v2/index.heta b/latest/cases/01476/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01476/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01476/l3v2/json/output.json b/latest/cases/01476/l3v2/json/output.json new file mode 100644 index 000000000..506ddc3a5 --- /dev/null +++ b/latest/cases/01476/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "extentconv", + "num": 1000 + } +] \ No newline at end of file diff --git a/latest/cases/01476/model-sbml-l3v2.xml b/latest/cases/01476/model-sbml-l3v2.xml new file mode 100644 index 000000000..31628eac5 --- /dev/null +++ b/latest/cases/01476/model-sbml-l3v2.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01476/output.heta b/latest/cases/01476/output.heta new file mode 100644 index 000000000..b3b1ce7e7 --- /dev/null +++ b/latest/cases/01476/output.heta @@ -0,0 +1,46 @@ +/* +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:ExtentConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (extentconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 0 / C; + +extentconv @Const { } = 1000; + diff --git a/latest/cases/01476/synopsis.txt b/latest/cases/01476/synopsis.txt new file mode 100644 index 000000000..fd3446860 --- /dev/null +++ b/latest/cases/01476/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A hierarchical model with a reaction modified by an extent conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:ExtentConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (extentconv) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $extentconv * 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species s1 | $0$ | variable | +| Initial value of parameter extentconv | $1000$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01477/l2v5/index.heta b/latest/cases/01477/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01477/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01477/l3v2/heta-code/output.heta b/latest/cases/01477/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9d5308baa --- /dev/null +++ b/latest/cases/01477/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 2; + +cf @Const { } = 10; + diff --git a/latest/cases/01477/l3v2/index.heta b/latest/cases/01477/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01477/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01477/l3v2/json/output.json b/latest/cases/01477/l3v2/json/output.json new file mode 100644 index 000000000..5866bc465 --- /dev/null +++ b/latest/cases/01477/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "cf", + "num": 10 + } +] \ No newline at end of file diff --git a/latest/cases/01477/model-sbml-l3v2.xml b/latest/cases/01477/model-sbml-l3v2.xml new file mode 100644 index 000000000..b4a6b6910 --- /dev/null +++ b/latest/cases/01477/model-sbml-l3v2.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01477/output.heta b/latest/cases/01477/output.heta new file mode 100644 index 000000000..9afeebe3e --- /dev/null +++ b/latest/cases/01477/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: A hierarchical model with a species modified by a conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the replaced species must be converted by the conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species s1 | $2$ | variable | +| Initial value of parameter cf | $10$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 2; + +cf @Const { } = 10; + diff --git a/latest/cases/01477/synopsis.txt b/latest/cases/01477/synopsis.txt new file mode 100644 index 000000000..29011ed54 --- /dev/null +++ b/latest/cases/01477/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a species modified by a conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The reaction in the replaced species must be converted by the conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species s1 | $2$ | variable | +| Initial value of parameter cf | $10$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01478/l2v5/heta-code/output.heta b/latest/cases/01478/l2v5/heta-code/output.heta new file mode 100644 index 000000000..47a909db0 --- /dev/null +++ b/latest/cases/01478/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; +getPointFour #defineFunction { arguments: [], math: 0.4, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := getPointFour(); +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01478/l2v5/index.heta b/latest/cases/01478/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01478/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01478/l2v5/json/output.json b/latest/cases/01478/l2v5/json/output.json new file mode 100644 index 000000000..6b0f5a892 --- /dev/null +++ b/latest/cases/01478/l2v5/json/output.json @@ -0,0 +1,83 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "getPointFour()" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + }, + { + "id": "getPointFour", + "math": "0.4", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01478/l3v2/heta-code/output.heta b/latest/cases/01478/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0e551adf6 --- /dev/null +++ b/latest/cases/01478/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + +getPointFour #defineFunction { arguments: [], math: 0.4, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := getPointFour(); +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01478/l3v2/index.heta b/latest/cases/01478/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01478/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01478/l3v2/json/output.json b/latest/cases/01478/l3v2/json/output.json new file mode 100644 index 000000000..d29d58712 --- /dev/null +++ b/latest/cases/01478/l3v2/json/output.json @@ -0,0 +1,58 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "getPointFour()" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "id": "getPointFour", + "math": "0.4", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01478/model-sbml-l2v5.xml b/latest/cases/01478/model-sbml-l2v5.xml new file mode 100644 index 000000000..b8a268be5 --- /dev/null +++ b/latest/cases/01478/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + 0.4 + + + + + + + + + + + + + + + + + + getPointFour + + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01478/model-sbml-l3v2.xml b/latest/cases/01478/model-sbml-l3v2.xml new file mode 100644 index 000000000..c6b1c521d --- /dev/null +++ b/latest/cases/01478/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + 0.4 + + + + + + + + + + + + + + + + + + getPointFour + + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01478/output.heta b/latest/cases/01478/output.heta new file mode 100644 index 000000000..795ae918f --- /dev/null +++ b/latest/cases/01478/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: A species and a compartment both under control of a rate rule. +componentTags: AssignmentRule, Compartment, FunctionDefinition, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. One of the rate rules is a function definition, just to ensure that is considered. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $getPointFour()$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getPointFour | | $0.4$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +*/ + + +getPointFour #defineFunction { arguments: [], math: 0.4, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := getPointFour(); +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01478/synopsis.txt b/latest/cases/01478/synopsis.txt new file mode 100644 index 000000000..0ccb5098c --- /dev/null +++ b/latest/cases/01478/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule. +componentTags: AssignmentRule, Compartment, FunctionDefinition, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. One of the rate rules is a function definition, just to ensure that is considered. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $getPointFour()$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getPointFour | | $0.4$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01479/l2v5/index.heta b/latest/cases/01479/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01479/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01479/l3v2/build.log b/latest/cases/01479/l3v2/build.log new file mode 100644 index 000000000..2cb2833a4 --- /dev/null +++ b/latest/cases/01479/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01479/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01479/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01479/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01479/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01479/l3v2/index.heta b/latest/cases/01479/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01479/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01479/model-sbml-l3v2.xml b/latest/cases/01479/model-sbml-l3v2.xml new file mode 100644 index 000000000..8e4d9d678 --- /dev/null +++ b/latest/cases/01479/model-sbml-l3v2.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + avogadro + 1 23 + + P1 + + + + + + diff --git a/latest/cases/01479/synopsis.txt b/latest/cases/01479/synopsis.txt new file mode 100644 index 000000000..bfa521e74 --- /dev/null +++ b/latest/cases/01479/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Using avogadro in an algebraic rule. +componentTags: AlgebraicRule, CSymbolAvogadro, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model assigns avogadro's number through an algebraic rule to a parameter. + +The model contains: +* 1 parameter (P1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $avogadro / 1e23 - P1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01480/l2v5/index.heta b/latest/cases/01480/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01480/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01480/l3v2/build.log b/latest/cases/01480/l3v2/build.log new file mode 100644 index 000000000..00b5a0477 --- /dev/null +++ b/latest/cases/01480/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01480/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01480/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01480/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01480/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01480/l3v2/index.heta b/latest/cases/01480/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01480/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01480/model-sbml-l3v2.xml b/latest/cases/01480/model-sbml-l3v2.xml new file mode 100644 index 000000000..9dd8df450 --- /dev/null +++ b/latest/cases/01480/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + delay + S1 + 1 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01480/synopsis.txt b/latest/cases/01480/synopsis.txt new file mode 100644 index 000000000..809bbc911 --- /dev/null +++ b/latest/cases/01480/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Assigned stoichiometry with a delay. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + +This model tests an assigned stoichiometry with a delay in it. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_sr S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_sr + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1_sr | $delay(S1, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_sr' | $delay(S1, 1)$ | variable |] + diff --git a/latest/cases/01481/l2v5/build.log b/latest/cases/01481/l2v5/build.log new file mode 100644 index 000000000..d36b182c5 --- /dev/null +++ b/latest/cases/01481/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01481/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01481/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01481/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01481/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01481/l2v5/index.heta b/latest/cases/01481/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01481/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01481/l3v2/index.heta b/latest/cases/01481/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01481/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01481/model-sbml-l2v5.xml b/latest/cases/01481/model-sbml-l2v5.xml new file mode 100644 index 000000000..efb69f79e --- /dev/null +++ b/latest/cases/01481/model-sbml-l2v5.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + + delay + S1 + 1 + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01481/synopsis.txt b/latest/cases/01481/synopsis.txt new file mode 100644 index 000000000..86dca36d5 --- /dev/null +++ b/latest/cases/01481/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Stoichiometry math with a delay. +componentTags: CSymbolDelay, Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric +packagesPresent: + +This model tests stoichiometry math with a delay in it. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_sr S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_sr + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_sr' | $delay(S1, 1)$ | variable |] + diff --git a/latest/cases/01482/l2v5/index.heta b/latest/cases/01482/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01482/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01482/l3v2/build.log b/latest/cases/01482/l3v2/build.log new file mode 100644 index 000000000..b155c8b6b --- /dev/null +++ b/latest/cases/01482/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01482/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01482/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01482/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01482/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01482/l3v2/index.heta b/latest/cases/01482/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01482/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01482/model-sbml-l3v2.xml b/latest/cases/01482/model-sbml-l3v2.xml new file mode 100644 index 000000000..0d9111653 --- /dev/null +++ b/latest/cases/01482/model-sbml-l3v2.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + 2 + + + + + + + + rateOf + S1 + + P1 + + + + + + diff --git a/latest/cases/01482/synopsis.txt b/latest/cases/01482/synopsis.txt new file mode 100644 index 000000000..1f06257ff --- /dev/null +++ b/latest/cases/01482/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: An algebraic rule with a 'rateOf' csymbol. +componentTags: AlgebraicRule, CSymbolRateOf, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, we have an algebraic rule that uses the 'rateOf' function. + +The model contains: +* 3 parameters (S1, x, P1) + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $2$ | +| Algebraic | $0$ | $rateOf(S1) - P1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S1 | $1$ | variable | +| Initial value of parameter x | $unknown$ | variable | +| Initial value of parameter P1 | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01483/l2v5/index.heta b/latest/cases/01483/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01483/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01483/l3v2/build.log b/latest/cases/01483/l3v2/build.log new file mode 100644 index 000000000..f7b2ec64d --- /dev/null +++ b/latest/cases/01483/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01483/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01483/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01483/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01483/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01483/l3v2/index.heta b/latest/cases/01483/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01483/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01483/model-sbml-l3v2.xml b/latest/cases/01483/model-sbml-l3v2.xml new file mode 100644 index 000000000..fd412b95a --- /dev/null +++ b/latest/cases/01483/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + rateOf + S1 + + P1 + + + + + + + + + + + + 2 + + + + + + diff --git a/latest/cases/01483/synopsis.txt b/latest/cases/01483/synopsis.txt new file mode 100644 index 000000000..84b74b958 --- /dev/null +++ b/latest/cases/01483/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: An algebraic rule with a 'rateOf' csymbol. +componentTags: AlgebraicRule, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, we have an algebraic rule that uses the 'rateOf' function. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $rateOf(S1) - P1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter P1 | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01484/l2v5/index.heta b/latest/cases/01484/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01484/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01484/l3v2/build.log b/latest/cases/01484/l3v2/build.log new file mode 100644 index 000000000..94693366b --- /dev/null +++ b/latest/cases/01484/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01484/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01484/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01484/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01484/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01484/l3v2/index.heta b/latest/cases/01484/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01484/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01484/model-sbml-l3v2.xml b/latest/cases/01484/model-sbml-l3v2.xml new file mode 100644 index 000000000..b29f6b0aa --- /dev/null +++ b/latest/cases/01484/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + P1 + S1 + + + + + + + + + + + + 2 + + + + + + diff --git a/latest/cases/01484/synopsis.txt b/latest/cases/01484/synopsis.txt new file mode 100644 index 000000000..0c5de33b6 --- /dev/null +++ b/latest/cases/01484/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: An algebraic rule with a 'rateOf' csymbol. +componentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, we have an algebraic rule that uses the 'rateOf' function. + +The model contains: +* 1 species (S1) +* 2 parameters (conversionFactor, P1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $2$ |] + +The conversion factor for the species 'S1' is 'conversionFactor' + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P1 - S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter conversionFactor | $3$ | constant | +| Initial value of parameter P1 | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01485/l2v5/build.log b/latest/cases/01485/l2v5/build.log new file mode 100644 index 000000000..0554c3ccc --- /dev/null +++ b/latest/cases/01485/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01485/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01485/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01485/model-sbml-l2v5.xml"... +[info] Setting references in elements, total length 136 +[error] FunctionDef "tanh" is not found as expected here: my_tanh { math: tanh(x) }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01485/l2v5/index.heta b/latest/cases/01485/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01485/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01485/l3v2/build.log b/latest/cases/01485/l3v2/build.log new file mode 100644 index 000000000..049b2facb --- /dev/null +++ b/latest/cases/01485/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01485/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01485/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01485/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 131 +[error] FunctionDef "tanh" is not found as expected here: my_tanh { math: tanh(x) }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01485/l3v2/index.heta b/latest/cases/01485/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01485/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01485/model-sbml-l2v5.xml b/latest/cases/01485/model-sbml-l2v5.xml new file mode 100644 index 000000000..c95b90158 --- /dev/null +++ b/latest/cases/01485/model-sbml-l2v5.xml @@ -0,0 +1,557 @@ + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + + 10 + + x + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + + x + 2 + + + + + + + + + x + + + + + 2 + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + my_abs + -1 + + + + + + + my_abs + 1 + + + + + + + my_acos + -1 + + + + + + + my_acos + 0.5 + + + + + + + my_asin + 1 + + + + + + + my_asin + -0.5 + + + + + + + my_atan + 2.8 + + + + + + + my_atan + -7.09 + + + + + + + my_ceil + 0.5 + + + + + + + my_ceil + 3.55 + + + + + + + my_ceil + -4.6 + + + + + + + my_cos + 9.1 + + + + + + + my_cos + -0.22 + + + + + + + my_exp + 0 + + + + + + + my_exp + 1 + + + + + + + my_exp + 0.77 + + + + + + + my_floor + -4.6 + + + + + + + my_floor + 9.1 + + + + + + + my_log + 0.2 + + + + + + + my_log + 1 + + + + + + + my_log10 + 0.2 + + + + + + + my_log10 + 1 + + + + + + + my_pow + 1 + 2 + + + + + + + my_pow + 2 + 2 + + + + + + + my_pow + 1.4 + 5.1 + + + + + + + my_sqr + 4 + + + + + + + my_sqr + 3.1 + + + + + + + my_sqrt + 4 + + + + + + + my_sqrt + 7.4 + + + + + + + my_sin + 2.1 + + + + + + + my_sin + 0 + + + + + + + my_sin + -5.9 + + + + + + + my_tan + 0 + + + + + + + my_tan + 1.11 + + + + + + + my_tan + -6 + + + + + + + my_tanh + -0.4 + + + + + + diff --git a/latest/cases/01485/model-sbml-l3v2.xml b/latest/cases/01485/model-sbml-l3v2.xml new file mode 100644 index 000000000..e455d4c18 --- /dev/null +++ b/latest/cases/01485/model-sbml-l3v2.xml @@ -0,0 +1,558 @@ + + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + + 10 + + x + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + + x + 2 + + + + + + + + + x + + + + + 2 + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + my_abs + -1 + + + + + + + my_abs + 1 + + + + + + + my_acos + -1 + + + + + + + my_acos + 0.5 + + + + + + + my_asin + 1 + + + + + + + my_asin + -0.5 + + + + + + + my_atan + 2.8 + + + + + + + my_atan + -7.09 + + + + + + + my_ceil + 0.5 + + + + + + + my_ceil + 3.55 + + + + + + + my_ceil + -4.6 + + + + + + + my_cos + 9.1 + + + + + + + my_cos + -0.22 + + + + + + + my_exp + 0 + + + + + + + my_exp + 1 + + + + + + + my_exp + 0.77 + + + + + + + my_floor + -4.6 + + + + + + + my_floor + 9.1 + + + + + + + my_log + 0.2 + + + + + + + my_log + 1 + + + + + + + my_log10 + 0.2 + + + + + + + my_log10 + 1 + + + + + + + my_pow + 1 + 2 + + + + + + + my_pow + 2 + 2 + + + + + + + my_pow + 1.4 + 5.1 + + + + + + + my_sqr + 4 + + + + + + + my_sqr + 3.1 + + + + + + + my_sqrt + 4 + + + + + + + my_sqrt + 7.4 + + + + + + + my_sin + 2.1 + + + + + + + my_sin + 0 + + + + + + + my_sin + -5.9 + + + + + + + my_tan + 0 + + + + + + + my_tan + 1.11 + + + + + + + my_tan + -6 + + + + + + + my_tanh + -0.4 + + + + + + diff --git a/latest/cases/01485/synopsis.txt b/latest/cases/01485/synopsis.txt new file mode 100644 index 000000000..700a8473e --- /dev/null +++ b/latest/cases/01485/synopsis.txt @@ -0,0 +1,118 @@ + +category: Test +synopsis: Several parameters with assignment rules, testing various L1 built-in functions acting on constants. +componentTags: AssignmentRule, FunctionDefinition, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various mathematical constructs present in L1, in a function definition. + +The model contains: +* 36 parameters (P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37) + +There are 36 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P2 | $my_abs(-1)$ | +| Assignment | P3 | $my_abs(1)$ | +| Assignment | P4 | $my_acos(-1)$ | +| Assignment | P5 | $my_acos(0.5)$ | +| Assignment | P6 | $my_asin(1)$ | +| Assignment | P7 | $my_asin(-0.5)$ | +| Assignment | P8 | $my_atan(2.8)$ | +| Assignment | P9 | $my_atan(-7.09)$ | +| Assignment | P10 | $my_ceil(0.5)$ | +| Assignment | P11 | $my_ceil(3.55)$ | +| Assignment | P12 | $my_ceil(-4.6)$ | +| Assignment | P13 | $my_cos(9.1)$ | +| Assignment | P14 | $my_cos(-0.22)$ | +| Assignment | P15 | $my_exp(0)$ | +| Assignment | P16 | $my_exp(1)$ | +| Assignment | P17 | $my_exp(0.77)$ | +| Assignment | P18 | $my_floor(-4.6)$ | +| Assignment | P19 | $my_floor(9.1)$ | +| Assignment | P20 | $my_log(0.2)$ | +| Assignment | P21 | $my_log(1)$ | +| Assignment | P22 | $my_log10(0.2)$ | +| Assignment | P23 | $my_log10(1)$ | +| Assignment | P24 | $my_pow(1, 2)$ | +| Assignment | P25 | $my_pow(2, 2)$ | +| Assignment | P26 | $my_pow(1.4, 5.1)$ | +| Assignment | P27 | $my_sqr(4)$ | +| Assignment | P28 | $my_sqr(3.1)$ | +| Assignment | P29 | $my_sqrt(4)$ | +| Assignment | P30 | $my_sqrt(7.4)$ | +| Assignment | P31 | $my_sin(2.1)$ | +| Assignment | P32 | $my_sin(0)$ | +| Assignment | P33 | $my_sin(-5.9)$ | +| Assignment | P34 | $my_tan(0)$ | +| Assignment | P35 | $my_tan(1.11)$ | +| Assignment | P36 | $my_tan(-6)$ | +| Assignment | P37 | $my_tanh(-0.4)$ |] + +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_abs | x | $abs(x)$ | + | my_acos | x | $acos(x)$ | + | my_asin | x | $asin(x)$ | + | my_atan | x | $atan(x)$ | + | my_ceil | x | $ceil(x)$ | + | my_cos | x | $cos(x)$ | + | my_exp | x | $exp(x)$ | + | my_floor | x | $floor(x)$ | + | my_log | x | $ln(x)$ | + | my_log10 | x | $log10(x)$ | + | my_pow | x, y | $x^y$ | + | my_sqr | x | $x^2$ | + | my_sqrt | x | $sqrt(x)$ | + | my_sin | x | $sin(x)$ | + | my_tan | x | $tan(x)$ | + | my_tanh | x | $tanh(x)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P2 | $my_abs(-1)$ | variable | +| Initial value of parameter P3 | $my_abs(1)$ | variable | +| Initial value of parameter P4 | $my_acos(-1)$ | variable | +| Initial value of parameter P5 | $my_acos(0.5)$ | variable | +| Initial value of parameter P6 | $my_asin(1)$ | variable | +| Initial value of parameter P7 | $my_asin(-0.5)$ | variable | +| Initial value of parameter P8 | $my_atan(2.8)$ | variable | +| Initial value of parameter P9 | $my_atan(-7.09)$ | variable | +| Initial value of parameter P10 | $my_ceil(0.5)$ | variable | +| Initial value of parameter P11 | $my_ceil(3.55)$ | variable | +| Initial value of parameter P12 | $my_ceil(-4.6)$ | variable | +| Initial value of parameter P13 | $my_cos(9.1)$ | variable | +| Initial value of parameter P14 | $my_cos(-0.22)$ | variable | +| Initial value of parameter P15 | $my_exp(0)$ | variable | +| Initial value of parameter P16 | $my_exp(1)$ | variable | +| Initial value of parameter P17 | $my_exp(0.77)$ | variable | +| Initial value of parameter P18 | $my_floor(-4.6)$ | variable | +| Initial value of parameter P19 | $my_floor(9.1)$ | variable | +| Initial value of parameter P20 | $my_log(0.2)$ | variable | +| Initial value of parameter P21 | $my_log(1)$ | variable | +| Initial value of parameter P22 | $my_log10(0.2)$ | variable | +| Initial value of parameter P23 | $my_log10(1)$ | variable | +| Initial value of parameter P24 | $my_pow(1, 2)$ | variable | +| Initial value of parameter P25 | $my_pow(2, 2)$ | variable | +| Initial value of parameter P26 | $my_pow(1.4, 5.1)$ | variable | +| Initial value of parameter P27 | $my_sqr(4)$ | variable | +| Initial value of parameter P28 | $my_sqr(3.1)$ | variable | +| Initial value of parameter P29 | $my_sqrt(4)$ | variable | +| Initial value of parameter P30 | $my_sqrt(7.4)$ | variable | +| Initial value of parameter P31 | $my_sin(2.1)$ | variable | +| Initial value of parameter P32 | $my_sin(0)$ | variable | +| Initial value of parameter P33 | $my_sin(-5.9)$ | variable | +| Initial value of parameter P34 | $my_tan(0)$ | variable | +| Initial value of parameter P35 | $my_tan(1.11)$ | variable | +| Initial value of parameter P36 | $my_tan(-6)$ | variable | +| Initial value of parameter P37 | $my_tanh(-0.4)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01486/l2v5/build.log b/latest/cases/01486/l2v5/build.log new file mode 100644 index 000000000..c4eb335a3 --- /dev/null +++ b/latest/cases/01486/l2v5/build.log @@ -0,0 +1,36 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01486/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01486/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01486/model-sbml-l2v5.xml"... +[error] Function math "my_gt" should be a numeric expression. +[error] Function math "my_geq" should be a numeric expression. +[error] Function math "my_lt" should be a numeric expression. +[error] Function math "my_leq" should be a numeric expression. +[error] Function math "my_eq" should be a numeric expression. +[error] Function math "my_neq" should be a numeric expression. +[error] Function math "my_and" should be a numeric expression. +[error] Function math "my_or" should be a numeric expression. +[error] Function math "my_xor" should be a numeric expression. +[error] Function math "my_not" should be a numeric expression. +[info] Setting references in elements, total length 131 +[error] FunctionDef "sinh" is not found as expected here: my_sinh { math: sinh(x) }; +[error] FunctionDef "cosh" is not found as expected here: my_cosh { math: cosh(x) }; +[error] FunctionDef "asinh" is not found as expected here: my_arcsinh { math: asinh(x) }; +[error] FunctionDef "acosh" is not found as expected here: my_arccosh { math: acosh(x) }; +[error] FunctionDef "atanh" is not found as expected here: my_arctanh { math: atanh(x) }; +[error] FunctionDef "asech" is not found as expected here: my_arcsech { math: asech(x) }; +[error] FunctionDef "acsch" is not found as expected here: my_arccsch { math: acsch(x) }; +[error] FunctionDef "acoth" is not found as expected here: my_arccoth { math: acoth(x) }; +[error] FunctionDef "my_gt" is not found as expected here: P3 { math: undefined }; +[error] FunctionDef "my_geq" is not found as expected here: P4 { math: undefined }; +[error] FunctionDef "my_lt" is not found as expected here: P5 { math: undefined }; +[error] FunctionDef "my_leq" is not found as expected here: P6 { math: undefined }; +[error] FunctionDef "my_eq" is not found as expected here: P7 { math: undefined }; +[error] FunctionDef "my_neq" is not found as expected here: P8 { math: undefined }; +[error] FunctionDef "my_and" is not found as expected here: P10 { math: undefined }; +[error] FunctionDef "my_or" is not found as expected here: P11 { math: undefined }; +[error] FunctionDef "my_xor" is not found as expected here: P12 { math: undefined }; +[error] FunctionDef "my_not" is not found as expected here: P13 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01486/l2v5/index.heta b/latest/cases/01486/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01486/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01486/l3v2/build.log b/latest/cases/01486/l3v2/build.log new file mode 100644 index 000000000..fa627bedc --- /dev/null +++ b/latest/cases/01486/l3v2/build.log @@ -0,0 +1,36 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01486/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01486/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01486/model-sbml-l3v2.xml"... +[error] Function math "my_gt" should be a numeric expression. +[error] Function math "my_geq" should be a numeric expression. +[error] Function math "my_lt" should be a numeric expression. +[error] Function math "my_leq" should be a numeric expression. +[error] Function math "my_eq" should be a numeric expression. +[error] Function math "my_neq" should be a numeric expression. +[error] Function math "my_and" should be a numeric expression. +[error] Function math "my_or" should be a numeric expression. +[error] Function math "my_xor" should be a numeric expression. +[error] Function math "my_not" should be a numeric expression. +[info] Setting references in elements, total length 126 +[error] FunctionDef "sinh" is not found as expected here: my_sinh { math: sinh(x) }; +[error] FunctionDef "cosh" is not found as expected here: my_cosh { math: cosh(x) }; +[error] FunctionDef "asinh" is not found as expected here: my_arcsinh { math: asinh(x) }; +[error] FunctionDef "acosh" is not found as expected here: my_arccosh { math: acosh(x) }; +[error] FunctionDef "atanh" is not found as expected here: my_arctanh { math: atanh(x) }; +[error] FunctionDef "asech" is not found as expected here: my_arcsech { math: asech(x) }; +[error] FunctionDef "acsch" is not found as expected here: my_arccsch { math: acsch(x) }; +[error] FunctionDef "acoth" is not found as expected here: my_arccoth { math: acoth(x) }; +[error] FunctionDef "my_gt" is not found as expected here: P3 { math: undefined }; +[error] FunctionDef "my_geq" is not found as expected here: P4 { math: undefined }; +[error] FunctionDef "my_lt" is not found as expected here: P5 { math: undefined }; +[error] FunctionDef "my_leq" is not found as expected here: P6 { math: undefined }; +[error] FunctionDef "my_eq" is not found as expected here: P7 { math: undefined }; +[error] FunctionDef "my_neq" is not found as expected here: P8 { math: undefined }; +[error] FunctionDef "my_and" is not found as expected here: P10 { math: undefined }; +[error] FunctionDef "my_or" is not found as expected here: P11 { math: undefined }; +[error] FunctionDef "my_xor" is not found as expected here: P12 { math: undefined }; +[error] FunctionDef "my_not" is not found as expected here: P13 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01486/l3v2/index.heta b/latest/cases/01486/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01486/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01486/model-sbml-l2v5.xml b/latest/cases/01486/model-sbml-l2v5.xml new file mode 100644 index 000000000..592b48179 --- /dev/null +++ b/latest/cases/01486/model-sbml-l2v5.xml @@ -0,0 +1,732 @@ + + + + + + + + + + + + + + + + x + + + y + + + z + + + + x + y + + + z + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + + x + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + 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+ my_piecewise + 2 + + my_not + + + 3 + + + + + + + my_sec + 0.5 + + + + + + + my_csc + 4.5 + + + + + + + my_cot + 0.2 + + + + + + + my_sinh + 0.3 + + + + + + + my_cosh + 1.7 + + + + + + + my_arcsec + 2.3 + + + + + + + my_arccsc + 1.1 + + + + + + + my_arccot + -0.1 + + + + + + + my_arcsinh + 99 + + + + + + + my_arccosh + 1.34 + + + + + + + my_arctanh + -0.7 + + + + + + + my_arcsech + 0.42 + + + + + + + my_arccsch + 0.01 + + + + + + + my_arccoth + 8.2 + + + + + + + my_exponentiale + + + + + + + my_exp + + + + + + + diff --git a/latest/cases/01486/model-sbml-l3v2.xml b/latest/cases/01486/model-sbml-l3v2.xml new file mode 100644 index 000000000..0ee738bc8 --- /dev/null +++ b/latest/cases/01486/model-sbml-l3v2.xml @@ -0,0 +1,733 @@ + + + + + + + + + + + + + + + + + x + + + y + + + z + + + + x + y + + + z + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + + x + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + my_pi + + + + + + + my_piecewise + 2 + + my_gt + 1 + 0.5 + + 3 + + + + + + + my_piecewise + 2 + + my_geq + 1 + 0.5 + + 3 + + + + + + + my_piecewise + 2 + + my_lt + 1 + 0.5 + + 3 + + + + + + + my_piecewise + 2 + + my_leq + 1 + 0.5 + + 3 + + + + + + + my_piecewise + 2 + + my_eq + P1 + + + 3 + + + + + + + my_piecewise + 2 + + my_neq + P1 + + + 3 + + + + + + + my_factorial + 4 + + + + + + + my_piecewise + 2 + + my_and + + + + 3 + + + + + + + my_piecewise + 2 + + my_or + + + + 3 + + + + + + + my_piecewise + 2 + + my_xor + + + + 3 + + + + + + + my_piecewise + 2 + + my_not + + + 3 + + + + + + + my_sec + 0.5 + + + + + + + my_csc + 4.5 + + + + + + + my_cot + 0.2 + + + + + + + my_sinh + 0.3 + + + + + + + my_cosh + 1.7 + + + + + + + my_arcsec + 2.3 + + + + + + + my_arccsc + 1.1 + + + + + + + my_arccot + -0.1 + + + + + + + my_arcsinh + 99 + + + + + + + my_arccosh + 1.34 + + + + + + + my_arctanh + -0.7 + + + + + + + my_arcsech + 0.42 + + + + + + + my_arccsch + 0.01 + + + + + + + my_arccoth + 8.2 + + + + + + + my_exponentiale + + + + + + + my_exp + + + + + + + diff --git a/latest/cases/01486/synopsis.txt b/latest/cases/01486/synopsis.txt new file mode 100644 index 000000000..3bcd3bee1 --- /dev/null +++ b/latest/cases/01486/synopsis.txt @@ -0,0 +1,115 @@ + +category: Test +synopsis: Several unusual MathML constructs, wrapped in function definitions. +componentTags: AssignmentRule, FunctionDefinition, Parameter +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests the various uncommon mathematical constructs wrapped in function definitions. + +The model contains: +* 28 parameters (P1, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29) + +There are 28 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $my_pi()$ | +| Assignment | P3 | $my_piecewise(2, my_gt(1, 0.5), 3)$ | +| Assignment | P4 | $my_piecewise(2, my_geq(1, 0.5), 3)$ | +| Assignment | P5 | $my_piecewise(2, my_lt(1, 0.5), 3)$ | +| Assignment | P6 | $my_piecewise(2, my_leq(1, 0.5), 3)$ | +| Assignment | P7 | $my_piecewise(2, my_eq(P1, pi), 3)$ | +| Assignment | P8 | $my_piecewise(2, my_neq(P1, pi), 3)$ | +| Assignment | P9 | $my_factorial(4)$ | +| Assignment | P10 | $my_piecewise(2, my_and(true, false), 3)$ | +| Assignment | P11 | $my_piecewise(2, my_or(true, false), 3)$ | +| Assignment | P12 | $my_piecewise(2, my_xor(true, false), 3)$ | +| Assignment | P13 | $my_piecewise(2, my_not(false), 3)$ | +| Assignment | P14 | $my_sec(0.5)$ | +| Assignment | P15 | $my_csc(4.5)$ | +| Assignment | P16 | $my_cot(0.2)$ | +| Assignment | P17 | $my_sinh(0.3)$ | +| Assignment | P18 | $my_cosh(1.7)$ | +| Assignment | P19 | $my_arcsec(2.3)$ | +| Assignment | P20 | $my_arccsc(1.1)$ | +| Assignment | P21 | $my_arccot(-0.1)$ | +| Assignment | P22 | $my_arcsinh(99)$ | +| Assignment | P23 | $my_arccosh(1.34)$ | +| Assignment | P24 | $my_arctanh(-0.7)$ | +| Assignment | P25 | $my_arcsech(0.42)$ | +| Assignment | P26 | $my_arccsch(0.01)$ | +| Assignment | P27 | $my_arccoth(8.2)$ | +| Assignment | P28 | $my_exponentiale()$ | +| Assignment | P29 | $my_exp(exponentiale)$ |] + +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_pi | | $pi$ | + | my_piecewise | x, y, z | $piecewise(x, y, z)$ | + | my_gt | x, y | $x > y$ | + | my_geq | x, y | $x >= y$ | + | my_lt | x, y | $x < y$ | + | my_leq | x, y | $x <= y$ | + | my_eq | x, y | $x == y$ | + | my_neq | x, y | $x != y$ | + | my_factorial | x | $factorial(x)$ | + | my_and | x, y | $x && y$ | + | my_or | x, y | $x || y$ | + | my_xor | x, y | $xor(x, y)$ | + | my_not | x | $!x$ | + | my_sec | x | $sec(x)$ | + | my_csc | x | $csc(x)$ | + | my_cot | x | $cot(x)$ | + | my_sinh | x | $sinh(x)$ | + | my_cosh | x | $cosh(x)$ | + | my_arcsec | x | $arcsec(x)$ | + | my_arccsc | x | $arccsc(x)$ | + | my_arccot | x | $arccot(x)$ | + | my_arcsinh | x | $arcsinh(x)$ | + | my_arccosh | x | $arccosh(x)$ | + | my_arctanh | x | $arctanh(x)$ | + | my_arcsech | x | $arcsech(x)$ | + | my_arccsch | x | $arccsch(x)$ | + | my_arccoth | x | $arccoth(x)$ | + | my_exponentiale | | $exponentiale$ | + | my_exp | x | $exp(x)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $my_pi()$ | variable | +| Initial value of parameter P3 | $my_piecewise(2, my_gt(1, 0.5), 3)$ | variable | +| Initial value of parameter P4 | $my_piecewise(2, my_geq(1, 0.5), 3)$ | variable | +| Initial value of parameter P5 | $my_piecewise(2, my_lt(1, 0.5), 3)$ | variable | +| Initial value of parameter P6 | $my_piecewise(2, my_leq(1, 0.5), 3)$ | variable | +| Initial value of parameter P7 | $my_piecewise(2, my_eq(P1, pi), 3)$ | variable | +| Initial value of parameter P8 | $my_piecewise(2, my_neq(P1, pi), 3)$ | variable | +| Initial value of parameter P9 | $my_factorial(4)$ | variable | +| Initial value of parameter P10 | $my_piecewise(2, my_and(true, false), 3)$ | variable | +| Initial value of parameter P11 | $my_piecewise(2, my_or(true, false), 3)$ | variable | +| Initial value of parameter P12 | $my_piecewise(2, my_xor(true, false), 3)$ | variable | +| Initial value of parameter P13 | $my_piecewise(2, my_not(false), 3)$ | variable | +| Initial value of parameter P14 | $my_sec(0.5)$ | variable | +| Initial value of parameter P15 | $my_csc(4.5)$ | variable | +| Initial value of parameter P16 | $my_cot(0.2)$ | variable | +| Initial value of parameter P17 | $my_sinh(0.3)$ | variable | +| Initial value of parameter P18 | $my_cosh(1.7)$ | variable | +| Initial value of parameter P19 | $my_arcsec(2.3)$ | variable | +| Initial value of parameter P20 | $my_arccsc(1.1)$ | variable | +| Initial value of parameter P21 | $my_arccot(-0.1)$ | variable | +| Initial value of parameter P22 | $my_arcsinh(99)$ | variable | +| Initial value of parameter P23 | $my_arccosh(1.34)$ | variable | +| Initial value of parameter P24 | $my_arctanh(-0.7)$ | variable | +| Initial value of parameter P25 | $my_arcsech(0.42)$ | variable | +| Initial value of parameter P26 | $my_arccsch(0.01)$ | variable | +| Initial value of parameter P27 | $my_arccoth(8.2)$ | variable | +| Initial value of parameter P28 | $my_exponentiale()$ | variable | +| Initial value of parameter P29 | $my_exp(exponentiale)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01487/l2v5/build.log b/latest/cases/01487/l2v5/build.log new file mode 100644 index 000000000..b2a55bec1 --- /dev/null +++ b/latest/cases/01487/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01487/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01487/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01487/model-sbml-l2v5.xml"... +[info] Setting references in elements, total length 127 +[error] FunctionDef "tanh" is not found as expected here: my_tanh { math: tanh(x) }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01487/l2v5/index.heta b/latest/cases/01487/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01487/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01487/l3v2/build.log b/latest/cases/01487/l3v2/build.log new file mode 100644 index 000000000..e8157db21 --- /dev/null +++ b/latest/cases/01487/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01487/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01487/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01487/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 122 +[error] FunctionDef "tanh" is not found as expected here: my_tanh { math: tanh(x) }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01487/l3v2/index.heta b/latest/cases/01487/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01487/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01487/model-sbml-l2v5.xml b/latest/cases/01487/model-sbml-l2v5.xml new file mode 100644 index 000000000..0bb457c45 --- /dev/null +++ b/latest/cases/01487/model-sbml-l2v5.xml @@ -0,0 +1,531 @@ + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + + 10 + + x + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + + x + 2 + + + + + + + + + x + + + + + 2 + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + + + + my_abs + time + + + + + + + my_abs + + + time + + + + + + + + my_acos + time + + + + + + + my_acos + + + time + + + + + + + + my_asin + time + + + + + + + my_asin + + + time + + + + + + + + my_atan + time + + + + + + + my_atan + + + time + + + + + + + + my_ceil + + + time + 0.001 + + + + + + + + my_ceil + + + + + time + + 0.001 + + + + + + + + my_cos + time + + + + + + + my_cos + + + time + + + + + + + + my_exp + time + + + + + + + my_exp + + + time + + + + + + + + my_floor + + + time + 0.001 + + + + + + + + my_floor + + + + + time + + 0.001 + + + + + + + + my_ln + + + time + 1 + + + + + + + + my_log10 + + + time + 1 + + + + + + + + my_sqrt + time + + + + + + + my_sin + time + + + + + + + my_sin + + + time + + + + + + + + my_tan + time + + + + + + + my_tan + + + time + + + + + + + + my_tanh + time + + + + + + + my_tanh + + + time + + + + + + + diff --git a/latest/cases/01487/model-sbml-l3v2.xml b/latest/cases/01487/model-sbml-l3v2.xml new file mode 100644 index 000000000..5fafdec51 --- /dev/null +++ b/latest/cases/01487/model-sbml-l3v2.xml @@ -0,0 +1,532 @@ + + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + + 10 + + x + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + + x + 2 + + + + + + + + + x + + + + + 2 + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + + + + my_abs + time + + + + + + + my_abs + + + time + + + + + + + + my_acos + time + + + + + + + my_acos + + + time + + + + + + + + my_asin + time + + + + + + + my_asin + + + time + + + + + + + + my_atan + time + + + + + + + my_atan + + + time + + + + + + + + my_ceil + + + time + 0.001 + + + + + + + + my_ceil + + + + + time + + 0.001 + + + + + + + + my_cos + time + + + + + + + my_cos + + + time + + + + + + + + my_exp + time + + + + + + + my_exp + + + time + + + + + + + + my_floor + + + time + 0.001 + + + + + + + + my_floor + + + + + time + + 0.001 + + + + + + + + my_ln + + + time + 1 + + + + + + + + my_log10 + + + time + 1 + + + + + + + + my_sqrt + time + + + + + + + my_sin + time + + + + + + + my_sin + + + time + + + + + + + + my_tan + time + + + + + + + my_tan + + + time + + + + + + + + my_tanh + time + + + + + + + my_tanh + + + time + + + + + + + diff --git a/latest/cases/01487/synopsis.txt b/latest/cases/01487/synopsis.txt new file mode 100644 index 000000000..b1bae3fb9 --- /dev/null +++ b/latest/cases/01487/synopsis.txt @@ -0,0 +1,99 @@ + +category: Test +synopsis: Several parameters with assignment rules involving time, testing various L1 built-in functions. +componentTags: AssignmentRule, CSymbolTime, FunctionDefinition, Parameter +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various mathematical constructs present in L1, as applied to the time variable, in a function definition. Ironically, this doesn't work in L1, since time isn't present, but hey. + +The model contains: +* 26 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P13, P14, P15, P16, P18, P19, P20, P22, P29, P31, P32, P34, P35, P36, P37) + +There are 26 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $time$ | +| Assignment | P2 | $my_abs(time)$ | +| Assignment | P3 | $my_abs(-time)$ | +| Assignment | P4 | $my_acos(time)$ | +| Assignment | P5 | $my_acos(-time)$ | +| Assignment | P6 | $my_asin(time)$ | +| Assignment | P7 | $my_asin(-time)$ | +| Assignment | P8 | $my_atan(time)$ | +| Assignment | P9 | $my_atan(-time)$ | +| Assignment | P10 | $my_ceil(time - 0.001)$ | +| Assignment | P11 | $my_ceil(-time - 0.001)$ | +| Assignment | P13 | $my_cos(time)$ | +| Assignment | P14 | $my_cos(-time)$ | +| Assignment | P15 | $my_exp(time)$ | +| Assignment | P16 | $my_exp(-time)$ | +| Assignment | P18 | $my_floor(time + 0.001)$ | +| Assignment | P19 | $my_floor(-time + 0.001)$ | +| Assignment | P20 | $my_ln(time + 1)$ | +| Assignment | P22 | $my_log10(time + 1)$ | +| Assignment | P29 | $my_sqrt(time)$ | +| Assignment | P31 | $my_sin(time)$ | +| Assignment | P32 | $my_sin(-time)$ | +| Assignment | P34 | $my_tan(time)$ | +| Assignment | P35 | $my_tan(-time)$ | +| Assignment | P36 | $my_tanh(time)$ | +| Assignment | P37 | $my_tanh(-time)$ |] + +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_abs | x | $abs(x)$ | + | my_acos | x | $acos(x)$ | + | my_asin | x | $asin(x)$ | + | my_atan | x | $atan(x)$ | + | my_ceil | x | $ceil(x)$ | + | my_cos | x | $cos(x)$ | + | my_exp | x | $exp(x)$ | + | my_floor | x | $floor(x)$ | + | my_log | x | $ln(x)$ | + | my_ln | x | $ln(x)$ | + | my_log10 | x | $log10(x)$ | + | my_pow | x, y | $x^y$ | + | my_sqr | x | $x^2$ | + | my_sqrt | x | $sqrt(x)$ | + | my_sin | x | $sin(x)$ | + | my_tan | x | $tan(x)$ | + | my_tanh | x | $tanh(x)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $time$ | variable | +| Initial value of parameter P2 | $my_abs(time)$ | variable | +| Initial value of parameter P3 | $my_abs(-time)$ | variable | +| Initial value of parameter P4 | $my_acos(time)$ | variable | +| Initial value of parameter P5 | $my_acos(-time)$ | variable | +| Initial value of parameter P6 | $my_asin(time)$ | variable | +| Initial value of parameter P7 | $my_asin(-time)$ | variable | +| Initial value of parameter P8 | $my_atan(time)$ | variable | +| Initial value of parameter P9 | $my_atan(-time)$ | variable | +| Initial value of parameter P10 | $my_ceil(time - 0.001)$ | variable | +| Initial value of parameter P11 | $my_ceil(-time - 0.001)$ | variable | +| Initial value of parameter P13 | $my_cos(time)$ | variable | +| Initial value of parameter P14 | $my_cos(-time)$ | variable | +| Initial value of parameter P15 | $my_exp(time)$ | variable | +| Initial value of parameter P16 | $my_exp(-time)$ | variable | +| Initial value of parameter P18 | $my_floor(time + 0.001)$ | variable | +| Initial value of parameter P19 | $my_floor(-time + 0.001)$ | variable | +| Initial value of parameter P20 | $my_ln(time + 1)$ | variable | +| Initial value of parameter P22 | $my_log10(time + 1)$ | variable | +| Initial value of parameter P29 | $my_sqrt(time)$ | variable | +| Initial value of parameter P31 | $my_sin(time)$ | variable | +| Initial value of parameter P32 | $my_sin(-time)$ | variable | +| Initial value of parameter P34 | $my_tan(time)$ | variable | +| Initial value of parameter P35 | $my_tan(-time)$ | variable | +| Initial value of parameter P36 | $my_tanh(time)$ | variable | +| Initial value of parameter P37 | $my_tanh(-time)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01488/l2v5/build.log b/latest/cases/01488/l2v5/build.log new file mode 100644 index 000000000..5a5029bba --- /dev/null +++ b/latest/cases/01488/l2v5/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01488/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01488/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01488/model-sbml-l2v5.xml"... +[info] Setting references in elements, total length 127 +[error] FunctionDef "sinh" is not found as expected here: my_sinh { math: sinh(x) }; +[error] FunctionDef "cosh" is not found as expected here: my_cosh { math: cosh(x) }; +[error] FunctionDef "asinh" is not found as expected here: my_arcsinh { math: asinh(x) }; +[error] FunctionDef "acosh" is not found as expected here: my_arccosh { math: acosh(x) }; +[error] FunctionDef "atanh" is not found as expected here: my_arctanh { math: atanh(x) }; +[error] FunctionDef "asech" is not found as expected here: my_arcsech { math: asech(x) }; +[error] FunctionDef "acsch" is not found as expected here: my_arccsch { math: acsch(x) }; +[error] FunctionDef "acoth" is not found as expected here: my_arccoth { math: acoth(x) }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01488/l2v5/index.heta b/latest/cases/01488/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01488/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01488/l3v2/build.log b/latest/cases/01488/l3v2/build.log new file mode 100644 index 000000000..0caadfeed --- /dev/null +++ b/latest/cases/01488/l3v2/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01488/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01488/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01488/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 122 +[error] FunctionDef "sinh" is not found as expected here: my_sinh { math: sinh(x) }; +[error] FunctionDef "cosh" is not found as expected here: my_cosh { math: cosh(x) }; +[error] FunctionDef "asinh" is not found as expected here: my_arcsinh { math: asinh(x) }; +[error] FunctionDef "acosh" is not found as expected here: my_arccosh { math: acosh(x) }; +[error] FunctionDef "atanh" is not found as expected here: my_arctanh { math: atanh(x) }; +[error] FunctionDef "asech" is not found as expected here: my_arcsech { math: asech(x) }; +[error] FunctionDef "acsch" is not found as expected here: my_arccsch { math: acsch(x) }; +[error] FunctionDef "acoth" is not found as expected here: my_arccoth { math: acoth(x) }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01488/l3v2/index.heta b/latest/cases/01488/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01488/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01488/model-sbml-l2v5.xml b/latest/cases/01488/model-sbml-l2v5.xml new file mode 100644 index 000000000..f13139943 --- /dev/null +++ b/latest/cases/01488/model-sbml-l2v5.xml @@ -0,0 +1,605 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + + + z + + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + my_sec + time + + + + + + + my_sec + + + time + + + + + + + + my_csc + + + time + 0.001 + + + + + + + + my_csc + + + + + time + + 0.001 + + + + + + + + my_cot + + + time + 0.001 + + + + + + + + my_cot + + + + + time + + 0.001 + + + + + + + + my_sinh + time + + + + + + + my_sinh + + + time + + + + + + + + my_cosh + time + + + + + + + my_cosh + + + time + + + + + + + + my_arcsec + + + time + 1 + + + + + + + + my_arcsec + + + + + time + + 1 + + + + + + + + my_arccsc + + + time + 1 + + + + + + + + my_arccsc + + + + + time + + 1 + + + + + + + + my_arccot + + + time + 0.001 + + + + + + + + my_arccot + + + + + time + + 0.001 + + + + + + + + my_arcsinh + time + + + + + + + my_arcsinh + + + time + + + + + + + + my_arccosh + + + time + 1 + + + + + + + + my_piecewise + + my_arctanh + time + + + + time + 1 + + 10 + + + + + + + my_piecewise + + my_arctanh + + + time + + + + + time + 1 + + -10 + + + + + + + my_piecewise + 0 + + + + + time + 0 + + + + time + 1 + + + + my_arcsech + time + + + + + + + + my_arccsch + + + time + 1 + + + + + + + + my_arccsch + + + + + time + + 1 + + + + + + + + my_arccoth + + + time + 1.001 + + + + + + + + my_arccoth + + + + + time + + 1.001 + + + + + + + diff --git a/latest/cases/01488/model-sbml-l3v2.xml b/latest/cases/01488/model-sbml-l3v2.xml new file mode 100644 index 000000000..d8241652b --- /dev/null +++ b/latest/cases/01488/model-sbml-l3v2.xml @@ -0,0 +1,606 @@ + + + + + + + + + + x + + + y + + + z + + + + x + y + + + z + + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + my_sec + time + + + + + + + my_sec + + + time + + + + + + + + my_csc + + + time + 0.001 + + + + + + + + my_csc + + + + + time + + 0.001 + + + + + + + + my_cot + + + time + 0.001 + + + + + + + + my_cot + + + + + time + + 0.001 + + + + + + + + my_sinh + time + + + + + + + my_sinh + + + time + + + + + + + + my_cosh + time + + + + + + + my_cosh + + + time + + + + + + + + my_arcsec + + + time + 1 + + + + + + + + my_arcsec + + + + + time + + 1 + + + + + + + + my_arccsc + + + time + 1 + + + + + + + + my_arccsc + + + + + time + + 1 + + + + + + + + my_arccot + + + time + 0.001 + + + + + + + + my_arccot + + + + + time + + 0.001 + + + + + + + + my_arcsinh + time + + + + + + + my_arcsinh + + + time + + + + + + + + my_arccosh + + + time + 1 + + + + + + + + my_piecewise + + my_arctanh + time + + + + time + 1 + + 10 + + + + + + + my_piecewise + + my_arctanh + + + time + + + + + time + 1 + + -10 + + + + + + + my_piecewise + 0 + + + + + time + 0 + + + + time + 1 + + + + my_arcsech + time + + + + + + + + my_arccsch + + + time + 1 + + + + + + + + my_arccsch + + + + + time + + 1 + + + + + + + + my_arccoth + + + time + 1.001 + + + + + + + + my_arccoth + + + + + time + + 1.001 + + + + + + + diff --git a/latest/cases/01488/synopsis.txt b/latest/cases/01488/synopsis.txt new file mode 100644 index 000000000..1677459d7 --- /dev/null +++ b/latest/cases/01488/synopsis.txt @@ -0,0 +1,99 @@ + +category: Test +synopsis: Various uncommon MathML constructs, wrapped in function definitions. +componentTags: AssignmentRule, CSymbolTime, FunctionDefinition, Parameter +testTags: InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various trigonometrical constructs added in L2v1, wrapped in function definitions. Some functions with weird boundary conditions have been set up with the 'piecewise' function so that the results are never 'inf', or 'nan'. + +The model contains: +* 26 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26) + +There are 26 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $my_sec(time)$ | +| Assignment | P2 | $my_sec(-time)$ | +| Assignment | P3 | $my_csc(time + 0.001)$ | +| Assignment | P4 | $my_csc(-time - 0.001)$ | +| Assignment | P5 | $my_cot(time + 0.001)$ | +| Assignment | P6 | $my_cot(-time - 0.001)$ | +| Assignment | P7 | $my_sinh(time)$ | +| Assignment | P8 | $my_sinh(-time)$ | +| Assignment | P9 | $my_cosh(time)$ | +| Assignment | P10 | $my_cosh(-time)$ | +| Assignment | P11 | $my_arcsec(time + 1)$ | +| Assignment | P12 | $my_arcsec(-time - 1)$ | +| Assignment | P13 | $my_arccsc(time + 1)$ | +| Assignment | P14 | $my_arccsc(-time - 1)$ | +| Assignment | P15 | $my_arccot(time + 0.001)$ | +| Assignment | P16 | $my_arccot(-time - 0.001)$ | +| Assignment | P17 | $my_arcsinh(time)$ | +| Assignment | P18 | $my_arcsinh(-time)$ | +| Assignment | P19 | $my_arccosh(time + 1)$ | +| Assignment | P20 | $my_piecewise(my_arctanh(time), time < 1, 10)$ | +| Assignment | P21 | $my_piecewise(my_arctanh(-time), time < 1, -10)$ | +| Assignment | P22 | $my_piecewise(0, (time <= 0) || (time >= 1), my_arcsech(time))$ | +| Assignment | P23 | $my_arccsch(time + 1)$ | +| Assignment | P24 | $my_arccsch(-time - 1)$ | +| Assignment | P25 | $my_arccoth(time + 1.001)$ | +| Assignment | P26 | $my_arccoth(-time - 1.001)$ |] + +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_piecewise | x, y, z | $piecewise(x, y, z)$ | + | my_sec | x | $sec(x)$ | + | my_csc | x | $csc(x)$ | + | my_cot | x | $cot(x)$ | + | my_sinh | x | $sinh(x)$ | + | my_cosh | x | $cosh(x)$ | + | my_arcsec | x | $arcsec(x)$ | + | my_arccsc | x | $arccsc(x)$ | + | my_arccot | x | $arccot(x)$ | + | my_arcsinh | x | $arcsinh(x)$ | + | my_arccosh | x | $arccosh(x)$ | + | my_arctanh | x | $arctanh(x)$ | + | my_arcsech | x | $arcsech(x)$ | + | my_arccsch | x | $arccsch(x)$ | + | my_arccoth | x | $arccoth(x)$ | + | my_exponentiale | | $plus(exponentiale)$ | + | my_exp | x | $exp(x)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $my_sec(time)$ | variable | +| Initial value of parameter P2 | $my_sec(-time)$ | variable | +| Initial value of parameter P3 | $my_csc(time + 0.001)$ | variable | +| Initial value of parameter P4 | $my_csc(-time - 0.001)$ | variable | +| Initial value of parameter P5 | $my_cot(time + 0.001)$ | variable | +| Initial value of parameter P6 | $my_cot(-time - 0.001)$ | variable | +| Initial value of parameter P7 | $my_sinh(time)$ | variable | +| Initial value of parameter P8 | $my_sinh(-time)$ | variable | +| Initial value of parameter P9 | $my_cosh(time)$ | variable | +| Initial value of parameter P10 | $my_cosh(-time)$ | variable | +| Initial value of parameter P11 | $my_arcsec(time + 1)$ | variable | +| Initial value of parameter P12 | $my_arcsec(-time - 1)$ | variable | +| Initial value of parameter P13 | $my_arccsc(time + 1)$ | variable | +| Initial value of parameter P14 | $my_arccsc(-time - 1)$ | variable | +| Initial value of parameter P15 | $my_arccot(time + 0.001)$ | variable | +| Initial value of parameter P16 | $my_arccot(-time - 0.001)$ | variable | +| Initial value of parameter P17 | $my_arcsinh(time)$ | variable | +| Initial value of parameter P18 | $my_arcsinh(-time)$ | variable | +| Initial value of parameter P19 | $my_arccosh(time + 1)$ | variable | +| Initial value of parameter P20 | $my_piecewise(my_arctanh(time), time < 1, 10)$ | variable | +| Initial value of parameter P21 | $my_piecewise(my_arctanh(-time), time < 1, -10)$ | variable | +| Initial value of parameter P22 | $my_piecewise(0, (time <= 0) || (time >= 1), my_arcsech(time))$ | variable | +| Initial value of parameter P23 | $my_arccsch(time + 1)$ | variable | +| Initial value of parameter P24 | $my_arccsch(-time - 1)$ | variable | +| Initial value of parameter P25 | $my_arccoth(time + 1.001)$ | variable | +| Initial value of parameter P26 | $my_arccoth(-time - 1.001)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01489/l2v5/build.log b/latest/cases/01489/l2v5/build.log new file mode 100644 index 000000000..1adeaa4ad --- /dev/null +++ b/latest/cases/01489/l2v5/build.log @@ -0,0 +1,25 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01489/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01489/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01489/model-sbml-l2v5.xml"... +[error] my_plus Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_times Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_and Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_or Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_xor Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[error] FunctionDef "my_plus" is not found as expected here: a { math: undefined }; +[error] FunctionDef "my_times" is not found as expected here: b { math: undefined }; +[error] FunctionDef "my_and" is not found as expected here: c { math: undefined }; +[error] FunctionDef "my_or" is not found as expected here: d { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01489/l2v5/index.heta b/latest/cases/01489/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01489/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01489/l3v2/build.log b/latest/cases/01489/l3v2/build.log new file mode 100644 index 000000000..8da49659e --- /dev/null +++ b/latest/cases/01489/l3v2/build.log @@ -0,0 +1,25 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01489/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01489/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01489/model-sbml-l3v2.xml"... +[error] my_plus Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_times Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_and Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_or Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_xor Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01489/l3v2/index.heta b/latest/cases/01489/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01489/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01489/model-sbml-l2v5.xml b/latest/cases/01489/model-sbml-l2v5.xml new file mode 100644 index 000000000..2d408e0dc --- /dev/null +++ b/latest/cases/01489/model-sbml-l2v5.xml @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + my_plus + + + + + + + my_times + + + + + + + + 1 + + my_and + + + + 0 + + + + + + + + + 1 + + my_or + + + + 0 + + + + + + + + + 1 + + my_xor + + + + 0 + + + + + + + diff --git a/latest/cases/01489/model-sbml-l3v2.xml b/latest/cases/01489/model-sbml-l3v2.xml new file mode 100644 index 000000000..40fbd8c05 --- /dev/null +++ b/latest/cases/01489/model-sbml-l3v2.xml @@ -0,0 +1,121 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + my_plus + + + + + + + my_times + + + + + + + + 1 + + my_and + + + + 0 + + + + + + + + + 1 + + my_or + + + + 0 + + + + + + + + + 1 + + my_xor + + + + 0 + + + + + + + diff --git a/latest/cases/01489/synopsis.txt b/latest/cases/01489/synopsis.txt new file mode 100644 index 000000000..62370f5de --- /dev/null +++ b/latest/cases/01489/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Test of 0-child MathML constructs in function definitions. +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In the official MathML spec, plus, times, and, or, and xor may all have 0 arguments. When they do, they are supposed return identity for that construct, namely: + *plus: 0 + *times: 1 + *and: true + *or: false + *xor: false + +This tests tests these constructs in function definitions. + +The model contains: +* 5 parameters (a, b, c, d, e) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_plus | | $plus()$ | + | my_times | | $times()$ | + | my_and | | $and()$ | + | my_or | | $or()$ | + | my_xor | | $xor()$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $my_plus()$ | constant | +| Initial value of parameter b | $my_times()$ | constant | +| Initial value of parameter c | $piecewise(1, my_and(), 0)$ | constant | +| Initial value of parameter d | $piecewise(1, my_or(), 0)$ | constant | +| Initial value of parameter e | $piecewise(1, my_xor(), 0)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01490/l2v5/build.log b/latest/cases/01490/l2v5/build.log new file mode 100644 index 000000000..256e5f435 --- /dev/null +++ b/latest/cases/01490/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01490/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01490/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01490/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 93 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01490/l2v5/index.heta b/latest/cases/01490/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01490/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01490/l3v2/build.log b/latest/cases/01490/l3v2/build.log new file mode 100644 index 000000000..62cccd7fe --- /dev/null +++ b/latest/cases/01490/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01490/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01490/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01490/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 88 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01490/l3v2/index.heta b/latest/cases/01490/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01490/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01490/model-sbml-l2v5.xml b/latest/cases/01490/model-sbml-l2v5.xml new file mode 100644 index 000000000..bde79986c --- /dev/null +++ b/latest/cases/01490/model-sbml-l2v5.xml @@ -0,0 +1,145 @@ + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + my_plus + 1 + + + + + + + my_times + 2 + + + + + + + + 1 + + my_and + + + + + 0 + + + + + + + + + 1 + + my_or + + + + + 0 + + + + + + + + + 1 + + my_xor + + + + + 0 + + + + + + + diff --git a/latest/cases/01490/model-sbml-l3v2.xml b/latest/cases/01490/model-sbml-l3v2.xml new file mode 100644 index 000000000..7079a2f77 --- /dev/null +++ b/latest/cases/01490/model-sbml-l3v2.xml @@ -0,0 +1,146 @@ + + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + my_plus + 1 + + + + + + + my_times + 2 + + + + + + + + 1 + + my_and + + + + + 0 + + + + + + + + + 1 + + my_or + + + + + 0 + + + + + + + + + 1 + + my_xor + + + + + 0 + + + + + + + diff --git a/latest/cases/01490/synopsis.txt b/latest/cases/01490/synopsis.txt new file mode 100644 index 000000000..d4f7819ef --- /dev/null +++ b/latest/cases/01490/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Test of 1-child MathML constructs plus, times, and, or, and xor in function definitions. +componentTags: AssignmentRule, FunctionDefinition, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In the official MathML spec, plus, times, and, or, and xor may all have 1 arguments. When they do, they are supposed return that argument. This tests tests these constructs in function definitions. + +The model contains: +* 5 parameters (a, b, c, d, e) + +There are 5 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | a | $my_plus(1)$ | +| Assignment | b | $my_times(2)$ | +| Assignment | c | $piecewise(1, my_and(true), 0)$ | +| Assignment | d | $piecewise(1, my_or(true), 0)$ | +| Assignment | e | $piecewise(1, my_xor(true), 0)$ |] + +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_plus | x | $plus(x)$ | + | my_times | x | $times(x)$ | + | my_and | x | $and(x)$ | + | my_or | x | $or(x)$ | + | my_xor | x | $xor(x)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $my_plus(1)$ | variable | +| Initial value of parameter b | $my_times(2)$ | variable | +| Initial value of parameter c | $piecewise(1, my_and(true), 0)$ | variable | +| Initial value of parameter d | $piecewise(1, my_or(true), 0)$ | variable | +| Initial value of parameter e | $piecewise(1, my_xor(true), 0)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01491/l2v5/build.log b/latest/cases/01491/l2v5/build.log new file mode 100644 index 000000000..6e24aa378 --- /dev/null +++ b/latest/cases/01491/l2v5/build.log @@ -0,0 +1,30 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01491/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01491/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01491/model-sbml-l2v5.xml"... +[error] my_plus0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_times0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_and0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_or0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_xor0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] Function math "my_and" should be a numeric expression. +[error] Function math "my_or" should be a numeric expression. +[error] Function math "my_xor" should be a numeric expression. +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 90 +[error] FunctionDef "my_plus0" is not found as expected here: a { math: undefined }; +[error] FunctionDef "my_times0" is not found as expected here: b { math: undefined }; +[error] FunctionDef "my_and" is not found as expected here: c { math: undefined }; +[error] FunctionDef "my_and0" is not found as expected here: c { math: undefined }; +[error] FunctionDef "my_or" is not found as expected here: d { math: undefined }; +[error] FunctionDef "my_or0" is not found as expected here: d { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01491/l2v5/index.heta b/latest/cases/01491/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01491/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01491/l3v2/build.log b/latest/cases/01491/l3v2/build.log new file mode 100644 index 000000000..3af49e857 --- /dev/null +++ b/latest/cases/01491/l3v2/build.log @@ -0,0 +1,30 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01491/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01491/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01491/model-sbml-l3v2.xml"... +[error] my_plus0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_times0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_and0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_or0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] my_xor0 Some of properties do not satisfy requirements for class "FunctionDef" + 1. /math should NOT be shorter than 1 characters +[error] Function math "my_and" should be a numeric expression. +[error] Function math "my_or" should be a numeric expression. +[error] Function math "my_xor" should be a numeric expression. +[error] id must not be a reserved word, got "e". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] e component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[error] FunctionDef "my_plus0" is not found as expected here: a { math: undefined }; +[error] FunctionDef "my_times0" is not found as expected here: b { math: undefined }; +[error] FunctionDef "my_and" is not found as expected here: c { math: undefined }; +[error] FunctionDef "my_and0" is not found as expected here: c { math: undefined }; +[error] FunctionDef "my_or" is not found as expected here: d { math: undefined }; +[error] FunctionDef "my_or0" is not found as expected here: d { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01491/l3v2/index.heta b/latest/cases/01491/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01491/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01491/model-sbml-l2v5.xml b/latest/cases/01491/model-sbml-l2v5.xml new file mode 100644 index 000000000..d81834ddf --- /dev/null +++ b/latest/cases/01491/model-sbml-l2v5.xml @@ -0,0 +1,245 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + my_plus + 1 + + my_plus + 1 + + my_plus0 + + + + + + + + + my_times + 2 + + my_times + 2 + + my_times0 + + + + + + + + + + 1 + + my_and + + my_and + + my_and0 + + + + + + + + 0 + + + + + + + + + 1 + + my_or + + my_or + + my_or0 + + + + + + + + 0 + + + + + + + + + 1 + + my_xor + + my_xor + + my_xor0 + + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01491/model-sbml-l3v2.xml b/latest/cases/01491/model-sbml-l3v2.xml new file mode 100644 index 000000000..d77602acb --- /dev/null +++ b/latest/cases/01491/model-sbml-l3v2.xml @@ -0,0 +1,246 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + + my_plus + 1 + + my_plus + 1 + + my_plus0 + + + + + + + + + my_times + 2 + + my_times + 2 + + my_times0 + + + + + + + + + + 1 + + my_and + + my_and + + my_and0 + + + + + + + + 0 + + + + + + + + + 1 + + my_or + + my_or + + my_or0 + + + + + + + + 0 + + + + + + + + + 1 + + my_xor + + my_xor + + my_xor0 + + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01491/synopsis.txt b/latest/cases/01491/synopsis.txt new file mode 100644 index 000000000..ef34896f8 --- /dev/null +++ b/latest/cases/01491/synopsis.txt @@ -0,0 +1,57 @@ + +category: Test +synopsis: Test of nested 0-child MathML constructs plus, times, and, or, and xor in function definitions. +componentTags: AssignmentRule, FunctionDefinition, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In the official MathML spec, plus, times, and, or, and xor may all have 0 arguments. When they do, they are supposed return identity for that construct, namely: + *plus: 0 + *times: 1 + *and: true + *or: false + *xor: false + +This tests tests these constructs in function definitions. + +The model contains: +* 5 parameters (a, b, c, d, e) + +There are 5 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | a | $my_plus(1, my_plus(1, my_plus0()))$ | +| Assignment | b | $my_times(2, my_times(2, my_times0()))$ | +| Assignment | c | $piecewise(1, my_and(my_and(my_and0(), true), true), 0)$ | +| Assignment | d | $piecewise(1, my_or(my_or(my_or0(), true), true), 0)$ | +| Assignment | e | $piecewise(1, my_xor(my_xor(my_xor0(), true), true), 0)$ |] + +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_plus0 | | $plus()$ | + | my_times0 | | $times()$ | + | my_and0 | | $and()$ | + | my_or0 | | $or()$ | + | my_xor0 | | $xor()$ | + | my_plus | x, y | $x + y$ | + | my_times | x, y | $x * y$ | + | my_and | x, y | $x && y$ | + | my_or | x, y | $x || y$ | + | my_xor | x, y | $xor(x, y)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter a | $my_plus(1, my_plus(1, my_plus0()))$ | variable | +| Initial value of parameter b | $my_times(2, my_times(2, my_times0()))$ | variable | +| Initial value of parameter c | $piecewise(1, my_and(my_and(my_and0(), true), true), 0)$ | variable | +| Initial value of parameter d | $piecewise(1, my_or(my_or(my_or0(), true), true), 0)$ | variable | +| Initial value of parameter e | $piecewise(1, my_xor(my_xor(my_xor0(), true), true), 0)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01492/l2v5/build.log b/latest/cases/01492/l2v5/build.log new file mode 100644 index 000000000..26f5658fc --- /dev/null +++ b/latest/cases/01492/l2v5/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01492/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01492/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01492/model-sbml-l2v5.xml"... +[error] Function math "my_gt" should be a numeric expression. +[error] Function math "my_lteq" should be a numeric expression. +[info] Setting references in elements, total length 90 +[error] FunctionDef "my_gt" is not found as expected here: z { math: undefined }; +[error] FunctionDef "my_lteq" is not found as expected here: z { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01492/l2v5/index.heta b/latest/cases/01492/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01492/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01492/l3v2/build.log b/latest/cases/01492/l3v2/build.log new file mode 100644 index 000000000..b315b70e7 --- /dev/null +++ b/latest/cases/01492/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01492/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01492/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01492/model-sbml-l3v2.xml"... +[error] Function math "my_gt" should be a numeric expression. +[error] Function math "my_lteq" should be a numeric expression. +[info] Setting references in elements, total length 85 +[error] FunctionDef "my_gt" is not found as expected here: z { math: undefined }; +[error] FunctionDef "my_lteq" is not found as expected here: z { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01492/l3v2/index.heta b/latest/cases/01492/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01492/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01492/model-sbml-l2v5.xml b/latest/cases/01492/model-sbml-l2v5.xml new file mode 100644 index 000000000..8de3bb20e --- /dev/null +++ b/latest/cases/01492/model-sbml-l2v5.xml @@ -0,0 +1,105 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + + + z + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + my_piecewise + + my_piecewise + 2 + + my_gt + y + 1.49 + + 1 + + + my_lteq + x + 0.49 + + 0 + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01492/model-sbml-l3v2.xml b/latest/cases/01492/model-sbml-l3v2.xml new file mode 100644 index 000000000..d45cc8c90 --- /dev/null +++ b/latest/cases/01492/model-sbml-l3v2.xml @@ -0,0 +1,106 @@ + + + + + + + + + + x + + + y + + + z + + + + x + y + + + z + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + my_piecewise + + my_piecewise + 2 + + my_gt + y + 1.49 + + 1 + + + my_lteq + x + 0.49 + + 0 + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01492/synopsis.txt b/latest/cases/01492/synopsis.txt new file mode 100644 index 000000000..6005ae274 --- /dev/null +++ b/latest/cases/01492/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Nested piecewise in function definitions. +componentTags: AssignmentRule, FunctionDefinition, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model has a nested 'piecewise' function, with the nested piecewise in the 'returned value' part of the function. This tests tests these constructs in function definitions. + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $my_piecewise(my_piecewise(2, my_gt(y, 1.49), 1), my_lteq(x, 0.49), 0)$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_piecewise | x, y, z | $piecewise(x, y, z)$ | + | my_gt | x, y | $x > y$ | + | my_lteq | x, y | $x <= y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $my_piecewise(my_piecewise(2, my_gt(y, 1.49), 1), my_lteq(x, 0.49), 0)$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01493/l2v5/build.log b/latest/cases/01493/l2v5/build.log new file mode 100644 index 000000000..d704616d9 --- /dev/null +++ b/latest/cases/01493/l2v5/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01493/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01493/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01493/model-sbml-l2v5.xml"... +[error] Function math "my_gt" should be a numeric expression. +[error] Function math "my_lteq" should be a numeric expression. +[info] Setting references in elements, total length 90 +[error] FunctionDef "my_gt" is not found as expected here: z { math: undefined }; +[error] FunctionDef "my_lteq" is not found as expected here: z { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01493/l2v5/index.heta b/latest/cases/01493/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01493/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01493/l3v2/build.log b/latest/cases/01493/l3v2/build.log new file mode 100644 index 000000000..a6f89db08 --- /dev/null +++ b/latest/cases/01493/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01493/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01493/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01493/model-sbml-l3v2.xml"... +[error] Function math "my_gt" should be a numeric expression. +[error] Function math "my_lteq" should be a numeric expression. +[info] Setting references in elements, total length 85 +[error] FunctionDef "my_gt" is not found as expected here: z { math: undefined }; +[error] FunctionDef "my_lteq" is not found as expected here: z { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01493/l3v2/index.heta b/latest/cases/01493/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01493/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01493/model-sbml-l2v5.xml b/latest/cases/01493/model-sbml-l2v5.xml new file mode 100644 index 000000000..e5cf4b1bf --- /dev/null +++ b/latest/cases/01493/model-sbml-l2v5.xml @@ -0,0 +1,114 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + + + z + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + my_piecewise + + my_piecewise + 2 + + my_gt + y + 1.49 + + 1 + + + my_lteq + x + 0.49 + + + my_piecewise + 1 + + my_gt + y + 0.49 + + 0 + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01493/model-sbml-l3v2.xml b/latest/cases/01493/model-sbml-l3v2.xml new file mode 100644 index 000000000..1bc84d9e4 --- /dev/null +++ b/latest/cases/01493/model-sbml-l3v2.xml @@ -0,0 +1,115 @@ + + + + + + + + + + x + + + y + + + z + + + + x + y + + + z + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + my_piecewise + + my_piecewise + 2 + + my_gt + y + 1.49 + + 1 + + + my_lteq + x + 0.49 + + + my_piecewise + 1 + + my_gt + y + 0.49 + + 0 + + + + + + + -2 + + + + + 1 + + + + + diff --git a/latest/cases/01493/synopsis.txt b/latest/cases/01493/synopsis.txt new file mode 100644 index 000000000..101688c04 --- /dev/null +++ b/latest/cases/01493/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: Nested piecewise in return and otherwise. +componentTags: AssignmentRule, FunctionDefinition, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The assignment rule for parameter 'z' has two nested piecewise functions in the return and otherwise parts of the containing piecewise function. This tests tests these constructs in function definitions. A combination of cases 01200 and 01202. + +The model contains: +* 3 parameters (z, y, x) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $my_piecewise(my_piecewise(2, my_gt(y, 1.49), 1), my_lteq(x, 0.49), my_piecewise(1, my_gt(y, 0.49), 0))$ | +| Rate | y | $-2$ | +| Rate | x | $1$ |] + +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_piecewise | x, y, z | $piecewise(x, y, z)$ | + | my_gt | x, y | $x > y$ | + | my_lteq | x, y | $x <= y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter z | $my_piecewise(my_piecewise(2, my_gt(y, 1.49), 1), my_lteq(x, 0.49), my_piecewise(1, my_gt(y, 0.49), 0))$ | variable | +| Initial value of parameter y | $2$ | variable | +| Initial value of parameter x | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01494/l2v5/build.log b/latest/cases/01494/l2v5/build.log new file mode 100644 index 000000000..90652e3c3 --- /dev/null +++ b/latest/cases/01494/l2v5/build.log @@ -0,0 +1,18 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01494/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01494/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01494/model-sbml-l2v5.xml"... +[error] Function math "my_lt" should be a numeric expression. +[error] Function math "my_gt" should be a numeric expression. +[error] Function math "my_leq" should be a numeric expression. +[error] Function math "my_geq" should be a numeric expression. +[error] Function math "my_eq" should be a numeric expression. +[info] Setting references in elements, total length 89 +[error] FunctionDef "my_lt" is not found as expected here: P1 { math: undefined }; +[error] FunctionDef "my_gt" is not found as expected here: P2 { math: undefined }; +[error] FunctionDef "my_leq" is not found as expected here: P3 { math: undefined }; +[error] FunctionDef "my_geq" is not found as expected here: P4 { math: undefined }; +[error] FunctionDef "my_eq" is not found as expected here: P5 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01494/l2v5/index.heta b/latest/cases/01494/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01494/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01494/l3v2/build.log b/latest/cases/01494/l3v2/build.log new file mode 100644 index 000000000..e460d8953 --- /dev/null +++ b/latest/cases/01494/l3v2/build.log @@ -0,0 +1,18 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01494/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01494/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01494/model-sbml-l3v2.xml"... +[error] Function math "my_lt" should be a numeric expression. +[error] Function math "my_gt" should be a numeric expression. +[error] Function math "my_leq" should be a numeric expression. +[error] Function math "my_geq" should be a numeric expression. +[error] Function math "my_eq" should be a numeric expression. +[info] Setting references in elements, total length 84 +[error] No required "num" property for "P1" of Const. +[error] No required "num" property for "P2" of Const. +[error] No required "num" property for "P3" of Const. +[error] No required "num" property for "P4" of Const. +[error] No required "num" property for "P5" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01494/l3v2/index.heta b/latest/cases/01494/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01494/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01494/model-sbml-l2v5.xml b/latest/cases/01494/model-sbml-l2v5.xml new file mode 100644 index 000000000..c578e873f --- /dev/null +++ b/latest/cases/01494/model-sbml-l2v5.xml @@ -0,0 +1,211 @@ + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + 1 + + my_lt + 1 + 2 + 1 + + + + 3 + + + + + + + + + 1 + + my_gt + 2 + 1 + 2 + + + + 3 + + + + + + + + + 1 + + my_leq + 1 + 2 + 1 + + + + 3 + + + + + + + + + 1 + + my_geq + 2 + 1 + 2 + + + + 3 + + + + + + + + + 1 + + my_eq + 1 + 1 + 2 + + + + 3 + + + + + + + diff --git a/latest/cases/01494/model-sbml-l3v2.xml b/latest/cases/01494/model-sbml-l3v2.xml new file mode 100644 index 000000000..552fd9749 --- /dev/null +++ b/latest/cases/01494/model-sbml-l3v2.xml @@ -0,0 +1,212 @@ + + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + x + + + y + + + z + + + + x + y + z + + + + + + + + + + + + + + + + + + 1 + + my_lt + 1 + 2 + 1 + + + + 3 + + + + + + + + + 1 + + my_gt + 2 + 1 + 2 + + + + 3 + + + + + + + + + 1 + + my_leq + 1 + 2 + 1 + + + + 3 + + + + + + + + + 1 + + my_geq + 2 + 1 + 2 + + + + 3 + + + + + + + + + 1 + + my_eq + 1 + 1 + 2 + + + + 3 + + + + + + + diff --git a/latest/cases/01494/synopsis.txt b/latest/cases/01494/synopsis.txt new file mode 100644 index 000000000..93ca1ebba --- /dev/null +++ b/latest/cases/01494/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An initial assignment with an nary relational element. +componentTags: FunctionDefinition, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as less than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. This tests tests these constructs in function definitions. + +The model contains: +* 5 parameters (P1, P2, P3, P4, P5) +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_lt | x, y, z | $x < y < z$ | + | my_gt | x, y, z | $x > y > z$ | + | my_leq | x, y, z | $x <= y <= z$ | + | my_geq | x, y, z | $x >= y >= z$ | + | my_eq | x, y, z | $x == y == z$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $piecewise(1, my_lt(1, 2, 1), 3)$ | constant | +| Initial value of parameter P2 | $piecewise(1, my_gt(2, 1, 2), 3)$ | constant | +| Initial value of parameter P3 | $piecewise(1, my_leq(1, 2, 1), 3)$ | constant | +| Initial value of parameter P4 | $piecewise(1, my_geq(2, 1, 2), 3)$ | constant | +| Initial value of parameter P5 | $piecewise(1, my_eq(1, 1, 2), 3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01495/l2v5/index.heta b/latest/cases/01495/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01495/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01495/l3v2/build.log b/latest/cases/01495/l3v2/build.log new file mode 100644 index 000000000..6f9d8358f --- /dev/null +++ b/latest/cases/01495/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01495/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01495/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01495/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] FunctionDef "quotient" is not found as expected here: my_quotient { math: quotient(x, y) }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01495/l3v2/index.heta b/latest/cases/01495/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01495/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01495/model-sbml-l3v2.xml b/latest/cases/01495/model-sbml-l3v2.xml new file mode 100644 index 000000000..d96840e24 --- /dev/null +++ b/latest/cases/01495/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + my_quotient + time + 2 + + + + + + diff --git a/latest/cases/01495/synopsis.txt b/latest/cases/01495/synopsis.txt new file mode 100644 index 000000000..77d3cf1ec --- /dev/null +++ b/latest/cases/01495/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Use of the 'quotient' MathML in an assignment rule. +componentTags: AssignmentRule, CSymbolTime, FunctionDefinition, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +In this model, the 'quotient' MathML symbol is used in an assignment rule function definition. + +The model contains: +* 1 parameter (p1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $my_quotient(time, 2)$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_quotient | x, y | $quotient(x, y)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $my_quotient(time, 2)$ | variable |] + diff --git a/latest/cases/01496/l2v5/index.heta b/latest/cases/01496/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01496/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01496/l3v2/build.log b/latest/cases/01496/l3v2/build.log new file mode 100644 index 000000000..c84648d57 --- /dev/null +++ b/latest/cases/01496/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01496/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01496/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01496/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] FunctionDef "rem" is not found as expected here: my_rem { math: rem(x, y) }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01496/l3v2/index.heta b/latest/cases/01496/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01496/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01496/model-sbml-l3v2.xml b/latest/cases/01496/model-sbml-l3v2.xml new file mode 100644 index 000000000..49c6083ad --- /dev/null +++ b/latest/cases/01496/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + my_rem + time + 2 + + + + + + diff --git a/latest/cases/01496/synopsis.txt b/latest/cases/01496/synopsis.txt new file mode 100644 index 000000000..167d776d1 --- /dev/null +++ b/latest/cases/01496/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Use of the 'rem' MathML in an assignment rule. +componentTags: AssignmentRule, CSymbolTime, FunctionDefinition, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + +In this model, the 'rem' MathML symbol is used in an assignment rule function definition. + +The model contains: +* 1 parameter (p1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | p1 | $my_rem(time, 2)$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_rem | x, y | $rem(x, y)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $my_rem(time, 2)$ | variable |] + diff --git a/latest/cases/01497/l2v5/index.heta b/latest/cases/01497/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01497/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01497/l3v2/build.log b/latest/cases/01497/l3v2/build.log new file mode 100644 index 000000000..072513d0c --- /dev/null +++ b/latest/cases/01497/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01497/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01497/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01497/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 84 +[error] FunctionDef "implies" is not found as expected here: my_implies { math: implies(x, y) }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01497/l3v2/index.heta b/latest/cases/01497/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01497/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01497/model-sbml-l3v2.xml b/latest/cases/01497/model-sbml-l3v2.xml new file mode 100644 index 000000000..75451a3a2 --- /dev/null +++ b/latest/cases/01497/model-sbml-l3v2.xml @@ -0,0 +1,101 @@ + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + + my_implies + + + time + 5.5 + + + + time + 2.5 + + + + + + + + my_implies + + + time + 5.5 + + + + time + 2.5 + + + + + + + + my_implies + + + time + 5.5 + + + + time + 2.5 + + + + + + + + my_implies + + + time + 5.5 + + + + time + 2.5 + + + + + + + diff --git a/latest/cases/01497/synopsis.txt b/latest/cases/01497/synopsis.txt new file mode 100644 index 000000000..1f3a3ac4d --- /dev/null +++ b/latest/cases/01497/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Use of the 'implies' MathML in assignment rules. +componentTags: AssignmentRule, CSymbolTime, FunctionDefinition, Parameter +testTags: InitialValueReassigned, L3v2MathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the 'implies' MathML symbol is used in assignment rule function definitions. 'Implies' means 'if A is true, then B is also true', or '(not A) or B'. With the automatic translation (in l3v2) of boolean values to numeric values, this means that p1 is always 1 (true); p2 becomes 0 (false) halfway through the run; p3 becomes 0 only from 2.5 5.5, time > 2.5)$ | +| Assignment | p2 | $my_implies(time > 5.5, time < 2.5)$ | +| Assignment | p3 | $my_implies(time < 5.5, time > 2.5)$ | +| Assignment | p4 | $my_implies(time < 5.5, time < 2.5)$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | my_implies | x, y | $implies(x, y)$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $my_implies(time > 5.5, time > 2.5)$ | variable | +| Initial value of parameter p2 | $my_implies(time > 5.5, time < 2.5)$ | variable | +| Initial value of parameter p3 | $my_implies(time < 5.5, time > 2.5)$ | variable | +| Initial value of parameter p4 | $my_implies(time < 5.5, time < 2.5)$ | variable |] + diff --git a/latest/cases/01498/l2v5/index.heta b/latest/cases/01498/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01498/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01498/l3v2/build.log b/latest/cases/01498/l3v2/build.log new file mode 100644 index 000000000..9357fae39 --- /dev/null +++ b/latest/cases/01498/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01498/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01498/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01498/model-sbml-l3v2.xml"... +[error] S2_sr component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[error] Component "S2_sr" is not found in space "nameless" as expected in expression: S1_proc [ode_]= S2_sr; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01498/l3v2/index.heta b/latest/cases/01498/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01498/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01498/model-sbml-l3v2.xml b/latest/cases/01498/model-sbml-l3v2.xml new file mode 100644 index 000000000..99adc85cf --- /dev/null +++ b/latest/cases/01498/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + 0.4 + + + + + + + S2_sr + + + + + 0.2 + + + + + S1 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01498/synopsis.txt b/latest/cases/01498/synopsis.txt new file mode 100644 index 000000000..c5e57a1d6 --- /dev/null +++ b/latest/cases/01498/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule. +componentTags: AssignmentRule, Compartment, InitialAssignment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath, VolumeConcentrationRates +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. One of the rate rules gets its value from a species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (x) +* 1 compartment (C1) +* 1 species reference (S2_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S2_sr S2 | $1$ |] +Note: the following stoichiometries are set separately: S2_sr + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $S2_sr$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable | +| Initial value of species reference 'S2_sr' | $0.4$ | constant |] + diff --git a/latest/cases/01499/l2v5/index.heta b/latest/cases/01499/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01499/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01499/l3v2/build.log b/latest/cases/01499/l3v2/build.log new file mode 100644 index 000000000..504c8795d --- /dev/null +++ b/latest/cases/01499/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01499/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01499/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01499/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01499/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01499/l3v2/index.heta b/latest/cases/01499/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01499/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01499/model-sbml-l3v2.xml b/latest/cases/01499/model-sbml-l3v2.xml new file mode 100644 index 000000000..dc9c92e68 --- /dev/null +++ b/latest/cases/01499/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + P0 + S1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01499/synopsis.txt b/latest/cases/01499/synopsis.txt new file mode 100644 index 000000000..6a2328adc --- /dev/null +++ b/latest/cases/01499/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A combination of a model converstion factor and an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the species are affected by a reaction, which is itself affected by a model-wide conversion factor. The parameter P0 equals S1 through an algebraic rule. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P0, conversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the model is 'conversion' + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P0 - S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter conversion | $2$ | constant | +| Initial value of parameter P0 | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01500/l2v5/index.heta b/latest/cases/01500/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01500/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01500/l3v2/build.log b/latest/cases/01500/l3v2/build.log new file mode 100644 index 000000000..5fefb680e --- /dev/null +++ b/latest/cases/01500/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01500/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01500/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01500/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01500/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01500/l3v2/index.heta b/latest/cases/01500/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01500/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01500/model-sbml-l3v2.xml b/latest/cases/01500/model-sbml-l3v2.xml new file mode 100644 index 000000000..8b589f6c1 --- /dev/null +++ b/latest/cases/01500/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + P0 + S1 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01500/synopsis.txt b/latest/cases/01500/synopsis.txt new file mode 100644 index 000000000..cf5005631 --- /dev/null +++ b/latest/cases/01500/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A combination of a species converstion factor and an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the species are affected by a reaction, one of which is affected by a species conversion factor. The parameter P0 equals S1 through an algebraic rule. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P0, conversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the species 'S1' is 'conversion' + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P0 - S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter conversion | $2$ | constant | +| Initial value of parameter P0 | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01501/l2v5/index.heta b/latest/cases/01501/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01501/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01501/l3v2/build.log b/latest/cases/01501/l3v2/build.log new file mode 100644 index 000000000..004402b8c --- /dev/null +++ b/latest/cases/01501/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01501/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01501/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01501/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01501/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01501/l3v2/index.heta b/latest/cases/01501/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01501/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01501/model-sbml-l3v2.xml b/latest/cases/01501/model-sbml-l3v2.xml new file mode 100644 index 000000000..1ce64b32b --- /dev/null +++ b/latest/cases/01501/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + P0 + S1 + + + + + + + + P1 + S2 + + + + + + + + + + + + + + + + + 0.1 + S1 + + + + + + + diff --git a/latest/cases/01501/synopsis.txt b/latest/cases/01501/synopsis.txt new file mode 100644 index 000000000..66e035b77 --- /dev/null +++ b/latest/cases/01501/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A combination of a species and model conversion factors and algebraic rules. +componentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + In this model, the species are affected by a reaction, one of which is affected by a species conversion factor, and the other of which is affected by the model conversion factor. The parameter P0 and P1 equal S1 and S2, respectively, through algebraic rules. + +The model contains: +* 2 species (S1, S2) +* 4 parameters (P0, P1, mconversion, sconversion) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.1 * S1$ |] + +The conversion factor for the model is 'mconversion' +The conversion factor for the species 'S1' is 'sconversion' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P0 - S1$ | +| Algebraic | $0$ | $P1 - S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $5$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial value of parameter mconversion | $3$ | constant | +| Initial value of parameter sconversion | $2$ | constant | +| Initial value of parameter P0 | $unknown$ | variable | +| Initial value of parameter P1 | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01502/l2v5/build.log b/latest/cases/01502/l2v5/build.log new file mode 100644 index 000000000..e5988a560 --- /dev/null +++ b/latest/cases/01502/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01502/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01502/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01502/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01502/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01502/l2v5/index.heta b/latest/cases/01502/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01502/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01502/l3v2/build.log b/latest/cases/01502/l3v2/build.log new file mode 100644 index 000000000..0a3a92f39 --- /dev/null +++ b/latest/cases/01502/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01502/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01502/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01502/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01502/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01502/l3v2/index.heta b/latest/cases/01502/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01502/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01502/model-sbml-l2v5.xml b/latest/cases/01502/model-sbml-l2v5.xml new file mode 100644 index 000000000..d87d092d9 --- /dev/null +++ b/latest/cases/01502/model-sbml-l2v5.xml @@ -0,0 +1,494 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + P2 + + + -1 + + + + + + + + + P3 + + + 1 + + + + + + + + + P4 + + + -1 + + + + + + + + + P5 + + + 0.5 + + + + + + + + + P6 + + + 1 + + + + + + + + + P7 + + + -0.5 + + + + + + + + + P8 + + + 2.8 + + + + + + + + + P9 + + + -7.09 + + + + + + + + + P10 + + + 0.5 + + + + + + + + + P11 + + + 3.55 + + + + + + + + + P12 + + + -4.6 + + + + + + + + + P13 + + + 9.1 + + + + + + + + + P14 + + + -0.22 + + + + + + + + + P15 + + + 0 + + + + + + + + + P16 + + + 1 + + + + + + + + + P17 + + + 0.77 + + + + + + + + + P18 + + + -4.6 + + + + + + + + + P19 + + + 9.1 + + + + + + + + + P20 + + + 0.2 + + + + + + + + + P21 + + + 1 + + + + + + + + + P22 + + + + 10 + + 0.2 + + + + + + + + + P23 + + + + 10 + + 1 + + + + + + + + + P24 + + + 1 + 2 + + + + + + + + + P25 + + + 2 + 2 + + + + + + + + + P26 + + + 1.4 + 5.1 + + + + + + + + + P27 + + + 4 + 2 + + + + + + + + + P28 + + + 3.1 + 2 + + + + + + + + + P29 + + + + 2 + + 4 + + + + + + + + + P30 + + + + 2 + + 7.4 + + + + + + + + + P31 + + + 2.1 + + + + + + + + + P32 + + + 0 + + + + + + + + + P33 + + + -5.9 + + + + + + + + + P34 + + + 0 + + + + + + + + + P35 + + + 1.11 + + + + + + + + + P36 + + + -6 + + + + + + + + + P37 + + + -0.4 + + + + + + + diff --git a/latest/cases/01502/model-sbml-l3v2.xml b/latest/cases/01502/model-sbml-l3v2.xml new file mode 100644 index 000000000..ff25c49eb --- /dev/null +++ b/latest/cases/01502/model-sbml-l3v2.xml @@ -0,0 +1,495 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + P2 + + + -1 + + + + + + + + + P3 + + + 1 + + + + + + + + + P4 + + + -1 + + + + + + + + + P5 + + + 0.5 + + + + + + + + + P6 + + + 1 + + + + + + + + + P7 + + + -0.5 + + + + + + + + + P8 + + + 2.8 + + + + + + + + + P9 + + + -7.09 + + + + + + + + + P10 + + + 0.5 + + + + + + + + + P11 + + + 3.55 + + + + + + + + + P12 + + + -4.6 + + + + + + + + + P13 + + + 9.1 + + + + + + + + + P14 + + + -0.22 + + + + + + + + + P15 + + + 0 + + + + + + + + + P16 + + + 1 + + + + + + + + + P17 + + + 0.77 + + + + + + + + + P18 + + + -4.6 + + + + + + + + + P19 + + + 9.1 + + + + + + + + + P20 + + + 0.2 + + + + + + + + + P21 + + + 1 + + + + + + + + + P22 + + + + 10 + + 0.2 + + + + + + + + + P23 + + + + 10 + + 1 + + + + + + + + + P24 + + + 1 + 2 + + + + + + + + + P25 + + + 2 + 2 + + + + + + + + + P26 + + + 1.4 + 5.1 + + + + + + + + + P27 + + + 4 + 2 + + + + + + + + + P28 + + + 3.1 + 2 + + + + + + + + + P29 + + + + 2 + + 4 + + + + + + + + + P30 + + + + 2 + + 7.4 + + + + + + + + + P31 + + + 2.1 + + + + + + + + + P32 + + + 0 + + + + + + + + + P33 + + + -5.9 + + + + + + + + + P34 + + + 0 + + + + + + + + + P35 + + + 1.11 + + + + + + + + + P36 + + + -6 + + + + + + + + + P37 + + + -0.4 + + + + + + + diff --git a/latest/cases/01502/synopsis.txt b/latest/cases/01502/synopsis.txt new file mode 100644 index 000000000..0d4e30bf0 --- /dev/null +++ b/latest/cases/01502/synopsis.txt @@ -0,0 +1,98 @@ + +category: Test +synopsis: Several parameters with algebraic rules, testing various L1 built-in functions acting on constants. +componentTags: AlgebraicRule, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various mathematical constructs present in L1, in algebraic rules. + +The model contains: +* 36 parameters (P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37) + +There are 36 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P2 - abs(-1)$ | +| Algebraic | $0$ | $P3 - abs(1)$ | +| Algebraic | $0$ | $P4 - acos(-1)$ | +| Algebraic | $0$ | $P5 - acos(0.5)$ | +| Algebraic | $0$ | $P6 - asin(1)$ | +| Algebraic | $0$ | $P7 - asin(-0.5)$ | +| Algebraic | $0$ | $P8 - atan(2.8)$ | +| Algebraic | $0$ | $P9 - atan(-7.09)$ | +| Algebraic | $0$ | $P10 - ceil(0.5)$ | +| Algebraic | $0$ | $P11 - ceil(3.55)$ | +| Algebraic | $0$ | $P12 - ceil(-4.6)$ | +| Algebraic | $0$ | $P13 - cos(9.1)$ | +| Algebraic | $0$ | $P14 - cos(-0.22)$ | +| Algebraic | $0$ | $P15 - exp(0)$ | +| Algebraic | $0$ | $P16 - exp(1)$ | +| Algebraic | $0$ | $P17 - exp(0.77)$ | +| Algebraic | $0$ | $P18 - floor(-4.6)$ | +| Algebraic | $0$ | $P19 - floor(9.1)$ | +| Algebraic | $0$ | $P20 - ln(0.2)$ | +| Algebraic | $0$ | $P21 - ln(1)$ | +| Algebraic | $0$ | $P22 - log10(0.2)$ | +| Algebraic | $0$ | $P23 - log10(1)$ | +| Algebraic | $0$ | $P24 - 1^2$ | +| Algebraic | $0$ | $P25 - 2^2$ | +| Algebraic | $0$ | $P26 - 1.4^5.1$ | +| Algebraic | $0$ | $P27 - 4^2$ | +| Algebraic | $0$ | $P28 - 3.1^2$ | +| Algebraic | $0$ | $P29 - sqrt(4)$ | +| Algebraic | $0$ | $P30 - sqrt(7.4)$ | +| Algebraic | $0$ | $P31 - sin(2.1)$ | +| Algebraic | $0$ | $P32 - sin(0)$ | +| Algebraic | $0$ | $P33 - sin(-5.9)$ | +| Algebraic | $0$ | $P34 - tan(0)$ | +| Algebraic | $0$ | $P35 - tan(1.11)$ | +| Algebraic | $0$ | $P36 - tan(-6)$ | +| Algebraic | $0$ | $P37 - tanh(-0.4)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P2 | $unknown$ | variable | +| Initial value of parameter P3 | $unknown$ | variable | +| Initial value of parameter P4 | $unknown$ | variable | +| Initial value of parameter P5 | $unknown$ | variable | +| Initial value of parameter P6 | $unknown$ | variable | +| Initial value of parameter P7 | $unknown$ | variable | +| Initial value of parameter P8 | $unknown$ | variable | +| Initial value of parameter P9 | $unknown$ | variable | +| Initial value of parameter P10 | $unknown$ | variable | +| Initial value of parameter P11 | $unknown$ | variable | +| Initial value of parameter P12 | $unknown$ | variable | +| Initial value of parameter P13 | $unknown$ | variable | +| Initial value of parameter P14 | $unknown$ | variable | +| Initial value of parameter P15 | $unknown$ | variable | +| Initial value of parameter P16 | $unknown$ | variable | +| Initial value of parameter P17 | $unknown$ | variable | +| Initial value of parameter P18 | $unknown$ | variable | +| Initial value of parameter P19 | $unknown$ | variable | +| Initial value of parameter P20 | $unknown$ | variable | +| Initial value of parameter P21 | $unknown$ | variable | +| Initial value of parameter P22 | $unknown$ | variable | +| Initial value of parameter P23 | $unknown$ | variable | +| Initial value of parameter P24 | $unknown$ | variable | +| Initial value of parameter P25 | $unknown$ | variable | +| Initial value of parameter P26 | $unknown$ | variable | +| Initial value of parameter P27 | $unknown$ | variable | +| Initial value of parameter P28 | $unknown$ | variable | +| Initial value of parameter P29 | $unknown$ | variable | +| Initial value of parameter P30 | $unknown$ | variable | +| Initial value of parameter P31 | $unknown$ | variable | +| Initial value of parameter P32 | $unknown$ | variable | +| Initial value of parameter P33 | $unknown$ | variable | +| Initial value of parameter P34 | $unknown$ | variable | +| Initial value of parameter P35 | $unknown$ | variable | +| Initial value of parameter P36 | $unknown$ | variable | +| Initial value of parameter P37 | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01503/l2v5/build.log b/latest/cases/01503/l2v5/build.log new file mode 100644 index 000000000..94cf47657 --- /dev/null +++ b/latest/cases/01503/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01503/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01503/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01503/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01503/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01503/l2v5/index.heta b/latest/cases/01503/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01503/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01503/l3v2/build.log b/latest/cases/01503/l3v2/build.log new file mode 100644 index 000000000..6e4eb52bc --- /dev/null +++ b/latest/cases/01503/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01503/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01503/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01503/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01503/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01503/l3v2/index.heta b/latest/cases/01503/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01503/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01503/model-sbml-l2v5.xml b/latest/cases/01503/model-sbml-l2v5.xml new file mode 100644 index 000000000..79435f50a --- /dev/null +++ b/latest/cases/01503/model-sbml-l2v5.xml @@ -0,0 +1,182 @@ + + + + + + + + + + + + + + + + + + + + + P1 + + + + + + + + + + + P2 + + + + + + + + + + + P3 + + + 1 + + + + + + 0 + + + + + + + + + + P4 + + + 1 + + + + + + 0 + + + + + + + + + + P5 + + + 1 + + + + + + 0 + + + + + + + + + + P6 + + + 3 + + + + + + + + + P7 + + + 4 + + + + + + + + + P8 + + + 1 + + + + + + + 0 + + + + + + + + + + P9 + + + 1 + + + + + + + 0 + + + + + + + + + + P10 + + + 1 + + + + + + + 0 + + + + + + + + diff --git a/latest/cases/01503/model-sbml-l3v2.xml b/latest/cases/01503/model-sbml-l3v2.xml new file mode 100644 index 000000000..fd0c956fb --- /dev/null +++ b/latest/cases/01503/model-sbml-l3v2.xml @@ -0,0 +1,183 @@ + + + + + + + + + + + + + + + + + + + + + + P1 + + + + + + + + + + + P2 + + + + + + + + + + + P3 + + + 1 + + + + + + 0 + + + + + + + + + + P4 + + + 1 + + + + + + 0 + + + + + + + + + + P5 + + + 1 + + + + + + 0 + + + + + + + + + + P6 + + + 3 + + + + + + + + + P7 + + + 4 + + + + + + + + + P8 + + + 1 + + + + + + + 0 + + + + + + + + + + P9 + + + 1 + + + + + + + 0 + + + + + + + + + + P10 + + + 1 + + + + + + + 0 + + + + + + + + diff --git a/latest/cases/01503/synopsis.txt b/latest/cases/01503/synopsis.txt new file mode 100644 index 000000000..5c987d571 --- /dev/null +++ b/latest/cases/01503/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Several parameters with algebraic rules, testing various L1 built-in functions acting on constants. +componentTags: AlgebraicRule, Parameter +testTags: InitialValueReassigned, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various uncommon mathematical constructs, in algebraic rules. + +The model contains: +* 10 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10) + +There are 10 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P1 - plus()$ | +| Algebraic | $0$ | $P2 - times()$ | +| Algebraic | $0$ | $P3 - piecewise(1, and(), 0)$ | +| Algebraic | $0$ | $P4 - piecewise(1, or(), 0)$ | +| Algebraic | $0$ | $P5 - piecewise(1, xor(), 0)$ | +| Algebraic | $0$ | $P6 - plus(3)$ | +| Algebraic | $0$ | $P7 - times(4)$ | +| Algebraic | $0$ | $P8 - piecewise(1, and(true), 0)$ | +| Algebraic | $0$ | $P9 - piecewise(1, or(false), 0)$ | +| Algebraic | $0$ | $P10 - piecewise(1, xor(true), 0)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $unknown$ | variable | +| Initial value of parameter P2 | $unknown$ | variable | +| Initial value of parameter P3 | $unknown$ | variable | +| Initial value of parameter P4 | $unknown$ | variable | +| Initial value of parameter P5 | $unknown$ | variable | +| Initial value of parameter P6 | $unknown$ | variable | +| Initial value of parameter P7 | $unknown$ | variable | +| Initial value of parameter P8 | $unknown$ | variable | +| Initial value of parameter P9 | $unknown$ | variable | +| Initial value of parameter P10 | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01504/l2v5/heta-code/output.heta b/latest/cases/01504/l2v5/heta-code/output.heta new file mode 100644 index 000000000..bc1fb6e86 --- /dev/null +++ b/latest/cases/01504/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; +S1 [_E0]= 0.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +_E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01504/l2v5/index.heta b/latest/cases/01504/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01504/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01504/l2v5/json/output.json b/latest/cases/01504/l2v5/json/output.json new file mode 100644 index 000000000..211151565 --- /dev/null +++ b/latest/cases/01504/l2v5/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0", + "_E0": "0.2" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t >= 0.45" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01504/l3v2/heta-code/output.heta b/latest/cases/01504/l3v2/heta-code/output.heta new file mode 100644 index 000000000..66878d609 --- /dev/null +++ b/latest/cases/01504/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; +S1 [_E0]= 0.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +_E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01504/l3v2/index.heta b/latest/cases/01504/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01504/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01504/l3v2/json/output.json b/latest/cases/01504/l3v2/json/output.json new file mode 100644 index 000000000..233421db4 --- /dev/null +++ b/latest/cases/01504/l3v2/json/output.json @@ -0,0 +1,59 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0", + "_E0": "0.2" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t >= 0.45" + } +] \ No newline at end of file diff --git a/latest/cases/01504/model-sbml-l2v5.xml b/latest/cases/01504/model-sbml-l2v5.xml new file mode 100644 index 000000000..a33aef453 --- /dev/null +++ b/latest/cases/01504/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01504/model-sbml-l3v2.xml b/latest/cases/01504/model-sbml-l3v2.xml new file mode 100644 index 000000000..37e9f57cf --- /dev/null +++ b/latest/cases/01504/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01504/output.heta b/latest/cases/01504/output.heta new file mode 100644 index 000000000..4fd590a3b --- /dev/null +++ b/latest/cases/01504/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: A species and a compartment both under control of a rate rule, then modified by an event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by an event partway through the simulation, affecting things all over again. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time >= 0.45$ | $S1 = 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; +S1 [_E0]= 0.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +_E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01504/synopsis.txt b/latest/cases/01504/synopsis.txt new file mode 100644 index 000000000..038c6de8d --- /dev/null +++ b/latest/cases/01504/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule, then modified by an event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by an event partway through the simulation, affecting things all over again. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time >= 0.45$ | $S1 = 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01505/l2v5/heta-code/output.heta b/latest/cases/01505/l2v5/heta-code/output.heta new file mode 100644 index 000000000..82cd3c168 --- /dev/null +++ b/latest/cases/01505/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [_E0]= 0.2; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +_E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01505/l2v5/index.heta b/latest/cases/01505/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01505/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01505/l2v5/json/output.json b/latest/cases/01505/l2v5/json/output.json new file mode 100644 index 000000000..8458c8af1 --- /dev/null +++ b/latest/cases/01505/l2v5/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5", + "_E0": "0.2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t >= 0.45" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01505/l3v2/heta-code/output.heta b/latest/cases/01505/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ec71eff5f --- /dev/null +++ b/latest/cases/01505/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [_E0]= 0.2; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +_E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01505/l3v2/index.heta b/latest/cases/01505/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01505/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01505/l3v2/json/output.json b/latest/cases/01505/l3v2/json/output.json new file mode 100644 index 000000000..f48543e96 --- /dev/null +++ b/latest/cases/01505/l3v2/json/output.json @@ -0,0 +1,59 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5", + "_E0": "0.2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t >= 0.45" + } +] \ No newline at end of file diff --git a/latest/cases/01505/model-sbml-l2v5.xml b/latest/cases/01505/model-sbml-l2v5.xml new file mode 100644 index 000000000..11c232eda --- /dev/null +++ b/latest/cases/01505/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01505/model-sbml-l3v2.xml b/latest/cases/01505/model-sbml-l3v2.xml new file mode 100644 index 000000000..7883bdc2c --- /dev/null +++ b/latest/cases/01505/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01505/output.heta b/latest/cases/01505/output.heta new file mode 100644 index 000000000..77ef06ee1 --- /dev/null +++ b/latest/cases/01505/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: A species and a compartment both under control of a rate rule, and affected by an event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Partway through the simulation, an event changes the level of the compartment, forcing yet another change. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time >= 0.45$ | $C1 = 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [_E0]= 0.2; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +_E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01505/synopsis.txt b/latest/cases/01505/synopsis.txt new file mode 100644 index 000000000..11909c060 --- /dev/null +++ b/latest/cases/01505/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule, and affected by an event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Partway through the simulation, an event changes the level of the compartment, forcing yet another change. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time >= 0.45$ | $C1 = 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01506/l2v5/heta-code/output.heta b/latest/cases/01506/l2v5/heta-code/output.heta new file mode 100644 index 000000000..19ddae152 --- /dev/null +++ b/latest/cases/01506/l2v5/heta-code/output.heta @@ -0,0 +1,25 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [E0]= 0.2; + +S1 @Species { compartment: C1, } .= 0; +S1 [E0]= 0.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01506/l2v5/index.heta b/latest/cases/01506/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01506/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01506/l2v5/json/output.json b/latest/cases/01506/l2v5/json/output.json new file mode 100644 index 000000000..61ba841a4 --- /dev/null +++ b/latest/cases/01506/l2v5/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5", + "E0": "0.2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0", + "E0": "0.2" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 0.45" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01506/l3v2/heta-code/output.heta b/latest/cases/01506/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4f2e4cbfe --- /dev/null +++ b/latest/cases/01506/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [E0]= 0.2; + +S1 @Species { compartment: C1, } .= 0; +S1 [E0]= 0.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01506/l3v2/index.heta b/latest/cases/01506/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01506/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01506/l3v2/json/output.json b/latest/cases/01506/l3v2/json/output.json new file mode 100644 index 000000000..e06ca1081 --- /dev/null +++ b/latest/cases/01506/l3v2/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5", + "E0": "0.2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0", + "E0": "0.2" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 0.45" + } +] \ No newline at end of file diff --git a/latest/cases/01506/model-sbml-l2v5.xml b/latest/cases/01506/model-sbml-l2v5.xml new file mode 100644 index 000000000..d42105ce0 --- /dev/null +++ b/latest/cases/01506/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01506/model-sbml-l3v2.xml b/latest/cases/01506/model-sbml-l3v2.xml new file mode 100644 index 000000000..90b7aff0d --- /dev/null +++ b/latest/cases/01506/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01506/output.heta b/latest/cases/01506/output.heta new file mode 100644 index 000000000..ecc27ae9f --- /dev/null +++ b/latest/cases/01506/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: A species and a compartment both under control of a rate rule, and affected by an event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + NOTE: This test is a more complicated version of test 1779. If this isn't passing, make sure you pass test 1779 first, as it is likely that the issue here is actually reflective of the more fundamental issue tested in that test (i.e. the simultaneous assignment to a species concentration and compartment). + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Partway through the simulation, an event changes the level of the species and of the compartment, forcing yet another change. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 0.45$ | $S1 = 0.2$ | +| | | $C1 = 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [E0]= 0.2; + +S1 @Species { compartment: C1, } .= 0; +S1 [E0]= 0.2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01506/synopsis.txt b/latest/cases/01506/synopsis.txt new file mode 100644 index 000000000..a4a3e8003 --- /dev/null +++ b/latest/cases/01506/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule, and affected by an event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + NOTE: This test is a more complicated version of test 1779. If this isn't passing, make sure you pass test 1779 first, as it is likely that the issue here is actually reflective of the more fundamental issue tested in that test (i.e. the simultaneous assignment to a species concentration and compartment). + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Partway through the simulation, an event changes the level of the species and of the compartment, forcing yet another change. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 0.45$ | $S1 = 0.2$ | +| | | $C1 = 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01507/l2v5/build.log b/latest/cases/01507/l2v5/build.log new file mode 100644 index 000000000..7a627ab66 --- /dev/null +++ b/latest/cases/01507/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01507/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01507/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01507/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01507/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01507/l2v5/index.heta b/latest/cases/01507/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01507/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01507/l3v2/build.log b/latest/cases/01507/l3v2/build.log new file mode 100644 index 000000000..049f88c75 --- /dev/null +++ b/latest/cases/01507/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01507/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01507/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01507/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01507/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01507/l3v2/index.heta b/latest/cases/01507/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01507/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01507/model-sbml-l2v5.xml b/latest/cases/01507/model-sbml-l2v5.xml new file mode 100644 index 000000000..0cc1615ca --- /dev/null +++ b/latest/cases/01507/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + + 1 + S1 + + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01507/model-sbml-l3v2.xml b/latest/cases/01507/model-sbml-l3v2.xml new file mode 100644 index 000000000..93c356239 --- /dev/null +++ b/latest/cases/01507/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + + 1 + S1 + + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01507/synopsis.txt b/latest/cases/01507/synopsis.txt new file mode 100644 index 000000000..36428e0c1 --- /dev/null +++ b/latest/cases/01507/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule, then modified by an event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventWithDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by an event partway through the simulation, affecting things all over again, and that event has a delay dependent on the correct value for S1. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time >= 0.45$ | $1 * S1$ | $S1 = 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01508/l2v5/build.log b/latest/cases/01508/l2v5/build.log new file mode 100644 index 000000000..7382d1714 --- /dev/null +++ b/latest/cases/01508/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01508/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01508/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01508/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01508/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01508/l2v5/index.heta b/latest/cases/01508/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01508/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01508/l3v2/build.log b/latest/cases/01508/l3v2/build.log new file mode 100644 index 000000000..031419b99 --- /dev/null +++ b/latest/cases/01508/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01508/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01508/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01508/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01508/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01508/l3v2/index.heta b/latest/cases/01508/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01508/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01508/model-sbml-l2v5.xml b/latest/cases/01508/model-sbml-l2v5.xml new file mode 100644 index 000000000..696c595ca --- /dev/null +++ b/latest/cases/01508/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + 0.1 + + + + + + + + S1 + 0.2 + + + + + + + + diff --git a/latest/cases/01508/model-sbml-l3v2.xml b/latest/cases/01508/model-sbml-l3v2.xml new file mode 100644 index 000000000..489c4bc03 --- /dev/null +++ b/latest/cases/01508/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + 0.1 + + + + + + + + S1 + 0.2 + + + + + + + + diff --git a/latest/cases/01508/synopsis.txt b/latest/cases/01508/synopsis.txt new file mode 100644 index 000000000..a1a88f693 --- /dev/null +++ b/latest/cases/01508/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule, then modified by an event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventWithDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, EventUsesTriggerTimeValues, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by an event partway through the simulation, affecting things all over again, and that event has a delay, with an assignment dependent on the correct value for S1, calculated at trigger time. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time >= 0.45$ | $0.1$ | $S1 = S1 + 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01509/l2v5/build.log b/latest/cases/01509/l2v5/build.log new file mode 100644 index 000000000..d4bbc3d19 --- /dev/null +++ b/latest/cases/01509/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01509/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01509/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01509/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01509/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01509/l2v5/index.heta b/latest/cases/01509/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01509/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01509/l3v2/build.log b/latest/cases/01509/l3v2/build.log new file mode 100644 index 000000000..d40db6583 --- /dev/null +++ b/latest/cases/01509/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01509/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01509/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01509/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01509/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01509/l3v2/index.heta b/latest/cases/01509/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01509/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01509/model-sbml-l2v5.xml b/latest/cases/01509/model-sbml-l2v5.xml new file mode 100644 index 000000000..47ad599aa --- /dev/null +++ b/latest/cases/01509/model-sbml-l2v5.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + 0.1 + + + + + + + + S1 + 0.2 + + + + + + + + diff --git a/latest/cases/01509/model-sbml-l3v2.xml b/latest/cases/01509/model-sbml-l3v2.xml new file mode 100644 index 000000000..2c18e322f --- /dev/null +++ b/latest/cases/01509/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + 0.1 + + + + + + + + S1 + 0.2 + + + + + + + + diff --git a/latest/cases/01509/synopsis.txt b/latest/cases/01509/synopsis.txt new file mode 100644 index 000000000..d35bd99f9 --- /dev/null +++ b/latest/cases/01509/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule, then modified by an event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventWithDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, EventUsesAssignmentTimeValues, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by an event partway through the simulation, affecting things all over again, and that event has a delay, with an assignment dependent on the correct value for S1, calculated at assignment time. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $time >= 0.45$ | Assignment time | $0.1$ | $S1 = S1 + 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01510/l2v5/index.heta b/latest/cases/01510/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01510/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01510/l3v2/heta-code/output.heta b/latest/cases/01510/l3v2/heta-code/output.heta new file mode 100644 index 000000000..53665b166 --- /dev/null +++ b/latest/cases/01510/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 1; +S1 [E0]= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: S1 > (-1), }; + diff --git a/latest/cases/01510/l3v2/index.heta b/latest/cases/01510/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01510/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01510/l3v2/json/output.json b/latest/cases/01510/l3v2/json/output.json new file mode 100644 index 000000000..6f98feb0f --- /dev/null +++ b/latest/cases/01510/l3v2/json/output.json @@ -0,0 +1,59 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1", + "E0": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "S1 > (-1)" + } +] \ No newline at end of file diff --git a/latest/cases/01510/model-sbml-l3v2.xml b/latest/cases/01510/model-sbml-l3v2.xml new file mode 100644 index 000000000..9fb8d1bed --- /dev/null +++ b/latest/cases/01510/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + S1 + -1 + + + + + + + 0 + + + + + + + diff --git a/latest/cases/01510/output.heta b/latest/cases/01510/output.heta new file mode 100644 index 000000000..61dff274d --- /dev/null +++ b/latest/cases/01510/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: A species and a compartment both under control of a rate rule, modified by an event at t0. +componentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, EventT0Firing, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by an event at t0. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $S1 > -1$ | false | $S1 = 0$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 1; +S1 [E0]= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: S1 > (-1), }; + diff --git a/latest/cases/01510/synopsis.txt b/latest/cases/01510/synopsis.txt new file mode 100644 index 000000000..2fd42a973 --- /dev/null +++ b/latest/cases/01510/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule, modified by an event at t0. +componentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, EventT0Firing, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by an event at t0. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $S1 > -1$ | false | $S1 = 0$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01511/l2v5/build.log b/latest/cases/01511/l2v5/build.log new file mode 100644 index 000000000..50f09cc0b --- /dev/null +++ b/latest/cases/01511/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01511/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01511/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01511/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01511/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01511/l2v5/index.heta b/latest/cases/01511/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01511/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01511/l3v2/build.log b/latest/cases/01511/l3v2/build.log new file mode 100644 index 000000000..b91b33234 --- /dev/null +++ b/latest/cases/01511/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01511/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01511/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01511/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01511/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01511/l3v2/index.heta b/latest/cases/01511/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01511/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01511/model-sbml-l2v5.xml b/latest/cases/01511/model-sbml-l2v5.xml new file mode 100644 index 000000000..948af6ff9 --- /dev/null +++ b/latest/cases/01511/model-sbml-l2v5.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + + + S1 + 0.18 + + + + S1 + 0.19 + + + + + + + 0.1 + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01511/model-sbml-l3v2.xml b/latest/cases/01511/model-sbml-l3v2.xml new file mode 100644 index 000000000..807bfee4e --- /dev/null +++ b/latest/cases/01511/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + + + S1 + 0.18 + + + + S1 + 0.19 + + + + + + + 0.1 + + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01511/synopsis.txt b/latest/cases/01511/synopsis.txt new file mode 100644 index 000000000..14dc7b65e --- /dev/null +++ b/latest/cases/01511/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule, modified by an persistent delayed event. +componentTags: AssignmentRule, Compartment, EventWithDelay, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, EventIsPersistent, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by a persistent delayed event, after the trigger reverts to being 'false'. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(S1 > 0.18) && (S1 < 0.19)$ | $0.1$ | $S1 = 0.2$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01512/l2v5/index.heta b/latest/cases/01512/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01512/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01512/l3v2/heta-code/output.heta b/latest/cases/01512/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b51351199 --- /dev/null +++ b/latest/cases/01512/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; +x2 @Record { } .= 0; +x2 [E0]= 3; +x2 [E1]= 5; + +E0 @DSwitcher { trigger: t > 0.45, }; +E1 @DSwitcher { trigger: t > 0.45, }; + diff --git a/latest/cases/01512/l3v2/index.heta b/latest/cases/01512/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01512/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01512/l3v2/json/output.json b/latest/cases/01512/l3v2/json/output.json new file mode 100644 index 000000000..675778cdf --- /dev/null +++ b/latest/cases/01512/l3v2/json/output.json @@ -0,0 +1,72 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Record", + "id": "x2", + "assignments": { + "start_": "0", + "E0": "3", + "E1": "5" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 0.45" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 0.45" + } +] \ No newline at end of file diff --git a/latest/cases/01512/model-sbml-l3v2.xml b/latest/cases/01512/model-sbml-l3v2.xml new file mode 100644 index 000000000..aa50c9b8a --- /dev/null +++ b/latest/cases/01512/model-sbml-l3v2.xml @@ -0,0 +1,81 @@ + + + + + + + + + + + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + S1 + + + + + + 3 + + + + + + + + + + time + 0.45 + + + + + + 0.15 + + + + + + 5 + + + + + + + diff --git a/latest/cases/01512/output.heta b/latest/cases/01512/output.heta new file mode 100644 index 000000000..74a2a4f07 --- /dev/null +++ b/latest/cases/01512/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: A species and a compartment both under control of a rate rule,that affects an event priority. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Two other simultaneous events fire, with the priority of one equal to S1, and the priority of the other equal to a value between the concentration of S1 and the amount of S1, to ensure that the order is correct. + +The model contains: +* 1 species (S1) +* 2 parameters (x, x2) +* 1 compartment (C1) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 0.45$ | $S1$ | $x2 = 3$ | +| E1 | $time > 0.45$ | $0.15$ | $x2 = 5$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial value of parameter x2 | $0$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 0; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; +x2 @Record { } .= 0; +x2 [E0]= 3; +x2 [E1]= 5; + +E0 @DSwitcher { trigger: t > 0.45, }; +E1 @DSwitcher { trigger: t > 0.45, }; + diff --git a/latest/cases/01512/synopsis.txt b/latest/cases/01512/synopsis.txt new file mode 100644 index 000000000..16d01ef4b --- /dev/null +++ b/latest/cases/01512/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule,that affects an event priority. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Two other simultaneous events fire, with the priority of one equal to S1, and the priority of the other equal to a value between the concentration of S1 and the amount of S1, to ensure that the order is correct. + +The model contains: +* 1 species (S1) +* 2 parameters (x, x2) +* 1 compartment (C1) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 0.45$ | $S1$ | $x2 = 3$ | +| E1 | $time > 0.45$ | $0.15$ | $x2 = 5$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial value of parameter x2 | $0$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + diff --git a/latest/cases/01513/l2v5/heta-code/output.heta b/latest/cases/01513/l2v5/heta-code/output.heta new file mode 100644 index 000000000..2face5969 --- /dev/null +++ b/latest/cases/01513/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 3 / 2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01513/l2v5/index.heta b/latest/cases/01513/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01513/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01513/l2v5/json/output.json b/latest/cases/01513/l2v5/json/output.json new file mode 100644 index 000000000..345af4ca1 --- /dev/null +++ b/latest/cases/01513/l2v5/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3 / 2" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01513/l3v2/heta-code/output.heta b/latest/cases/01513/l3v2/heta-code/output.heta new file mode 100644 index 000000000..839e0641e --- /dev/null +++ b/latest/cases/01513/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 3 / 2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01513/l3v2/index.heta b/latest/cases/01513/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01513/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01513/l3v2/json/output.json b/latest/cases/01513/l3v2/json/output.json new file mode 100644 index 000000000..ceb676cf1 --- /dev/null +++ b/latest/cases/01513/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3 / 2" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01513/model-sbml-l2v5.xml b/latest/cases/01513/model-sbml-l2v5.xml new file mode 100644 index 000000000..e60f371e2 --- /dev/null +++ b/latest/cases/01513/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + 3 + 2 + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01513/model-sbml-l3v2.xml b/latest/cases/01513/model-sbml-l3v2.xml new file mode 100644 index 000000000..0746cfeac --- /dev/null +++ b/latest/cases/01513/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + + 3 + 2 + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01513/output.heta b/latest/cases/01513/output.heta new file mode 100644 index 000000000..d572f8c77 --- /dev/null +++ b/latest/cases/01513/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: A species and a compartment both under control of a rate rule,with an initial assignment to the species. +componentTags: AssignmentRule, Compartment, InitialAssignment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Its concentration is set with an initial assignment (not its amount). + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3 / 2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; + +S1 @Species { compartment: C1, } .= 3 / 2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01513/synopsis.txt b/latest/cases/01513/synopsis.txt new file mode 100644 index 000000000..872b28022 --- /dev/null +++ b/latest/cases/01513/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule,with an initial assignment to the species. +componentTags: AssignmentRule, Compartment, InitialAssignment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Its concentration is set with an initial assignment (not its amount). + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3 / 2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01514/l2v5/heta-code/output.heta b/latest/cases/01514/l2v5/heta-code/output.heta new file mode 100644 index 000000000..041c461e2 --- /dev/null +++ b/latest/cases/01514/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 1 / 2; + +S1 @Species { compartment: C1, } .= 3 / 2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01514/l2v5/index.heta b/latest/cases/01514/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01514/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01514/l2v5/json/output.json b/latest/cases/01514/l2v5/json/output.json new file mode 100644 index 000000000..da8e05c82 --- /dev/null +++ b/latest/cases/01514/l2v5/json/output.json @@ -0,0 +1,78 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "1 / 2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3 / 2" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01514/l3v2/heta-code/output.heta b/latest/cases/01514/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1f2f35395 --- /dev/null +++ b/latest/cases/01514/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 1 / 2; + +S1 @Species { compartment: C1, } .= 3 / 2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01514/l3v2/index.heta b/latest/cases/01514/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01514/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01514/l3v2/json/output.json b/latest/cases/01514/l3v2/json/output.json new file mode 100644 index 000000000..a3e8c2647 --- /dev/null +++ b/latest/cases/01514/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "1 / 2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "3 / 2" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "0.4" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.2" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01514/model-sbml-l2v5.xml b/latest/cases/01514/model-sbml-l2v5.xml new file mode 100644 index 000000000..371bf4509 --- /dev/null +++ b/latest/cases/01514/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + 3 + 2 + + + + + + + + 1 + 2 + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01514/model-sbml-l3v2.xml b/latest/cases/01514/model-sbml-l3v2.xml new file mode 100644 index 000000000..d9d922f38 --- /dev/null +++ b/latest/cases/01514/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + 3 + 2 + + + + + + + + 1 + 2 + + + + + + + + 0.4 + + + + + 0.2 + + + + + S1 + + + + + diff --git a/latest/cases/01514/output.heta b/latest/cases/01514/output.heta new file mode 100644 index 000000000..a926321b5 --- /dev/null +++ b/latest/cases/01514/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: A species and a compartment both under control of a rate rule,with an initial assignment to the species and compartment. +componentTags: AssignmentRule, Compartment, InitialAssignment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Its concentration is set with an initial assignment (not its amount), and the compartment itself also has an initial assignment. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3 / 2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $1 / 2$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 1 / 2; + +S1 @Species { compartment: C1, } .= 3 / 2; + +S1_proc @Process { actors: = S1, }; +S1_proc := 0.4; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.2; + +x @Record { }; +x := S1; + diff --git a/latest/cases/01514/synopsis.txt b/latest/cases/01514/synopsis.txt new file mode 100644 index 000000000..b8495d368 --- /dev/null +++ b/latest/cases/01514/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A species and a compartment both under control of a rate rule,with an initial assignment to the species and compartment. +componentTags: AssignmentRule, Compartment, InitialAssignment, Parameter, RateRule, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Numeric +packagesPresent: + + A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Its concentration is set with an initial assignment (not its amount), and the compartment itself also has an initial assignment. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.4$ | +| Rate | C1 | $0.2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3 / 2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $1 / 2$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + diff --git a/latest/cases/01515/l2v5/build.log b/latest/cases/01515/l2v5/build.log new file mode 100644 index 000000000..2e2089df3 --- /dev/null +++ b/latest/cases/01515/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01515/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01515/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01515/model-sbml-l2v5.xml"... +[info] Setting references in elements, total length 160 +[error] FunctionDef "tanh" is not found as expected here: P37_proc { math: undefined }; +[error] FunctionDef "tanh" is not found as expected here: P38_proc { math: undefined }; +[error] FunctionDef "tanh" is not found as expected here: P39_proc { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01515/l2v5/index.heta b/latest/cases/01515/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01515/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01515/l3v2/build.log b/latest/cases/01515/l3v2/build.log new file mode 100644 index 000000000..1171845ca --- /dev/null +++ b/latest/cases/01515/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01515/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01515/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01515/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 155 +[error] FunctionDef "tanh" is not found as expected here: P37_proc { math: undefined }; +[error] FunctionDef "tanh" is not found as expected here: P38_proc { math: undefined }; +[error] FunctionDef "tanh" is not found as expected here: P39_proc { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01515/l3v2/index.heta b/latest/cases/01515/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01515/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01515/model-sbml-l2v5.xml b/latest/cases/01515/model-sbml-l2v5.xml new file mode 100644 index 000000000..313a2151e --- /dev/null +++ b/latest/cases/01515/model-sbml-l2v5.xml @@ -0,0 +1,368 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + + + 1 + + + + + + + + -1 + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + -0.5 + + + + + + + + 2.8 + + + + + + + + -7.09 + + + + + + + + 0.5 + + + + + + + + 3.55 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + -0.22 + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + 0.77 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + 10 + + 0.2 + + + + + + + + + 10 + + 1 + + + + + + + + 1 + 2 + + + + + + + + 2 + 2 + + + + + + + + 1.4 + 5.1 + + + + + + + + 4 + 2 + + + + + + + + 3.1 + 2 + + + + + + + + + 2 + + 4 + + + + + + + + + 2 + + 7.4 + + + + + + + + 2.1 + + + + + + + + 0 + + + + + + + + -5.9 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + diff --git a/latest/cases/01515/model-sbml-l3v2.xml b/latest/cases/01515/model-sbml-l3v2.xml new file mode 100644 index 000000000..1f22096e9 --- /dev/null +++ b/latest/cases/01515/model-sbml-l3v2.xml @@ -0,0 +1,369 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + + + 1 + + + + + + + + -1 + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + -0.5 + + + + + + + + 2.8 + + + + + + + + -7.09 + + + + + + + + 0.5 + + + + + + + + 3.55 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + -0.22 + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + 0.77 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + 10 + + 0.2 + + + + + + + + + 10 + + 1 + + + + + + + + 1 + 2 + + + + + + + + 2 + 2 + + + + + + + + 1.4 + 5.1 + + + + + + + + 4 + 2 + + + + + + + + 3.1 + 2 + + + + + + + + + 2 + + 4 + + + + + + + + + 2 + + 7.4 + + + + + + + + 2.1 + + + + + + + + 0 + + + + + + + + -5.9 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + diff --git a/latest/cases/01515/synopsis.txt b/latest/cases/01515/synopsis.txt new file mode 100644 index 000000000..10b2e0634 --- /dev/null +++ b/latest/cases/01515/synopsis.txt @@ -0,0 +1,102 @@ + +category: Test +synopsis: Several parameters with rate rules, testing various unusual MathML constructs. +componentTags: Parameter, RateRule +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests various unusual MathML elements in rate rules. + +The model contains: +* 38 parameters (P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39) + +There are 38 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P2 | $abs(-1)$ | +| Rate | P3 | $abs(1)$ | +| Rate | P4 | $acos(-1)$ | +| Rate | P5 | $acos(0.5)$ | +| Rate | P6 | $asin(1)$ | +| Rate | P7 | $asin(-0.5)$ | +| Rate | P8 | $atan(2.8)$ | +| Rate | P9 | $atan(-7.09)$ | +| Rate | P10 | $ceil(0.5)$ | +| Rate | P11 | $ceil(3.55)$ | +| Rate | P12 | $ceil(-4.6)$ | +| Rate | P13 | $cos(9.1)$ | +| Rate | P14 | $cos(-0.22)$ | +| Rate | P15 | $exp(0)$ | +| Rate | P16 | $exp(1)$ | +| Rate | P17 | $exp(0.77)$ | +| Rate | P18 | $floor(-4.6)$ | +| Rate | P19 | $floor(9.1)$ | +| Rate | P20 | $ln(0.2)$ | +| Rate | P21 | $ln(1)$ | +| Rate | P22 | $log10(0.2)$ | +| Rate | P23 | $log10(1)$ | +| Rate | P24 | $1^2$ | +| Rate | P25 | $2^2$ | +| Rate | P26 | $1.4^5.1$ | +| Rate | P27 | $4^2$ | +| Rate | P28 | $3.1^2$ | +| Rate | P29 | $sqrt(4)$ | +| Rate | P30 | $sqrt(7.4)$ | +| Rate | P31 | $sin(2.1)$ | +| Rate | P32 | $sin(0)$ | +| Rate | P33 | $sin(-5.9)$ | +| Rate | P34 | $tan(0)$ | +| Rate | P35 | $tan(1.11)$ | +| Rate | P36 | $tan(-6)$ | +| Rate | P37 | $tanh(0)$ | +| Rate | P38 | $tanh(1.11)$ | +| Rate | P39 | $tanh(-6)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P2 | $0$ | variable | +| Initial value of parameter P3 | $0$ | variable | +| Initial value of parameter P4 | $0$ | variable | +| Initial value of parameter P5 | $0$ | variable | +| Initial value of parameter P6 | $0$ | variable | +| Initial value of parameter P7 | $0$ | variable | +| Initial value of parameter P8 | $0$ | variable | +| Initial value of parameter P9 | $0$ | variable | +| Initial value of parameter P10 | $0$ | variable | +| Initial value of parameter P11 | $0$ | variable | +| Initial value of parameter P12 | $0$ | variable | +| Initial value of parameter P13 | $0$ | variable | +| Initial value of parameter P14 | $0$ | variable | +| Initial value of parameter P15 | $0$ | variable | +| Initial value of parameter P16 | $0$ | variable | +| Initial value of parameter P17 | $0$ | variable | +| Initial value of parameter P18 | $0$ | variable | +| Initial value of parameter P19 | $0$ | variable | +| Initial value of parameter P20 | $0$ | variable | +| Initial value of parameter P21 | $0$ | variable | +| Initial value of parameter P22 | $0$ | variable | +| Initial value of parameter P23 | $0$ | variable | +| Initial value of parameter P24 | $0$ | variable | +| Initial value of parameter P25 | $0$ | variable | +| Initial value of parameter P26 | $0$ | variable | +| Initial value of parameter P27 | $0$ | variable | +| Initial value of parameter P28 | $0$ | variable | +| Initial value of parameter P29 | $0$ | variable | +| Initial value of parameter P30 | $0$ | variable | +| Initial value of parameter P31 | $0$ | variable | +| Initial value of parameter P32 | $0$ | variable | +| Initial value of parameter P33 | $0$ | variable | +| Initial value of parameter P34 | $0$ | variable | +| Initial value of parameter P35 | $0$ | variable | +| Initial value of parameter P36 | $0$ | variable | +| Initial value of parameter P37 | $0$ | variable | +| Initial value of parameter P38 | $0$ | variable | +| Initial value of parameter P39 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01516/l2v5/index.heta b/latest/cases/01516/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01516/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01516/l3v2/build.log b/latest/cases/01516/l3v2/build.log new file mode 100644 index 000000000..9af42bf9f --- /dev/null +++ b/latest/cases/01516/l3v2/build.log @@ -0,0 +1,46 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01516/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01516/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01516/model-sbml-l3v2.xml"... +[error] P2_sr component does not exist which is not allowed for the "update" action. +[error] P3_sr component does not exist which is not allowed for the "update" action. +[error] P4_sr component does not exist which is not allowed for the "update" action. +[error] P5_sr component does not exist which is not allowed for the "update" action. +[error] P6_sr component does not exist which is not allowed for the "update" action. +[error] P7_sr component does not exist which is not allowed for the "update" action. +[error] P8_sr component does not exist which is not allowed for the "update" action. +[error] P9_sr component does not exist which is not allowed for the "update" action. +[error] P10_sr component does not exist which is not allowed for the "update" action. +[error] P11_sr component does not exist which is not allowed for the "update" action. +[error] P12_sr component does not exist which is not allowed for the "update" action. +[error] P13_sr component does not exist which is not allowed for the "update" action. +[error] P14_sr component does not exist which is not allowed for the "update" action. +[error] P15_sr component does not exist which is not allowed for the "update" action. +[error] P16_sr component does not exist which is not allowed for the "update" action. +[error] P17_sr component does not exist which is not allowed for the "update" action. +[error] P18_sr component does not exist which is not allowed for the "update" action. +[error] P19_sr component does not exist which is not allowed for the "update" action. +[error] P20_sr component does not exist which is not allowed for the "update" action. +[error] P21_sr component does not exist which is not allowed for the "update" action. +[error] P22_sr component does not exist which is not allowed for the "update" action. +[error] P23_sr component does not exist which is not allowed for the "update" action. +[error] P24_sr component does not exist which is not allowed for the "update" action. +[error] P25_sr component does not exist which is not allowed for the "update" action. +[error] P26_sr component does not exist which is not allowed for the "update" action. +[error] P27_sr component does not exist which is not allowed for the "update" action. +[error] P28_sr component does not exist which is not allowed for the "update" action. +[error] P29_sr component does not exist which is not allowed for the "update" action. +[error] P30_sr component does not exist which is not allowed for the "update" action. +[error] P31_sr component does not exist which is not allowed for the "update" action. +[error] P32_sr component does not exist which is not allowed for the "update" action. +[error] P33_sr component does not exist which is not allowed for the "update" action. +[error] P34_sr component does not exist which is not allowed for the "update" action. +[error] P35_sr component does not exist which is not allowed for the "update" action. +[error] P36_sr component does not exist which is not allowed for the "update" action. +[error] P37_sr component does not exist which is not allowed for the "update" action. +[error] P38_sr component does not exist which is not allowed for the "update" action. +[error] P39_sr component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 119 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01516/l3v2/index.heta b/latest/cases/01516/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01516/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01516/model-sbml-l3v2.xml b/latest/cases/01516/model-sbml-l3v2.xml new file mode 100644 index 000000000..facfe8d0c --- /dev/null +++ b/latest/cases/01516/model-sbml-l3v2.xml @@ -0,0 +1,421 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + + + 1 + + + + + + + + -1 + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + -0.5 + + + + + + + + 2.8 + + + + + + + + -7.09 + + + + + + + + 0.5 + + + + + + + + 3.55 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + -0.22 + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + 0.77 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + 10 + + 0.2 + + + + + + + + + 10 + + 1 + + + + + + + + 1 + 2 + + + + + + + + 2 + 2 + + + + + + + + 1.4 + 5.1 + + + + + + + + 4 + 2 + + + + + + + + 3.1 + 2 + + + + + + + + + 2 + + 4 + + + + + + + + + 2 + + 7.4 + + + + + + + + 2.1 + + + + + + + + 0 + + + + + + + + -5.9 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01516/synopsis.txt b/latest/cases/01516/synopsis.txt new file mode 100644 index 000000000..4276486ae --- /dev/null +++ b/latest/cases/01516/synopsis.txt @@ -0,0 +1,107 @@ + +category: Test +synopsis: The use of unusual MathML constructs assigned to stoichiometries. +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonUnityStoichiometry, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests various unusual MathML elements in stoichiometries. It is numerically identical to model 01515, which uses rate rules. + +The model contains: +* 38 species (P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39) +* 1 compartment (C) +* 38 species references (P2_sr, P3_sr, P4_sr, P5_sr, P6_sr, P7_sr, P8_sr, P9_sr, P10_sr, P11_sr, P12_sr, P13_sr, P14_sr, P15_sr, P16_sr, P17_sr, P18_sr, P19_sr, P20_sr, P21_sr, P22_sr, P23_sr, P24_sr, P25_sr, P26_sr, P27_sr, P28_sr, P29_sr, P30_sr, P31_sr, P32_sr, P33_sr, P34_sr, P35_sr, P36_sr, P37_sr, P38_sr, P39_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> P2_sr P2 + P3_sr P3 + P4_sr P4 + P5_sr P5 + P6_sr P6 + P7_sr P7 + P8_sr P8 + P9_sr P9 + P10_sr P10 + P11_sr P11 + P12_sr P12 + P13_sr P13 + P14_sr P14 + P15_sr P15 + P16_sr P16 + P17_sr P17 + P18_sr P18 + P19_sr P19 + P20_sr P20 + P21_sr P21 + P22_sr P22 + P23_sr P23 + P24_sr P24 + P25_sr P25 + P26_sr P26 + P27_sr P27 + P28_sr P28 + P29_sr P29 + P30_sr P30 + P31_sr P31 + P32_sr P32 + P33_sr P33 + P34_sr P34 + P35_sr P35 + P36_sr P36 + P37_sr P37 + P38_sr P38 + P39_sr P39 | $1$ |] +Note: the following stoichiometries are set separately: P2_sr, P3_sr, P4_sr, P5_sr, P6_sr, P7_sr, P8_sr, P9_sr, P10_sr, P11_sr, P12_sr, P13_sr, P14_sr, P15_sr, P16_sr, P17_sr, P18_sr, P19_sr, P20_sr, P21_sr, P22_sr, P23_sr, P24_sr, P25_sr, P26_sr, P27_sr, P28_sr, P29_sr, P30_sr, P31_sr, P32_sr, P33_sr, P34_sr, P35_sr, P36_sr, P37_sr, P38_sr, P39_sr + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species P2 | $0$ | variable | +| Initial concentration of species P3 | $0$ | variable | +| Initial concentration of species P4 | $0$ | variable | +| Initial concentration of species P5 | $0$ | variable | +| Initial concentration of species P6 | $0$ | variable | +| Initial concentration of species P7 | $0$ | variable | +| Initial concentration of species P8 | $0$ | variable | +| Initial concentration of species P9 | $0$ | variable | +| Initial concentration of species P10 | $0$ | variable | +| Initial concentration of species P11 | $0$ | variable | +| Initial concentration of species P12 | $0$ | variable | +| Initial concentration of species P13 | $0$ | variable | +| Initial concentration of species P14 | $0$ | variable | +| Initial concentration of species P15 | $0$ | variable | +| Initial concentration of species P16 | $0$ | variable | +| Initial concentration of species P17 | $0$ | variable | +| Initial concentration of species P18 | $0$ | variable | +| Initial concentration of species P19 | $0$ | variable | +| Initial concentration of species P20 | $0$ | variable | +| Initial concentration of species P21 | $0$ | variable | +| Initial concentration of species P22 | $0$ | variable | +| Initial concentration of species P23 | $0$ | variable | +| Initial concentration of species P24 | $0$ | variable | +| Initial concentration of species P25 | $0$ | variable | +| Initial concentration of species P26 | $0$ | variable | +| Initial concentration of species P27 | $0$ | variable | +| Initial concentration of species P28 | $0$ | variable | +| Initial concentration of species P29 | $0$ | variable | +| Initial concentration of species P30 | $0$ | variable | +| Initial concentration of species P31 | $0$ | variable | +| Initial concentration of species P32 | $0$ | variable | +| Initial concentration of species P33 | $0$ | variable | +| Initial concentration of species P34 | $0$ | variable | +| Initial concentration of species P35 | $0$ | variable | +| Initial concentration of species P36 | $0$ | variable | +| Initial concentration of species P37 | $0$ | variable | +| Initial concentration of species P38 | $0$ | variable | +| Initial concentration of species P39 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'P2_sr' | $abs(-1)$ | constant | +| Initial value of species reference 'P3_sr' | $abs(1)$ | constant | +| Initial value of species reference 'P4_sr' | $acos(-1)$ | constant | +| Initial value of species reference 'P5_sr' | $acos(0.5)$ | constant | +| Initial value of species reference 'P6_sr' | $asin(1)$ | constant | +| Initial value of species reference 'P7_sr' | $asin(-0.5)$ | constant | +| Initial value of species reference 'P8_sr' | $atan(2.8)$ | constant | +| Initial value of species reference 'P9_sr' | $atan(-7.09)$ | constant | +| Initial value of species reference 'P10_sr' | $ceil(0.5)$ | constant | +| Initial value of species reference 'P11_sr' | $ceil(3.55)$ | constant | +| Initial value of species reference 'P12_sr' | $ceil(-4.6)$ | constant | +| Initial value of species reference 'P13_sr' | $cos(9.1)$ | constant | +| Initial value of species reference 'P14_sr' | $cos(-0.22)$ | constant | +| Initial value of species reference 'P15_sr' | $exp(0)$ | constant | +| Initial value of species reference 'P16_sr' | $exp(1)$ | constant | +| Initial value of species reference 'P17_sr' | $exp(0.77)$ | constant | +| Initial value of species reference 'P18_sr' | $floor(-4.6)$ | constant | +| Initial value of species reference 'P19_sr' | $floor(9.1)$ | constant | +| Initial value of species reference 'P20_sr' | $ln(0.2)$ | constant | +| Initial value of species reference 'P21_sr' | $ln(1)$ | constant | +| Initial value of species reference 'P22_sr' | $log10(0.2)$ | constant | +| Initial value of species reference 'P23_sr' | $log10(1)$ | constant | +| Initial value of species reference 'P24_sr' | $1^2$ | constant | +| Initial value of species reference 'P25_sr' | $2^2$ | constant | +| Initial value of species reference 'P26_sr' | $1.4^5.1$ | constant | +| Initial value of species reference 'P27_sr' | $4^2$ | constant | +| Initial value of species reference 'P28_sr' | $3.1^2$ | constant | +| Initial value of species reference 'P29_sr' | $sqrt(4)$ | constant | +| Initial value of species reference 'P30_sr' | $sqrt(7.4)$ | constant | +| Initial value of species reference 'P31_sr' | $sin(2.1)$ | constant | +| Initial value of species reference 'P32_sr' | $sin(0)$ | constant | +| Initial value of species reference 'P33_sr' | $sin(-5.9)$ | constant | +| Initial value of species reference 'P34_sr' | $tan(0)$ | constant | +| Initial value of species reference 'P35_sr' | $tan(1.11)$ | constant | +| Initial value of species reference 'P36_sr' | $tan(-6)$ | constant | +| Initial value of species reference 'P37_sr' | $tanh(0)$ | constant | +| Initial value of species reference 'P38_sr' | $tanh(1.11)$ | constant | +| Initial value of species reference 'P39_sr' | $tanh(-6)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01517/l2v5/build.log b/latest/cases/01517/l2v5/build.log new file mode 100644 index 000000000..2c2378b06 --- /dev/null +++ b/latest/cases/01517/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01517/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01517/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01517/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01517/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01517/l2v5/index.heta b/latest/cases/01517/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01517/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01517/l3v2/index.heta b/latest/cases/01517/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01517/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01517/model-sbml-l2v5.xml b/latest/cases/01517/model-sbml-l2v5.xml new file mode 100644 index 000000000..8d1240214 --- /dev/null +++ b/latest/cases/01517/model-sbml-l2v5.xml @@ -0,0 +1,456 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + + + + + 1 + + + + + + + + + + -1 + + + + + + + + + + 0.5 + + + + + + + + + + 1 + + + + + + + + + + -0.5 + + + + + + + + + + 2.8 + + + + + + + + + + -7.09 + + + + + + + + + + 0.5 + + + + + + + + + + 3.55 + + + + + + + + + + -4.6 + + + + + + + + + + 9.1 + + + + + + + + + + -0.22 + + + + + + + + + + 0 + + + + + + + + + + 1 + + + + + + + + + + 0.77 + + + + + + + + + + -4.6 + + + + + + + + + + 9.1 + + + + + + + + + + 0.2 + + + + + + + + + + 1 + + + + + + + + + + + 10 + + 0.2 + + + + + + + + + + + 10 + + 1 + + + + + + + + + + 1 + 2 + + + + + + + + + + 2 + 2 + + + + + + + + + + 1.4 + 5.1 + + + + + + + + + + 4 + 2 + + + + + + + + + + 3.1 + 2 + + + + + + + + + + + 2 + + 4 + + + + + + + + + + + 2 + + 7.4 + + + + + + + + + + 2.1 + + + + + + + + + + 0 + + + + + + + + + + -5.9 + + + + + + + + + + 0 + + + + + + + + + + 1.11 + + + + + + + + + + -6 + + + + + + + + + + 0 + + + + + + + + + + 1.11 + + + + + + + + + + -6 + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01517/synopsis.txt b/latest/cases/01517/synopsis.txt new file mode 100644 index 000000000..abd3323f2 --- /dev/null +++ b/latest/cases/01517/synopsis.txt @@ -0,0 +1,107 @@ + +category: Test +synopsis: The use of unusual MathML constructs in StoichiometryMath. +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + The model tests various unusual MathML elements in stoichiometries. It is numerically identical to model 01515, which uses rate rules. + +The model contains: +* 38 species (P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39) +* 1 compartment (C) +* 38 species references (P2_sr, P3_sr, P4_sr, P5_sr, P6_sr, P7_sr, P8_sr, P9_sr, P10_sr, P11_sr, P12_sr, P13_sr, P14_sr, P15_sr, P16_sr, P17_sr, P18_sr, P19_sr, P20_sr, P21_sr, P22_sr, P23_sr, P24_sr, P25_sr, P26_sr, P27_sr, P28_sr, P29_sr, P30_sr, P31_sr, P32_sr, P33_sr, P34_sr, P35_sr, P36_sr, P37_sr, P38_sr, P39_sr) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> P2_sr P2 + P3_sr P3 + P4_sr P4 + P5_sr P5 + P6_sr P6 + P7_sr P7 + P8_sr P8 + P9_sr P9 + P10_sr P10 + P11_sr P11 + P12_sr P12 + P13_sr P13 + P14_sr P14 + P15_sr P15 + P16_sr P16 + P17_sr P17 + P18_sr P18 + P19_sr P19 + P20_sr P20 + P21_sr P21 + P22_sr P22 + P23_sr P23 + P24_sr P24 + P25_sr P25 + P26_sr P26 + P27_sr P27 + P28_sr P28 + P29_sr P29 + P30_sr P30 + P31_sr P31 + P32_sr P32 + P33_sr P33 + P34_sr P34 + P35_sr P35 + P36_sr P36 + P37_sr P37 + P38_sr P38 + P39_sr P39 | $1$ |] +Note: the following stoichiometries are set separately: P2_sr, P3_sr, P4_sr, P5_sr, P6_sr, P7_sr, P8_sr, P9_sr, P10_sr, P11_sr, P12_sr, P13_sr, P14_sr, P15_sr, P16_sr, P17_sr, P18_sr, P19_sr, P20_sr, P21_sr, P22_sr, P23_sr, P24_sr, P25_sr, P26_sr, P27_sr, P28_sr, P29_sr, P30_sr, P31_sr, P32_sr, P33_sr, P34_sr, P35_sr, P36_sr, P37_sr, P38_sr, P39_sr + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species P2 | $0$ | variable | +| Initial concentration of species P3 | $0$ | variable | +| Initial concentration of species P4 | $0$ | variable | +| Initial concentration of species P5 | $0$ | variable | +| Initial concentration of species P6 | $0$ | variable | +| Initial concentration of species P7 | $0$ | variable | +| Initial concentration of species P8 | $0$ | variable | +| Initial concentration of species P9 | $0$ | variable | +| Initial concentration of species P10 | $0$ | variable | +| Initial concentration of species P11 | $0$ | variable | +| Initial concentration of species P12 | $0$ | variable | +| Initial concentration of species P13 | $0$ | variable | +| Initial concentration of species P14 | $0$ | variable | +| Initial concentration of species P15 | $0$ | variable | +| Initial concentration of species P16 | $0$ | variable | +| Initial concentration of species P17 | $0$ | variable | +| Initial concentration of species P18 | $0$ | variable | +| Initial concentration of species P19 | $0$ | variable | +| Initial concentration of species P20 | $0$ | variable | +| Initial concentration of species P21 | $0$ | variable | +| Initial concentration of species P22 | $0$ | variable | +| Initial concentration of species P23 | $0$ | variable | +| Initial concentration of species P24 | $0$ | variable | +| Initial concentration of species P25 | $0$ | variable | +| Initial concentration of species P26 | $0$ | variable | +| Initial concentration of species P27 | $0$ | variable | +| Initial concentration of species P28 | $0$ | variable | +| Initial concentration of species P29 | $0$ | variable | +| Initial concentration of species P30 | $0$ | variable | +| Initial concentration of species P31 | $0$ | variable | +| Initial concentration of species P32 | $0$ | variable | +| Initial concentration of species P33 | $0$ | variable | +| Initial concentration of species P34 | $0$ | variable | +| Initial concentration of species P35 | $0$ | variable | +| Initial concentration of species P36 | $0$ | variable | +| Initial concentration of species P37 | $0$ | variable | +| Initial concentration of species P38 | $0$ | variable | +| Initial concentration of species P39 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'P2_sr' | $abs(-1)$ | variable | +| Initial value of species reference 'P3_sr' | $abs(1)$ | variable | +| Initial value of species reference 'P4_sr' | $acos(-1)$ | variable | +| Initial value of species reference 'P5_sr' | $acos(0.5)$ | variable | +| Initial value of species reference 'P6_sr' | $asin(1)$ | variable | +| Initial value of species reference 'P7_sr' | $asin(-0.5)$ | variable | +| Initial value of species reference 'P8_sr' | $atan(2.8)$ | variable | +| Initial value of species reference 'P9_sr' | $atan(-7.09)$ | variable | +| Initial value of species reference 'P10_sr' | $ceil(0.5)$ | variable | +| Initial value of species reference 'P11_sr' | $ceil(3.55)$ | variable | +| Initial value of species reference 'P12_sr' | $ceil(-4.6)$ | variable | +| Initial value of species reference 'P13_sr' | $cos(9.1)$ | variable | +| Initial value of species reference 'P14_sr' | $cos(-0.22)$ | variable | +| Initial value of species reference 'P15_sr' | $exp(0)$ | variable | +| Initial value of species reference 'P16_sr' | $exp(1)$ | variable | +| Initial value of species reference 'P17_sr' | $exp(0.77)$ | variable | +| Initial value of species reference 'P18_sr' | $floor(-4.6)$ | variable | +| Initial value of species reference 'P19_sr' | $floor(9.1)$ | variable | +| Initial value of species reference 'P20_sr' | $ln(0.2)$ | variable | +| Initial value of species reference 'P21_sr' | $ln(1)$ | variable | +| Initial value of species reference 'P22_sr' | $log10(0.2)$ | variable | +| Initial value of species reference 'P23_sr' | $log10(1)$ | variable | +| Initial value of species reference 'P24_sr' | $1^2$ | variable | +| Initial value of species reference 'P25_sr' | $2^2$ | variable | +| Initial value of species reference 'P26_sr' | $1.4^5.1$ | variable | +| Initial value of species reference 'P27_sr' | $4^2$ | variable | +| Initial value of species reference 'P28_sr' | $3.1^2$ | variable | +| Initial value of species reference 'P29_sr' | $sqrt(4)$ | variable | +| Initial value of species reference 'P30_sr' | $sqrt(7.4)$ | variable | +| Initial value of species reference 'P31_sr' | $sin(2.1)$ | variable | +| Initial value of species reference 'P32_sr' | $sin(0)$ | variable | +| Initial value of species reference 'P33_sr' | $sin(-5.9)$ | variable | +| Initial value of species reference 'P34_sr' | $tan(0)$ | variable | +| Initial value of species reference 'P35_sr' | $tan(1.11)$ | variable | +| Initial value of species reference 'P36_sr' | $tan(-6)$ | variable | +| Initial value of species reference 'P37_sr' | $tanh(0)$ | variable | +| Initial value of species reference 'P38_sr' | $tanh(1.11)$ | variable | +| Initial value of species reference 'P39_sr' | $tanh(-6)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01518/l2v5/build.log b/latest/cases/01518/l2v5/build.log new file mode 100644 index 000000000..52a7abf1e --- /dev/null +++ b/latest/cases/01518/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01518/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01518/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01518/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01518/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01518/l2v5/index.heta b/latest/cases/01518/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01518/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01518/l3v2/build.log b/latest/cases/01518/l3v2/build.log new file mode 100644 index 000000000..162928036 --- /dev/null +++ b/latest/cases/01518/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01518/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01518/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01518/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01518/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01518/l3v2/index.heta b/latest/cases/01518/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01518/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01518/model-sbml-l2v5.xml b/latest/cases/01518/model-sbml-l2v5.xml new file mode 100644 index 000000000..6cd8707fa --- /dev/null +++ b/latest/cases/01518/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + 1 + + + + + + + + + + + + + delay + P1 + 1 + + 1.5 + + + + + delay + P1 + 1 + + 2 + + + + + + + 1 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01518/model-sbml-l3v2.xml b/latest/cases/01518/model-sbml-l3v2.xml new file mode 100644 index 000000000..66aba3173 --- /dev/null +++ b/latest/cases/01518/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + 1 + + + + + + + + + + + + + delay + P1 + 1 + + 1.5 + + + + + delay + P1 + 1 + + 2 + + + + + + + 1 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01518/synopsis.txt b/latest/cases/01518/synopsis.txt new file mode 100644 index 000000000..8bc0e2569 --- /dev/null +++ b/latest/cases/01518/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An event with a delay that has triggers with variable delays. +componentTags: CSymbolDelay, EventWithDelay, Parameter, RateRule +testTags: DelayInTrigger, EventIsPersistent, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests whether the delayed value of a parameter is within a window of values, assigning a value to another parameter if so. The event is persistent, so even when the tested parameter leaves the window before the event assignment, the assignment is carried out anyway. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(delay(P1, 1) > 1.5) && (delay(P1, 1) < 2)$ | $1$ | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01519/l2v5/index.heta b/latest/cases/01519/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01519/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01519/l3v2/build.log b/latest/cases/01519/l3v2/build.log new file mode 100644 index 000000000..96e9fe3dc --- /dev/null +++ b/latest/cases/01519/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01519/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01519/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01519/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01519/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01519/l3v2/index.heta b/latest/cases/01519/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01519/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01519/model-sbml-l3v2.xml b/latest/cases/01519/model-sbml-l3v2.xml new file mode 100644 index 000000000..bbd72c00b --- /dev/null +++ b/latest/cases/01519/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + 1 + + + + + + + + + + + + + delay + P1 + 1 + + 1.5 + + + + + delay + P1 + 1 + + 2 + + + + + + + 1 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01519/synopsis.txt b/latest/cases/01519/synopsis.txt new file mode 100644 index 000000000..7a39c0264 --- /dev/null +++ b/latest/cases/01519/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An event with a delay that has triggers with variable delays. +componentTags: CSymbolDelay, EventWithDelay, Parameter, RateRule +testTags: DelayInTrigger, EventIsNotPersistent, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests whether the delayed value of a parameter is within a window of values, assigning a value to another parameter if so. The event is not persistent, so even when the tested parameter leaves the window before the event assignment, the assignment is not carried out. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E0 | $(delay(P1, 1) > 1.5) && (delay(P1, 1) < 2)$ | false | $1$ | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01520/l2v5/index.heta b/latest/cases/01520/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01520/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01520/l3v2/build.log b/latest/cases/01520/l3v2/build.log new file mode 100644 index 000000000..496d2b8df --- /dev/null +++ b/latest/cases/01520/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01520/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01520/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01520/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01520/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01520/l3v2/index.heta b/latest/cases/01520/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01520/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01520/model-sbml-l3v2.xml b/latest/cases/01520/model-sbml-l3v2.xml new file mode 100644 index 000000000..edc0e231a --- /dev/null +++ b/latest/cases/01520/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + 1 + + + + + + + + + + + + + delay + P1 + 1 + + 1.5 + + + + + delay + P1 + 1 + + 2.6 + + + + + + + 1 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01520/synopsis.txt b/latest/cases/01520/synopsis.txt new file mode 100644 index 000000000..30d6dbf31 --- /dev/null +++ b/latest/cases/01520/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An event with a delay that has triggers with variable delays. +componentTags: CSymbolDelay, EventWithDelay, Parameter, RateRule +testTags: DelayInTrigger, EventIsNotPersistent, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests whether the delayed value of a parameter is within a window of values, assigning a value to another parameter if so. The event is not persistent, but the the tested parameter does not leave the window before the event assignment, so the assignment is carried out. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E0 | $(delay(P1, 1) > 1.5) && (delay(P1, 1) < 2.6)$ | false | $1$ | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01521/l2v5/index.heta b/latest/cases/01521/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01521/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01521/l3v2/heta-code/output.heta b/latest/cases/01521/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d068f5ff1 --- /dev/null +++ b/latest/cases/01521/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +P1_proc @Process { actors: = P1, }; +P1_proc := 1; + +P1 @Record { } .= 0; +P2 @Record { } .= 0; +P2 [E0]= 3; +P2 [E1]= 5; + +E0 @DSwitcher { trigger: P1 > 1.5, }; +E1 @DSwitcher { trigger: P1 > 1.5, }; + diff --git a/latest/cases/01521/l3v2/index.heta b/latest/cases/01521/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01521/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01521/l3v2/json/output.json b/latest/cases/01521/l3v2/json/output.json new file mode 100644 index 000000000..957becb4e --- /dev/null +++ b/latest/cases/01521/l3v2/json/output.json @@ -0,0 +1,44 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "0" + } + }, + { + "class": "Record", + "id": "P2", + "assignments": { + "start_": "0", + "E0": "3", + "E1": "5" + } + }, + { + "class": "Process", + "id": "P1_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "P1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "P1 > 1.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "P1 > 1.5" + } +] \ No newline at end of file diff --git a/latest/cases/01521/model-sbml-l3v2.xml b/latest/cases/01521/model-sbml-l3v2.xml new file mode 100644 index 000000000..39a912ecf --- /dev/null +++ b/latest/cases/01521/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + 1 + + + + + + + + + + P1 + 1.5 + + + + + + + delay + P1 + 1 + + + + + + + 3 + + + + + + + + + + P1 + 1.5 + + + + + + 1 + + + + + + 5 + + + + + + + diff --git a/latest/cases/01521/output.heta b/latest/cases/01521/output.heta new file mode 100644 index 000000000..8946fa6da --- /dev/null +++ b/latest/cases/01521/output.heta @@ -0,0 +1,53 @@ +/* +category: Test +synopsis: Two simultaneous events with a priority using a delay. +componentTags: CSymbolDelay, EventNoDelay, EventPriority, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events fire simultaneously, with the priority of one being set using the delay function for another parameter, making its priority lower, and therefore firing second. + +The model contains: +* 2 parameters (P1, P2) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $P1 > 1.5$ | $delay(P1, 1)$ | $P2 = 3$ | +| E1 | $P1 > 1.5$ | $1$ | $P2 = 5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P1_proc @Process { actors: = P1, }; +P1_proc := 1; + +P1 @Record { } .= 0; +P2 @Record { } .= 0; +P2 [E0]= 3; +P2 [E1]= 5; + +E0 @DSwitcher { trigger: P1 > 1.5, }; +E1 @DSwitcher { trigger: P1 > 1.5, }; + diff --git a/latest/cases/01521/synopsis.txt b/latest/cases/01521/synopsis.txt new file mode 100644 index 000000000..63bf1622f --- /dev/null +++ b/latest/cases/01521/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: Two simultaneous events with a priority using a delay. +componentTags: CSymbolDelay, EventNoDelay, EventPriority, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events fire simultaneously, with the priority of one being set using the delay function for another parameter, making its priority lower, and therefore firing second. + +The model contains: +* 2 parameters (P1, P2) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $P1 > 1.5$ | $delay(P1, 1)$ | $P2 = 3$ | +| E1 | $P1 > 1.5$ | $1$ | $P2 = 5$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01522/l2v5/index.heta b/latest/cases/01522/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01522/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01522/l3v2/build.log b/latest/cases/01522/l3v2/build.log new file mode 100644 index 000000000..fcacf6651 --- /dev/null +++ b/latest/cases/01522/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01522/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01522/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01522/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01522/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01522/l3v2/index.heta b/latest/cases/01522/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01522/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01522/model-sbml-l3v2.xml b/latest/cases/01522/model-sbml-l3v2.xml new file mode 100644 index 000000000..d63909fa3 --- /dev/null +++ b/latest/cases/01522/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + time + + + + + + + + + + + delay + P1 + 1 + + -0.5 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01522/synopsis.txt b/latest/cases/01522/synopsis.txt new file mode 100644 index 000000000..6bd7fa7fc --- /dev/null +++ b/latest/cases/01522/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An event triggered at t0 by a delayed value in its trigger. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, EventNoDelay, Parameter +testTags: DelayInTrigger, EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event tests whether the delayed value of a parameter is less than -0.5. Since that parameter has an assignment rule to be equal to 'time', which applies at all times, including before the beginning of the simulation, that trigger evaluates to true, and fires because it is set to have an initial value of 'false'. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $delay(P1, 1) < -0.5$ | false | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $time$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01523/l2v5/build.log b/latest/cases/01523/l2v5/build.log new file mode 100644 index 000000000..44f713bbf --- /dev/null +++ b/latest/cases/01523/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01523/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01523/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01523/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01523/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01523/l2v5/index.heta b/latest/cases/01523/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01523/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01523/l3v2/build.log b/latest/cases/01523/l3v2/build.log new file mode 100644 index 000000000..0f8cf66de --- /dev/null +++ b/latest/cases/01523/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01523/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01523/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01523/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01523/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01523/l3v2/index.heta b/latest/cases/01523/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01523/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01523/model-sbml-l2v5.xml b/latest/cases/01523/model-sbml-l2v5.xml new file mode 100644 index 000000000..b26d7b0e4 --- /dev/null +++ b/latest/cases/01523/model-sbml-l2v5.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + 1 + + + + + + + + + + P1 + 1.5 + + + + + + 2 + + + + + + + delay + P1 + 1 + + + + + + + + diff --git a/latest/cases/01523/model-sbml-l3v2.xml b/latest/cases/01523/model-sbml-l3v2.xml new file mode 100644 index 000000000..b500c9310 --- /dev/null +++ b/latest/cases/01523/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + 1 + + + + + + + + + + P1 + 1.5 + + + + + + 2 + + + + + + + delay + P1 + 1 + + + + + + + + diff --git a/latest/cases/01523/synopsis.txt b/latest/cases/01523/synopsis.txt new file mode 100644 index 000000000..34f7e4924 --- /dev/null +++ b/latest/cases/01523/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A delayed event that assigns the value of a delayed parameter +componentTags: CSymbolDelay, EventWithDelay, Parameter, RateRule +testTags: DelayInEventAssignment, EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event assigns a value of a delayed parameter from the trigger time of the event, since the value of its 'userValuesFromTriggerTime' attribute is 'true'. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $P1 > 1.5$ | $2$ | $P2 = delay(P1, 1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01524/l2v5/build.log b/latest/cases/01524/l2v5/build.log new file mode 100644 index 000000000..25490c0e8 --- /dev/null +++ b/latest/cases/01524/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01524/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01524/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01524/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01524/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01524/l2v5/index.heta b/latest/cases/01524/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01524/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01524/l3v2/build.log b/latest/cases/01524/l3v2/build.log new file mode 100644 index 000000000..bca051922 --- /dev/null +++ b/latest/cases/01524/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01524/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01524/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01524/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01524/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01524/l3v2/index.heta b/latest/cases/01524/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01524/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01524/model-sbml-l2v5.xml b/latest/cases/01524/model-sbml-l2v5.xml new file mode 100644 index 000000000..79dbbfb78 --- /dev/null +++ b/latest/cases/01524/model-sbml-l2v5.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + 1 + + + + + + + + + + P1 + 1.5 + + + + + + 2 + + + + + + + delay + P1 + 1 + + + + + + + + diff --git a/latest/cases/01524/model-sbml-l3v2.xml b/latest/cases/01524/model-sbml-l3v2.xml new file mode 100644 index 000000000..5cccd4379 --- /dev/null +++ b/latest/cases/01524/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + 1 + + + + + + + + + + P1 + 1.5 + + + + + + 2 + + + + + + + delay + P1 + 1 + + + + + + + + diff --git a/latest/cases/01524/synopsis.txt b/latest/cases/01524/synopsis.txt new file mode 100644 index 000000000..dc222b9b1 --- /dev/null +++ b/latest/cases/01524/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A delayed event that assigns the value of a delayed parameter +componentTags: CSymbolDelay, EventWithDelay, Parameter, RateRule +testTags: DelayInEventAssignment, EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event assigns a value of a delayed parameter from the assignment time of the event, since the value of its 'userValuesFromTriggerTime' attribute is 'false'. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $P1 > 1.5$ | Assignment time | $2$ | $P2 = delay(P1, 1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01525/l2v5/index.heta b/latest/cases/01525/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01525/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01525/l3v2/build.log b/latest/cases/01525/l3v2/build.log new file mode 100644 index 000000000..094d0ce64 --- /dev/null +++ b/latest/cases/01525/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01525/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01525/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01525/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01525/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01525/l3v2/index.heta b/latest/cases/01525/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01525/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01525/model-sbml-l3v2.xml b/latest/cases/01525/model-sbml-l3v2.xml new file mode 100644 index 000000000..973ad81c3 --- /dev/null +++ b/latest/cases/01525/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + time + + + + + + + + + + + + + rateOf + P1 + + 1.5 + + + + + rateOf + P1 + + 2.5 + + + + + + + 2 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01525/synopsis.txt b/latest/cases/01525/synopsis.txt new file mode 100644 index 000000000..f222835be --- /dev/null +++ b/latest/cases/01525/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A delayed event with a trigger window for the rateOf another parameter. +componentTags: CSymbolRateOf, CSymbolTime, EventWithDelay, Parameter, RateRule +testTags: EventIsPersistent, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event triggers based on whether the value of the rate of change of a parameter is within a window. The event is persistent, meaning that it will assign its value even though the rate of change is outside the window upon execution. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(rateOf(P1) > 1.5) && (rateOf(P1) < 2.5)$ | $2$ | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01526/l2v5/index.heta b/latest/cases/01526/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01526/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01526/l3v2/build.log b/latest/cases/01526/l3v2/build.log new file mode 100644 index 000000000..174af6bff --- /dev/null +++ b/latest/cases/01526/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01526/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01526/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01526/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01526/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01526/l3v2/index.heta b/latest/cases/01526/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01526/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01526/model-sbml-l3v2.xml b/latest/cases/01526/model-sbml-l3v2.xml new file mode 100644 index 000000000..86582ec3d --- /dev/null +++ b/latest/cases/01526/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + time + + + + + + + + + + + + + rateOf + P1 + + 1.5 + + + + + rateOf + P1 + + 2.5 + + + + + + + 2 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01526/synopsis.txt b/latest/cases/01526/synopsis.txt new file mode 100644 index 000000000..156cf980f --- /dev/null +++ b/latest/cases/01526/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A delayed event with a trigger window for the rateOf another parameter. +componentTags: CSymbolRateOf, CSymbolTime, EventWithDelay, Parameter, RateRule +testTags: EventIsNotPersistent, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event triggers based on whether the value of the rate of change of a parameter is within a window. The event is not persistent, meaning that it will not assign its value because the rate of change goes outside the window before execution. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E0 | $(rateOf(P1) > 1.5) && (rateOf(P1) < 2.5)$ | false | $2$ | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01527/l2v5/index.heta b/latest/cases/01527/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01527/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01527/l3v2/build.log b/latest/cases/01527/l3v2/build.log new file mode 100644 index 000000000..2547b6e67 --- /dev/null +++ b/latest/cases/01527/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01527/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01527/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01527/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01527/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01527/l3v2/index.heta b/latest/cases/01527/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01527/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01527/model-sbml-l3v2.xml b/latest/cases/01527/model-sbml-l3v2.xml new file mode 100644 index 000000000..665868889 --- /dev/null +++ b/latest/cases/01527/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + 1 + + + + + + + + + + + rateOf + P1 + + 0.5 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01527/synopsis.txt b/latest/cases/01527/synopsis.txt new file mode 100644 index 000000000..88a5b4214 --- /dev/null +++ b/latest/cases/01527/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An event that fires at t0 because of the rate of a parameter. +componentTags: CSymbolRateOf, EventNoDelay, Parameter, RateRule +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event fires at t0 because the rate of P1 is greater than 0.5. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $rateOf(P1) > 0.5$ | false | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01528/l2v5/index.heta b/latest/cases/01528/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01528/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01528/l3v2/build.log b/latest/cases/01528/l3v2/build.log new file mode 100644 index 000000000..ba7fe60a8 --- /dev/null +++ b/latest/cases/01528/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01528/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01528/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01528/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01528/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01528/l3v2/index.heta b/latest/cases/01528/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01528/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01528/model-sbml-l3v2.xml b/latest/cases/01528/model-sbml-l3v2.xml new file mode 100644 index 000000000..152c0ddea --- /dev/null +++ b/latest/cases/01528/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + time + + + + + + + + + + time + 1.5 + + + + + + 2 + + + + + + + rateOf + P1 + + + + + + + + diff --git a/latest/cases/01528/synopsis.txt b/latest/cases/01528/synopsis.txt new file mode 100644 index 000000000..cbf6ce5ea --- /dev/null +++ b/latest/cases/01528/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An event that assigns the rate of change of a parameter. +componentTags: CSymbolRateOf, CSymbolTime, EventWithDelay, Parameter, RateRule +testTags: EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event assigns the rate of change of a parameter, from the value it had at the trigger time of the event. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time > 1.5$ | $2$ | $P2 = rateOf(P1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01529/l2v5/index.heta b/latest/cases/01529/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01529/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01529/l3v2/build.log b/latest/cases/01529/l3v2/build.log new file mode 100644 index 000000000..c22b30197 --- /dev/null +++ b/latest/cases/01529/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01529/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01529/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01529/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01529/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01529/l3v2/index.heta b/latest/cases/01529/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01529/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01529/model-sbml-l3v2.xml b/latest/cases/01529/model-sbml-l3v2.xml new file mode 100644 index 000000000..af38e1c8e --- /dev/null +++ b/latest/cases/01529/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + time + + + + + + + + + + time + 1.5 + + + + + + 2 + + + + + + + rateOf + P1 + + + + + + + + diff --git a/latest/cases/01529/synopsis.txt b/latest/cases/01529/synopsis.txt new file mode 100644 index 000000000..a99cb7cd6 --- /dev/null +++ b/latest/cases/01529/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An event that assigns the rate of change of a parameter. +componentTags: CSymbolRateOf, CSymbolTime, EventWithDelay, Parameter, RateRule +testTags: EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event assigns the rate of change of a parameter, from the value it has at the asignment time of the event. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $time > 1.5$ | Assignment time | $2$ | $P2 = rateOf(P1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01530/l2v5/build.log b/latest/cases/01530/l2v5/build.log new file mode 100644 index 000000000..a1a7ef944 --- /dev/null +++ b/latest/cases/01530/l2v5/build.log @@ -0,0 +1,20 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01530/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01530/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01530/model-sbml-l2v5.xml"... +[error] P52 Some of properties do not satisfy requirements for class "Record" + 1. /assignments/E50 should NOT be shorter than 1 characters + 2. /assignments/E50 should be number + 3. /assignments/E50 should match exactly one schema in oneOf +[warn] Some of component properties will not be updated. +[info] Setting references in elements, total length 188 +[error] FunctionDef "sinh" is not found as expected here: P40 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: P41 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: P45 { math: undefined }; +[error] FunctionDef "acosh" is not found as expected here: P46 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: P47 { math: undefined }; +[error] FunctionDef "asech" is not found as expected here: P48 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: P49 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01530/l2v5/index.heta b/latest/cases/01530/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01530/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01530/l3v2/build.log b/latest/cases/01530/l3v2/build.log new file mode 100644 index 000000000..a95275ee4 --- /dev/null +++ b/latest/cases/01530/l3v2/build.log @@ -0,0 +1,20 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01530/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01530/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01530/model-sbml-l3v2.xml"... +[error] P52 Some of properties do not satisfy requirements for class "Record" + 1. /assignments/E50 should NOT be shorter than 1 characters + 2. /assignments/E50 should be number + 3. /assignments/E50 should match exactly one schema in oneOf +[warn] Some of component properties will not be updated. +[info] Setting references in elements, total length 183 +[error] FunctionDef "sinh" is not found as expected here: P40 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: P41 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: P45 { math: undefined }; +[error] FunctionDef "acosh" is not found as expected here: P46 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: P47 { math: undefined }; +[error] FunctionDef "asech" is not found as expected here: P48 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: P49 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01530/l3v2/index.heta b/latest/cases/01530/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01530/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01530/model-sbml-l2v5.xml b/latest/cases/01530/model-sbml-l2v5.xml new file mode 100644 index 000000000..fd0a7696a --- /dev/null +++ b/latest/cases/01530/model-sbml-l2v5.xml @@ -0,0 +1,1146 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 1.5 + + + + + + + + + + + + + + + + + time + 1.5 + + + + + + + + + + + + + + + + + + + + time + 1.5 + + + + + + + + + -1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + -1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + -0.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 2.8 + + + + + + + + + + + time + 1.5 + + + + + + + + + -7.09 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 3.55 + + + + + + + + + + + time + 1.5 + + + + + + + + + -4.6 + + + + + + + + + + + time + 1.5 + + + + + + + + + 9.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + -0.22 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.77 + + + + + + + + + + + time + 1.5 + + + + + + + + + -4.6 + + + + + + + + + + + time + 1.5 + + + + + + + + + 9.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + + 10 + + 0.2 + + + + + + + + + + + time + 1.5 + + + + + + + + + + 10 + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + 2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 2 + 2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.4 + 5.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 4 + 2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 3.1 + 2 + + + + + + + + + + + time + 1.5 + + + + + + + + + + 2 + + 4 + + + + + + + + + + + time + 1.5 + + + + + + + + + + 2 + + 7.4 + + + + + + + + + + + time + 1.5 + + + + + + + + + 2.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0 + + + + + + + + + + + time + 1.5 + + + + + + + + + -5.9 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.11 + + + + + + + + + + + time + 1.5 + + + + + + + + + -6 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 4.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.3 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.7 + + + + + + + + + + + time + 1.5 + + + + + + + + + 2.3 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + -0.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 99 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.34 + + + + + + + + + + + time + 1.5 + + + + + + + + + -0.7 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.42 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.01 + + + + + + + + + + + time + 1.5 + + + + + + + + + + + + + + + + diff --git a/latest/cases/01530/model-sbml-l3v2.xml b/latest/cases/01530/model-sbml-l3v2.xml new file mode 100644 index 000000000..9fb94234a --- /dev/null +++ b/latest/cases/01530/model-sbml-l3v2.xml @@ -0,0 +1,1147 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + 1.5 + + + + + + + + + + + + + + + + + time + 1.5 + + + + + + + + + + + + + + + + + + + + time + 1.5 + + + + + + + + + -1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + -1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + -0.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 2.8 + + + + + + + + + + + time + 1.5 + + + + + + + + + -7.09 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 3.55 + + + + + + + + + + + time + 1.5 + + + + + + + + + -4.6 + + + + + + + + + + + time + 1.5 + + + + + + + + + 9.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + -0.22 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.77 + + + + + + + + + + + time + 1.5 + + + + + + + + + -4.6 + + + + + + + + + + + time + 1.5 + + + + + + + + + 9.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + + 10 + + 0.2 + + + + + + + + + + + time + 1.5 + + + + + + + + + + 10 + + 1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1 + 2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 2 + 2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.4 + 5.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 4 + 2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 3.1 + 2 + + + + + + + + + + + time + 1.5 + + + + + + + + + + 2 + + 4 + + + + + + + + + + + time + 1.5 + + + + + + + + + + 2 + + 7.4 + + + + + + + + + + + time + 1.5 + + + + + + + + + 2.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0 + + + + + + + + + + + time + 1.5 + + + + + + + + + -5.9 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.11 + + + + + + + + + + + time + 1.5 + + + + + + + + + -6 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 4.5 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.2 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.3 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.7 + + + + + + + + + + + time + 1.5 + + + + + + + + + 2.3 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + -0.1 + + + + + + + + + + + time + 1.5 + + + + + + + + + 99 + + + + + + + + + + + time + 1.5 + + + + + + + + + 1.34 + + + + + + + + + + + time + 1.5 + + + + + + + + + -0.7 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.42 + + + + + + + + + + + time + 1.5 + + + + + + + + + 0.01 + + + + + + + + + + + time + 1.5 + + + + + + + + + + + + + + + + diff --git a/latest/cases/01530/synopsis.txt b/latest/cases/01530/synopsis.txt new file mode 100644 index 000000000..56573f5a8 --- /dev/null +++ b/latest/cases/01530/synopsis.txt @@ -0,0 +1,130 @@ + +category: Test +synopsis: Uncommon MathML in event assignments. +componentTags: CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests various uncommon mathematical constructs in event assignments. + +The model contains: +* 53 parameters (P0, P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40, P41, P42, P43, P44, P45, P46, P47, P48, P49, P52, P50, P51) + +There are 51 events: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 1.5$ | $P0 = exponentiale$ | +| E1 | $time > 1.5$ | $P1 = exp(exponentiale)$ | +| E2 | $time > 1.5$ | $P2 = abs(-1)$ | +| E3 | $time > 1.5$ | $P3 = abs(1)$ | +| E4 | $time > 1.5$ | $P4 = acos(-1)$ | +| E5 | $time > 1.5$ | $P5 = acos(0.5)$ | +| E6 | $time > 1.5$ | $P6 = asin(1)$ | +| E7 | $time > 1.5$ | $P7 = asin(-0.5)$ | +| E8 | $time > 1.5$ | $P8 = atan(2.8)$ | +| E9 | $time > 1.5$ | $P9 = atan(-7.09)$ | +| E10 | $time > 1.5$ | $P10 = ceil(0.5)$ | +| E11 | $time > 1.5$ | $P11 = ceil(3.55)$ | +| E12 | $time > 1.5$ | $P12 = ceil(-4.6)$ | +| E13 | $time > 1.5$ | $P13 = cos(9.1)$ | +| E14 | $time > 1.5$ | $P14 = cos(-0.22)$ | +| E15 | $time > 1.5$ | $P15 = exp(0)$ | +| E16 | $time > 1.5$ | $P16 = exp(1)$ | +| E17 | $time > 1.5$ | $P17 = exp(0.77)$ | +| E18 | $time > 1.5$ | $P18 = floor(-4.6)$ | +| E19 | $time > 1.5$ | $P19 = floor(9.1)$ | +| E20 | $time > 1.5$ | $P20 = ln(0.2)$ | +| E21 | $time > 1.5$ | $P21 = ln(1)$ | +| E22 | $time > 1.5$ | $P22 = log10(0.2)$ | +| E23 | $time > 1.5$ | $P23 = log10(1)$ | +| E24 | $time > 1.5$ | $P24 = 1^2$ | +| E25 | $time > 1.5$ | $P25 = 2^2$ | +| E26 | $time > 1.5$ | $P26 = 1.4^5.1$ | +| E27 | $time > 1.5$ | $P27 = 4^2$ | +| E28 | $time > 1.5$ | $P28 = 3.1^2$ | +| E29 | $time > 1.5$ | $P29 = sqrt(4)$ | +| E30 | $time > 1.5$ | $P30 = sqrt(7.4)$ | +| E31 | $time > 1.5$ | $P31 = sin(2.1)$ | +| E32 | $time > 1.5$ | $P32 = sin(0)$ | +| E33 | $time > 1.5$ | $P33 = sin(-5.9)$ | +| E34 | $time > 1.5$ | $P34 = tan(0)$ | +| E35 | $time > 1.5$ | $P35 = tan(1.11)$ | +| E36 | $time > 1.5$ | $P36 = tan(-6)$ | +| E37 | $time > 1.5$ | $P37 = sec(0.5)$ | +| E38 | $time > 1.5$ | $P38 = csc(4.5)$ | +| E39 | $time > 1.5$ | $P39 = cot(0.2)$ | +| E40 | $time > 1.5$ | $P40 = sinh(0.3)$ | +| E41 | $time > 1.5$ | $P41 = cosh(1.7)$ | +| E42 | $time > 1.5$ | $P42 = arcsec(2.3)$ | +| E43 | $time > 1.5$ | $P43 = arccsc(1.1)$ | +| E44 | $time > 1.5$ | $P44 = arccot(-0.1)$ | +| E45 | $time > 1.5$ | $P45 = arcsinh(99)$ | +| E46 | $time > 1.5$ | $P46 = arccosh(1.34)$ | +| E47 | $time > 1.5$ | $P47 = arctanh(-0.7)$ | +| E48 | $time > 1.5$ | $P48 = arcsech(0.42)$ | +| E49 | $time > 1.5$ | $P49 = arccsch(0.01)$ | +| E50 | $time > 1.5$ | $P52 = times()$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P50 | $0$ | constant | +| Initial value of parameter P51 | $0$ | constant | +| Initial value of parameter P0 | $0$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable | +| Initial value of parameter P3 | $0$ | variable | +| Initial value of parameter P4 | $0$ | variable | +| Initial value of parameter P5 | $0$ | variable | +| Initial value of parameter P6 | $0$ | variable | +| Initial value of parameter P7 | $0$ | variable | +| Initial value of parameter P8 | $0$ | variable | +| Initial value of parameter P9 | $0$ | variable | +| Initial value of parameter P10 | $0$ | variable | +| Initial value of parameter P11 | $0$ | variable | +| Initial value of parameter P12 | $0$ | variable | +| Initial value of parameter P13 | $0$ | variable | +| Initial value of parameter P14 | $0$ | variable | +| Initial value of parameter P15 | $0$ | variable | +| Initial value of parameter P16 | $0$ | variable | +| Initial value of parameter P17 | $0$ | variable | +| Initial value of parameter P18 | $0$ | variable | +| Initial value of parameter P19 | $0$ | variable | +| Initial value of parameter P20 | $0$ | variable | +| Initial value of parameter P21 | $0$ | variable | +| Initial value of parameter P22 | $0$ | variable | +| Initial value of parameter P23 | $0$ | variable | +| Initial value of parameter P24 | $0$ | variable | +| Initial value of parameter P25 | $0$ | variable | +| Initial value of parameter P26 | $0$ | variable | +| Initial value of parameter P27 | $0$ | variable | +| Initial value of parameter P28 | $0$ | variable | +| Initial value of parameter P29 | $0$ | variable | +| Initial value of parameter P30 | $0$ | variable | +| Initial value of parameter P31 | $0$ | variable | +| Initial value of parameter P32 | $0$ | variable | +| Initial value of parameter P33 | $0$ | variable | +| Initial value of parameter P34 | $0$ | variable | +| Initial value of parameter P35 | $0$ | variable | +| Initial value of parameter P36 | $0$ | variable | +| Initial value of parameter P37 | $0$ | variable | +| Initial value of parameter P38 | $0$ | variable | +| Initial value of parameter P39 | $0$ | variable | +| Initial value of parameter P40 | $0$ | variable | +| Initial value of parameter P41 | $0$ | variable | +| Initial value of parameter P42 | $0$ | variable | +| Initial value of parameter P43 | $0$ | variable | +| Initial value of parameter P44 | $0$ | variable | +| Initial value of parameter P45 | $0$ | variable | +| Initial value of parameter P46 | $0$ | variable | +| Initial value of parameter P47 | $0$ | variable | +| Initial value of parameter P48 | $0$ | variable | +| Initial value of parameter P49 | $0$ | variable | +| Initial value of parameter P52 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01531/l2v5/build.log b/latest/cases/01531/l2v5/build.log new file mode 100644 index 000000000..c69f23298 --- /dev/null +++ b/latest/cases/01531/l2v5/build.log @@ -0,0 +1,26 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01531/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01531/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01531/model-sbml-l2v5.xml"... +[error] E51 Cannot parse MathExpr properly. Value expected (char 11) " trig > ()" +[error] E52 Cannot parse MathExpr properly. Value expected (char 11) " trig > ()" +[error] E53 Cannot parse MathExpr properly. Unexpected end of expression (char 18) " trig > 0 and " +[error] E54 Cannot parse MathExpr properly. Unexpected end of expression (char 22) " trig > 0 and not " +[error] E55 Cannot parse MathExpr properly. Unexpected end of expression (char 22) " trig > 0 and not " +[info] Setting references in elements, total length 198 +[error] FunctionDef "sinh" is not found as expected here: E40 { trigger: trig > sinh(0.3) }; +[error] FunctionDef "cosh" is not found as expected here: E41 { trigger: trig > cosh(1.7) }; +[error] FunctionDef "asinh" is not found as expected here: E45 { trigger: trig > asinh(99) }; +[error] FunctionDef "acosh" is not found as expected here: E46 { trigger: trig > acosh(1.34) }; +[error] FunctionDef "atanh" is not found as expected here: E47 { trigger: trig > atanh((-0.7)) }; +[error] FunctionDef "asech" is not found as expected here: E48 { trigger: trig > asech(0.42) }; +[error] FunctionDef "acsch" is not found as expected here: E49 { trigger: trig > acsch(0.01) }; +[error] FunctionDef "acoth" is not found as expected here: E50 { trigger: trig > acoth(8.2) }; +[error] No required "trigger" property for "E51" of DSwitcher. +[error] No required "trigger" property for "E52" of DSwitcher. +[error] No required "trigger" property for "E53" of DSwitcher. +[error] No required "trigger" property for "E54" of DSwitcher. +[error] No required "trigger" property for "E55" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01531/l2v5/index.heta b/latest/cases/01531/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01531/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01531/l3v2/build.log b/latest/cases/01531/l3v2/build.log new file mode 100644 index 000000000..1797fce6d --- /dev/null +++ b/latest/cases/01531/l3v2/build.log @@ -0,0 +1,26 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01531/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01531/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01531/model-sbml-l3v2.xml"... +[error] E51 Cannot parse MathExpr properly. Value expected (char 11) " trig > ()" +[error] E52 Cannot parse MathExpr properly. Value expected (char 11) " trig > ()" +[error] E53 Cannot parse MathExpr properly. Unexpected end of expression (char 18) " trig > 0 and " +[error] E54 Cannot parse MathExpr properly. Unexpected end of expression (char 22) " trig > 0 and not " +[error] E55 Cannot parse MathExpr properly. Unexpected end of expression (char 22) " trig > 0 and not " +[info] Setting references in elements, total length 193 +[error] FunctionDef "sinh" is not found as expected here: E40 { trigger: trig > sinh(0.3) }; +[error] FunctionDef "cosh" is not found as expected here: E41 { trigger: trig > cosh(1.7) }; +[error] FunctionDef "asinh" is not found as expected here: E45 { trigger: trig > asinh(99) }; +[error] FunctionDef "acosh" is not found as expected here: E46 { trigger: trig > acosh(1.34) }; +[error] FunctionDef "atanh" is not found as expected here: E47 { trigger: trig > atanh((-0.7)) }; +[error] FunctionDef "asech" is not found as expected here: E48 { trigger: trig > asech(0.42) }; +[error] FunctionDef "acsch" is not found as expected here: E49 { trigger: trig > acsch(0.01) }; +[error] FunctionDef "acoth" is not found as expected here: E50 { trigger: trig > acoth(8.2) }; +[error] No required "trigger" property for "E51" of DSwitcher. +[error] No required "trigger" property for "E52" of DSwitcher. +[error] No required "trigger" property for "E53" of DSwitcher. +[error] No required "trigger" property for "E54" of DSwitcher. +[error] No required "trigger" property for "E55" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01531/l3v2/index.heta b/latest/cases/01531/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01531/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01531/model-sbml-l2v5.xml b/latest/cases/01531/model-sbml-l2v5.xml new file mode 100644 index 000000000..59afcbe1c --- /dev/null +++ b/latest/cases/01531/model-sbml-l2v5.xml @@ -0,0 +1,1276 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + trig + + + + + + + + 2 + + + + + + + + + + trig + + + + + + + + + + + 2 + + + + + + + + + + trig + + + -1 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + -1 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + -0.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 2.8 + + + + + + + + 2 + + + + + + + + + + trig + + + -7.09 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 3.55 + + + + + + + + 2 + + + + + + + + + + trig + + + -4.6 + + + + + + + + 2 + + + + + + + + + + trig + + + 9.1 + + + + + + + + 2 + + + + + + + + + + trig + + + -0.22 + + + + + + + + 2 + + + + + + + + + + trig + + + 0 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.77 + + + + + + + + 2 + + + + + + + + + + trig + + + -4.6 + + + + + + + + 2 + + + + + + + + + + trig + + + 9.1 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.2 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + + 10 + + 0.2 + + + + + + + + 2 + + + + + + + + + + trig + + + + 10 + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + 2 + + + + + + + + 2 + + + + + + + + + + trig + + + 2 + 2 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.4 + 5.1 + + + + + + + + 2 + + + + + + + + + + trig + + + 4 + 2 + + + + + + + + 2 + + + + + + + + + + trig + + + 3.1 + 2 + + + + + + + + 2 + + + + + + + + + + trig + + + + 2 + + 4 + + + + + + + + 2 + + + + + + + + + + trig + + + + 2 + + 7.4 + + + + + + + + 2 + + + + + + + + + + trig + + + 2.1 + + + + + + + + 2 + + + + + + + + + + trig + + + 0 + + + + + + + + 2 + + + + + + + + + + trig + + + -5.9 + + + + + + + + 2 + + + + + + + + + + trig + + + 0 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.11 + + + + + + + + 2 + + + + + + + + + + trig + + + -6 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 4.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.2 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.3 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.7 + + + + + + + + 2 + + + + + + + + + + trig + + + 2.3 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.1 + + + + + + + + 2 + + + + + + + + + + trig + + + -0.1 + + + + + + + + 2 + + + + + + + + + + trig + + + 99 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.34 + + + + + + + + 2 + + + + + + + + + + trig + + + -0.7 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.42 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.01 + + + + + + + + 2 + + + + + + + + + + trig + + + 8.2 + + + + + + + + 2 + + + + + + + + + + trig + + + + + + + + + + 2 + + + + + + + + + + trig + + + + + + + + + + 2 + + + + + + + + + + + + trig + 0 + + + + + + + + + + + 2 + + + + + + + + + + + + trig + 0 + + + + + + + + + + + + + + 2 + + + + + + + + + + + + trig + 0 + + + + + + + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01531/model-sbml-l3v2.xml b/latest/cases/01531/model-sbml-l3v2.xml new file mode 100644 index 000000000..e48868b4a --- /dev/null +++ b/latest/cases/01531/model-sbml-l3v2.xml @@ -0,0 +1,1277 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + trig + + + + + + + + 2 + + + + + + + + + + trig + + + + + + + + + + + 2 + + + + + + + + + + trig + + + -1 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + -1 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + -0.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 2.8 + + + + + + + + 2 + + + + + + + + + + trig + + + -7.09 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 3.55 + + + + + + + + 2 + + + + + + + + + + trig + + + -4.6 + + + + + + + + 2 + + + + + + + + + + trig + + + 9.1 + + + + + + + + 2 + + + + + + + + + + trig + + + -0.22 + + + + + + + + 2 + + + + + + + + + + trig + + + 0 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.77 + + + + + + + + 2 + + + + + + + + + + trig + + + -4.6 + + + + + + + + 2 + + + + + + + + + + trig + + + 9.1 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.2 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + + 10 + + 0.2 + + + + + + + + 2 + + + + + + + + + + trig + + + + 10 + + 1 + + + + + + + + 2 + + + + + + + + + + trig + + + 1 + 2 + + + + + + + + 2 + + + + + + + + + + trig + + + 2 + 2 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.4 + 5.1 + + + + + + + + 2 + + + + + + + + + + trig + + + 4 + 2 + + + + + + + + 2 + + + + + + + + + + trig + + + 3.1 + 2 + + + + + + + + 2 + + + + + + + + + + trig + + + + 2 + + 4 + + + + + + + + 2 + + + + + + + + + + trig + + + + 2 + + 7.4 + + + + + + + + 2 + + + + + + + + + + trig + + + 2.1 + + + + + + + + 2 + + + + + + + + + + trig + + + 0 + + + + + + + + 2 + + + + + + + + + + trig + + + -5.9 + + + + + + + + 2 + + + + + + + + + + trig + + + 0 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.11 + + + + + + + + 2 + + + + + + + + + + trig + + + -6 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 4.5 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.2 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.3 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.7 + + + + + + + + 2 + + + + + + + + + + trig + + + 2.3 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.1 + + + + + + + + 2 + + + + + + + + + + trig + + + -0.1 + + + + + + + + 2 + + + + + + + + + + trig + + + 99 + + + + + + + + 2 + + + + + + + + + + trig + + + 1.34 + + + + + + + + 2 + + + + + + + + + + trig + + + -0.7 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.42 + + + + + + + + 2 + + + + + + + + + + trig + + + 0.01 + + + + + + + + 2 + + + + + + + + + + trig + + + 8.2 + + + + + + + + 2 + + + + + + + + + + trig + + + + + + + + + + 2 + + + + + + + + + + trig + + + + + + + + + + 2 + + + + + + + + + + + + trig + 0 + + + + + + + + + + + 2 + + + + + + + + + + + + trig + 0 + + + + + + + + + + + + + + 2 + + + + + + + + + + + + trig + 0 + + + + + + + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01531/synopsis.txt b/latest/cases/01531/synopsis.txt new file mode 100644 index 000000000..74bcecee7 --- /dev/null +++ b/latest/cases/01531/synopsis.txt @@ -0,0 +1,145 @@ + +category: Test +synopsis: Uncommon MathML used in event triggers. +componentTags: EventNoDelay, Parameter, RateRule +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests the various unusual mathematical constructs in event triggers. + +The model contains: +* 57 parameters (trig, P0, P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40, P41, P42, P43, P44, P45, P46, P47, P48, P49, P50, P51, P52, P53, P54, P55) + +There are 56 events: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $trig > exponentiale$ | $P0 = 2$ | +| E1 | $trig > exp(exponentiale)$ | $P1 = 2$ | +| E2 | $trig > abs(-1)$ | $P2 = 2$ | +| E3 | $trig > abs(1)$ | $P3 = 2$ | +| E4 | $trig > acos(-1)$ | $P4 = 2$ | +| E5 | $trig > acos(0.5)$ | $P5 = 2$ | +| E6 | $trig > asin(1)$ | $P6 = 2$ | +| E7 | $trig > asin(-0.5)$ | $P7 = 2$ | +| E8 | $trig > atan(2.8)$ | $P8 = 2$ | +| E9 | $trig > atan(-7.09)$ | $P9 = 2$ | +| E10 | $trig > ceil(0.5)$ | $P10 = 2$ | +| E11 | $trig > ceil(3.55)$ | $P11 = 2$ | +| E12 | $trig > ceil(-4.6)$ | $P12 = 2$ | +| E13 | $trig > cos(9.1)$ | $P13 = 2$ | +| E14 | $trig > cos(-0.22)$ | $P14 = 2$ | +| E15 | $trig > exp(0)$ | $P15 = 2$ | +| E16 | $trig > exp(1)$ | $P16 = 2$ | +| E17 | $trig > exp(0.77)$ | $P17 = 2$ | +| E18 | $trig > floor(-4.6)$ | $P18 = 2$ | +| E19 | $trig > floor(9.1)$ | $P19 = 2$ | +| E20 | $trig > ln(0.2)$ | $P20 = 2$ | +| E21 | $trig > ln(1)$ | $P21 = 2$ | +| E22 | $trig > log10(0.2)$ | $P22 = 2$ | +| E23 | $trig > log10(1)$ | $P23 = 2$ | +| E24 | $trig > (1^2)$ | $P24 = 2$ | +| E25 | $trig > (2^2)$ | $P25 = 2$ | +| E26 | $trig > (1.4^5.1)$ | $P26 = 2$ | +| E27 | $trig > (4^2)$ | $P27 = 2$ | +| E28 | $trig > (3.1^2)$ | $P28 = 2$ | +| E29 | $trig > sqrt(4)$ | $P29 = 2$ | +| E30 | $trig > sqrt(7.4)$ | $P30 = 2$ | +| E31 | $trig > sin(2.1)$ | $P31 = 2$ | +| E32 | $trig > sin(0)$ | $P32 = 2$ | +| E33 | $trig > sin(-5.9)$ | $P33 = 2$ | +| E34 | $trig > tan(0)$ | $P34 = 2$ | +| E35 | $trig > tan(1.11)$ | $P35 = 2$ | +| E36 | $trig > tan(-6)$ | $P36 = 2$ | +| E37 | $trig > sec(0.5)$ | $P37 = 2$ | +| E38 | $trig > csc(4.5)$ | $P38 = 2$ | +| E39 | $trig > cot(0.2)$ | $P39 = 2$ | +| E40 | $trig > sinh(0.3)$ | $P40 = 2$ | +| E41 | $trig > cosh(1.7)$ | $P41 = 2$ | +| E42 | $trig > arcsec(2.3)$ | $P42 = 2$ | +| E43 | $trig > arccsc(1.1)$ | $P43 = 2$ | +| E44 | $trig > arccot(-0.1)$ | $P44 = 2$ | +| E45 | $trig > arcsinh(99)$ | $P45 = 2$ | +| E46 | $trig > arccosh(1.34)$ | $P46 = 2$ | +| E47 | $trig > arctanh(-0.7)$ | $P47 = 2$ | +| E48 | $trig > arcsech(0.42)$ | $P48 = 2$ | +| E49 | $trig > arccsch(0.01)$ | $P49 = 2$ | +| E50 | $trig > arccoth(8.2)$ | $P50 = 2$ | +| E51 | $trig > times()$ | $P51 = 2$ | +| E52 | $trig > plus()$ | $P52 = 2$ | +| E53 | $(trig > 0) && and()$ | $P53 = 2$ | +| E54 | $(trig > 0) && !or()$ | $P54 = 2$ | +| E55 | $(trig > 0) && !xor()$ | $P55 = 2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | trig | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter trig | $-5.3$ | variable | +| Initial value of parameter P0 | $0$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable | +| Initial value of parameter P3 | $0$ | variable | +| Initial value of parameter P4 | $0$ | variable | +| Initial value of parameter P5 | $0$ | variable | +| Initial value of parameter P6 | $0$ | variable | +| Initial value of parameter P7 | $0$ | variable | +| Initial value of parameter P8 | $0$ | variable | +| Initial value of parameter P9 | $0$ | variable | +| Initial value of parameter P10 | $0$ | variable | +| Initial value of parameter P11 | $0$ | variable | +| Initial value of parameter P12 | $0$ | variable | +| Initial value of parameter P13 | $0$ | variable | +| Initial value of parameter P14 | $0$ | variable | +| Initial value of parameter P15 | $0$ | variable | +| Initial value of parameter P16 | $0$ | variable | +| Initial value of parameter P17 | $0$ | variable | +| Initial value of parameter P18 | $0$ | variable | +| Initial value of parameter P19 | $0$ | variable | +| Initial value of parameter P20 | $0$ | variable | +| Initial value of parameter P21 | $0$ | variable | +| Initial value of parameter P22 | $0$ | variable | +| Initial value of parameter P23 | $0$ | variable | +| Initial value of parameter P24 | $0$ | variable | +| Initial value of parameter P25 | $0$ | variable | +| Initial value of parameter P26 | $0$ | variable | +| Initial value of parameter P27 | $0$ | variable | +| Initial value of parameter P28 | $0$ | variable | +| Initial value of parameter P29 | $0$ | variable | +| Initial value of parameter P30 | $0$ | variable | +| Initial value of parameter P31 | $0$ | variable | +| Initial value of parameter P32 | $0$ | variable | +| Initial value of parameter P33 | $0$ | variable | +| Initial value of parameter P34 | $0$ | variable | +| Initial value of parameter P35 | $0$ | variable | +| Initial value of parameter P36 | $0$ | variable | +| Initial value of parameter P37 | $0$ | variable | +| Initial value of parameter P38 | $0$ | variable | +| Initial value of parameter P39 | $0$ | variable | +| Initial value of parameter P40 | $0$ | variable | +| Initial value of parameter P41 | $0$ | variable | +| Initial value of parameter P42 | $0$ | variable | +| Initial value of parameter P43 | $0$ | variable | +| Initial value of parameter P44 | $0$ | variable | +| Initial value of parameter P45 | $0$ | variable | +| Initial value of parameter P46 | $0$ | variable | +| Initial value of parameter P47 | $0$ | variable | +| Initial value of parameter P48 | $0$ | variable | +| Initial value of parameter P49 | $0$ | variable | +| Initial value of parameter P50 | $0$ | variable | +| Initial value of parameter P51 | $0$ | variable | +| Initial value of parameter P52 | $0$ | variable | +| Initial value of parameter P53 | $0$ | variable | +| Initial value of parameter P54 | $0$ | variable | +| Initial value of parameter P55 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01532/l2v5/build.log b/latest/cases/01532/l2v5/build.log new file mode 100644 index 000000000..f54787ab2 --- /dev/null +++ b/latest/cases/01532/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01532/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01532/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01532/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01532/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01532/l2v5/index.heta b/latest/cases/01532/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01532/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01532/l3v2/build.log b/latest/cases/01532/l3v2/build.log new file mode 100644 index 000000000..e5f6ba330 --- /dev/null +++ b/latest/cases/01532/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01532/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01532/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01532/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01532/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01532/l3v2/index.heta b/latest/cases/01532/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01532/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01532/model-sbml-l2v5.xml b/latest/cases/01532/model-sbml-l2v5.xml new file mode 100644 index 000000000..fbf77b13a --- /dev/null +++ b/latest/cases/01532/model-sbml-l2v5.xml @@ -0,0 +1,1881 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + -1 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 1 + + + + + + + + + 2 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+ 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 0.42 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 0.01 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 8.2 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01532/model-sbml-l3v2.xml b/latest/cases/01532/model-sbml-l3v2.xml new file mode 100644 index 000000000..833eff05c --- /dev/null +++ b/latest/cases/01532/model-sbml-l3v2.xml @@ -0,0 +1,1882 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + -1 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 1 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + -1 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 0.5 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 1 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + -0.5 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 2.8 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + -7.09 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 0.5 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 3.55 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + -4.6 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + 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+ -5.2 + + + + + + + + 1 + + + 5.3 + + + 1.11 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + -6 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 0.5 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 4.5 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 0.2 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 0.3 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 1.7 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 2.3 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 1.1 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + -0.1 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 99 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 1.34 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + -0.7 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 0.42 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 0.01 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + 8.2 + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + + + + + + + + + 2 + + + + + + + + + + trig + -5.2 + + + + + + + + 1 + + + 5.3 + + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01532/synopsis.txt b/latest/cases/01532/synopsis.txt new file mode 100644 index 000000000..49aba35e6 --- /dev/null +++ b/latest/cases/01532/synopsis.txt @@ -0,0 +1,142 @@ + +category: Test +synopsis: Uncommon MathML used in event delays. +componentTags: EventWithDelay, Parameter, RateRule +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests the various unusual mathematical constructs in event delays. + +The model contains: +* 57 parameters (trig, P0, P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40, P41, P42, P43, P44, P45, P46, P47, P48, P49, P50, P51, P52, P53, P54, P55) + +There are 53 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $trig > -5.2$ | $1 * (5.3 + exponentiale)$ | $P0 = 2$ | +| E1 | $trig > -5.2$ | $1 * (5.3 + exp(exponentiale))$ | $P1 = 2$ | +| E2 | $trig > -5.2$ | $1 * (5.3 + abs(-1))$ | $P2 = 2$ | +| E3 | $trig > -5.2$ | $1 * (5.3 + abs(1))$ | $P3 = 2$ | +| E4 | $trig > -5.2$ | $1 * (5.3 + acos(-1))$ | $P4 = 2$ | +| E5 | $trig > -5.2$ | $1 * (5.3 + acos(0.5))$ | $P5 = 2$ | +| E6 | $trig > -5.2$ | $1 * (5.3 + asin(1))$ | $P6 = 2$ | +| E7 | $trig > -5.2$ | $1 * (5.3 + asin(-0.5))$ | $P7 = 2$ | +| E8 | $trig > -5.2$ | $1 * (5.3 + atan(2.8))$ | $P8 = 2$ | +| E9 | $trig > -5.2$ | $1 * (5.3 + atan(-7.09))$ | $P9 = 2$ | +| E10 | $trig > -5.2$ | $1 * (5.3 + ceil(0.5))$ | $P10 = 2$ | +| E11 | $trig > -5.2$ | $1 * (5.3 + ceil(3.55))$ | $P11 = 2$ | +| E12 | $trig > -5.2$ | $1 * (5.3 + ceil(-4.6))$ | $P12 = 2$ | +| E13 | $trig > -5.2$ | $1 * (5.3 + cos(9.1))$ | $P13 = 2$ | +| E14 | $trig > -5.2$ | $1 * (5.3 + cos(-0.22))$ | $P14 = 2$ | +| E15 | $trig > -5.2$ | $1 * (5.3 + exp(0))$ | $P15 = 2$ | +| E16 | $trig > -5.2$ | $1 * (5.3 + exp(1))$ | $P16 = 2$ | +| E17 | $trig > -5.2$ | $1 * (5.3 + exp(0.77))$ | $P17 = 2$ | +| E18 | $trig > -5.2$ | $1 * (5.3 + floor(-4.6))$ | $P18 = 2$ | +| E19 | $trig > -5.2$ | $1 * (5.3 + floor(9.1))$ | $P19 = 2$ | +| E20 | $trig > -5.2$ | $1 * (5.3 + ln(0.2))$ | $P20 = 2$ | +| E21 | $trig > -5.2$ | $1 * (5.3 + ln(1))$ | $P21 = 2$ | +| E22 | $trig > -5.2$ | $1 * (5.3 + log10(0.2))$ | $P22 = 2$ | +| E23 | $trig > -5.2$ | $1 * (5.3 + log10(1))$ | $P23 = 2$ | +| E24 | $trig > -5.2$ | $1 * (5.3 + 1^2)$ | $P24 = 2$ | +| E25 | $trig > -5.2$ | $1 * (5.3 + 2^2)$ | $P25 = 2$ | +| E26 | $trig > -5.2$ | $1 * (5.3 + 1.4^5.1)$ | $P26 = 2$ | +| E27 | $trig > -5.2$ | $1 * (5.3 + 4^2)$ | $P27 = 2$ | +| E28 | $trig > -5.2$ | $1 * (5.3 + 3.1^2)$ | $P28 = 2$ | +| E29 | $trig > -5.2$ | $1 * (5.3 + sqrt(4))$ | $P29 = 2$ | +| E30 | $trig > -5.2$ | $1 * (5.3 + sqrt(7.4))$ | $P30 = 2$ | +| E31 | $trig > -5.2$ | $1 * (5.3 + sin(2.1))$ | $P31 = 2$ | +| E32 | $trig > -5.2$ | $1 * (5.3 + sin(0))$ | $P32 = 2$ | +| E33 | $trig > -5.2$ | $1 * (5.3 + sin(-5.9))$ | $P33 = 2$ | +| E34 | $trig > -5.2$ | $1 * (5.3 + tan(0))$ | $P34 = 2$ | +| E35 | $trig > -5.2$ | $1 * (5.3 + tan(1.11))$ | $P35 = 2$ | +| E36 | $trig > -5.2$ | $1 * (5.3 + tan(-6))$ | $P36 = 2$ | +| E37 | $trig > -5.2$ | $1 * (5.3 + sec(0.5))$ | $P37 = 2$ | +| E38 | $trig > -5.2$ | $1 * (5.3 + csc(4.5))$ | $P38 = 2$ | +| E39 | $trig > -5.2$ | $1 * (5.3 + cot(0.2))$ | $P39 = 2$ | +| E40 | $trig > -5.2$ | $1 * (5.3 + sinh(0.3))$ | $P40 = 2$ | +| E41 | $trig > -5.2$ | $1 * (5.3 + cosh(1.7))$ | $P41 = 2$ | +| E42 | $trig > -5.2$ | $1 * (5.3 + arcsec(2.3))$ | $P42 = 2$ | +| E43 | $trig > -5.2$ | $1 * (5.3 + arccsc(1.1))$ | $P43 = 2$ | +| E44 | $trig > -5.2$ | $1 * (5.3 + arccot(-0.1))$ | $P44 = 2$ | +| E45 | $trig > -5.2$ | $1 * (5.3 + arcsinh(99))$ | $P45 = 2$ | +| E46 | $trig > -5.2$ | $1 * (5.3 + arccosh(1.34))$ | $P46 = 2$ | +| E47 | $trig > -5.2$ | $1 * (5.3 + arctanh(-0.7))$ | $P47 = 2$ | +| E48 | $trig > -5.2$ | $1 * (5.3 + arcsech(0.42))$ | $P48 = 2$ | +| E49 | $trig > -5.2$ | $1 * (5.3 + arccsch(0.01))$ | $P49 = 2$ | +| E50 | $trig > -5.2$ | $1 * (5.3 + arccoth(8.2))$ | $P50 = 2$ | +| E51 | $trig > -5.2$ | $1 * (5.3 + times())$ | $P51 = 2$ | +| E52 | $trig > -5.2$ | $1 * plus(5.3)$ | $P52 = 2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | trig | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter trig | $-5.3$ | variable | +| Initial value of parameter P0 | $0$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable | +| Initial value of parameter P3 | $0$ | variable | +| Initial value of parameter P4 | $0$ | variable | +| Initial value of parameter P5 | $0$ | variable | +| Initial value of parameter P6 | $0$ | variable | +| Initial value of parameter P7 | $0$ | variable | +| Initial value of parameter P8 | $0$ | variable | +| Initial value of parameter P9 | $0$ | variable | +| Initial value of parameter P10 | $0$ | variable | +| Initial value of parameter P11 | $0$ | variable | +| Initial value of parameter P12 | $0$ | variable | +| Initial value of parameter P13 | $0$ | variable | +| Initial value of parameter P14 | $0$ | variable | +| Initial value of parameter P15 | $0$ | variable | +| Initial value of parameter P16 | $0$ | variable | +| Initial value of parameter P17 | $0$ | variable | +| Initial value of parameter P18 | $0$ | variable | +| Initial value of parameter P19 | $0$ | variable | +| Initial value of parameter P20 | $0$ | variable | +| Initial value of parameter P21 | $0$ | variable | +| Initial value of parameter P22 | $0$ | variable | +| Initial value of parameter P23 | $0$ | variable | +| Initial value of parameter P24 | $0$ | variable | +| Initial value of parameter P25 | $0$ | variable | +| Initial value of parameter P26 | $0$ | variable | +| Initial value of parameter P27 | $0$ | variable | +| Initial value of parameter P28 | $0$ | variable | +| Initial value of parameter P29 | $0$ | variable | +| Initial value of parameter P30 | $0$ | variable | +| Initial value of parameter P31 | $0$ | variable | +| Initial value of parameter P32 | $0$ | variable | +| Initial value of parameter P33 | $0$ | variable | +| Initial value of parameter P34 | $0$ | variable | +| Initial value of parameter P35 | $0$ | variable | +| Initial value of parameter P36 | $0$ | variable | +| Initial value of parameter P37 | $0$ | variable | +| Initial value of parameter P38 | $0$ | variable | +| Initial value of parameter P39 | $0$ | variable | +| Initial value of parameter P40 | $0$ | variable | +| Initial value of parameter P41 | $0$ | variable | +| Initial value of parameter P42 | $0$ | variable | +| Initial value of parameter P43 | $0$ | variable | +| Initial value of parameter P44 | $0$ | variable | +| Initial value of parameter P45 | $0$ | variable | +| Initial value of parameter P46 | $0$ | variable | +| Initial value of parameter P47 | $0$ | variable | +| Initial value of parameter P48 | $0$ | variable | +| Initial value of parameter P49 | $0$ | variable | +| Initial value of parameter P50 | $0$ | variable | +| Initial value of parameter P51 | $0$ | variable | +| Initial value of parameter P52 | $0$ | variable | +| Initial value of parameter P53 | $0$ | variable | +| Initial value of parameter P54 | $0$ | variable | +| Initial value of parameter P55 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01533/l2v5/index.heta b/latest/cases/01533/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01533/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01533/l3v2/heta-code/output.heta b/latest/cases/01533/l3v2/heta-code/output.heta new file mode 100644 index 000000000..846b6e57a --- /dev/null +++ b/latest/cases/01533/l3v2/heta-code/output.heta @@ -0,0 +1,271 @@ + + +t @TimeScale { }; + +P0 @Record { } .= 0; +P0 [E0]= 2; +P0 [Ep0]= 3; +P1 @Record { } .= 0; +P1 [E1]= 2; +P1 [Ep1]= 3; +P2 @Record { } .= 0; +P2 [E2]= 2; +P2 [Ep2]= 3; +P3 @Record { } .= 0; +P3 [E3]= 2; +P3 [Ep3]= 3; +P4 @Record { } .= 0; +P4 [E4]= 2; +P4 [Ep4]= 3; +P5 @Record { } .= 0; +P5 [E5]= 2; +P5 [Ep5]= 3; +P6 @Record { } .= 0; +P6 [E6]= 2; +P6 [Ep6]= 3; +P7 @Record { } .= 0; +P7 [E7]= 2; +P7 [Ep7]= 3; +P8 @Record { } .= 0; +P8 [E8]= 2; +P8 [Ep8]= 3; +P9 @Record { } .= 0; +P9 [E9]= 2; +P9 [Ep9]= 3; +P10 @Record { } .= 0; +P10 [E10]= 2; +P10 [Ep10]= 3; +P11 @Record { } .= 0; +P11 [E11]= 2; +P11 [Ep11]= 3; +P12 @Record { } .= 0; +P12 [E12]= 2; +P12 [Ep12]= 3; +P13 @Record { } .= 0; +P13 [E13]= 2; +P13 [Ep13]= 3; +P14 @Record { } .= 0; +P14 [E14]= 2; +P14 [Ep14]= 3; +P15 @Record { } .= 0; +P15 [E15]= 2; +P15 [Ep15]= 3; +P16 @Record { } .= 0; +P16 [E16]= 2; +P16 [Ep16]= 3; +P17 @Record { } .= 0; +P17 [E17]= 2; +P17 [Ep17]= 3; +P18 @Record { } .= 0; +P18 [E18]= 2; +P18 [Ep18]= 3; +P19 @Record { } .= 0; +P19 [E19]= 2; +P19 [Ep19]= 3; +P20 @Record { } .= 0; +P20 [E20]= 2; +P20 [Ep20]= 3; +P21 @Record { } .= 0; +P21 [E21]= 2; +P21 [Ep21]= 3; +P22 @Record { } .= 0; +P22 [E22]= 2; +P22 [Ep22]= 3; +P23 @Record { } .= 0; +P23 [E23]= 2; +P23 [Ep23]= 3; +P24 @Record { } .= 0; +P24 [E24]= 2; +P24 [Ep24]= 3; +P25 @Record { } .= 0; +P25 [E25]= 2; +P25 [Ep25]= 3; +P26 @Record { } .= 0; +P26 [E26]= 2; +P26 [Ep26]= 3; +P27 @Record { } .= 0; +P27 [E27]= 2; +P27 [Ep27]= 3; +P28 @Record { } .= 0; +P28 [E28]= 2; +P28 [Ep28]= 3; +P29 @Record { } .= 0; +P29 [E29]= 2; +P29 [Ep29]= 3; +P30 @Record { } .= 0; +P30 [E30]= 2; +P30 [Ep30]= 3; +P31 @Record { } .= 0; +P31 [E31]= 2; +P31 [Ep31]= 3; +P32 @Record { } .= 0; +P32 [E32]= 2; +P32 [Ep32]= 3; +P33 @Record { } .= 0; +P33 [E33]= 2; +P33 [Ep33]= 3; +P34 @Record { } .= 0; +P34 [E34]= 2; +P34 [Ep34]= 3; +P35 @Record { } .= 0; +P35 [E35]= 2; +P35 [Ep35]= 3; +P36 @Record { } .= 0; +P36 [E36]= 2; +P36 [Ep36]= 3; +P37 @Record { } .= 0; +P37 [E37]= 2; +P37 [Ep37]= 3; +P38 @Record { } .= 0; +P38 [E38]= 2; +P38 [Ep38]= 3; +P39 @Record { } .= 0; +P39 [E39]= 2; +P39 [Ep39]= 3; +P40 @Record { } .= 0; +P40 [E40]= 2; +P40 [Ep40]= 3; +P41 @Record { } .= 0; +P41 [E41]= 2; +P41 [Ep41]= 3; +P42 @Record { } .= 0; +P42 [E42]= 2; +P42 [Ep42]= 3; +P43 @Record { } .= 0; +P43 [E43]= 2; +P43 [Ep43]= 3; +P44 @Record { } .= 0; +P44 [E44]= 2; +P44 [Ep44]= 3; +P45 @Record { } .= 0; +P45 [E45]= 2; +P45 [Ep45]= 3; +P46 @Record { } .= 0; +P46 [E46]= 2; +P46 [Ep46]= 3; +P47 @Record { } .= 0; +P47 [E47]= 2; +P47 [Ep47]= 3; +P48 @Record { } .= 0; +P48 [E48]= 2; +P48 [Ep48]= 3; +P49 @Record { } .= 0; +P49 [E49]= 2; +P49 [Ep49]= 3; +P50 @Record { } .= 0; +P50 [E50]= 2; +P50 [Ep50]= 3; +P51 @Record { } .= 0; +P51 [E51]= 2; +P51 [Ep51]= 3; +P52 @Record { } .= 0; +P52 [E52]= 2; +P52 [Ep52]= 3; + +E0 @DSwitcher { trigger: t > 1.5, }; +E1 @DSwitcher { trigger: t > 1.5, }; +E2 @DSwitcher { trigger: t > 1.5, }; +E3 @DSwitcher { trigger: t > 1.5, }; +E4 @DSwitcher { trigger: t > 1.5, }; +E5 @DSwitcher { trigger: t > 1.5, }; +E6 @DSwitcher { trigger: t > 1.5, }; +E7 @DSwitcher { trigger: t > 1.5, }; +E8 @DSwitcher { trigger: t > 1.5, }; +E9 @DSwitcher { trigger: t > 1.5, }; +E10 @DSwitcher { trigger: t > 1.5, }; +E11 @DSwitcher { trigger: t > 1.5, }; +E12 @DSwitcher { trigger: t > 1.5, }; +E13 @DSwitcher { trigger: t > 1.5, }; +E14 @DSwitcher { trigger: t > 1.5, }; +E15 @DSwitcher { trigger: t > 1.5, }; +E16 @DSwitcher { trigger: t > 1.5, }; +E17 @DSwitcher { trigger: t > 1.5, }; +E18 @DSwitcher { trigger: t > 1.5, }; +E19 @DSwitcher { trigger: t > 1.5, }; +E20 @DSwitcher { trigger: t > 1.5, }; +E21 @DSwitcher { trigger: t > 1.5, }; +E22 @DSwitcher { trigger: t > 1.5, }; +E23 @DSwitcher { trigger: t > 1.5, }; +E24 @DSwitcher { trigger: t > 1.5, }; +E25 @DSwitcher { trigger: t > 1.5, }; +E26 @DSwitcher { trigger: t > 1.5, }; +E27 @DSwitcher { trigger: t > 1.5, }; +E28 @DSwitcher { trigger: t > 1.5, }; +E29 @DSwitcher { trigger: t > 1.5, }; +E30 @DSwitcher { trigger: t > 1.5, }; +E31 @DSwitcher { trigger: t > 1.5, }; +E32 @DSwitcher { trigger: t > 1.5, }; +E33 @DSwitcher { trigger: t > 1.5, }; +E34 @DSwitcher { trigger: t > 1.5, }; +E35 @DSwitcher { trigger: t > 1.5, }; +E36 @DSwitcher { trigger: t > 1.5, }; +E37 @DSwitcher { trigger: t > 1.5, }; +E38 @DSwitcher { trigger: t > 1.5, }; +E39 @DSwitcher { trigger: t > 1.5, }; +E40 @DSwitcher { trigger: t > 1.5, }; +E41 @DSwitcher { trigger: t > 1.5, }; +E42 @DSwitcher { trigger: t > 1.5, }; +E43 @DSwitcher { trigger: t > 1.5, }; +E44 @DSwitcher { trigger: t > 1.5, }; +E45 @DSwitcher { trigger: t > 1.5, }; +E46 @DSwitcher { trigger: t > 1.5, }; +E47 @DSwitcher { trigger: t > 1.5, }; +E48 @DSwitcher { trigger: t > 1.5, }; +E49 @DSwitcher { trigger: t > 1.5, }; +E50 @DSwitcher { trigger: t > 1.5, }; +E51 @DSwitcher { trigger: t > 1.5, }; +E52 @DSwitcher { trigger: t > 1.5, }; +Ep0 @DSwitcher { trigger: t > 1.5, }; +Ep1 @DSwitcher { trigger: t > 1.5, }; +Ep2 @DSwitcher { trigger: t > 1.5, }; +Ep3 @DSwitcher { trigger: t > 1.5, }; +Ep4 @DSwitcher { trigger: t > 1.5, }; +Ep5 @DSwitcher { trigger: t > 1.5, }; +Ep6 @DSwitcher { trigger: t > 1.5, }; +Ep7 @DSwitcher { trigger: t > 1.5, }; +Ep8 @DSwitcher { trigger: t > 1.5, }; +Ep9 @DSwitcher { trigger: t > 1.5, }; +Ep10 @DSwitcher { trigger: t > 1.5, }; +Ep11 @DSwitcher { trigger: t > 1.5, }; +Ep12 @DSwitcher { trigger: t > 1.5, }; +Ep13 @DSwitcher { trigger: t > 1.5, }; +Ep14 @DSwitcher { trigger: t > 1.5, }; +Ep15 @DSwitcher { trigger: t > 1.5, }; +Ep16 @DSwitcher { trigger: t > 1.5, }; +Ep17 @DSwitcher { trigger: t > 1.5, }; +Ep18 @DSwitcher { trigger: t > 1.5, }; +Ep19 @DSwitcher { trigger: t > 1.5, }; +Ep20 @DSwitcher { trigger: t > 1.5, }; +Ep21 @DSwitcher { trigger: t > 1.5, }; +Ep22 @DSwitcher { trigger: t > 1.5, }; +Ep23 @DSwitcher { trigger: t > 1.5, }; +Ep24 @DSwitcher { trigger: t > 1.5, }; +Ep25 @DSwitcher { trigger: t > 1.5, }; +Ep26 @DSwitcher { trigger: t > 1.5, }; +Ep27 @DSwitcher { trigger: t > 1.5, }; +Ep28 @DSwitcher { trigger: t > 1.5, }; +Ep29 @DSwitcher { trigger: t > 1.5, }; +Ep30 @DSwitcher { trigger: t > 1.5, }; +Ep31 @DSwitcher { trigger: t > 1.5, }; +Ep32 @DSwitcher { trigger: t > 1.5, }; +Ep33 @DSwitcher { trigger: t > 1.5, }; +Ep34 @DSwitcher { trigger: t > 1.5, }; +Ep35 @DSwitcher { trigger: t > 1.5, }; +Ep36 @DSwitcher { trigger: t > 1.5, }; +Ep37 @DSwitcher { trigger: t > 1.5, }; +Ep38 @DSwitcher { trigger: t > 1.5, }; +Ep39 @DSwitcher { trigger: t > 1.5, }; +Ep40 @DSwitcher { trigger: t > 1.5, }; +Ep41 @DSwitcher { trigger: t > 1.5, }; +Ep42 @DSwitcher { trigger: t > 1.5, }; +Ep43 @DSwitcher { trigger: t > 1.5, }; +Ep44 @DSwitcher { trigger: t > 1.5, }; +Ep45 @DSwitcher { trigger: t > 1.5, }; +Ep46 @DSwitcher { trigger: t > 1.5, }; +Ep47 @DSwitcher { trigger: t > 1.5, }; +Ep48 @DSwitcher { trigger: t > 1.5, }; +Ep49 @DSwitcher { trigger: t > 1.5, }; +Ep50 @DSwitcher { trigger: t > 1.5, }; +Ep51 @DSwitcher { trigger: t > 1.5, }; +Ep52 @DSwitcher { trigger: t > 1.5, }; + diff --git a/latest/cases/01533/l3v2/index.heta b/latest/cases/01533/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01533/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01533/l3v2/json/output.json b/latest/cases/01533/l3v2/json/output.json new file mode 100644 index 000000000..be8876458 --- /dev/null +++ b/latest/cases/01533/l3v2/json/output.json @@ -0,0 +1,1012 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P0", + "assignments": { + "start_": "0", + "E0": "2", + "Ep0": "3" + } + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "0", + "E1": "2", + "Ep1": "3" + } + }, + { + "class": "Record", + "id": "P2", + "assignments": { + "start_": "0", + "E2": "2", + "Ep2": "3" + } + }, + { + "class": "Record", + "id": "P3", + "assignments": { + "start_": "0", + "E3": "2", + "Ep3": "3" + } + }, + { + "class": "Record", + "id": "P4", + "assignments": { + "start_": "0", + "E4": "2", + "Ep4": "3" + } + }, + { + "class": "Record", + "id": "P5", + "assignments": { + "start_": "0", + "E5": "2", + "Ep5": "3" + } + }, + { + "class": "Record", + "id": "P6", + "assignments": { + "start_": "0", + "E6": "2", + "Ep6": "3" + } + }, + { + "class": "Record", + "id": "P7", + "assignments": { + "start_": "0", + "E7": "2", + "Ep7": "3" + } + }, + { + "class": "Record", + "id": "P8", + "assignments": { + "start_": "0", + "E8": "2", + "Ep8": "3" + } + }, + { + "class": "Record", + "id": "P9", + "assignments": { + "start_": "0", + "E9": "2", + "Ep9": "3" + } + }, + { + "class": "Record", + "id": "P10", + "assignments": { + "start_": "0", + "E10": "2", + "Ep10": "3" + } + }, + { + "class": "Record", + "id": "P11", + "assignments": { + "start_": "0", + "E11": "2", + "Ep11": "3" + } + }, + { + "class": "Record", + "id": "P12", + "assignments": { + "start_": "0", + "E12": "2", + "Ep12": "3" + } + }, + { + "class": "Record", + "id": "P13", + "assignments": { + "start_": "0", + "E13": "2", + "Ep13": "3" + } + }, + { + "class": "Record", + "id": "P14", + "assignments": { + "start_": "0", + "E14": "2", + "Ep14": "3" + } + }, + { + "class": "Record", + "id": "P15", + "assignments": { + "start_": "0", + "E15": "2", + "Ep15": "3" + } + }, + { + "class": "Record", + "id": "P16", + "assignments": { + "start_": "0", + "E16": "2", + "Ep16": "3" + } + }, + { + "class": "Record", + "id": "P17", + "assignments": { + "start_": "0", + "E17": "2", + "Ep17": "3" + } + }, + { + "class": "Record", + "id": "P18", + "assignments": { + "start_": "0", + "E18": "2", + "Ep18": "3" + } + }, + { + "class": "Record", + "id": "P19", + "assignments": { + "start_": "0", + "E19": "2", + "Ep19": "3" + } + }, + { + "class": "Record", + "id": "P20", + "assignments": { + "start_": "0", + "E20": "2", + "Ep20": "3" + } + }, + { + "class": "Record", + "id": "P21", + "assignments": { + "start_": "0", + "E21": "2", + "Ep21": "3" + } + }, + { + "class": "Record", + "id": "P22", + "assignments": { + "start_": "0", + "E22": "2", + "Ep22": "3" + } + }, + { + "class": "Record", + "id": "P23", + "assignments": { + "start_": "0", + "E23": "2", + "Ep23": "3" + } + }, + { + "class": "Record", + "id": "P24", + "assignments": { + "start_": "0", + "E24": "2", + "Ep24": "3" + } + }, + { + "class": "Record", + "id": "P25", + "assignments": { + "start_": "0", + "E25": "2", + "Ep25": "3" + } + }, + { + "class": "Record", + "id": "P26", + "assignments": { + "start_": "0", + "E26": "2", + "Ep26": "3" + } + }, + { + "class": "Record", + "id": "P27", + "assignments": { + "start_": "0", + "E27": "2", + "Ep27": "3" + } + }, + { + "class": "Record", + "id": "P28", + "assignments": { + "start_": "0", + "E28": "2", + "Ep28": "3" + } + }, + { + "class": "Record", + "id": "P29", + "assignments": { + "start_": "0", + "E29": "2", + "Ep29": "3" + } + }, + { + "class": "Record", + "id": "P30", + "assignments": { + "start_": "0", + "E30": "2", + "Ep30": "3" + } + }, + { + "class": "Record", + "id": "P31", + "assignments": { + "start_": "0", + "E31": "2", + "Ep31": "3" + } + }, + { + "class": "Record", + "id": "P32", + "assignments": { + "start_": "0", + "E32": "2", + "Ep32": "3" + } + }, + { + "class": "Record", + "id": "P33", + "assignments": { + "start_": "0", + "E33": "2", + "Ep33": "3" + } + }, + { + "class": "Record", + "id": "P34", + "assignments": { + "start_": "0", + "E34": "2", + "Ep34": "3" + } + }, + { + "class": "Record", + "id": "P35", + "assignments": { + "start_": "0", + "E35": "2", + "Ep35": "3" + } + }, + { + "class": "Record", + "id": "P36", + "assignments": { + "start_": "0", + "E36": "2", + "Ep36": "3" + } + }, + { + "class": "Record", + "id": "P37", + "assignments": { + "start_": "0", + "E37": "2", + "Ep37": "3" + } + }, + { + "class": "Record", + "id": "P38", + "assignments": { + "start_": "0", + "E38": "2", + "Ep38": "3" + } + }, + { + "class": "Record", + "id": "P39", + "assignments": { + "start_": "0", + "E39": "2", + "Ep39": "3" + } + }, + { + "class": "Record", + "id": "P40", + "assignments": { + "start_": "0", + "E40": "2", + "Ep40": "3" + } + }, + { + "class": "Record", + "id": "P41", + "assignments": { + "start_": "0", + "E41": "2", + "Ep41": "3" + } + }, + { + "class": "Record", + "id": "P42", + "assignments": { + "start_": "0", + "E42": "2", + "Ep42": "3" + } + }, + { + "class": "Record", + "id": "P43", + "assignments": { + "start_": "0", + "E43": "2", + "Ep43": "3" + } + }, + { + "class": "Record", + "id": "P44", + "assignments": { + "start_": "0", + "E44": "2", + "Ep44": "3" + } + }, + { + "class": "Record", + "id": "P45", + "assignments": { + "start_": "0", + "E45": "2", + "Ep45": "3" + } + }, + { + "class": "Record", + "id": "P46", + "assignments": { + "start_": "0", + "E46": "2", + "Ep46": "3" + } + }, + { + "class": "Record", + "id": "P47", + "assignments": { + "start_": "0", + "E47": "2", + "Ep47": "3" + } + }, + { + "class": "Record", + "id": "P48", + "assignments": { + "start_": "0", + "E48": "2", + "Ep48": "3" + } + }, + { + "class": "Record", + "id": "P49", + "assignments": { + "start_": "0", + "E49": "2", + "Ep49": "3" + } + }, + { + "class": "Record", + "id": "P50", + "assignments": { + "start_": "0", + "E50": "2", + "Ep50": "3" + } + }, + { + "class": "Record", + "id": "P51", + "assignments": { + "start_": "0", + "E51": "2", + "Ep51": "3" + } + }, + { + "class": "Record", + "id": "P52", + "assignments": { + "start_": "0", + "E52": "2", + "Ep52": "3" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 1.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 1.5" + }, + { + "class": "DSwitcher", + "id": "E2", + "trigger": "t > 1.5" + }, + { + "class": "DSwitcher", + "id": "E3", + "trigger": "t > 1.5" + }, + { + "class": "DSwitcher", + "id": "E4", + "trigger": "t > 1.5" + }, + { + "class": "DSwitcher", + "id": "E5", + "trigger": "t > 1.5" + }, + { + "class": 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+ + + + + + + + + time + 1.5 + + + + + + 0.55 + + + + + + 3 + + + + + + + + + + time + 1.5 + + + + + + 0.55 + + + + + + 3 + + + + + + + + + + time + 1.5 + + + + + + 0.55 + + + + + + 3 + + + + + + + + + + time + 1.5 + + + + + + 0.55 + + + + + + 3 + + + + + + + + + + time + 1.5 + + + + + + 0.55 + + + + + + 3 + + + + + + + + + + time + 1.5 + + + + + + 0.55 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01533/output.heta b/latest/cases/01533/output.heta new file mode 100644 index 000000000..b4bd45abe --- /dev/null +++ b/latest/cases/01533/output.heta @@ -0,0 +1,458 @@ +/* +category: Test +synopsis: Uncommon MathML used in event priorities. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various unusual mathematical constructs in event priorities, essentially comparing them to 0.55 to see which is greater. + +The model contains: +* 53 parameters (P0, P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40, P41, P42, P43, P44, P45, P46, P47, P48, P49, P50, P51, P52) + +There are 106 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 1.5$ | $exponentiale$ | $P0 = 2$ | +| E1 | $time > 1.5$ | $exp(exponentiale)$ | $P1 = 2$ | +| E2 | $time > 1.5$ | $abs(-1)$ | $P2 = 2$ | +| E3 | $time > 1.5$ | $abs(1)$ | $P3 = 2$ | +| E4 | $time > 1.5$ | $acos(-1)$ | $P4 = 2$ | +| E5 | $time > 1.5$ | $acos(0.5)$ | $P5 = 2$ | +| E6 | $time > 1.5$ | $asin(1)$ | $P6 = 2$ | +| E7 | $time > 1.5$ | $asin(-0.5)$ | $P7 = 2$ | +| E8 | $time > 1.5$ | $atan(2.8)$ | $P8 = 2$ | +| E9 | $time > 1.5$ | $atan(-7.09)$ | $P9 = 2$ | +| E10 | $time > 1.5$ | $ceil(0.5)$ | $P10 = 2$ | +| E11 | $time > 1.5$ | $ceil(3.55)$ | $P11 = 2$ | +| E12 | $time > 1.5$ | $ceil(-4.6)$ | $P12 = 2$ | +| E13 | $time > 1.5$ | $cos(9.1)$ | $P13 = 2$ | +| E14 | $time > 1.5$ | $cos(-0.22)$ | $P14 = 2$ | +| E15 | $time > 1.5$ | $exp(0)$ | $P15 = 2$ | +| E16 | $time > 1.5$ | $exp(1)$ | $P16 = 2$ | +| E17 | $time > 1.5$ | $exp(0.77)$ | $P17 = 2$ | +| E18 | $time > 1.5$ | $floor(-4.6)$ | $P18 = 2$ | +| E19 | $time > 1.5$ | $floor(9.1)$ | $P19 = 2$ | +| E20 | $time > 1.5$ | $ln(0.2)$ | $P20 = 2$ | +| E21 | $time > 1.5$ | $ln(1)$ | $P21 = 2$ | +| E22 | $time > 1.5$ | $log10(0.2)$ | $P22 = 2$ | +| E23 | $time > 1.5$ | $log10(1)$ | $P23 = 2$ | +| E24 | $time > 1.5$ | $1^2$ | $P24 = 2$ | +| E25 | $time > 1.5$ | $2^2$ | $P25 = 2$ | +| E26 | $time > 1.5$ | $1.4^5.1$ | $P26 = 2$ | +| E27 | $time > 1.5$ | $4^2$ | $P27 = 2$ | +| E28 | $time > 1.5$ | $3.1^2$ | $P28 = 2$ | +| E29 | $time > 1.5$ | $sqrt(4)$ | $P29 = 2$ | +| E30 | $time > 1.5$ | $sqrt(7.4)$ | $P30 = 2$ | +| E31 | $time > 1.5$ | $sin(2.1)$ | $P31 = 2$ | +| E32 | $time > 1.5$ | $sin(0)$ | $P32 = 2$ | +| E33 | $time > 1.5$ | $sin(-5.9)$ | $P33 = 2$ | +| E34 | $time > 1.5$ | $tan(0)$ | $P34 = 2$ | +| E35 | $time > 1.5$ | $tan(1.11)$ | $P35 = 2$ | +| E36 | $time > 1.5$ | $tan(-6)$ | $P36 = 2$ | +| E37 | $time > 1.5$ | $sec(0.5)$ | $P37 = 2$ | +| E38 | $time > 1.5$ | $csc(4.5)$ | $P38 = 2$ | +| E39 | $time > 1.5$ | $cot(0.2)$ | $P39 = 2$ | +| E40 | $time > 1.5$ | $sinh(0.3)$ | $P40 = 2$ | +| E41 | $time > 1.5$ | $cosh(1.7)$ | $P41 = 2$ | +| E42 | $time > 1.5$ | $arcsec(2.3)$ | $P42 = 2$ | +| E43 | $time > 1.5$ | $arccsc(1.1)$ | $P43 = 2$ | +| E44 | $time > 1.5$ | $arccot(-0.1)$ | $P44 = 2$ | +| E45 | $time > 1.5$ | $arcsinh(99)$ | $P45 = 2$ | +| E46 | $time > 1.5$ | $arccosh(1.34)$ | $P46 = 2$ | +| E47 | $time > 1.5$ | $arctanh(-0.7)$ | $P47 = 2$ | +| E48 | $time > 1.5$ | $arcsech(0.42)$ | $P48 = 2$ | +| E49 | $time > 1.5$ | $arccsch(0.01)$ | $P49 = 2$ | +| E50 | $time > 1.5$ | $arccoth(8.2)$ | $P50 = 2$ | +| E51 | $time > 1.5$ | $times()$ | $P51 = 2$ | +| E52 | $time > 1.5$ | $plus()$ | $P52 = 2$ | +| Ep0 | $time > 1.5$ | $0.55$ | $P0 = 3$ | +| Ep1 | $time > 1.5$ | $0.55$ | $P1 = 3$ | +| Ep2 | $time > 1.5$ | $0.55$ | $P2 = 3$ | +| Ep3 | $time > 1.5$ | $0.55$ | $P3 = 3$ | +| Ep4 | $time > 1.5$ | $0.55$ | $P4 = 3$ | +| Ep5 | $time > 1.5$ | $0.55$ | $P5 = 3$ | +| Ep6 | $time > 1.5$ | $0.55$ | $P6 = 3$ | +| Ep7 | $time > 1.5$ | $0.55$ | $P7 = 3$ | +| Ep8 | $time > 1.5$ | $0.55$ | $P8 = 3$ | +| Ep9 | $time > 1.5$ | $0.55$ | $P9 = 3$ | +| Ep10 | $time > 1.5$ | $0.55$ | $P10 = 3$ | +| Ep11 | $time > 1.5$ | $0.55$ | $P11 = 3$ | +| Ep12 | $time > 1.5$ | $0.55$ | $P12 = 3$ | +| Ep13 | $time > 1.5$ | $0.55$ | $P13 = 3$ | +| Ep14 | $time > 1.5$ | $0.55$ | $P14 = 3$ | +| Ep15 | $time > 1.5$ | $0.55$ | $P15 = 3$ | +| Ep16 | $time > 1.5$ | $0.55$ | $P16 = 3$ | +| Ep17 | $time > 1.5$ | $0.55$ | $P17 = 3$ | +| Ep18 | $time > 1.5$ | $0.55$ | $P18 = 3$ | +| Ep19 | $time > 1.5$ | $0.55$ | $P19 = 3$ | +| Ep20 | $time > 1.5$ | $0.55$ | $P20 = 3$ | +| Ep21 | $time > 1.5$ | $0.55$ | $P21 = 3$ | +| Ep22 | $time > 1.5$ | $0.55$ | $P22 = 3$ | +| Ep23 | $time > 1.5$ | $0.55$ | $P23 = 3$ | +| Ep24 | $time > 1.5$ | $0.55$ | $P24 = 3$ | +| Ep25 | $time > 1.5$ | $0.55$ | $P25 = 3$ | +| Ep26 | $time > 1.5$ | $0.55$ | $P26 = 3$ | +| Ep27 | $time > 1.5$ | $0.55$ | $P27 = 3$ | +| Ep28 | $time > 1.5$ | $0.55$ | $P28 = 3$ | +| Ep29 | $time > 1.5$ | $0.55$ | $P29 = 3$ | +| Ep30 | $time > 1.5$ | $0.55$ | $P30 = 3$ | +| Ep31 | $time > 1.5$ | $0.55$ | $P31 = 3$ | +| Ep32 | $time > 1.5$ | $0.55$ | $P32 = 3$ | +| Ep33 | $time > 1.5$ | $0.55$ | $P33 = 3$ | +| Ep34 | $time > 1.5$ | $0.55$ | $P34 = 3$ | +| Ep35 | $time > 1.5$ | $0.55$ | $P35 = 3$ | +| Ep36 | $time > 1.5$ | $0.55$ | $P36 = 3$ | +| Ep37 | $time > 1.5$ | $0.55$ | $P37 = 3$ | +| Ep38 | $time > 1.5$ | $0.55$ | $P38 = 3$ | +| Ep39 | $time > 1.5$ | $0.55$ | $P39 = 3$ | +| Ep40 | $time > 1.5$ | $0.55$ | $P40 = 3$ | +| Ep41 | $time > 1.5$ | $0.55$ | $P41 = 3$ | +| Ep42 | $time > 1.5$ | $0.55$ | $P42 = 3$ | +| Ep43 | $time > 1.5$ | $0.55$ | $P43 = 3$ | +| Ep44 | $time > 1.5$ | $0.55$ | $P44 = 3$ | +| Ep45 | $time > 1.5$ | $0.55$ | $P45 = 3$ | +| Ep46 | $time > 1.5$ | $0.55$ | $P46 = 3$ | +| Ep47 | $time > 1.5$ | $0.55$ | $P47 = 3$ | +| Ep48 | $time > 1.5$ | $0.55$ | $P48 = 3$ | +| Ep49 | $time > 1.5$ | $0.55$ | $P49 = 3$ | +| Ep50 | $time > 1.5$ | $0.55$ | $P50 = 3$ | +| Ep51 | $time > 1.5$ | $0.55$ | $P51 = 3$ | +| Ep52 | $time > 1.5$ | $0.55$ | $P52 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P0 | $0$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable | +| Initial value of parameter P3 | $0$ | variable | +| Initial value of parameter P4 | $0$ | variable | +| Initial value of parameter P5 | $0$ | variable | +| Initial value of parameter P6 | $0$ | variable | +| Initial value of parameter P7 | $0$ | variable | +| Initial value of parameter P8 | $0$ | variable | +| Initial value of parameter P9 | $0$ | variable | +| Initial value of parameter P10 | $0$ | variable | +| Initial value of parameter P11 | $0$ | variable | +| Initial value of parameter P12 | $0$ | variable | +| Initial value of parameter P13 | $0$ | variable | +| Initial value of parameter P14 | $0$ | variable | +| Initial value of parameter P15 | $0$ | variable | +| Initial value of parameter P16 | $0$ | variable | +| Initial value of parameter P17 | $0$ | variable | +| Initial value of parameter P18 | $0$ | variable | +| Initial value of parameter P19 | $0$ | variable | +| Initial value of parameter P20 | $0$ | variable | +| Initial value of parameter P21 | $0$ | variable | +| Initial value of parameter P22 | $0$ | variable | +| Initial value of parameter P23 | $0$ | variable | +| Initial value of parameter P24 | $0$ | variable | +| Initial value of parameter P25 | $0$ | variable | +| Initial value of parameter P26 | $0$ | variable | +| Initial value of parameter P27 | $0$ | variable | +| Initial value of parameter P28 | $0$ | variable | +| Initial value of parameter P29 | $0$ | variable | +| Initial value of parameter P30 | $0$ | variable | +| Initial value of parameter P31 | $0$ | variable | +| Initial value of parameter P32 | $0$ | variable | +| Initial value of parameter P33 | $0$ | variable | +| Initial value of parameter P34 | $0$ | variable | +| Initial value of parameter P35 | $0$ | variable | +| Initial value of parameter P36 | $0$ | variable | +| Initial value of parameter P37 | $0$ | variable | +| Initial value of parameter P38 | $0$ | variable | +| Initial value of parameter P39 | $0$ | variable | +| Initial value of parameter P40 | $0$ | variable | +| Initial value of parameter P41 | $0$ | variable | +| Initial value of parameter P42 | $0$ | variable | +| Initial value of parameter P43 | $0$ | variable | +| Initial value of parameter P44 | $0$ | variable | +| Initial value of parameter P45 | $0$ | variable | +| Initial value of parameter P46 | $0$ | variable | +| Initial value of parameter P47 | $0$ | variable | +| Initial value of parameter P48 | $0$ | variable | +| Initial value of parameter P49 | $0$ | variable | +| Initial value of parameter P50 | $0$ | variable | +| Initial value of parameter P51 | $0$ | variable | +| Initial value of parameter P52 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P0 @Record { } .= 0; +P0 [E0]= 2; +P0 [Ep0]= 3; +P1 @Record { } .= 0; +P1 [E1]= 2; +P1 [Ep1]= 3; +P2 @Record { } .= 0; +P2 [E2]= 2; +P2 [Ep2]= 3; +P3 @Record { } .= 0; +P3 [E3]= 2; +P3 [Ep3]= 3; +P4 @Record { } .= 0; +P4 [E4]= 2; +P4 [Ep4]= 3; +P5 @Record { } .= 0; +P5 [E5]= 2; +P5 [Ep5]= 3; +P6 @Record { } .= 0; +P6 [E6]= 2; +P6 [Ep6]= 3; +P7 @Record { } .= 0; +P7 [E7]= 2; +P7 [Ep7]= 3; +P8 @Record { } .= 0; +P8 [E8]= 2; +P8 [Ep8]= 3; +P9 @Record { } .= 0; +P9 [E9]= 2; +P9 [Ep9]= 3; +P10 @Record { } .= 0; +P10 [E10]= 2; +P10 [Ep10]= 3; +P11 @Record { } .= 0; +P11 [E11]= 2; +P11 [Ep11]= 3; +P12 @Record { } .= 0; +P12 [E12]= 2; +P12 [Ep12]= 3; +P13 @Record { } .= 0; +P13 [E13]= 2; +P13 [Ep13]= 3; +P14 @Record { } .= 0; +P14 [E14]= 2; +P14 [Ep14]= 3; +P15 @Record { } .= 0; +P15 [E15]= 2; +P15 [Ep15]= 3; +P16 @Record { } .= 0; +P16 [E16]= 2; +P16 [Ep16]= 3; +P17 @Record { } .= 0; +P17 [E17]= 2; +P17 [Ep17]= 3; +P18 @Record { } .= 0; +P18 [E18]= 2; +P18 [Ep18]= 3; +P19 @Record { } .= 0; +P19 [E19]= 2; +P19 [Ep19]= 3; +P20 @Record { } .= 0; +P20 [E20]= 2; +P20 [Ep20]= 3; +P21 @Record { } .= 0; +P21 [E21]= 2; +P21 [Ep21]= 3; +P22 @Record { } .= 0; +P22 [E22]= 2; +P22 [Ep22]= 3; +P23 @Record { } .= 0; +P23 [E23]= 2; +P23 [Ep23]= 3; +P24 @Record { } .= 0; +P24 [E24]= 2; +P24 [Ep24]= 3; +P25 @Record { } .= 0; +P25 [E25]= 2; +P25 [Ep25]= 3; +P26 @Record { } .= 0; +P26 [E26]= 2; +P26 [Ep26]= 3; +P27 @Record { } .= 0; +P27 [E27]= 2; +P27 [Ep27]= 3; +P28 @Record { } .= 0; +P28 [E28]= 2; +P28 [Ep28]= 3; +P29 @Record { } .= 0; +P29 [E29]= 2; +P29 [Ep29]= 3; +P30 @Record { } .= 0; +P30 [E30]= 2; +P30 [Ep30]= 3; +P31 @Record { } .= 0; +P31 [E31]= 2; +P31 [Ep31]= 3; +P32 @Record { } .= 0; +P32 [E32]= 2; +P32 [Ep32]= 3; +P33 @Record { } .= 0; +P33 [E33]= 2; +P33 [Ep33]= 3; +P34 @Record { } .= 0; +P34 [E34]= 2; +P34 [Ep34]= 3; +P35 @Record { } .= 0; +P35 [E35]= 2; +P35 [Ep35]= 3; +P36 @Record { } .= 0; +P36 [E36]= 2; +P36 [Ep36]= 3; +P37 @Record { } .= 0; +P37 [E37]= 2; +P37 [Ep37]= 3; +P38 @Record { } .= 0; +P38 [E38]= 2; +P38 [Ep38]= 3; +P39 @Record { } .= 0; +P39 [E39]= 2; +P39 [Ep39]= 3; +P40 @Record { } .= 0; +P40 [E40]= 2; +P40 [Ep40]= 3; +P41 @Record { } .= 0; +P41 [E41]= 2; +P41 [Ep41]= 3; +P42 @Record { } .= 0; +P42 [E42]= 2; +P42 [Ep42]= 3; +P43 @Record { } .= 0; +P43 [E43]= 2; +P43 [Ep43]= 3; +P44 @Record { } .= 0; +P44 [E44]= 2; +P44 [Ep44]= 3; +P45 @Record { } .= 0; +P45 [E45]= 2; +P45 [Ep45]= 3; +P46 @Record { } .= 0; +P46 [E46]= 2; +P46 [Ep46]= 3; +P47 @Record { } .= 0; +P47 [E47]= 2; +P47 [Ep47]= 3; +P48 @Record { } .= 0; +P48 [E48]= 2; +P48 [Ep48]= 3; +P49 @Record { } .= 0; +P49 [E49]= 2; +P49 [Ep49]= 3; +P50 @Record { } .= 0; +P50 [E50]= 2; +P50 [Ep50]= 3; +P51 @Record { } .= 0; +P51 [E51]= 2; +P51 [Ep51]= 3; +P52 @Record { } .= 0; +P52 [E52]= 2; +P52 [Ep52]= 3; + +E0 @DSwitcher { trigger: t > 1.5, }; +E1 @DSwitcher { trigger: t > 1.5, }; +E2 @DSwitcher { trigger: t > 1.5, }; +E3 @DSwitcher { trigger: t > 1.5, }; +E4 @DSwitcher { trigger: t > 1.5, }; +E5 @DSwitcher { trigger: t > 1.5, }; +E6 @DSwitcher { trigger: t > 1.5, }; +E7 @DSwitcher { trigger: t > 1.5, }; +E8 @DSwitcher { trigger: t > 1.5, }; +E9 @DSwitcher { trigger: t > 1.5, }; +E10 @DSwitcher { trigger: t > 1.5, }; +E11 @DSwitcher { trigger: t > 1.5, }; +E12 @DSwitcher { trigger: t > 1.5, }; +E13 @DSwitcher { trigger: t > 1.5, }; +E14 @DSwitcher { trigger: t > 1.5, }; +E15 @DSwitcher { trigger: t > 1.5, }; +E16 @DSwitcher { trigger: t > 1.5, }; +E17 @DSwitcher { trigger: t > 1.5, }; +E18 @DSwitcher { trigger: t > 1.5, }; +E19 @DSwitcher { trigger: t > 1.5, }; +E20 @DSwitcher { trigger: t > 1.5, }; +E21 @DSwitcher { trigger: t > 1.5, }; +E22 @DSwitcher { trigger: t > 1.5, }; +E23 @DSwitcher { trigger: t > 1.5, }; +E24 @DSwitcher { trigger: t > 1.5, }; +E25 @DSwitcher { trigger: t > 1.5, }; +E26 @DSwitcher { trigger: t > 1.5, }; +E27 @DSwitcher { trigger: t > 1.5, }; +E28 @DSwitcher { trigger: t > 1.5, }; +E29 @DSwitcher { trigger: t > 1.5, }; +E30 @DSwitcher { trigger: t > 1.5, }; +E31 @DSwitcher { trigger: t > 1.5, }; +E32 @DSwitcher { trigger: t > 1.5, }; +E33 @DSwitcher { trigger: t > 1.5, }; +E34 @DSwitcher { trigger: t > 1.5, }; +E35 @DSwitcher { trigger: t > 1.5, }; +E36 @DSwitcher { trigger: t > 1.5, }; +E37 @DSwitcher { trigger: t > 1.5, }; +E38 @DSwitcher { trigger: t > 1.5, }; +E39 @DSwitcher { trigger: t > 1.5, }; +E40 @DSwitcher { trigger: t > 1.5, }; +E41 @DSwitcher { trigger: t > 1.5, }; +E42 @DSwitcher { trigger: t > 1.5, }; +E43 @DSwitcher { trigger: t > 1.5, }; +E44 @DSwitcher { trigger: t > 1.5, }; +E45 @DSwitcher { trigger: t > 1.5, }; +E46 @DSwitcher { trigger: t > 1.5, }; +E47 @DSwitcher { trigger: t > 1.5, }; +E48 @DSwitcher { trigger: t > 1.5, }; +E49 @DSwitcher { trigger: t > 1.5, }; +E50 @DSwitcher { trigger: t > 1.5, }; +E51 @DSwitcher { trigger: t > 1.5, }; +E52 @DSwitcher { trigger: t > 1.5, }; +Ep0 @DSwitcher { trigger: t > 1.5, }; +Ep1 @DSwitcher { trigger: t > 1.5, }; +Ep2 @DSwitcher { trigger: t > 1.5, }; +Ep3 @DSwitcher { trigger: t > 1.5, }; +Ep4 @DSwitcher { trigger: t > 1.5, }; +Ep5 @DSwitcher { trigger: t > 1.5, }; +Ep6 @DSwitcher { trigger: t > 1.5, }; +Ep7 @DSwitcher { trigger: t > 1.5, }; +Ep8 @DSwitcher { trigger: t > 1.5, }; +Ep9 @DSwitcher { trigger: t > 1.5, }; +Ep10 @DSwitcher { trigger: t > 1.5, }; +Ep11 @DSwitcher { trigger: t > 1.5, }; +Ep12 @DSwitcher { trigger: t > 1.5, }; +Ep13 @DSwitcher { trigger: t > 1.5, }; +Ep14 @DSwitcher { trigger: t > 1.5, }; +Ep15 @DSwitcher { trigger: t > 1.5, }; +Ep16 @DSwitcher { trigger: t > 1.5, }; +Ep17 @DSwitcher { trigger: t > 1.5, }; +Ep18 @DSwitcher { trigger: t > 1.5, }; +Ep19 @DSwitcher { trigger: t > 1.5, }; +Ep20 @DSwitcher { trigger: t > 1.5, }; +Ep21 @DSwitcher { trigger: t > 1.5, }; +Ep22 @DSwitcher { trigger: t > 1.5, }; +Ep23 @DSwitcher { trigger: t > 1.5, }; +Ep24 @DSwitcher { trigger: t > 1.5, }; +Ep25 @DSwitcher { trigger: t > 1.5, }; +Ep26 @DSwitcher { trigger: t > 1.5, }; +Ep27 @DSwitcher { trigger: t > 1.5, }; +Ep28 @DSwitcher { trigger: t > 1.5, }; +Ep29 @DSwitcher { trigger: t > 1.5, }; +Ep30 @DSwitcher { trigger: t > 1.5, }; +Ep31 @DSwitcher { trigger: t > 1.5, }; +Ep32 @DSwitcher { trigger: t > 1.5, }; +Ep33 @DSwitcher { trigger: t > 1.5, }; +Ep34 @DSwitcher { trigger: t > 1.5, }; +Ep35 @DSwitcher { trigger: t > 1.5, }; +Ep36 @DSwitcher { trigger: t > 1.5, }; +Ep37 @DSwitcher { trigger: t > 1.5, }; +Ep38 @DSwitcher { trigger: t > 1.5, }; +Ep39 @DSwitcher { trigger: t > 1.5, }; +Ep40 @DSwitcher { trigger: t > 1.5, }; +Ep41 @DSwitcher { trigger: t > 1.5, }; +Ep42 @DSwitcher { trigger: t > 1.5, }; +Ep43 @DSwitcher { trigger: t > 1.5, }; +Ep44 @DSwitcher { trigger: t > 1.5, }; +Ep45 @DSwitcher { trigger: t > 1.5, }; +Ep46 @DSwitcher { trigger: t > 1.5, }; +Ep47 @DSwitcher { trigger: t > 1.5, }; +Ep48 @DSwitcher { trigger: t > 1.5, }; +Ep49 @DSwitcher { trigger: t > 1.5, }; +Ep50 @DSwitcher { trigger: t > 1.5, }; +Ep51 @DSwitcher { trigger: t > 1.5, }; +Ep52 @DSwitcher { trigger: t > 1.5, }; + diff --git a/latest/cases/01533/synopsis.txt b/latest/cases/01533/synopsis.txt new file mode 100644 index 000000000..0fc5c8238 --- /dev/null +++ b/latest/cases/01533/synopsis.txt @@ -0,0 +1,185 @@ + +category: Test +synopsis: Uncommon MathML used in event priorities. +componentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model tests the various unusual mathematical constructs in event priorities, essentially comparing them to 0.55 to see which is greater. + +The model contains: +* 53 parameters (P0, P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40, P41, P42, P43, P44, P45, P46, P47, P48, P49, P50, P51, P52) + +There are 106 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 1.5$ | $exponentiale$ | $P0 = 2$ | +| E1 | $time > 1.5$ | $exp(exponentiale)$ | $P1 = 2$ | +| E2 | $time > 1.5$ | $abs(-1)$ | $P2 = 2$ | +| E3 | $time > 1.5$ | $abs(1)$ | $P3 = 2$ | +| E4 | $time > 1.5$ | $acos(-1)$ | $P4 = 2$ | +| E5 | $time > 1.5$ | $acos(0.5)$ | $P5 = 2$ | +| E6 | $time > 1.5$ | $asin(1)$ | $P6 = 2$ | +| E7 | $time > 1.5$ | $asin(-0.5)$ | $P7 = 2$ | +| E8 | $time > 1.5$ | $atan(2.8)$ | $P8 = 2$ | +| E9 | $time > 1.5$ | $atan(-7.09)$ | $P9 = 2$ | +| E10 | $time > 1.5$ | $ceil(0.5)$ | $P10 = 2$ | +| E11 | $time > 1.5$ | $ceil(3.55)$ | $P11 = 2$ | +| E12 | $time > 1.5$ | $ceil(-4.6)$ | $P12 = 2$ | +| E13 | $time > 1.5$ | $cos(9.1)$ | $P13 = 2$ | +| E14 | $time > 1.5$ | $cos(-0.22)$ | $P14 = 2$ | +| E15 | $time > 1.5$ | $exp(0)$ | $P15 = 2$ | +| E16 | $time > 1.5$ | $exp(1)$ | $P16 = 2$ | +| E17 | $time > 1.5$ | $exp(0.77)$ | $P17 = 2$ | +| E18 | $time > 1.5$ | $floor(-4.6)$ | $P18 = 2$ | +| E19 | $time > 1.5$ | $floor(9.1)$ | $P19 = 2$ | +| E20 | $time > 1.5$ | $ln(0.2)$ | $P20 = 2$ | +| E21 | $time > 1.5$ | $ln(1)$ | $P21 = 2$ | +| E22 | $time > 1.5$ | $log10(0.2)$ | $P22 = 2$ | +| E23 | $time > 1.5$ | $log10(1)$ | $P23 = 2$ | +| E24 | $time > 1.5$ | $1^2$ | $P24 = 2$ | +| E25 | $time > 1.5$ | $2^2$ | $P25 = 2$ | +| E26 | $time > 1.5$ | $1.4^5.1$ | $P26 = 2$ | +| E27 | $time > 1.5$ | $4^2$ | $P27 = 2$ | +| E28 | $time > 1.5$ | $3.1^2$ | $P28 = 2$ | +| E29 | $time > 1.5$ | $sqrt(4)$ | $P29 = 2$ | +| E30 | $time > 1.5$ | $sqrt(7.4)$ | $P30 = 2$ | +| E31 | $time > 1.5$ | $sin(2.1)$ | $P31 = 2$ | +| E32 | $time > 1.5$ | $sin(0)$ | $P32 = 2$ | +| E33 | $time > 1.5$ | $sin(-5.9)$ | $P33 = 2$ | +| E34 | $time > 1.5$ | $tan(0)$ | $P34 = 2$ | +| E35 | $time > 1.5$ | $tan(1.11)$ | $P35 = 2$ | +| E36 | $time > 1.5$ | $tan(-6)$ | $P36 = 2$ | +| E37 | $time > 1.5$ | $sec(0.5)$ | $P37 = 2$ | +| E38 | $time > 1.5$ | $csc(4.5)$ | $P38 = 2$ | +| E39 | $time > 1.5$ | $cot(0.2)$ | $P39 = 2$ | +| E40 | $time > 1.5$ | $sinh(0.3)$ | $P40 = 2$ | +| E41 | $time > 1.5$ | $cosh(1.7)$ | $P41 = 2$ | +| E42 | $time > 1.5$ | $arcsec(2.3)$ | $P42 = 2$ | +| E43 | $time > 1.5$ | $arccsc(1.1)$ | $P43 = 2$ | +| E44 | $time > 1.5$ | $arccot(-0.1)$ | $P44 = 2$ | +| E45 | $time > 1.5$ | $arcsinh(99)$ | $P45 = 2$ | +| E46 | $time > 1.5$ | $arccosh(1.34)$ | $P46 = 2$ | +| E47 | $time > 1.5$ | $arctanh(-0.7)$ | $P47 = 2$ | +| E48 | $time > 1.5$ | $arcsech(0.42)$ | $P48 = 2$ | +| E49 | $time > 1.5$ | $arccsch(0.01)$ | $P49 = 2$ | +| E50 | $time > 1.5$ | $arccoth(8.2)$ | $P50 = 2$ | +| E51 | $time > 1.5$ | $times()$ | $P51 = 2$ | +| E52 | $time > 1.5$ | $plus()$ | $P52 = 2$ | +| Ep0 | $time > 1.5$ | $0.55$ | $P0 = 3$ | +| Ep1 | $time > 1.5$ | $0.55$ | $P1 = 3$ | +| Ep2 | $time > 1.5$ | $0.55$ | $P2 = 3$ | +| Ep3 | $time > 1.5$ | $0.55$ | $P3 = 3$ | +| Ep4 | $time > 1.5$ | $0.55$ | $P4 = 3$ | +| Ep5 | $time > 1.5$ | $0.55$ | $P5 = 3$ | +| Ep6 | $time > 1.5$ | $0.55$ | $P6 = 3$ | +| Ep7 | $time > 1.5$ | $0.55$ | $P7 = 3$ | +| Ep8 | $time > 1.5$ | $0.55$ | $P8 = 3$ | +| Ep9 | $time > 1.5$ | $0.55$ | $P9 = 3$ | +| Ep10 | $time > 1.5$ | $0.55$ | $P10 = 3$ | +| Ep11 | $time > 1.5$ | $0.55$ | $P11 = 3$ | +| Ep12 | $time > 1.5$ | $0.55$ | $P12 = 3$ | +| Ep13 | $time > 1.5$ | $0.55$ | $P13 = 3$ | +| Ep14 | $time > 1.5$ | $0.55$ | $P14 = 3$ | +| Ep15 | $time > 1.5$ | $0.55$ | $P15 = 3$ | +| Ep16 | $time > 1.5$ | $0.55$ | $P16 = 3$ | +| Ep17 | $time > 1.5$ | $0.55$ | $P17 = 3$ | +| Ep18 | $time > 1.5$ | $0.55$ | $P18 = 3$ | +| Ep19 | $time > 1.5$ | $0.55$ | $P19 = 3$ | +| Ep20 | $time > 1.5$ | $0.55$ | $P20 = 3$ | +| Ep21 | $time > 1.5$ | $0.55$ | $P21 = 3$ | +| Ep22 | $time > 1.5$ | $0.55$ | $P22 = 3$ | +| Ep23 | $time > 1.5$ | $0.55$ | $P23 = 3$ | +| Ep24 | $time > 1.5$ | $0.55$ | $P24 = 3$ | +| Ep25 | $time > 1.5$ | $0.55$ | $P25 = 3$ | +| Ep26 | $time > 1.5$ | $0.55$ | $P26 = 3$ | +| Ep27 | $time > 1.5$ | $0.55$ | $P27 = 3$ | +| Ep28 | $time > 1.5$ | $0.55$ | $P28 = 3$ | +| Ep29 | $time > 1.5$ | $0.55$ | $P29 = 3$ | +| Ep30 | $time > 1.5$ | $0.55$ | $P30 = 3$ | +| Ep31 | $time > 1.5$ | $0.55$ | $P31 = 3$ | +| Ep32 | $time > 1.5$ | $0.55$ | $P32 = 3$ | +| Ep33 | $time > 1.5$ | $0.55$ | $P33 = 3$ | +| Ep34 | $time > 1.5$ | $0.55$ | $P34 = 3$ | +| Ep35 | $time > 1.5$ | $0.55$ | $P35 = 3$ | +| Ep36 | $time > 1.5$ | $0.55$ | $P36 = 3$ | +| Ep37 | $time > 1.5$ | $0.55$ | $P37 = 3$ | +| Ep38 | $time > 1.5$ | $0.55$ | $P38 = 3$ | +| Ep39 | $time > 1.5$ | $0.55$ | $P39 = 3$ | +| Ep40 | $time > 1.5$ | $0.55$ | $P40 = 3$ | +| Ep41 | $time > 1.5$ | $0.55$ | $P41 = 3$ | +| Ep42 | $time > 1.5$ | $0.55$ | $P42 = 3$ | +| Ep43 | $time > 1.5$ | $0.55$ | $P43 = 3$ | +| Ep44 | $time > 1.5$ | $0.55$ | $P44 = 3$ | +| Ep45 | $time > 1.5$ | $0.55$ | $P45 = 3$ | +| Ep46 | $time > 1.5$ | $0.55$ | $P46 = 3$ | +| Ep47 | $time > 1.5$ | $0.55$ | $P47 = 3$ | +| Ep48 | $time > 1.5$ | $0.55$ | $P48 = 3$ | +| Ep49 | $time > 1.5$ | $0.55$ | $P49 = 3$ | +| Ep50 | $time > 1.5$ | $0.55$ | $P50 = 3$ | +| Ep51 | $time > 1.5$ | $0.55$ | $P51 = 3$ | +| Ep52 | $time > 1.5$ | $0.55$ | $P52 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P0 | $0$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable | +| Initial value of parameter P3 | $0$ | variable | +| Initial value of parameter P4 | $0$ | variable | +| Initial value of parameter P5 | $0$ | variable | +| Initial value of parameter P6 | $0$ | variable | +| Initial value of parameter P7 | $0$ | variable | +| Initial value of parameter P8 | $0$ | variable | +| Initial value of parameter P9 | $0$ | variable | +| Initial value of parameter P10 | $0$ | variable | +| Initial value of parameter P11 | $0$ | variable | +| Initial value of parameter P12 | $0$ | variable | +| Initial value of parameter P13 | $0$ | variable | +| Initial value of parameter P14 | $0$ | variable | +| Initial value of parameter P15 | $0$ | variable | +| Initial value of parameter P16 | $0$ | variable | +| Initial value of parameter P17 | $0$ | variable | +| Initial value of parameter P18 | $0$ | variable | +| Initial value of parameter P19 | $0$ | variable | +| Initial value of parameter P20 | $0$ | variable | +| Initial value of parameter P21 | $0$ | variable | +| Initial value of parameter P22 | $0$ | variable | +| Initial value of parameter P23 | $0$ | variable | +| Initial value of parameter P24 | $0$ | variable | +| Initial value of parameter P25 | $0$ | variable | +| Initial value of parameter P26 | $0$ | variable | +| Initial value of parameter P27 | $0$ | variable | +| Initial value of parameter P28 | $0$ | variable | +| Initial value of parameter P29 | $0$ | variable | +| Initial value of parameter P30 | $0$ | variable | +| Initial value of parameter P31 | $0$ | variable | +| Initial value of parameter P32 | $0$ | variable | +| Initial value of parameter P33 | $0$ | variable | +| Initial value of parameter P34 | $0$ | variable | +| Initial value of parameter P35 | $0$ | variable | +| Initial value of parameter P36 | $0$ | variable | +| Initial value of parameter P37 | $0$ | variable | +| Initial value of parameter P38 | $0$ | variable | +| Initial value of parameter P39 | $0$ | variable | +| Initial value of parameter P40 | $0$ | variable | +| Initial value of parameter P41 | $0$ | variable | +| Initial value of parameter P42 | $0$ | variable | +| Initial value of parameter P43 | $0$ | variable | +| Initial value of parameter P44 | $0$ | variable | +| Initial value of parameter P45 | $0$ | variable | +| Initial value of parameter P46 | $0$ | variable | +| Initial value of parameter P47 | $0$ | variable | +| Initial value of parameter P48 | $0$ | variable | +| Initial value of parameter P49 | $0$ | variable | +| Initial value of parameter P50 | $0$ | variable | +| Initial value of parameter P51 | $0$ | variable | +| Initial value of parameter P52 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01534/l2v5/index.heta b/latest/cases/01534/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01534/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01534/l3v2/build.log b/latest/cases/01534/l3v2/build.log new file mode 100644 index 000000000..65181bae0 --- /dev/null +++ b/latest/cases/01534/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01534/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01534/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01534/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01534/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01534/l3v2/index.heta b/latest/cases/01534/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01534/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01534/model-sbml-l3v2.xml b/latest/cases/01534/model-sbml-l3v2.xml new file mode 100644 index 000000000..f3a6586a6 --- /dev/null +++ b/latest/cases/01534/model-sbml-l3v2.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + 1 + 2 + + + + + + + + + delay + S1 + 1 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01534/synopsis.txt b/latest/cases/01534/synopsis.txt new file mode 100644 index 000000000..396466599 --- /dev/null +++ b/latest/cases/01534/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A delay for a species changed by an assigned stoichiometry +componentTags: AssignmentRule, CSymbolDelay, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, P0 is assigned the delayed value for S1, which is under control of a reaction with an assigned stoichiometry. + +The model contains: +* 1 species (S1) +* 1 parameter (P0) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $delay(S1, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of parameter P0 | $delay(S1, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1 / 2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01535/l2v5/index.heta b/latest/cases/01535/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01535/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01535/l3v2/build.log b/latest/cases/01535/l3v2/build.log new file mode 100644 index 000000000..722b69c0a --- /dev/null +++ b/latest/cases/01535/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01535/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01535/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01535/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01535/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01535/l3v2/index.heta b/latest/cases/01535/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01535/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01535/model-sbml-l3v2.xml b/latest/cases/01535/model-sbml-l3v2.xml new file mode 100644 index 000000000..ebd7b50c0 --- /dev/null +++ b/latest/cases/01535/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + 1 + 2 + + + + + + + + + delay + S1 + 1 + + + + + + 0.1 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01535/synopsis.txt b/latest/cases/01535/synopsis.txt new file mode 100644 index 000000000..68a59dc9d --- /dev/null +++ b/latest/cases/01535/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: A delay for a species changed by an assigned variable stoichiometry +componentTags: AssignmentRule, CSymbolDelay, Compartment, InitialAssignment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, P0 is assigned the delayed value for S1, which is under control of a reaction with an assigned variable stoichiometry. + +The model contains: +* 1 species (S1) +* 1 parameter (P0) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $delay(S1, 1)$ | +| Rate | S1_stoich | $0.1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of parameter P0 | $delay(S1, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1 / 2$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01536/l2v5/index.heta b/latest/cases/01536/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01536/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01536/l3v2/build.log b/latest/cases/01536/l3v2/build.log new file mode 100644 index 000000000..c445e019c --- /dev/null +++ b/latest/cases/01536/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01536/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01536/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01536/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01536/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01536/l3v2/index.heta b/latest/cases/01536/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01536/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01536/model-sbml-l3v2.xml b/latest/cases/01536/model-sbml-l3v2.xml new file mode 100644 index 000000000..183e75bd2 --- /dev/null +++ b/latest/cases/01536/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + 1 + + + + + + + + + + + time + 3 + + + + + + + + delay + P1 + 1 + + + + + + + + diff --git a/latest/cases/01536/synopsis.txt b/latest/cases/01536/synopsis.txt new file mode 100644 index 000000000..7810343ae --- /dev/null +++ b/latest/cases/01536/synopsis.txt @@ -0,0 +1,52 @@ + +category: Test +synopsis: An assigned variable stoichiometry is given a delay. +componentTags: CSymbolDelay, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, DelayInEventAssignment, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the delayed value of P0 is assigned to the stoichiometry of the reaction J0. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > 3$ | $S1_stoich = delay(P1, 1)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01537/l2v5/build.log b/latest/cases/01537/l2v5/build.log new file mode 100644 index 000000000..9ef6a40c0 --- /dev/null +++ b/latest/cases/01537/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01537/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01537/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01537/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01537/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01537/l2v5/index.heta b/latest/cases/01537/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01537/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01537/l3v2/build.log b/latest/cases/01537/l3v2/build.log new file mode 100644 index 000000000..f1cc338ee --- /dev/null +++ b/latest/cases/01537/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01537/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01537/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01537/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01537/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01537/l3v2/index.heta b/latest/cases/01537/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01537/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01537/model-sbml-l2v5.xml b/latest/cases/01537/model-sbml-l2v5.xml new file mode 100644 index 000000000..5e1e34a0d --- /dev/null +++ b/latest/cases/01537/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + delay + S1 + 1 + + + + + + + delay + S2 + 1 + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01537/model-sbml-l3v2.xml b/latest/cases/01537/model-sbml-l3v2.xml new file mode 100644 index 000000000..2e059a979 --- /dev/null +++ b/latest/cases/01537/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + delay + S1 + 1 + + + + + + + delay + S2 + 1 + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01537/synopsis.txt b/latest/cases/01537/synopsis.txt new file mode 100644 index 000000000..b24e7a468 --- /dev/null +++ b/latest/cases/01537/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A delay of a boundary species that does not change. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, Reaction, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the delayed value of S1 and S2 are assigned to P1 and P2, with S1 being a boundary species that does not change. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P1, P2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $delay(S1, 1)$ | +| Assignment | P2 | $delay(S2, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter P1 | $delay(S1, 1)$ | variable | +| Initial value of parameter P2 | $delay(S2, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01538/l2v5/build.log b/latest/cases/01538/l2v5/build.log new file mode 100644 index 000000000..98babb885 --- /dev/null +++ b/latest/cases/01538/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01538/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01538/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01538/model-sbml-l2v5.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01538/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01538/l2v5/index.heta b/latest/cases/01538/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01538/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01538/l3v2/build.log b/latest/cases/01538/l3v2/build.log new file mode 100644 index 000000000..23d6ac15c --- /dev/null +++ b/latest/cases/01538/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01538/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01538/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01538/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01538/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01538/l3v2/index.heta b/latest/cases/01538/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01538/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01538/model-sbml-l2v5.xml b/latest/cases/01538/model-sbml-l2v5.xml new file mode 100644 index 000000000..7fd95d265 --- /dev/null +++ b/latest/cases/01538/model-sbml-l2v5.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + 0.5 + + + + + + delay + S1 + 1 + + + + + + + delay + S2 + 1 + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01538/model-sbml-l3v2.xml b/latest/cases/01538/model-sbml-l3v2.xml new file mode 100644 index 000000000..df693566e --- /dev/null +++ b/latest/cases/01538/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + 0.5 + + + + + + delay + S1 + 1 + + + + + + + delay + S2 + 1 + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01538/synopsis.txt b/latest/cases/01538/synopsis.txt new file mode 100644 index 000000000..94bb03938 --- /dev/null +++ b/latest/cases/01538/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: A delay of a boundary species that changes. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the delayed value of S1 and S2 are assigned to P1 and P2, with S1 being a boundary species that changes due to a rate rule. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P1, P2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $1$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.5$ | +| Assignment | P1 | $delay(S1, 1)$ | +| Assignment | P2 | $delay(S2, 1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter P1 | $delay(S1, 1)$ | variable | +| Initial value of parameter P2 | $delay(S2, 1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01539/l2v5/build.log b/latest/cases/01539/l2v5/build.log new file mode 100644 index 000000000..7d641be88 --- /dev/null +++ b/latest/cases/01539/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01539/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01539/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01539/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01539/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01539/l2v5/index.heta b/latest/cases/01539/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01539/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01539/l3v2/index.heta b/latest/cases/01539/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01539/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01539/model-sbml-l2v5.xml b/latest/cases/01539/model-sbml-l2v5.xml new file mode 100644 index 000000000..ceeb8e31c --- /dev/null +++ b/latest/cases/01539/model-sbml-l2v5.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + delay + S1 + 1.5 + + + + + + + delay + S2 + 1.5 + + + + + + + + + + + + + + + + + S1 + 1 + + + + + + + diff --git a/latest/cases/01539/synopsis.txt b/latest/cases/01539/synopsis.txt new file mode 100644 index 000000000..944facc70 --- /dev/null +++ b/latest/cases/01539/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A delay of species from a fast reaction. +componentTags: AssignmentRule, CSymbolDelay, Compartment, Parameter, Reaction, Species +testTags: Amount, FastReaction, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, the delayed value of S1 and S2 are assigned to P1 and P2, with S1 and S2 participating in a fast reaction, which goes to completion at t0, but not before t0. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P1, P2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $S1 * 1$ | fast |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $delay(S1, 1.5)$ | +| Assignment | P2 | $delay(S2, 1.5)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter P1 | $delay(S1, 1.5)$ | variable | +| Initial value of parameter P2 | $delay(S2, 1.5)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01540/l2v5/index.heta b/latest/cases/01540/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01540/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01540/l3v2/build.log b/latest/cases/01540/l3v2/build.log new file mode 100644 index 000000000..41b6a8ae0 --- /dev/null +++ b/latest/cases/01540/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01540/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01540/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01540/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01540/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01540/l3v2/index.heta b/latest/cases/01540/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01540/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01540/model-sbml-l3v2.xml b/latest/cases/01540/model-sbml-l3v2.xml new file mode 100644 index 000000000..3ad4cb49a --- /dev/null +++ b/latest/cases/01540/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + 0.5 + + + + + + rateOf + S1 + + + + + + + rateOf + S2 + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01540/synopsis.txt b/latest/cases/01540/synopsis.txt new file mode 100644 index 000000000..a826eb122 --- /dev/null +++ b/latest/cases/01540/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: A rateOf of a boundary species that changes. +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the rates of S1 and S2 are assigned to P1 and P2, with S1 being a boundary species that changes due to a rate rule. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P1, P2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $1$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $0.5$ | +| Assignment | P1 | $rateOf(S1)$ | +| Assignment | P2 | $rateOf(S2)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter P1 | $rateOf(S1)$ | variable | +| Initial value of parameter P2 | $rateOf(S2)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01541/l2v5/index.heta b/latest/cases/01541/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01541/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01541/l3v2/build.log b/latest/cases/01541/l3v2/build.log new file mode 100644 index 000000000..5f32f4608 --- /dev/null +++ b/latest/cases/01541/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01541/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01541/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01541/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01541/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01541/l3v2/index.heta b/latest/cases/01541/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01541/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01541/model-sbml-l3v2.xml b/latest/cases/01541/model-sbml-l3v2.xml new file mode 100644 index 000000000..46d065aee --- /dev/null +++ b/latest/cases/01541/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + rateOf + S1 + + + + + + + rateOf + S2 + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01541/synopsis.txt b/latest/cases/01541/synopsis.txt new file mode 100644 index 000000000..f44415c0e --- /dev/null +++ b/latest/cases/01541/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A rate of a boundary species that does not change. +componentTags: AssignmentRule, CSymbolRateOf, Compartment, Parameter, Reaction, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the rate of S1 and S2 are assigned to P1 and P2, with S1 being a boundary species that does not change. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (P1, P2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $rateOf(S1)$ | +| Assignment | P2 | $rateOf(S2)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter P1 | $rateOf(S1)$ | variable | +| Initial value of parameter P2 | $rateOf(S2)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01542/l2v5/index.heta b/latest/cases/01542/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01542/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01542/l3v2/build.log b/latest/cases/01542/l3v2/build.log new file mode 100644 index 000000000..a3790300b --- /dev/null +++ b/latest/cases/01542/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01542/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01542/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01542/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01542/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01542/l3v2/index.heta b/latest/cases/01542/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01542/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01542/model-sbml-l3v2.xml b/latest/cases/01542/model-sbml-l3v2.xml new file mode 100644 index 000000000..343186739 --- /dev/null +++ b/latest/cases/01542/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + 1 + 2 + + + + + + + + + rateOf + S1 + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01542/synopsis.txt b/latest/cases/01542/synopsis.txt new file mode 100644 index 000000000..f92563f2c --- /dev/null +++ b/latest/cases/01542/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A rate of a species changed by an assigned stoichiometry +componentTags: AssignmentRule, CSymbolRateOf, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, P0 is assigned the rate of S1, which is under control of a reaction with an assigned stoichiometry. + +The model contains: +* 1 species (S1) +* 1 parameter (P0) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1 / 2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01543/l2v5/index.heta b/latest/cases/01543/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01543/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01543/l3v2/build.log b/latest/cases/01543/l3v2/build.log new file mode 100644 index 000000000..a89b65c63 --- /dev/null +++ b/latest/cases/01543/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01543/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01543/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01543/model-sbml-l3v2.xml"... +[error] csymbol with url http://www.sbml.org/sbml/symbols/rateOf in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01543/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01543/l3v2/index.heta b/latest/cases/01543/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01543/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01543/model-sbml-l3v2.xml b/latest/cases/01543/model-sbml-l3v2.xml new file mode 100644 index 000000000..3810c0703 --- /dev/null +++ b/latest/cases/01543/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + 1 + 2 + + + + + + + + + rateOf + S1 + + + + + + 0.1 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01543/synopsis.txt b/latest/cases/01543/synopsis.txt new file mode 100644 index 000000000..b44360416 --- /dev/null +++ b/latest/cases/01543/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: A rate of a species changed by an assigned variable stoichiometry +componentTags: AssignmentRule, CSymbolRateOf, Compartment, InitialAssignment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, P0 is assigned the rate of S1, which is under control of a reaction with an assigned variable stoichiometry. + +The model contains: +* 1 species (S1) +* 1 parameter (P0) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P0 | $rateOf(S1)$ | +| Rate | S1_stoich | $0.1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of parameter P0 | $rateOf(S1)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1 / 2$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01544/l2v5/index.heta b/latest/cases/01544/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01544/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01544/l3v2/index.heta b/latest/cases/01544/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01544/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01544/synopsis.txt b/latest/cases/01544/synopsis.txt new file mode 100644 index 000000000..90e352991 --- /dev/null +++ b/latest/cases/01544/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Model and species conversion factors affecting a fast reaction. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, FastReaction +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors affect a fast reaction, changing the final levels of S1 and S2. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $S1 * 0.01$ | fast |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01545/l2v5/index.heta b/latest/cases/01545/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01545/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01545/l3v2/index.heta b/latest/cases/01545/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01545/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01545/synopsis.txt b/latest/cases/01545/synopsis.txt new file mode 100644 index 000000000..7ecf04b02 --- /dev/null +++ b/latest/cases/01545/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A species conversion factor affecting a fast reaction. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, FastReaction +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor affects a fast reaction, changing the final levels of S1 and S2. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $S1 * 0.01$ | fast |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01546/l2v5/index.heta b/latest/cases/01546/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01546/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01546/l3v2/index.heta b/latest/cases/01546/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01546/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01546/synopsis.txt b/latest/cases/01546/synopsis.txt new file mode 100644 index 000000000..9f4eb62e8 --- /dev/null +++ b/latest/cases/01546/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A model conversion factor affecting a fast reaction. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, FastReaction +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor affects a fast reaction, changing the final levels of S1 and S2. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $S1 * 0.01$ | fast |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01547/l2v5/build.log b/latest/cases/01547/l2v5/build.log new file mode 100644 index 000000000..d22e1c005 --- /dev/null +++ b/latest/cases/01547/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01547/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01547/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01547/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01547/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01547/l2v5/index.heta b/latest/cases/01547/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01547/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01547/l3v2/index.heta b/latest/cases/01547/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01547/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01547/model-sbml-l2v5.xml b/latest/cases/01547/model-sbml-l2v5.xml new file mode 100644 index 000000000..d10e9af3d --- /dev/null +++ b/latest/cases/01547/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + 0.01 + + + + + + + + + + + + + + + + + + + + + + + + S1 + + ispos + + + + + + + + diff --git a/latest/cases/01547/synopsis.txt b/latest/cases/01547/synopsis.txt new file mode 100644 index 000000000..c84d7557b --- /dev/null +++ b/latest/cases/01547/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A fast reaction using a function definition. +componentTags: Compartment, FunctionDefinition, Reaction, Species +testTags: Amount, FastReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, the kinetic law of a fast reaction is positive because of a function definition. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $S1 * ispos()$ | fast |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | ispos | | $0.01$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01548/l2v5/build.log b/latest/cases/01548/l2v5/build.log new file mode 100644 index 000000000..0d7f3d4dc --- /dev/null +++ b/latest/cases/01548/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01548/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01548/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01548/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01548/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01548/l2v5/index.heta b/latest/cases/01548/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01548/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01548/l3v2/index.heta b/latest/cases/01548/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01548/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01548/model-sbml-l2v5.xml b/latest/cases/01548/model-sbml-l2v5.xml new file mode 100644 index 000000000..2e1945077 --- /dev/null +++ b/latest/cases/01548/model-sbml-l2v5.xml @@ -0,0 +1,42 @@ + + + + + + + + -0.01 + + + + + + + + + + + + + + + + + + + + + + + + S2 + + isneg + + + + + + + + diff --git a/latest/cases/01548/synopsis.txt b/latest/cases/01548/synopsis.txt new file mode 100644 index 000000000..5e1e2d452 --- /dev/null +++ b/latest/cases/01548/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A fast reaction using a function definition. +componentTags: Compartment, FunctionDefinition, Reaction, Species +testTags: Amount, FastReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, the kinetic law of a fast reaction is negative because of a function definition. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $S2 * isneg()$ | fast |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | isneg | | $-0.01$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01549/l2v5/build.log b/latest/cases/01549/l2v5/build.log new file mode 100644 index 000000000..e2dd9974c --- /dev/null +++ b/latest/cases/01549/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01549/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01549/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01549/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01549/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01549/l2v5/index.heta b/latest/cases/01549/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01549/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01549/l3v2/index.heta b/latest/cases/01549/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01549/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01549/model-sbml-l2v5.xml b/latest/cases/01549/model-sbml-l2v5.xml new file mode 100644 index 000000000..6b0e6a40a --- /dev/null +++ b/latest/cases/01549/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + x + + + + 0.01 + x + + + + + + + + + + + + + + + + + + + + + + + + getpos + S1 + + + + + + + diff --git a/latest/cases/01549/synopsis.txt b/latest/cases/01549/synopsis.txt new file mode 100644 index 000000000..317dfd390 --- /dev/null +++ b/latest/cases/01549/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A fast reaction using a function definition. +componentTags: Compartment, FunctionDefinition, Reaction, Species +testTags: Amount, FastReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, the kinetic law of a fast reaction is positive because of a function definition. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $getpos(S1)$ | fast |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getpos | x | $0.01 * x$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01550/l2v5/build.log b/latest/cases/01550/l2v5/build.log new file mode 100644 index 000000000..3a74792c9 --- /dev/null +++ b/latest/cases/01550/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01550/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01550/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01550/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01550/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01550/l2v5/index.heta b/latest/cases/01550/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01550/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01550/l3v2/index.heta b/latest/cases/01550/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01550/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01550/model-sbml-l2v5.xml b/latest/cases/01550/model-sbml-l2v5.xml new file mode 100644 index 000000000..4c2559396 --- /dev/null +++ b/latest/cases/01550/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + x + + + + -0.01 + x + + + + + + + + + + + + + + + + + + + + + + + + getneg + S2 + + + + + + + diff --git a/latest/cases/01550/synopsis.txt b/latest/cases/01550/synopsis.txt new file mode 100644 index 000000000..e63ed423d --- /dev/null +++ b/latest/cases/01550/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A fast reaction using a function definition. +componentTags: Compartment, FunctionDefinition, Reaction, Species +testTags: Amount, FastReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, the kinetic law of a fast reaction is negative because of a function definition. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $getneg(S2)$ | fast |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getneg | x | $-0.01 * x$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01551/l2v5/build.log b/latest/cases/01551/l2v5/build.log new file mode 100644 index 000000000..ce9e20522 --- /dev/null +++ b/latest/cases/01551/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01551/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01551/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01551/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01551/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01551/l2v5/index.heta b/latest/cases/01551/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01551/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01551/l3v2/index.heta b/latest/cases/01551/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01551/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01551/model-sbml-l2v5.xml b/latest/cases/01551/model-sbml-l2v5.xml new file mode 100644 index 000000000..869500a39 --- /dev/null +++ b/latest/cases/01551/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + x + + + + x + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + getneg + S2 + + + + + + + + diff --git a/latest/cases/01551/synopsis.txt b/latest/cases/01551/synopsis.txt new file mode 100644 index 000000000..1f73ba298 --- /dev/null +++ b/latest/cases/01551/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A fast reaction using a function definition. +componentTags: Compartment, FunctionDefinition, Reaction, Species +testTags: Amount, FastReaction, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, the kinetic law of a fast reaction is negative because of a function definition. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $1 * getneg(S2)$ | fast |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getneg | x | $-x$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01552/l2v5/index.heta b/latest/cases/01552/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01552/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01552/l3v2/build.log b/latest/cases/01552/l3v2/build.log new file mode 100644 index 000000000..2526d0b1f --- /dev/null +++ b/latest/cases/01552/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01552/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01552/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01552/model-sbml-l3v2.xml"... +[error] S2_stoch component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01552/l3v2/index.heta b/latest/cases/01552/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01552/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01552/model-sbml-l3v2.xml b/latest/cases/01552/model-sbml-l3v2.xml new file mode 100644 index 000000000..792f840e4 --- /dev/null +++ b/latest/cases/01552/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01552/synopsis.txt b/latest/cases/01552/synopsis.txt new file mode 100644 index 000000000..1e1bea89b --- /dev/null +++ b/latest/cases/01552/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: A reaction stoichiometry with an assignment rule with no math. +componentTags: AssignmentRule, Compartment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the stoichiometry of an element is 2, with an assignment rule to change it that doesn't have any mathML, leaving the value at 2. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) +* 1 species reference (S2_stoch) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2_stoch S2 | $0.1$ |] +Note: the following stoichiometries are set separately: S2_stoch + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S2_stoch | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S2_stoch' | $2$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01553/l2v5/index.heta b/latest/cases/01553/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01553/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01553/l3v2/build.log b/latest/cases/01553/l3v2/build.log new file mode 100644 index 000000000..7d7312bfa --- /dev/null +++ b/latest/cases/01553/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01553/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01553/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01553/model-sbml-l3v2.xml"... +[error] S2_stoch component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] S2_stoch_proc Property "actors[0].target" has lost reference "S2_stoch". +[error] Record "S2_stoch_proc" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01553/l3v2/index.heta b/latest/cases/01553/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01553/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01553/model-sbml-l3v2.xml b/latest/cases/01553/model-sbml-l3v2.xml new file mode 100644 index 000000000..afa775876 --- /dev/null +++ b/latest/cases/01553/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01553/synopsis.txt b/latest/cases/01553/synopsis.txt new file mode 100644 index 000000000..d23b2211b --- /dev/null +++ b/latest/cases/01553/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: A reaction stoichiometry with a rate rule with no math. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the stoichiometry of an element is 2, with a rate rule to change it that doesn't have any mathML, leaving the value at 2. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) +* 1 species reference (S2_stoch) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2_stoch S2 | $0.1$ |] +Note: the following stoichiometries are set separately: S2_stoch + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S2_stoch | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S2_stoch' | $2$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01554/l2v5/index.heta b/latest/cases/01554/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01554/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01554/l3v2/build.log b/latest/cases/01554/l3v2/build.log new file mode 100644 index 000000000..57c1c810d --- /dev/null +++ b/latest/cases/01554/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01554/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01554/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01554/model-sbml-l3v2.xml"... +[error] S2_stoch component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01554/l3v2/index.heta b/latest/cases/01554/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01554/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01554/model-sbml-l3v2.xml b/latest/cases/01554/model-sbml-l3v2.xml new file mode 100644 index 000000000..288fa7d3f --- /dev/null +++ b/latest/cases/01554/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01554/synopsis.txt b/latest/cases/01554/synopsis.txt new file mode 100644 index 000000000..803187b4b --- /dev/null +++ b/latest/cases/01554/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A reaction stoichiometry with an initial assignment with no math. +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the stoichiometry of an element is 2, with an initial assignment to change it that doesn't have any mathML, leaving the value at 2. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) +* 1 species reference (S2_stoch) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2_stoch S2 | $0.1$ |] +Note: the following stoichiometries are set separately: S2_stoch + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S2_stoch' | $2$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01555/l2v5/index.heta b/latest/cases/01555/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01555/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01555/l3v2/heta-code/output.heta b/latest/cases/01555/l3v2/heta-code/output.heta new file mode 100644 index 000000000..532526821 --- /dev/null +++ b/latest/cases/01555/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = 2*S2, }; +J0 := 0.1; + diff --git a/latest/cases/01555/l3v2/index.heta b/latest/cases/01555/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01555/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01555/l3v2/json/output.json b/latest/cases/01555/l3v2/json/output.json new file mode 100644 index 000000000..73e6e18d9 --- /dev/null +++ b/latest/cases/01555/l3v2/json/output.json @@ -0,0 +1,47 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01555/model-sbml-l3v2.xml b/latest/cases/01555/model-sbml-l3v2.xml new file mode 100644 index 000000000..a899d00c0 --- /dev/null +++ b/latest/cases/01555/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01555/output.heta b/latest/cases/01555/output.heta new file mode 100644 index 000000000..fb5a8cdc0 --- /dev/null +++ b/latest/cases/01555/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: A boundary species with an assignment rule with no math. +componentTags: AssignmentRule, Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the initial amount of a boundary species is 2, with an assignment rule to change it that doesn't have any mathML, leaving the value at 2. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> 2S2 | $0.1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1 | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = 2*S2, }; +J0 := 0.1; + diff --git a/latest/cases/01555/synopsis.txt b/latest/cases/01555/synopsis.txt new file mode 100644 index 000000000..be6f6c832 --- /dev/null +++ b/latest/cases/01555/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: A boundary species with an assignment rule with no math. +componentTags: AssignmentRule, Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the initial amount of a boundary species is 2, with an assignment rule to change it that doesn't have any mathML, leaving the value at 2. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> 2S2 | $0.1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1 | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01556/l2v5/index.heta b/latest/cases/01556/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01556/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01556/l3v2/build.log b/latest/cases/01556/l3v2/build.log new file mode 100644 index 000000000..9053899f5 --- /dev/null +++ b/latest/cases/01556/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01556/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01556/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01556/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 84 +[error] Record "S1_proc" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01556/l3v2/index.heta b/latest/cases/01556/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01556/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01556/model-sbml-l3v2.xml b/latest/cases/01556/model-sbml-l3v2.xml new file mode 100644 index 000000000..61d32ec03 --- /dev/null +++ b/latest/cases/01556/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01556/synopsis.txt b/latest/cases/01556/synopsis.txt new file mode 100644 index 000000000..549961d53 --- /dev/null +++ b/latest/cases/01556/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: A boundary species with a rate rule with no math. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, BoundaryCondition, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the initial amount of a boundary species is 2, with a rate rule to change it that doesn't have any mathML, leaving the value at 2. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> 2S2 | $0.1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01557/l2v5/index.heta b/latest/cases/01557/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01557/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01557/l3v2/heta-code/output.heta b/latest/cases/01557/l3v2/heta-code/output.heta new file mode 100644 index 000000000..532526821 --- /dev/null +++ b/latest/cases/01557/l3v2/heta-code/output.heta @@ -0,0 +1,12 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = 2*S2, }; +J0 := 0.1; + diff --git a/latest/cases/01557/l3v2/index.heta b/latest/cases/01557/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01557/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01557/l3v2/json/output.json b/latest/cases/01557/l3v2/json/output.json new file mode 100644 index 000000000..73e6e18d9 --- /dev/null +++ b/latest/cases/01557/l3v2/json/output.json @@ -0,0 +1,47 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01557/model-sbml-l3v2.xml b/latest/cases/01557/model-sbml-l3v2.xml new file mode 100644 index 000000000..48395155c --- /dev/null +++ b/latest/cases/01557/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01557/output.heta b/latest/cases/01557/output.heta new file mode 100644 index 000000000..c353ff265 --- /dev/null +++ b/latest/cases/01557/output.heta @@ -0,0 +1,50 @@ +/* +category: Test +synopsis: A boundary species with an initial assignment with no math. +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, BoundaryCondition, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the initial amount of a boundary species is 2, with an initial assignment to change it that doesn't have any mathML, leaving the value at 2. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> 2S2 | $0.1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = 2*S2, }; +J0 := 0.1; + diff --git a/latest/cases/01557/synopsis.txt b/latest/cases/01557/synopsis.txt new file mode 100644 index 000000000..28d5df857 --- /dev/null +++ b/latest/cases/01557/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A boundary species with an initial assignment with no math. +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, BoundaryCondition, NoMathML, NonUnityStoichiometry +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the initial amount of a boundary species is 2, with an initial assignment to change it that doesn't have any mathML, leaving the value at 2. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> 2S2 | $0.1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01558/l2v5/index.heta b/latest/cases/01558/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01558/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01558/l3v2/index.heta b/latest/cases/01558/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01558/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01558/synopsis.txt b/latest/cases/01558/synopsis.txt new file mode 100644 index 000000000..99f2b2821 --- /dev/null +++ b/latest/cases/01558/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A fast reaction with a species reference used in an initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, FastReaction, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a fast reaction contains a species reference which is itself referenced in a parameter's initial assignment. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (P1) +* 1 compartment (C) +* 1 species reference (S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> 2S2 | $S1 * 0.1$ | fast |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter P1 | $S2_stoich$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S2_stoich' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01559/l2v5/index.heta b/latest/cases/01559/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01559/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01559/l3v2/index.heta b/latest/cases/01559/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01559/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01559/synopsis.txt b/latest/cases/01559/synopsis.txt new file mode 100644 index 000000000..b25e85897 --- /dev/null +++ b/latest/cases/01559/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A fast reaction with a species reference used in an assignment rule. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, FastReaction, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a fast reaction contains a species reference which is itself referenced in a parameter's assignment rule. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (P1) +* 1 compartment (C) +* 1 species reference (S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> 2S2 | $S1 * 0.1$ | fast |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $S2_stoich$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter P1 | $S2_stoich$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S2_stoich' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01560/l2v5/index.heta b/latest/cases/01560/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01560/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01560/l3v2/index.heta b/latest/cases/01560/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01560/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01560/synopsis.txt b/latest/cases/01560/synopsis.txt new file mode 100644 index 000000000..7813ff552 --- /dev/null +++ b/latest/cases/01560/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A fast reaction with a species reference used in a rate rule. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, FastReaction, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a fast reaction contains a species reference which is itself referenced in a parameter's rate rule. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (P1) +* 1 compartment (C) +* 1 species reference (S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> 2S2 | $S1 * 0.1$ | fast |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $S2_stoich$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S2_stoich' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01561/l2v5/index.heta b/latest/cases/01561/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01561/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01561/l3v2/build.log b/latest/cases/01561/l3v2/build.log new file mode 100644 index 000000000..143b9b5ba --- /dev/null +++ b/latest/cases/01561/l3v2/build.log @@ -0,0 +1,60 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01561/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01561/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01561/model-sbml-l3v2.xml"... +[error] S0_stoich component does not exist which is not allowed for the "update" action. +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[error] S3_stoich component does not exist which is not allowed for the "update" action. +[error] S4_stoich component does not exist which is not allowed for the "update" action. +[error] S5_stoich component does not exist which is not allowed for the "update" action. +[error] S6_stoich component does not exist which is not allowed for the "update" action. +[error] S7_stoich component does not exist which is not allowed for the "update" action. +[error] S8_stoich component does not exist which is not allowed for the "update" action. +[error] S9_stoich component does not exist which is not allowed for the "update" action. +[error] S10_stoich component does not exist which is not allowed for the "update" action. +[error] S11_stoich component does not exist which is not allowed for the "update" action. +[error] S12_stoich component does not exist which is not allowed for the "update" action. +[error] S13_stoich component does not exist which is not allowed for the "update" action. +[error] S14_stoich component does not exist which is not allowed for the "update" action. +[error] S15_stoich component does not exist which is not allowed for the "update" action. +[error] S16_stoich component does not exist which is not allowed for the "update" action. +[error] S17_stoich component does not exist which is not allowed for the "update" action. +[error] S18_stoich component does not exist which is not allowed for the "update" action. +[error] S19_stoich component does not exist which is not allowed for the "update" action. +[error] S20_stoich component does not exist which is not allowed for the "update" action. +[error] S21_stoich component does not exist which is not allowed for the "update" action. +[error] S22_stoich component does not exist which is not allowed for the "update" action. +[error] S23_stoich component does not exist which is not allowed for the "update" action. +[error] S24_stoich component does not exist which is not allowed for the "update" action. +[error] S25_stoich component does not exist which is not allowed for the "update" action. +[error] S26_stoich component does not exist which is not allowed for the "update" action. +[error] S27_stoich component does not exist which is not allowed for the "update" action. +[error] S28_stoich component does not exist which is not allowed for the "update" action. +[error] S29_stoich component does not exist which is not allowed for the "update" action. +[error] S30_stoich component does not exist which is not allowed for the "update" action. +[error] S31_stoich component does not exist which is not allowed for the "update" action. +[error] S32_stoich component does not exist which is not allowed for the "update" action. +[error] S33_stoich component does not exist which is not allowed for the "update" action. +[error] S34_stoich component does not exist which is not allowed for the "update" action. +[error] S35_stoich component does not exist which is not allowed for the "update" action. +[error] S36_stoich component does not exist which is not allowed for the "update" action. +[error] S37_stoich component does not exist which is not allowed for the "update" action. +[error] S38_stoich component does not exist which is not allowed for the "update" action. +[error] S39_stoich component does not exist which is not allowed for the "update" action. +[error] S40_stoich component does not exist which is not allowed for the "update" action. +[error] S41_stoich component does not exist which is not allowed for the "update" action. +[error] S42_stoich component does not exist which is not allowed for the "update" action. +[error] S43_stoich component does not exist which is not allowed for the "update" action. +[error] S44_stoich component does not exist which is not allowed for the "update" action. +[error] S45_stoich component does not exist which is not allowed for the "update" action. +[error] S46_stoich component does not exist which is not allowed for the "update" action. +[error] S47_stoich component does not exist which is not allowed for the "update" action. +[error] S48_stoich component does not exist which is not allowed for the "update" action. +[error] S49_stoich component does not exist which is not allowed for the "update" action. +[error] S50_stoich component does not exist which is not allowed for the "update" action. +[error] S51_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 184 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01561/l3v2/index.heta b/latest/cases/01561/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01561/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01561/model-sbml-l3v2.xml b/latest/cases/01561/model-sbml-l3v2.xml new file mode 100644 index 000000000..b09e6f486 --- /dev/null +++ b/latest/cases/01561/model-sbml-l3v2.xml @@ -0,0 +1,1015 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + + + 1 + + + + + + + + -1 + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + -0.5 + + + + + + + + 2.8 + + + + + + + + -7.09 + + + + + + + + 0.5 + + + + + + + + 3.55 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + -0.22 + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + 0.77 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + 10 + + 0.2 + + + + + + + + + 10 + + 1 + + + + + + + + 1 + 2 + + + + + + + + 2 + 2 + + + + + + + + 1.4 + 5.1 + + + + + + + + 4 + 2 + + + + + + + + 3.1 + 2 + + + + + + + + + 2 + + 4 + + + + + + + + + 2 + + 7.4 + + + + + + + + 2.1 + + + + + + + + 0 + + + + + + + + -5.9 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + 0.5 + + + + + + + + 4.5 + + + + + + + + 0.2 + + + + + + + + 0.3 + + + + + + + + 1.7 + + + + + + + + 2.3 + + + + + + + + 1.1 + + + + + + + + -0.1 + + + + + + + + 99 + + + + + + + + 1.34 + + + + + + + + -0.7 + + + + + + + + 0.42 + + + + + + + + 0.01 + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01561/synopsis.txt b/latest/cases/01561/synopsis.txt new file mode 100644 index 000000000..dbf58b266 --- /dev/null +++ b/latest/cases/01561/synopsis.txt @@ -0,0 +1,186 @@ + +category: Test +synopsis: Uncommon MathML assigned to stoichiometries. +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonUnityStoichiometry, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests various uncommon mathematical constructs assigned to stoichiometries. + +The model contains: +* 52 species (S0, S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17, S18, S19, S20, S21, S22, S23, S24, S25, S26, S27, S28, S29, S30, S31, S32, S33, S34, S35, S36, S37, S38, S39, S40, S41, S42, S43, S44, S45, S46, S47, S48, S49, S50, S51) +* 1 compartment (C) +* 52 species references (S0_stoich, S1_stoich, S2_stoich, S3_stoich, S4_stoich, S5_stoich, S6_stoich, S7_stoich, S8_stoich, S9_stoich, S10_stoich, S11_stoich, S12_stoich, S13_stoich, S14_stoich, S15_stoich, S16_stoich, S17_stoich, S18_stoich, S19_stoich, S20_stoich, S21_stoich, S22_stoich, S23_stoich, S24_stoich, S25_stoich, S26_stoich, S27_stoich, S28_stoich, S29_stoich, S30_stoich, S31_stoich, S32_stoich, S33_stoich, S34_stoich, S35_stoich, S36_stoich, S37_stoich, S38_stoich, S39_stoich, S40_stoich, S41_stoich, S42_stoich, S43_stoich, S44_stoich, S45_stoich, S46_stoich, S47_stoich, S48_stoich, S49_stoich, S50_stoich, S51_stoich) + +There are 52 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S0_stoich S0 | $1$ | +| J1: -> S1_stoich S1 | $1$ | +| J2: -> S2_stoich S2 | $1$ | +| J3: -> S3_stoich S3 | $1$ | +| J4: -> S4_stoich S4 | $1$ | +| J5: -> S5_stoich S5 | $1$ | +| J6: -> S6_stoich S6 | $1$ | +| J7: -> S7_stoich S7 | $1$ | +| J8: -> S8_stoich S8 | $1$ | +| J9: -> S9_stoich S9 | $1$ | +| J10: -> S10_stoich S10 | $1$ | +| J11: -> S11_stoich S11 | $1$ | +| J12: -> S12_stoich S12 | $1$ | +| J13: -> S13_stoich S13 | $1$ | +| J14: -> S14_stoich S14 | $1$ | +| J15: -> S15_stoich S15 | $1$ | +| J16: -> S16_stoich S16 | $1$ | +| J17: -> S17_stoich S17 | $1$ | +| J18: -> S18_stoich S18 | $1$ | +| J19: -> S19_stoich S19 | $1$ | +| J20: -> S20_stoich S20 | $1$ | +| J21: -> S21_stoich S21 | $1$ | +| J22: -> S22_stoich S22 | $1$ | +| J23: -> S23_stoich S23 | $1$ | +| J24: -> S24_stoich S24 | $1$ | +| J25: -> S25_stoich S25 | $1$ | +| J26: -> S26_stoich S26 | $1$ | +| J27: -> S27_stoich S27 | $1$ | +| J28: -> S28_stoich S28 | $1$ | +| J29: -> S29_stoich S29 | $1$ | +| J30: -> S30_stoich S30 | $1$ | +| J31: -> S31_stoich S31 | $1$ | +| J32: -> S32_stoich S32 | $1$ | +| J33: -> S33_stoich S33 | $1$ | +| J34: -> S34_stoich S34 | $1$ | +| J35: -> S35_stoich S35 | $1$ | +| J36: -> S36_stoich S36 | $1$ | +| J37: -> S37_stoich S37 | $1$ | +| J38: -> S38_stoich S38 | $1$ | +| J39: -> S39_stoich S39 | $1$ | +| J40: -> S40_stoich S40 | $1$ | +| J41: -> S41_stoich S41 | $1$ | +| J42: -> S42_stoich S42 | $1$ | +| J43: -> S43_stoich S43 | $1$ | +| J44: -> S44_stoich S44 | $1$ | +| J45: -> S45_stoich S45 | $1$ | +| J46: -> S46_stoich S46 | $1$ | +| J47: -> S47_stoich S47 | $1$ | +| J48: -> S48_stoich S48 | $1$ | +| J49: -> S49_stoich S49 | $1$ | +| J50: -> S50_stoich S50 | $1$ | +| J51: -> S51_stoich S51 | $1$ |] +Note: the following stoichiometries are set separately: S0_stoich, S1_stoich, S2_stoich, S3_stoich, S4_stoich, S5_stoich, S6_stoich, S7_stoich, S8_stoich, S9_stoich, S10_stoich, S11_stoich, S12_stoich, S13_stoich, S14_stoich, S15_stoich, S16_stoich, S17_stoich, S18_stoich, S19_stoich, S20_stoich, S21_stoich, S22_stoich, S23_stoich, S24_stoich, S25_stoich, S26_stoich, S27_stoich, S28_stoich, S29_stoich, S30_stoich, S31_stoich, S32_stoich, S33_stoich, S34_stoich, S35_stoich, S36_stoich, S37_stoich, S38_stoich, S39_stoich, S40_stoich, S41_stoich, S42_stoich, S43_stoich, S44_stoich, S45_stoich, S46_stoich, S47_stoich, S48_stoich, S49_stoich, S50_stoich, S51_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S0 | $0$ | variable | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial concentration of species S3 | $0$ | variable | +| Initial concentration of species S4 | $0$ | variable | +| Initial concentration of species S5 | $0$ | variable | +| Initial concentration of species S6 | $0$ | variable | +| Initial concentration of species S7 | $0$ | variable | +| Initial concentration of species S8 | $0$ | variable | +| Initial concentration of species S9 | $0$ | variable | +| Initial concentration of species S10 | $0$ | variable | +| Initial concentration of species S11 | $0$ | variable | +| Initial concentration of species S12 | $0$ | variable | +| Initial concentration of species S13 | $0$ | variable | +| Initial concentration of species S14 | $0$ | variable | +| Initial concentration of species S15 | $0$ | variable | +| Initial concentration of species S16 | $0$ | variable | +| Initial concentration of species S17 | $0$ | variable | +| Initial concentration of species S18 | $0$ | variable | +| Initial concentration of species S19 | $0$ | variable | +| Initial concentration of species S20 | $0$ | variable | +| Initial concentration of species S21 | $0$ | variable | +| Initial concentration of species S22 | $0$ | variable | +| Initial concentration of species S23 | $0$ | variable | +| Initial concentration of species S24 | $0$ | variable | +| Initial concentration of species S25 | $0$ | variable | +| Initial concentration of species S26 | $0$ | variable | +| Initial concentration of species S27 | $0$ | variable | +| Initial concentration of species S28 | $0$ | variable | +| Initial concentration of species S29 | $0$ | variable | +| Initial concentration of species S30 | $0$ | variable | +| Initial concentration of species S31 | $0$ | variable | +| Initial concentration of species S32 | $0$ | variable | +| Initial concentration of species S33 | $0$ | variable | +| Initial concentration of species S34 | $0$ | variable | +| Initial concentration of species S35 | $0$ | variable | +| Initial concentration of species S36 | $0$ | variable | +| Initial concentration of species S37 | $0$ | variable | +| Initial concentration of species S38 | $0$ | variable | +| Initial concentration of species S39 | $0$ | variable | +| Initial concentration of species S40 | $0$ | variable | +| Initial concentration of species S41 | $0$ | variable | +| Initial concentration of species S42 | $0$ | variable | +| Initial concentration of species S43 | $0$ | variable | +| Initial concentration of species S44 | $0$ | variable | +| Initial concentration of species S45 | $0$ | variable | +| Initial concentration of species S46 | $0$ | variable | +| Initial concentration of species S47 | $0$ | variable | +| Initial concentration of species S48 | $0$ | variable | +| Initial concentration of species S49 | $0$ | variable | +| Initial concentration of species S50 | $0$ | variable | +| Initial concentration of species S51 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S0_stoich' | $exponentiale$ | constant | +| Initial value of species reference 'S1_stoich' | $exp(exponentiale)$ | constant | +| Initial value of species reference 'S2_stoich' | $abs(-1)$ | constant | +| Initial value of species reference 'S3_stoich' | $abs(1)$ | constant | +| Initial value of species reference 'S4_stoich' | $acos(-1)$ | constant | +| Initial value of species reference 'S5_stoich' | $acos(0.5)$ | constant | +| Initial value of species reference 'S6_stoich' | $asin(1)$ | constant | +| Initial value of species reference 'S7_stoich' | $asin(-0.5)$ | constant | +| Initial value of species reference 'S8_stoich' | $atan(2.8)$ | constant | +| Initial value of species reference 'S9_stoich' | $atan(-7.09)$ | constant | +| Initial value of species reference 'S10_stoich' | $ceil(0.5)$ | constant | +| Initial value of species reference 'S11_stoich' | $ceil(3.55)$ | constant | +| Initial value of species reference 'S12_stoich' | $ceil(-4.6)$ | constant | +| Initial value of species reference 'S13_stoich' | $cos(9.1)$ | constant | +| Initial value of species reference 'S14_stoich' | $cos(-0.22)$ | constant | +| Initial value of species reference 'S15_stoich' | $exp(0)$ | constant | +| Initial value of species reference 'S16_stoich' | $exp(1)$ | constant | +| Initial value of species reference 'S17_stoich' | $exp(0.77)$ | constant | +| Initial value of species reference 'S18_stoich' | $floor(-4.6)$ | constant | +| Initial value of species reference 'S19_stoich' | $floor(9.1)$ | constant | +| Initial value of species reference 'S20_stoich' | $ln(0.2)$ | constant | +| Initial value of species reference 'S21_stoich' | $ln(1)$ | constant | +| Initial value of species reference 'S22_stoich' | $log10(0.2)$ | constant | +| Initial value of species reference 'S23_stoich' | $log10(1)$ | constant | +| Initial value of species reference 'S24_stoich' | $1^2$ | constant | +| Initial value of species reference 'S25_stoich' | $2^2$ | constant | +| Initial value of species reference 'S26_stoich' | $1.4^5.1$ | constant | +| Initial value of species reference 'S27_stoich' | $4^2$ | constant | +| Initial value of species reference 'S28_stoich' | $3.1^2$ | constant | +| Initial value of species reference 'S29_stoich' | $sqrt(4)$ | constant | +| Initial value of species reference 'S30_stoich' | $sqrt(7.4)$ | constant | +| Initial value of species reference 'S31_stoich' | $sin(2.1)$ | constant | +| Initial value of species reference 'S32_stoich' | $sin(0)$ | constant | +| Initial value of species reference 'S33_stoich' | $sin(-5.9)$ | constant | +| Initial value of species reference 'S34_stoich' | $tan(0)$ | constant | +| Initial value of species reference 'S35_stoich' | $tan(1.11)$ | constant | +| Initial value of species reference 'S36_stoich' | $tan(-6)$ | constant | +| Initial value of species reference 'S37_stoich' | $sec(0.5)$ | constant | +| Initial value of species reference 'S38_stoich' | $csc(4.5)$ | constant | +| Initial value of species reference 'S39_stoich' | $cot(0.2)$ | constant | +| Initial value of species reference 'S40_stoich' | $sinh(0.3)$ | constant | +| Initial value of species reference 'S41_stoich' | $cosh(1.7)$ | constant | +| Initial value of species reference 'S42_stoich' | $arcsec(2.3)$ | constant | +| Initial value of species reference 'S43_stoich' | $arccsc(1.1)$ | constant | +| Initial value of species reference 'S44_stoich' | $arccot(-0.1)$ | constant | +| Initial value of species reference 'S45_stoich' | $arcsinh(99)$ | constant | +| Initial value of species reference 'S46_stoich' | $arccosh(1.34)$ | constant | +| Initial value of species reference 'S47_stoich' | $arctanh(-0.7)$ | constant | +| Initial value of species reference 'S48_stoich' | $arcsech(0.42)$ | constant | +| Initial value of species reference 'S49_stoich' | $arccsch(0.01)$ | constant | +| Initial value of species reference 'S50_stoich' | $times()$ | constant | +| Initial value of species reference 'S51_stoich' | $plus()$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01562/l2v5/build.log b/latest/cases/01562/l2v5/build.log new file mode 100644 index 000000000..55aeb1bcc --- /dev/null +++ b/latest/cases/01562/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01562/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01562/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01562/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01562/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01562/l2v5/index.heta b/latest/cases/01562/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01562/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01562/l3v2/index.heta b/latest/cases/01562/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01562/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01562/model-sbml-l2v5.xml b/latest/cases/01562/model-sbml-l2v5.xml new file mode 100644 index 000000000..0155b9f69 --- /dev/null +++ b/latest/cases/01562/model-sbml-l2v5.xml @@ -0,0 +1,1064 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + -1 + + + + + + + + 1 + + + + + + + + + + + 1 + + + + + + + + 1 + + + + + + + + + + + -1 + + + + + + + + 1 + + + + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + + + + 1 + + + + + + + + 1 + + + + + + + + + + + -0.5 + + + + + + + + 1 + + + + + + + + + + + 2.8 + + + + + + + + 1 + + + + + + + + + + + -7.09 + + + + + + + + 1 + + + + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + + + + 3.55 + + + + + + + + 1 + + + + + + + + + + + -4.6 + + + + + + + + 1 + + + + + + + + + + + 9.1 + + + + + + + + 1 + + + + + + + + + + + -0.22 + + + + + + + + 1 + + + + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + + + + 1 + + + + + + + + 1 + + + + + + + + + + + 0.77 + + + + + + + + 1 + + + + + + + + + + + -4.6 + + + + + + + + 1 + + + + + + + + + + + 9.1 + + + + + + + + 1 + + + + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + + + 1 + + + + + + + + 1 + + + + + + + + + + + + 10 + + 0.2 + + + + + + + + 1 + + + + + + + + + + + + 10 + + 1 + + + + + + + + 1 + + + + + + + + + + + 1 + 2 + + + + + + + + 1 + + + + + + + + + + + 2 + 2 + + + + + + + + 1 + + + + + + + + + + + 1.4 + 5.1 + + + + + + + + 1 + + + + + + + + + + + 4 + 2 + + + + + + + + 1 + + + + + + + + + + + 3.1 + 2 + + + + + + + + 1 + + + + + + + + + + + + 2 + + 4 + + + + + + + + 1 + + + + + + + + + + + + 2 + + 7.4 + + + + + + + + 1 + + + + + + + + + + + 2.1 + + + + + + + + 1 + + + + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + + + + -5.9 + + + + + + + + 1 + + + + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + + + + 1.11 + + + + + + + + 1 + + + + + + + + + + + -6 + + + + + + + + 1 + + + + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + + + + 4.5 + + + + + + + + 1 + + + + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + + + 0.3 + + + + + + + + 1 + + + + + + + + + + + 1.7 + + + + + + + + 1 + + + + + + + + + + + 2.3 + + + + + + + + 1 + + + + + + + + + + + 1.1 + + + + + + + + 1 + + + + + + + + + + + -0.1 + + + + + + + + 1 + + + + + + + + + + + 99 + + + + + + + + 1 + + + + + + + + + + + 1.34 + + + + + + + + 1 + + + + + + + + + + + -0.7 + + + + + + + + 1 + + + + + + + + + + + 0.42 + + + + + + + + 1 + + + + + + + + + + + 0.01 + + + + + + + + 1 + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01562/synopsis.txt b/latest/cases/01562/synopsis.txt new file mode 100644 index 000000000..a8e2cf152 --- /dev/null +++ b/latest/cases/01562/synopsis.txt @@ -0,0 +1,186 @@ + +category: Test +synopsis: Uncommon MathML assigned to stoichiometries. +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, NonUnityStoichiometry, UncommonMathML +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +The model tests various uncommon mathematical constructs assigned to stoichiometries. + +The model contains: +* 52 species (S0, S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17, S18, S19, S20, S21, S22, S23, S24, S25, S26, S27, S28, S29, S30, S31, S32, S33, S34, S35, S36, S37, S38, S39, S40, S41, S42, S43, S44, S45, S46, S47, S48, S49, S50, S51) +* 1 compartment (C) +* 52 species references (S0_stoich, S1_stoich, S2_stoich, S3_stoich, S4_stoich, S5_stoich, S6_stoich, S7_stoich, S8_stoich, S9_stoich, S10_stoich, S11_stoich, S12_stoich, S13_stoich, S14_stoich, S15_stoich, S16_stoich, S17_stoich, S18_stoich, S19_stoich, S20_stoich, S21_stoich, S22_stoich, S23_stoich, S24_stoich, S25_stoich, S26_stoich, S27_stoich, S28_stoich, S29_stoich, S30_stoich, S31_stoich, S32_stoich, S33_stoich, S34_stoich, S35_stoich, S36_stoich, S37_stoich, S38_stoich, S39_stoich, S40_stoich, S41_stoich, S42_stoich, S43_stoich, S44_stoich, S45_stoich, S46_stoich, S47_stoich, S48_stoich, S49_stoich, S50_stoich, S51_stoich) + +There are 52 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S0_stoich S0 | $1$ | +| J1: -> S1_stoich S1 | $1$ | +| J2: -> S2_stoich S2 | $1$ | +| J3: -> S3_stoich S3 | $1$ | +| J4: -> S4_stoich S4 | $1$ | +| J5: -> S5_stoich S5 | $1$ | +| J6: -> S6_stoich S6 | $1$ | +| J7: -> S7_stoich S7 | $1$ | +| J8: -> S8_stoich S8 | $1$ | +| J9: -> S9_stoich S9 | $1$ | +| J10: -> S10_stoich S10 | $1$ | +| J11: -> S11_stoich S11 | $1$ | +| J12: -> S12_stoich S12 | $1$ | +| J13: -> S13_stoich S13 | $1$ | +| J14: -> S14_stoich S14 | $1$ | +| J15: -> S15_stoich S15 | $1$ | +| J16: -> S16_stoich S16 | $1$ | +| J17: -> S17_stoich S17 | $1$ | +| J18: -> S18_stoich S18 | $1$ | +| J19: -> S19_stoich S19 | $1$ | +| J20: -> S20_stoich S20 | $1$ | +| J21: -> S21_stoich S21 | $1$ | +| J22: -> S22_stoich S22 | $1$ | +| J23: -> S23_stoich S23 | $1$ | +| J24: -> S24_stoich S24 | $1$ | +| J25: -> S25_stoich S25 | $1$ | +| J26: -> S26_stoich S26 | $1$ | +| J27: -> S27_stoich S27 | $1$ | +| J28: -> S28_stoich S28 | $1$ | +| J29: -> S29_stoich S29 | $1$ | +| J30: -> S30_stoich S30 | $1$ | +| J31: -> S31_stoich S31 | $1$ | +| J32: -> S32_stoich S32 | $1$ | +| J33: -> S33_stoich S33 | $1$ | +| J34: -> S34_stoich S34 | $1$ | +| J35: -> S35_stoich S35 | $1$ | +| J36: -> S36_stoich S36 | $1$ | +| J37: -> S37_stoich S37 | $1$ | +| J38: -> S38_stoich S38 | $1$ | +| J39: -> S39_stoich S39 | $1$ | +| J40: -> S40_stoich S40 | $1$ | +| J41: -> S41_stoich S41 | $1$ | +| J42: -> S42_stoich S42 | $1$ | +| J43: -> S43_stoich S43 | $1$ | +| J44: -> S44_stoich S44 | $1$ | +| J45: -> S45_stoich S45 | $1$ | +| J46: -> S46_stoich S46 | $1$ | +| J47: -> S47_stoich S47 | $1$ | +| J48: -> S48_stoich S48 | $1$ | +| J49: -> S49_stoich S49 | $1$ | +| J50: -> S50_stoich S50 | $1$ | +| J51: -> S51_stoich S51 | $1$ |] +Note: the following stoichiometries are set separately: S0_stoich, S1_stoich, S2_stoich, S3_stoich, S4_stoich, S5_stoich, S6_stoich, S7_stoich, S8_stoich, S9_stoich, S10_stoich, S11_stoich, S12_stoich, S13_stoich, S14_stoich, S15_stoich, S16_stoich, S17_stoich, S18_stoich, S19_stoich, S20_stoich, S21_stoich, S22_stoich, S23_stoich, S24_stoich, S25_stoich, S26_stoich, S27_stoich, S28_stoich, S29_stoich, S30_stoich, S31_stoich, S32_stoich, S33_stoich, S34_stoich, S35_stoich, S36_stoich, S37_stoich, S38_stoich, S39_stoich, S40_stoich, S41_stoich, S42_stoich, S43_stoich, S44_stoich, S45_stoich, S46_stoich, S47_stoich, S48_stoich, S49_stoich, S50_stoich, S51_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S0 | $0$ | variable | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial concentration of species S3 | $0$ | variable | +| Initial concentration of species S4 | $0$ | variable | +| Initial concentration of species S5 | $0$ | variable | +| Initial concentration of species S6 | $0$ | variable | +| Initial concentration of species S7 | $0$ | variable | +| Initial concentration of species S8 | $0$ | variable | +| Initial concentration of species S9 | $0$ | variable | +| Initial concentration of species S10 | $0$ | variable | +| Initial concentration of species S11 | $0$ | variable | +| Initial concentration of species S12 | $0$ | variable | +| Initial concentration of species S13 | $0$ | variable | +| Initial concentration of species S14 | $0$ | variable | +| Initial concentration of species S15 | $0$ | variable | +| Initial concentration of species S16 | $0$ | variable | +| Initial concentration of species S17 | $0$ | variable | +| Initial concentration of species S18 | $0$ | variable | +| Initial concentration of species S19 | $0$ | variable | +| Initial concentration of species S20 | $0$ | variable | +| Initial concentration of species S21 | $0$ | variable | +| Initial concentration of species S22 | $0$ | variable | +| Initial concentration of species S23 | $0$ | variable | +| Initial concentration of species S24 | $0$ | variable | +| Initial concentration of species S25 | $0$ | variable | +| Initial concentration of species S26 | $0$ | variable | +| Initial concentration of species S27 | $0$ | variable | +| Initial concentration of species S28 | $0$ | variable | +| Initial concentration of species S29 | $0$ | variable | +| Initial concentration of species S30 | $0$ | variable | +| Initial concentration of species S31 | $0$ | variable | +| Initial concentration of species S32 | $0$ | variable | +| Initial concentration of species S33 | $0$ | variable | +| Initial concentration of species S34 | $0$ | variable | +| Initial concentration of species S35 | $0$ | variable | +| Initial concentration of species S36 | $0$ | variable | +| Initial concentration of species S37 | $0$ | variable | +| Initial concentration of species S38 | $0$ | variable | +| Initial concentration of species S39 | $0$ | variable | +| Initial concentration of species S40 | $0$ | variable | +| Initial concentration of species S41 | $0$ | variable | +| Initial concentration of species S42 | $0$ | variable | +| Initial concentration of species S43 | $0$ | variable | +| Initial concentration of species S44 | $0$ | variable | +| Initial concentration of species S45 | $0$ | variable | +| Initial concentration of species S46 | $0$ | variable | +| Initial concentration of species S47 | $0$ | variable | +| Initial concentration of species S48 | $0$ | variable | +| Initial concentration of species S49 | $0$ | variable | +| Initial concentration of species S50 | $0$ | variable | +| Initial concentration of species S51 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S0_stoich' | $exponentiale$ | variable | +| Initial value of species reference 'S1_stoich' | $exp(exponentiale)$ | variable | +| Initial value of species reference 'S2_stoich' | $abs(-1)$ | variable | +| Initial value of species reference 'S3_stoich' | $abs(1)$ | variable | +| Initial value of species reference 'S4_stoich' | $acos(-1)$ | variable | +| Initial value of species reference 'S5_stoich' | $acos(0.5)$ | variable | +| Initial value of species reference 'S6_stoich' | $asin(1)$ | variable | +| Initial value of species reference 'S7_stoich' | $asin(-0.5)$ | variable | +| Initial value of species reference 'S8_stoich' | $atan(2.8)$ | variable | +| Initial value of species reference 'S9_stoich' | $atan(-7.09)$ | variable | +| Initial value of species reference 'S10_stoich' | $ceil(0.5)$ | variable | +| Initial value of species reference 'S11_stoich' | $ceil(3.55)$ | variable | +| Initial value of species reference 'S12_stoich' | $ceil(-4.6)$ | variable | +| Initial value of species reference 'S13_stoich' | $cos(9.1)$ | variable | +| Initial value of species reference 'S14_stoich' | $cos(-0.22)$ | variable | +| Initial value of species reference 'S15_stoich' | $exp(0)$ | variable | +| Initial value of species reference 'S16_stoich' | $exp(1)$ | variable | +| Initial value of species reference 'S17_stoich' | $exp(0.77)$ | variable | +| Initial value of species reference 'S18_stoich' | $floor(-4.6)$ | variable | +| Initial value of species reference 'S19_stoich' | $floor(9.1)$ | variable | +| Initial value of species reference 'S20_stoich' | $ln(0.2)$ | variable | +| Initial value of species reference 'S21_stoich' | $ln(1)$ | variable | +| Initial value of species reference 'S22_stoich' | $log10(0.2)$ | variable | +| Initial value of species reference 'S23_stoich' | $log10(1)$ | variable | +| Initial value of species reference 'S24_stoich' | $1^2$ | variable | +| Initial value of species reference 'S25_stoich' | $2^2$ | variable | +| Initial value of species reference 'S26_stoich' | $1.4^5.1$ | variable | +| Initial value of species reference 'S27_stoich' | $4^2$ | variable | +| Initial value of species reference 'S28_stoich' | $3.1^2$ | variable | +| Initial value of species reference 'S29_stoich' | $sqrt(4)$ | variable | +| Initial value of species reference 'S30_stoich' | $sqrt(7.4)$ | variable | +| Initial value of species reference 'S31_stoich' | $sin(2.1)$ | variable | +| Initial value of species reference 'S32_stoich' | $sin(0)$ | variable | +| Initial value of species reference 'S33_stoich' | $sin(-5.9)$ | variable | +| Initial value of species reference 'S34_stoich' | $tan(0)$ | variable | +| Initial value of species reference 'S35_stoich' | $tan(1.11)$ | variable | +| Initial value of species reference 'S36_stoich' | $tan(-6)$ | variable | +| Initial value of species reference 'S37_stoich' | $sec(0.5)$ | variable | +| Initial value of species reference 'S38_stoich' | $csc(4.5)$ | variable | +| Initial value of species reference 'S39_stoich' | $cot(0.2)$ | variable | +| Initial value of species reference 'S40_stoich' | $sinh(0.3)$ | variable | +| Initial value of species reference 'S41_stoich' | $cosh(1.7)$ | variable | +| Initial value of species reference 'S42_stoich' | $arcsec(2.3)$ | variable | +| Initial value of species reference 'S43_stoich' | $arccsc(1.1)$ | variable | +| Initial value of species reference 'S44_stoich' | $arccot(-0.1)$ | variable | +| Initial value of species reference 'S45_stoich' | $arcsinh(99)$ | variable | +| Initial value of species reference 'S46_stoich' | $arccosh(1.34)$ | variable | +| Initial value of species reference 'S47_stoich' | $arctanh(-0.7)$ | variable | +| Initial value of species reference 'S48_stoich' | $arcsech(0.42)$ | variable | +| Initial value of species reference 'S49_stoich' | $arccsch(0.01)$ | variable | +| Initial value of species reference 'S50_stoich' | $times()$ | variable | +| Initial value of species reference 'S51_stoich' | $plus()$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01563/l2v5/index.heta b/latest/cases/01563/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01563/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01563/l3v2/build.log b/latest/cases/01563/l3v2/build.log new file mode 100644 index 000000000..bf125d4e4 --- /dev/null +++ b/latest/cases/01563/l3v2/build.log @@ -0,0 +1,131 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01563/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01563/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01563/model-sbml-l3v2.xml"... +[error] S0_stoich component does not exist which is not allowed for the "update" action. +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[error] S3_stoich component does not exist which is not allowed for the "update" action. +[error] S4_stoich component does not exist which is not allowed for the "update" action. +[error] S5_stoich component does not exist which is not allowed for the "update" action. +[error] S6_stoich component does not exist which is not allowed for the "update" action. +[error] S7_stoich component does not exist which is not allowed for the "update" action. +[error] S8_stoich component does not exist which is not allowed for the "update" action. +[error] S9_stoich component does not exist which is not allowed for the "update" action. +[error] S10_stoich component does not exist which is not allowed for the "update" action. +[error] S11_stoich component does not exist which is not allowed for the "update" action. +[error] S12_stoich component does not exist which is not allowed for the "update" action. +[error] S13_stoich component does not exist which is not allowed for the "update" action. +[error] S14_stoich component does not exist which is not allowed for the "update" action. +[error] S15_stoich component does not exist which is not allowed for the "update" action. +[error] S16_stoich component does not exist which is not allowed for the "update" action. +[error] S17_stoich component does not exist which is not allowed for the "update" action. +[error] S18_stoich component does not exist which is not allowed for the "update" action. +[error] S19_stoich component does not exist which is not allowed for the "update" action. +[error] S20_stoich component does not exist which is not allowed for the "update" action. +[error] S21_stoich component does not exist which is not allowed for the "update" action. +[error] S22_stoich component does not exist which is not allowed for the "update" action. +[error] S23_stoich component does not exist which is not allowed for the "update" action. +[error] S24_stoich component does not exist which is not allowed for the "update" action. +[error] S25_stoich component does not exist which is not allowed for the "update" action. +[error] S26_stoich component does not exist which is not allowed for the "update" action. +[error] S27_stoich component does not exist which is not allowed for the "update" action. +[error] S28_stoich component does not exist which is not allowed for the "update" action. +[error] S29_stoich component does not exist which is not allowed for the "update" action. +[error] S30_stoich component does not exist which is not allowed for the "update" action. +[error] S31_stoich component does not exist which is not allowed for the "update" action. +[error] S32_stoich component does not exist which is not allowed for the "update" action. +[error] S33_stoich component does not exist which is not allowed for the "update" action. +[error] S34_stoich component does not exist which is not allowed for the "update" action. +[error] S35_stoich component does not exist which is not allowed for the "update" action. +[error] S36_stoich component does not exist which is not allowed for the "update" action. +[error] S37_stoich component does not exist which is not allowed for the "update" action. +[error] S38_stoich component does not exist which is not allowed for the "update" action. +[error] S39_stoich component does not exist which is not allowed for the "update" action. +[error] S40_stoich component does not exist which is not allowed for the "update" action. +[error] S41_stoich component does not exist which is not allowed for the "update" action. +[error] S42_stoich component does not exist which is not allowed for the "update" action. +[error] S43_stoich component does not exist which is not allowed for the "update" action. +[error] S44_stoich component does not exist which is not allowed for the "update" action. +[error] S45_stoich component does not exist which is not allowed for the "update" action. +[error] S46_stoich component does not exist which is not allowed for the "update" action. +[error] S47_stoich component does not exist which is not allowed for the "update" action. +[error] S48_stoich component does not exist which is not allowed for the "update" action. +[error] S49_stoich component does not exist which is not allowed for the "update" action. +[error] S50_stoich_proc Some of properties do not satisfy requirements for class "Record" + 1. /assignments/ode_ should NOT be shorter than 1 characters + 2. /assignments/ode_ should be number + 3. /assignments/ode_ should match exactly one schema in oneOf +[warn] Some of component properties will not be updated. +[error] S50_stoich component does not exist which is not allowed for the "update" action. +[error] S51_stoich_proc Some of properties do not satisfy requirements for class "Record" + 1. /assignments/ode_ should NOT be shorter than 1 characters + 2. /assignments/ode_ should be number + 3. /assignments/ode_ should match exactly one schema in oneOf +[warn] Some of component properties will not be updated. +[error] S51_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 236 +[error] S0_stoich_proc Property "actors[0].target" has lost reference "S0_stoich". +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[error] S2_stoich_proc Property "actors[0].target" has lost reference "S2_stoich". +[error] S3_stoich_proc Property "actors[0].target" has lost reference "S3_stoich". +[error] S4_stoich_proc Property "actors[0].target" has lost reference "S4_stoich". +[error] S5_stoich_proc Property "actors[0].target" has lost reference "S5_stoich". +[error] S6_stoich_proc Property "actors[0].target" has lost reference "S6_stoich". +[error] S7_stoich_proc Property "actors[0].target" has lost reference "S7_stoich". +[error] S8_stoich_proc Property "actors[0].target" has lost reference "S8_stoich". +[error] S9_stoich_proc Property "actors[0].target" has lost reference "S9_stoich". +[error] S10_stoich_proc Property "actors[0].target" has lost reference "S10_stoich". +[error] S11_stoich_proc Property "actors[0].target" has lost reference "S11_stoich". +[error] S12_stoich_proc Property "actors[0].target" has lost reference "S12_stoich". +[error] S13_stoich_proc Property "actors[0].target" has lost reference "S13_stoich". +[error] S14_stoich_proc Property "actors[0].target" has lost reference "S14_stoich". +[error] S15_stoich_proc Property "actors[0].target" has lost reference "S15_stoich". +[error] S16_stoich_proc Property "actors[0].target" has lost reference "S16_stoich". +[error] S17_stoich_proc Property "actors[0].target" has lost reference "S17_stoich". +[error] S18_stoich_proc Property "actors[0].target" has lost reference "S18_stoich". +[error] S19_stoich_proc Property "actors[0].target" has lost reference "S19_stoich". +[error] S20_stoich_proc Property "actors[0].target" has lost reference "S20_stoich". +[error] S21_stoich_proc Property "actors[0].target" has lost reference "S21_stoich". +[error] S22_stoich_proc Property "actors[0].target" has lost reference "S22_stoich". +[error] S23_stoich_proc Property "actors[0].target" has lost reference "S23_stoich". +[error] S24_stoich_proc Property "actors[0].target" has lost reference "S24_stoich". +[error] S25_stoich_proc Property "actors[0].target" has lost reference "S25_stoich". +[error] S26_stoich_proc Property "actors[0].target" has lost reference "S26_stoich". +[error] S27_stoich_proc Property "actors[0].target" has lost reference "S27_stoich". +[error] S28_stoich_proc Property "actors[0].target" has lost reference "S28_stoich". +[error] S29_stoich_proc Property "actors[0].target" has lost reference "S29_stoich". +[error] S30_stoich_proc Property "actors[0].target" has lost reference "S30_stoich". +[error] S31_stoich_proc Property "actors[0].target" has lost reference "S31_stoich". +[error] S32_stoich_proc Property "actors[0].target" has lost reference "S32_stoich". +[error] S33_stoich_proc Property "actors[0].target" has lost reference "S33_stoich". +[error] S34_stoich_proc Property "actors[0].target" has lost reference "S34_stoich". +[error] S35_stoich_proc Property "actors[0].target" has lost reference "S35_stoich". +[error] S36_stoich_proc Property "actors[0].target" has lost reference "S36_stoich". +[error] S37_stoich_proc Property "actors[0].target" has lost reference "S37_stoich". +[error] S38_stoich_proc Property "actors[0].target" has lost reference "S38_stoich". +[error] S39_stoich_proc Property "actors[0].target" has lost reference "S39_stoich". +[error] S40_stoich_proc Property "actors[0].target" has lost reference "S40_stoich". +[error] FunctionDef "sinh" is not found as expected here: S40_stoich_proc { math: undefined }; +[error] S41_stoich_proc Property "actors[0].target" has lost reference "S41_stoich". +[error] FunctionDef "cosh" is not found as expected here: S41_stoich_proc { math: undefined }; +[error] S42_stoich_proc Property "actors[0].target" has lost reference "S42_stoich". +[error] S43_stoich_proc Property "actors[0].target" has lost reference "S43_stoich". +[error] S44_stoich_proc Property "actors[0].target" has lost reference "S44_stoich". +[error] S45_stoich_proc Property "actors[0].target" has lost reference "S45_stoich". +[error] FunctionDef "asinh" is not found as expected here: S45_stoich_proc { math: undefined }; +[error] S46_stoich_proc Property "actors[0].target" has lost reference "S46_stoich". +[error] FunctionDef "acosh" is not found as expected here: S46_stoich_proc { math: undefined }; +[error] S47_stoich_proc Property "actors[0].target" has lost reference "S47_stoich". +[error] FunctionDef "atanh" is not found as expected here: S47_stoich_proc { math: undefined }; +[error] S48_stoich_proc Property "actors[0].target" has lost reference "S48_stoich". +[error] FunctionDef "asech" is not found as expected here: S48_stoich_proc { math: undefined }; +[error] S49_stoich_proc Property "actors[0].target" has lost reference "S49_stoich". +[error] FunctionDef "acsch" is not found as expected here: S49_stoich_proc { math: undefined }; +[error] S50_stoich_proc Property "actors[0].target" has lost reference "S50_stoich". +[error] Record "S50_stoich_proc" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] S51_stoich_proc Property "actors[0].target" has lost reference "S51_stoich". +[error] Record "S51_stoich_proc" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01563/l3v2/index.heta b/latest/cases/01563/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01563/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01563/model-sbml-l3v2.xml b/latest/cases/01563/model-sbml-l3v2.xml new file mode 100644 index 000000000..d3a532dff --- /dev/null +++ b/latest/cases/01563/model-sbml-l3v2.xml @@ -0,0 +1,1014 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + + + + + + + + 1 + + + + + + + + -1 + + + + + + + + 0.5 + + + + + + + + 1 + + + + + + + + -0.5 + + + + + + + + 2.8 + + + + + + + + -7.09 + + + + + + + + 0.5 + + + + + + + + 3.55 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + -0.22 + + + + + + + + 0 + + + + + + + + 1 + + + + + + + + 0.77 + + + + + + + + -4.6 + + + + + + + + 9.1 + + + + + + + + 0.2 + + + + + + + + 1 + + + + + + + + + 10 + + 0.2 + + + + + + + + + 10 + + 1 + + + + + + + + 1 + 2 + + + + + + + + 2 + 2 + + + + + + + + 1.4 + 5.1 + + + + + + + + 4 + 2 + + + + + + + + 3.1 + 2 + + + + + + + + + 2 + + 4 + + + + + + + + + 2 + + 7.4 + + + + + + + + 2.1 + + + + + + + + 0 + + + + + + + + -5.9 + + + + + + + + 0 + + + + + + + + 1.11 + + + + + + + + -6 + + + + + + + + 0.5 + + + + + + + + 4.5 + + + + + + + + 0.2 + + + + + + + + 0.3 + + + + + + + + 1.7 + + + + + + + + 2.3 + + + + + + + + 1.1 + + + + + + + + -0.1 + + + + + + + + 99 + + + + + + + + 1.34 + + + + + + + + -0.7 + + + + + + + + 0.42 + + + + + + + + 0.01 + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01563/synopsis.txt b/latest/cases/01563/synopsis.txt new file mode 100644 index 000000000..c58c5c4e1 --- /dev/null +++ b/latest/cases/01563/synopsis.txt @@ -0,0 +1,243 @@ + +category: Test +synopsis: Uncommon MathML assigned to stoichiometries. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NonUnityStoichiometry, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests various uncommon mathematical constructs assigned to stoichiometries. + +The model contains: +* 52 species (S0, S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17, S18, S19, S20, S21, S22, S23, S24, S25, S26, S27, S28, S29, S30, S31, S32, S33, S34, S35, S36, S37, S38, S39, S40, S41, S42, S43, S44, S45, S46, S47, S48, S49, S50, S51) +* 1 compartment (C) +* 52 species references (S0_stoich, S1_stoich, S2_stoich, S3_stoich, S4_stoich, S5_stoich, S6_stoich, S7_stoich, S8_stoich, S9_stoich, S10_stoich, S11_stoich, S12_stoich, S13_stoich, S14_stoich, S15_stoich, S16_stoich, S17_stoich, S18_stoich, S19_stoich, S20_stoich, S21_stoich, S22_stoich, S23_stoich, S24_stoich, S25_stoich, S26_stoich, S27_stoich, S28_stoich, S29_stoich, S30_stoich, S31_stoich, S32_stoich, S33_stoich, S34_stoich, S35_stoich, S36_stoich, S37_stoich, S38_stoich, S39_stoich, S40_stoich, S41_stoich, S42_stoich, S43_stoich, S44_stoich, S45_stoich, S46_stoich, S47_stoich, S48_stoich, S49_stoich, S50_stoich, S51_stoich) + +There are 52 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S0_stoich S0 | $1$ | +| J1: -> S1_stoich S1 | $1$ | +| J2: -> S2_stoich S2 | $1$ | +| J3: -> S3_stoich S3 | $1$ | +| J4: -> S4_stoich S4 | $1$ | +| J5: -> S5_stoich S5 | $1$ | +| J6: -> S6_stoich S6 | $1$ | +| J7: -> S7_stoich S7 | $1$ | +| J8: -> S8_stoich S8 | $1$ | +| J9: -> S9_stoich S9 | $1$ | +| J10: -> S10_stoich S10 | $1$ | +| J11: -> S11_stoich S11 | $1$ | +| J12: -> S12_stoich S12 | $1$ | +| J13: -> S13_stoich S13 | $1$ | +| J14: -> S14_stoich S14 | $1$ | +| J15: -> S15_stoich S15 | $1$ | +| J16: -> S16_stoich S16 | $1$ | +| J17: -> S17_stoich S17 | $1$ | +| J18: -> S18_stoich S18 | $1$ | +| J19: -> S19_stoich S19 | $1$ | +| J20: -> S20_stoich S20 | $1$ | +| J21: -> S21_stoich S21 | $1$ | +| J22: -> S22_stoich S22 | $1$ | +| J23: -> S23_stoich S23 | $1$ | +| J24: -> S24_stoich S24 | $1$ | +| J25: -> S25_stoich S25 | $1$ | +| J26: -> S26_stoich S26 | $1$ | +| J27: -> S27_stoich S27 | $1$ | +| J28: -> S28_stoich S28 | $1$ | +| J29: -> S29_stoich S29 | $1$ | +| J30: -> S30_stoich S30 | $1$ | +| J31: -> S31_stoich S31 | $1$ | +| J32: -> S32_stoich S32 | $1$ | +| J33: -> S33_stoich S33 | $1$ | +| J34: -> S34_stoich S34 | $1$ | +| J35: -> S35_stoich S35 | $1$ | +| J36: -> S36_stoich S36 | $1$ | +| J37: -> S37_stoich S37 | $1$ | +| J38: -> S38_stoich S38 | $1$ | +| J39: -> S39_stoich S39 | $1$ | +| J40: -> S40_stoich S40 | $1$ | +| J41: -> S41_stoich S41 | $1$ | +| J42: -> S42_stoich S42 | $1$ | +| J43: -> S43_stoich S43 | $1$ | +| J44: -> S44_stoich S44 | $1$ | +| J45: -> S45_stoich S45 | $1$ | +| J46: -> S46_stoich S46 | $1$ | +| J47: -> S47_stoich S47 | $1$ | +| J48: -> S48_stoich S48 | $1$ | +| J49: -> S49_stoich S49 | $1$ | +| J50: -> S50_stoich S50 | $1$ | +| J51: -> S51_stoich S51 | $1$ |] +Note: the following stoichiometries are set separately: S0_stoich, S1_stoich, S2_stoich, S3_stoich, S4_stoich, S5_stoich, S6_stoich, S7_stoich, S8_stoich, S9_stoich, S10_stoich, S11_stoich, S12_stoich, S13_stoich, S14_stoich, S15_stoich, S16_stoich, S17_stoich, S18_stoich, S19_stoich, S20_stoich, S21_stoich, S22_stoich, S23_stoich, S24_stoich, S25_stoich, S26_stoich, S27_stoich, S28_stoich, S29_stoich, S30_stoich, S31_stoich, S32_stoich, S33_stoich, S34_stoich, S35_stoich, S36_stoich, S37_stoich, S38_stoich, S39_stoich, S40_stoich, S41_stoich, S42_stoich, S43_stoich, S44_stoich, S45_stoich, S46_stoich, S47_stoich, S48_stoich, S49_stoich, S50_stoich, S51_stoich + + +There are 52 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S0_stoich | $exponentiale$ | +| Rate | S1_stoich | $exp(exponentiale)$ | +| Rate | S2_stoich | $abs(-1)$ | +| Rate | S3_stoich | $abs(1)$ | +| Rate | S4_stoich | $acos(-1)$ | +| Rate | S5_stoich | $acos(0.5)$ | +| Rate | S6_stoich | $asin(1)$ | +| Rate | S7_stoich | $asin(-0.5)$ | +| Rate | S8_stoich | $atan(2.8)$ | +| Rate | S9_stoich | $atan(-7.09)$ | +| Rate | S10_stoich | $ceil(0.5)$ | +| Rate | S11_stoich | $ceil(3.55)$ | +| Rate | S12_stoich | $ceil(-4.6)$ | +| Rate | S13_stoich | $cos(9.1)$ | +| Rate | S14_stoich | $cos(-0.22)$ | +| Rate | S15_stoich | $exp(0)$ | +| Rate | S16_stoich | $exp(1)$ | +| Rate | S17_stoich | $exp(0.77)$ | +| Rate | S18_stoich | $floor(-4.6)$ | +| Rate | S19_stoich | $floor(9.1)$ | +| Rate | S20_stoich | $ln(0.2)$ | +| Rate | S21_stoich | $ln(1)$ | +| Rate | S22_stoich | $log10(0.2)$ | +| Rate | S23_stoich | $log10(1)$ | +| Rate | S24_stoich | $1^2$ | +| Rate | S25_stoich | $2^2$ | +| Rate | S26_stoich | $1.4^5.1$ | +| Rate | S27_stoich | $4^2$ | +| Rate | S28_stoich | $3.1^2$ | +| Rate | S29_stoich | $sqrt(4)$ | +| Rate | S30_stoich | $sqrt(7.4)$ | +| Rate | S31_stoich | $sin(2.1)$ | +| Rate | S32_stoich | $sin(0)$ | +| Rate | S33_stoich | $sin(-5.9)$ | +| Rate | S34_stoich | $tan(0)$ | +| Rate | S35_stoich | $tan(1.11)$ | +| Rate | S36_stoich | $tan(-6)$ | +| Rate | S37_stoich | $sec(0.5)$ | +| Rate | S38_stoich | $csc(4.5)$ | +| Rate | S39_stoich | $cot(0.2)$ | +| Rate | S40_stoich | $sinh(0.3)$ | +| Rate | S41_stoich | $cosh(1.7)$ | +| Rate | S42_stoich | $arcsec(2.3)$ | +| Rate | S43_stoich | $arccsc(1.1)$ | +| Rate | S44_stoich | $arccot(-0.1)$ | +| Rate | S45_stoich | $arcsinh(99)$ | +| Rate | S46_stoich | $arccosh(1.34)$ | +| Rate | S47_stoich | $arctanh(-0.7)$ | +| Rate | S48_stoich | $arcsech(0.42)$ | +| Rate | S49_stoich | $arccsch(0.01)$ | +| Rate | S50_stoich | $times()$ | +| Rate | S51_stoich | $plus()$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S0 | $0$ | variable | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial concentration of species S3 | $0$ | variable | +| Initial concentration of species S4 | $0$ | variable | +| Initial concentration of species S5 | $0$ | variable | +| Initial concentration of species S6 | $0$ | variable | +| Initial concentration of species S7 | $0$ | variable | +| Initial concentration of species S8 | $0$ | variable | +| Initial concentration of species S9 | $0$ | variable | +| Initial concentration of species S10 | $0$ | variable | +| Initial concentration of species S11 | $0$ | variable | +| Initial concentration of species S12 | $0$ | variable | +| Initial concentration of species S13 | $0$ | variable | +| Initial concentration of species S14 | $0$ | variable | +| Initial concentration of species S15 | $0$ | variable | +| Initial concentration of species S16 | $0$ | variable | +| Initial concentration of species S17 | $0$ | variable | +| Initial concentration of species S18 | $0$ | variable | +| Initial concentration of species S19 | $0$ | variable | +| Initial concentration of species S20 | $0$ | variable | +| Initial concentration of species S21 | $0$ | variable | +| Initial concentration of species S22 | $0$ | variable | +| Initial concentration of species S23 | $0$ | variable | +| Initial concentration of species S24 | $0$ | variable | +| Initial concentration of species S25 | $0$ | variable | +| Initial concentration of species S26 | $0$ | variable | +| Initial concentration of species S27 | $0$ | variable | +| Initial concentration of species S28 | $0$ | variable | +| Initial concentration of species S29 | $0$ | variable | +| Initial concentration of species S30 | $0$ | variable | +| Initial concentration of species S31 | $0$ | variable | +| Initial concentration of species S32 | $0$ | variable | +| Initial concentration of species S33 | $0$ | variable | +| Initial concentration of species S34 | $0$ | variable | +| Initial concentration of species S35 | $0$ | variable | +| Initial concentration of species S36 | $0$ | variable | +| Initial concentration of species S37 | $0$ | variable | +| Initial concentration of species S38 | $0$ | variable | +| Initial concentration of species S39 | $0$ | variable | +| Initial concentration of species S40 | $0$ | variable | +| Initial concentration of species S41 | $0$ | variable | +| Initial concentration of species S42 | $0$ | variable | +| Initial concentration of species S43 | $0$ | variable | +| Initial concentration of species S44 | $0$ | variable | +| Initial concentration of species S45 | $0$ | variable | +| Initial concentration of species S46 | $0$ | variable | +| Initial concentration of species S47 | $0$ | variable | +| Initial concentration of species S48 | $0$ | variable | +| Initial concentration of species S49 | $0$ | variable | +| Initial concentration of species S50 | $0$ | variable | +| Initial concentration of species S51 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S0_stoich' | $0$ | variable | +| Initial value of species reference 'S1_stoich' | $0$ | variable | +| Initial value of species reference 'S2_stoich' | $0$ | variable | +| Initial value of species reference 'S3_stoich' | $0$ | variable | +| Initial value of species reference 'S4_stoich' | $0$ | variable | +| Initial value of species reference 'S5_stoich' | $0$ | variable | +| Initial value of species reference 'S6_stoich' | $0$ | variable | +| Initial value of species reference 'S7_stoich' | $0$ | variable | +| Initial value of species reference 'S8_stoich' | $0$ | variable | +| Initial value of species reference 'S9_stoich' | $0$ | variable | +| Initial value of species reference 'S10_stoich' | $0$ | variable | +| Initial value of species reference 'S11_stoich' | $0$ | variable | +| Initial value of species reference 'S12_stoich' | $0$ | variable | +| Initial value of species reference 'S13_stoich' | $0$ | variable | +| Initial value of species reference 'S14_stoich' | $0$ | variable | +| Initial value of species reference 'S15_stoich' | $0$ | variable | +| Initial value of species reference 'S16_stoich' | $0$ | variable | +| Initial value of species reference 'S17_stoich' | $0$ | variable | +| Initial value of species reference 'S18_stoich' | $0$ | variable | +| Initial value of species reference 'S19_stoich' | $0$ | variable | +| Initial value of species reference 'S20_stoich' | $0$ | variable | +| Initial value of species reference 'S21_stoich' | $0$ | variable | +| Initial value of species reference 'S22_stoich' | $0$ | variable | +| Initial value of species reference 'S23_stoich' | $0$ | variable | +| Initial value of species reference 'S24_stoich' | $0$ | variable | +| Initial value of species reference 'S25_stoich' | $0$ | variable | +| Initial value of species reference 'S26_stoich' | $0$ | variable | +| Initial value of species reference 'S27_stoich' | $0$ | variable | +| Initial value of species reference 'S28_stoich' | $0$ | variable | +| Initial value of species reference 'S29_stoich' | $0$ | variable | +| Initial value of species reference 'S30_stoich' | $0$ | variable | +| Initial value of species reference 'S31_stoich' | $0$ | variable | +| Initial value of species reference 'S32_stoich' | $0$ | variable | +| Initial value of species reference 'S33_stoich' | $0$ | variable | +| Initial value of species reference 'S34_stoich' | $0$ | variable | +| Initial value of species reference 'S35_stoich' | $0$ | variable | +| Initial value of species reference 'S36_stoich' | $0$ | variable | +| Initial value of species reference 'S37_stoich' | $0$ | variable | +| Initial value of species reference 'S38_stoich' | $0$ | variable | +| Initial value of species reference 'S39_stoich' | $0$ | variable | +| Initial value of species reference 'S40_stoich' | $0$ | variable | +| Initial value of species reference 'S41_stoich' | $0$ | variable | +| Initial value of species reference 'S42_stoich' | $0$ | variable | +| Initial value of species reference 'S43_stoich' | $0$ | variable | +| Initial value of species reference 'S44_stoich' | $0$ | variable | +| Initial value of species reference 'S45_stoich' | $0$ | variable | +| Initial value of species reference 'S46_stoich' | $0$ | variable | +| Initial value of species reference 'S47_stoich' | $0$ | variable | +| Initial value of species reference 'S48_stoich' | $0$ | variable | +| Initial value of species reference 'S49_stoich' | $0$ | variable | +| Initial value of species reference 'S50_stoich' | $0$ | variable | +| Initial value of species reference 'S51_stoich' | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01564/l2v5/build.log b/latest/cases/01564/l2v5/build.log new file mode 100644 index 000000000..0877d0ec9 --- /dev/null +++ b/latest/cases/01564/l2v5/build.log @@ -0,0 +1,17 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01564/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01564/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01564/model-sbml-l2v5.xml"... +[error] J51: Cannot parse MathExpr properly. Value expected (char 8) in " 1 * ()" +[info] Setting references in elements, total length 189 +[error] FunctionDef "sinh" is not found as expected here: J40 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: J41 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: J45 { math: undefined }; +[error] FunctionDef "acosh" is not found as expected here: J46 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: J47 { math: undefined }; +[error] FunctionDef "asech" is not found as expected here: J48 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: J49 { math: undefined }; +[error] Record "J51" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01564/l2v5/index.heta b/latest/cases/01564/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01564/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01564/l3v2/build.log b/latest/cases/01564/l3v2/build.log new file mode 100644 index 000000000..e21f95273 --- /dev/null +++ b/latest/cases/01564/l3v2/build.log @@ -0,0 +1,17 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01564/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01564/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01564/model-sbml-l3v2.xml"... +[error] J51: Cannot parse MathExpr properly. Value expected (char 8) in " 1 * ()" +[info] Setting references in elements, total length 184 +[error] FunctionDef "sinh" is not found as expected here: J40 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: J41 { math: undefined }; +[error] FunctionDef "asinh" is not found as expected here: J45 { math: undefined }; +[error] FunctionDef "acosh" is not found as expected here: J46 { math: undefined }; +[error] FunctionDef "atanh" is not found as expected here: J47 { math: undefined }; +[error] FunctionDef "asech" is not found as expected here: J48 { math: undefined }; +[error] FunctionDef "acsch" is not found as expected here: J49 { math: undefined }; +[error] Record "J51" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01564/l3v2/index.heta b/latest/cases/01564/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01564/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01564/model-sbml-l2v5.xml b/latest/cases/01564/model-sbml-l2v5.xml new file mode 100644 index 000000000..30df0b670 --- /dev/null +++ b/latest/cases/01564/model-sbml-l2v5.xml @@ -0,0 +1,957 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + 1 + + + -1 + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + + + 1 + + + -1 + + + + + + + + + + + + + + 1 + + + 0.5 + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + + + 1 + + + -0.5 + + + + + + + + + + + + + + 1 + + + 2.8 + + + + + + + + + + + + + + 1 + + + -7.09 + + + + + + + + + + + + + + 1 + + + 0.5 + + + + + + + + + + + + + + 1 + + + 3.55 + + + + + + + + + + + + + + 1 + + + -4.6 + + + + + + + + + + + + + + 1 + + + 9.1 + + + + + + + + + + + + + + 1 + + + -0.22 + + + + + + + + + + + + + + 1 + + + 0 + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + + + 1 + + + 0.77 + + + + + + + + + + + + + + 1 + + + -4.6 + + + + + + + + + + + + + + 1 + + + 9.1 + + + + + + + + + + + + + + 1 + + + 0.2 + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + + + 1 + + + + 10 + + 0.2 + + + + + + + + + + + + + + 1 + + + + 10 + + 1 + + + + + + + + + + + + + + 1 + + + 1 + 2 + + + + + + + + + + + + + + 1 + + + 2 + 2 + + + + + + + + + + + + + + 1 + + + 1.4 + 5.1 + + + + + + + + + + + + + + 1 + + + 4 + 2 + + + + + + + + + + + + + + 1 + + + 3.1 + 2 + + + + + + + + + + + + + + 1 + + + + 2 + + 4 + + + + + + + + + + + + + + 1 + + + + 2 + + 7.4 + + + + + + + + + + + + + + 1 + + + 2.1 + + + + + + + + + + + + + + 1 + + + 0 + + + + + + + + + + + + + + 1 + + + -5.9 + + + + + + + + + + + + + + 1 + + + 0 + + + + + + + + + + + + + + 1 + + + 1.11 + + + + + + + + + + + + + + 1 + + + -6 + + + + + + + + + + + + + + 1 + + + 0.5 + + + + + + + + + + + + + + 1 + + + 4.5 + + + + + + + + + + + + + + 1 + + + 0.2 + + + + + + + + + + + + + + 1 + + + 0.3 + + + + + + + + + + + + + + 1 + + + 1.7 + + + + + + + + + + + + + + 1 + + + 2.3 + + + + + + + + + + + + + + 1 + + + 1.1 + + + + + + + + + + + + + + 1 + + + -0.1 + + + + + + + + + + + + + + 1 + + + 99 + + + + + + + + + + + + + + 1 + + + 1.34 + + + + + + + + + + + + + + 1 + + + -0.7 + + + + + + + + + + + + + + 1 + + + 0.42 + + + + + + + + + + + + + + 1 + + + 0.01 + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + 1 + + + + + + + + + + diff --git a/latest/cases/01564/model-sbml-l3v2.xml b/latest/cases/01564/model-sbml-l3v2.xml new file mode 100644 index 000000000..c26f3d27b --- /dev/null +++ b/latest/cases/01564/model-sbml-l3v2.xml @@ -0,0 +1,958 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + 1 + + + -1 + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + + + 1 + + + -1 + + + + + + + + + + + + + + 1 + + + 0.5 + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + + + 1 + + + -0.5 + + + + + + + + + + + + + + 1 + + + 2.8 + + + + + + + + + + + + + + 1 + + + -7.09 + + + + + + + + + + + + + + 1 + + + 0.5 + + + + + + + + + + + + + + 1 + + + 3.55 + + + + + + + + + + + + + + 1 + + + -4.6 + + + + + + + + + + + + + + 1 + + + 9.1 + + + + + + + + + + + + + + 1 + + + -0.22 + + + + + + + + + + + + + + 1 + + + 0 + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + + + 1 + + + 0.77 + + + + + + + + + + + + + + 1 + + + -4.6 + + + + + + + + + + + + + + 1 + + + 9.1 + + + + + + + + + + + + + + 1 + + + 0.2 + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + + + + + + + + 1 + + + + 10 + + 0.2 + + + + + + + + + + + + + + 1 + + + + 10 + + 1 + + + + + + + + + + + + + + 1 + + + 1 + 2 + + + + + + + + + + + + + + 1 + + + 2 + 2 + + + + + + + + + + + + + + 1 + + + 1.4 + 5.1 + + + + + + + + + + + + + + 1 + + + 4 + 2 + + + + + + + + + + + + + + 1 + + + 3.1 + 2 + + + + + + + + + + + + + + 1 + + + + 2 + + 4 + + + + + + + + + + + + + + 1 + + + + 2 + + 7.4 + + + + + + + + + + + + + + 1 + + + 2.1 + + + + + + + + + + + + + + 1 + + + 0 + + + + + + + + + + + + + + 1 + + + -5.9 + + + + + + + + + + + + + + 1 + + + 0 + + + + + + + + + + + + + + 1 + + + 1.11 + + + + + + + + + + + + + + 1 + + + -6 + + + + + + + + + + + + + + 1 + + + 0.5 + + + + + + + + + + + + + + 1 + + + 4.5 + + + + + + + + + + + + + + 1 + + + 0.2 + + + + + + + + + + + + + + 1 + + + 0.3 + + + + + + + + + + + + + + 1 + + + 1.7 + + + + + + + + + + + + + + 1 + + + 2.3 + + + + + + + + + + + + + + 1 + + + 1.1 + + + + + + + + + + + + + + 1 + + + -0.1 + + + + + + + + + + + + + + 1 + + + 99 + + + + + + + + + + + + + + 1 + + + 1.34 + + + + + + + + + + + + + + 1 + + + -0.7 + + + + + + + + + + + + + + 1 + + + 0.42 + + + + + + + + + + + + + + 1 + + + 0.01 + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + 1 + + + + + + + + + + diff --git a/latest/cases/01564/synopsis.txt b/latest/cases/01564/synopsis.txt new file mode 100644 index 000000000..6b4dfc7c9 --- /dev/null +++ b/latest/cases/01564/synopsis.txt @@ -0,0 +1,132 @@ + +category: Test +synopsis: Uncommon MathML in kinetic laws. +componentTags: Compartment, Reaction, Species +testTags: Amount, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests various uncommon mathematical constructs in kinetic laws. + +The model contains: +* 52 species (S0, S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17, S18, S19, S20, S21, S22, S23, S24, S25, S26, S27, S28, S29, S30, S31, S32, S33, S34, S35, S36, S37, S38, S39, S40, S41, S42, S43, S44, S45, S46, S47, S48, S49, S50, S51) +* 1 compartment (C) + +There are 52 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S0 | $1 * exponentiale$ | +| J1: -> S1 | $1 * exp(exponentiale)$ | +| J2: -> S2 | $1 * abs(-1)$ | +| J3: -> S3 | $1 * abs(1)$ | +| J4: -> S4 | $1 * acos(-1)$ | +| J5: -> S5 | $1 * acos(0.5)$ | +| J6: -> S6 | $1 * asin(1)$ | +| J7: -> S7 | $1 * asin(-0.5)$ | +| J8: -> S8 | $1 * atan(2.8)$ | +| J9: -> S9 | $1 * atan(-7.09)$ | +| J10: -> S10 | $1 * ceil(0.5)$ | +| J11: -> S11 | $1 * ceil(3.55)$ | +| J12: -> S12 | $1 * ceil(-4.6)$ | +| J13: -> S13 | $1 * cos(9.1)$ | +| J14: -> S14 | $1 * cos(-0.22)$ | +| J15: -> S15 | $1 * exp(0)$ | +| J16: -> S16 | $1 * exp(1)$ | +| J17: -> S17 | $1 * exp(0.77)$ | +| J18: -> S18 | $1 * floor(-4.6)$ | +| J19: -> S19 | $1 * floor(9.1)$ | +| J20: -> S20 | $1 * ln(0.2)$ | +| J21: -> S21 | $1 * ln(1)$ | +| J22: -> S22 | $1 * log10(0.2)$ | +| J23: -> S23 | $1 * log10(1)$ | +| J24: -> S24 | $1 * 1^2$ | +| J25: -> S25 | $1 * 2^2$ | +| J26: -> S26 | $1 * 1.4^5.1$ | +| J27: -> S27 | $1 * 4^2$ | +| J28: -> S28 | $1 * 3.1^2$ | +| J29: -> S29 | $1 * sqrt(4)$ | +| J30: -> S30 | $1 * sqrt(7.4)$ | +| J31: -> S31 | $1 * sin(2.1)$ | +| J32: -> S32 | $1 * sin(0)$ | +| J33: -> S33 | $1 * sin(-5.9)$ | +| J34: -> S34 | $1 * tan(0)$ | +| J35: -> S35 | $1 * tan(1.11)$ | +| J36: -> S36 | $1 * tan(-6)$ | +| J37: -> S37 | $1 * sec(0.5)$ | +| J38: -> S38 | $1 * csc(4.5)$ | +| J39: -> S39 | $1 * cot(0.2)$ | +| J40: -> S40 | $1 * sinh(0.3)$ | +| J41: -> S41 | $1 * cosh(1.7)$ | +| J42: -> S42 | $1 * arcsec(2.3)$ | +| J43: -> S43 | $1 * arccsc(1.1)$ | +| J44: -> S44 | $1 * arccot(-0.1)$ | +| J45: -> S45 | $1 * arcsinh(99)$ | +| J46: -> S46 | $1 * arccosh(1.34)$ | +| J47: -> S47 | $1 * arctanh(-0.7)$ | +| J48: -> S48 | $1 * arcsech(0.42)$ | +| J49: -> S49 | $1 * arccsch(0.01)$ | +| J50: -> S50 | $times(1)$ | +| J51: -> S51 | $1 * plus()$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S0 | $0$ | variable | +| Initial concentration of species S1 | $0$ | variable | +| Initial concentration of species S2 | $0$ | variable | +| Initial concentration of species S3 | $0$ | variable | +| Initial concentration of species S4 | $0$ | variable | +| Initial concentration of species S5 | $0$ | variable | +| Initial concentration of species S6 | $0$ | variable | +| Initial concentration of species S7 | $0$ | variable | +| Initial concentration of species S8 | $0$ | variable | +| Initial concentration of species S9 | $0$ | variable | +| Initial concentration of species S10 | $0$ | variable | +| Initial concentration of species S11 | $0$ | variable | +| Initial concentration of species S12 | $0$ | variable | +| Initial concentration of species S13 | $0$ | variable | +| Initial concentration of species S14 | $0$ | variable | +| Initial concentration of species S15 | $0$ | variable | +| Initial concentration of species S16 | $0$ | variable | +| Initial concentration of species S17 | $0$ | variable | +| Initial concentration of species S18 | $0$ | variable | +| Initial concentration of species S19 | $0$ | variable | +| Initial concentration of species S20 | $0$ | variable | +| Initial concentration of species S21 | $0$ | variable | +| Initial concentration of species S22 | $0$ | variable | +| Initial concentration of species S23 | $0$ | variable | +| Initial concentration of species S24 | $0$ | variable | +| Initial concentration of species S25 | $0$ | variable | +| Initial concentration of species S26 | $0$ | variable | +| Initial concentration of species S27 | $0$ | variable | +| Initial concentration of species S28 | $0$ | variable | +| Initial concentration of species S29 | $0$ | variable | +| Initial concentration of species S30 | $0$ | variable | +| Initial concentration of species S31 | $0$ | variable | +| Initial concentration of species S32 | $0$ | variable | +| Initial concentration of species S33 | $0$ | variable | +| Initial concentration of species S34 | $0$ | variable | +| Initial concentration of species S35 | $0$ | variable | +| Initial concentration of species S36 | $0$ | variable | +| Initial concentration of species S37 | $0$ | variable | +| Initial concentration of species S38 | $0$ | variable | +| Initial concentration of species S39 | $0$ | variable | +| Initial concentration of species S40 | $0$ | variable | +| Initial concentration of species S41 | $0$ | variable | +| Initial concentration of species S42 | $0$ | variable | +| Initial concentration of species S43 | $0$ | variable | +| Initial concentration of species S44 | $0$ | variable | +| Initial concentration of species S45 | $0$ | variable | +| Initial concentration of species S46 | $0$ | variable | +| Initial concentration of species S47 | $0$ | variable | +| Initial concentration of species S48 | $0$ | variable | +| Initial concentration of species S49 | $0$ | variable | +| Initial concentration of species S50 | $0$ | variable | +| Initial concentration of species S51 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01565/l2v5/build.log b/latest/cases/01565/l2v5/build.log new file mode 100644 index 000000000..2c766718f --- /dev/null +++ b/latest/cases/01565/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01565/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01565/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01565/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01565/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01565/l2v5/index.heta b/latest/cases/01565/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01565/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01565/l3v2/index.heta b/latest/cases/01565/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01565/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01565/model-sbml-l2v5.xml b/latest/cases/01565/model-sbml-l2v5.xml new file mode 100644 index 000000000..a6d3579db --- /dev/null +++ b/latest/cases/01565/model-sbml-l2v5.xml @@ -0,0 +1,1269 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + S0 + S0b + + + + + + + + + + + + + + + + + 1 + S1 + S1b + + + + + + + + + + + + + + + + + + + + 1 + S2 + S2b + + + -1 + + + + + + + + + + + + + + + + + 1 + S3 + S3b + + + 1 + + + + + + + + + + + + + + + + + 1 + S4 + S4b + + + -1 + + + + + + + + + + + + + + + + + 1 + S5 + S5b + + + 0.5 + + + + + + + + + + + + + + + + + 1 + S6 + S6b + + + 1 + + + + + + + + + + + + + + + + + 1 + S7 + S7b + + + -0.5 + + + + + + + + + + + + + + + + + 1 + S8 + S8b + + + 2.8 + + + + + + + + + + + + + + + + + 1 + S9 + S9b + + + -7.09 + + + + + + + + + + + + + + + + + 1 + S10 + S10b + + + 0.5 + + + + + + + + + + + + + + + + + 1 + S11 + S11b + + + 3.55 + + + + + + + + + + + + + + + + + 1 + S12 + S12b + + + -4.6 + + + + + + + + + + + + + + + + + 1 + S13 + S13b + + + 9.1 + + + + + + + + + + + + + + + + + 1 + S14 + S14b + + + -0.22 + + + + + + + + + + + + + + + + + 1 + S15 + S15b + + + 0 + + + + + + + + + + + + + + + + + 1 + S16 + S16b + + + 1 + + + + + + + + + + + + + + + + + 1 + S17 + S17b + + + 0.77 + + + + + + + + + + + + + + + + + 1 + S18 + S18b + + + -4.6 + + + + + + + + + + + + + + + + + 1 + S19 + S19b + + + 9.1 + + + + + + + + + + + + + + + + + 1 + S20 + S20b + + + 0.2 + + + + + + + + + + + + + + + + + 1 + S21 + S21b + + + 1 + + + + + + + + + + + + + + + + + 1 + S22 + S22b + + + + 10 + + 0.2 + + + + + + + + + + + + + + + + + 1 + S23 + S23b + + + + 10 + + 1 + + + + + + + + + + + + + + + + + 1 + S24 + S24b + + + 1 + 2 + + + + + + + + + + + + + + + + + 1 + S25 + S25b + + + 2 + 2 + + + + + + + + + + + + + + + + + 1 + S26 + S26b + + + 1.4 + 5.1 + + + + + + + + + + + + + + + + + 1 + S27 + S27b + + + 4 + 2 + + + + + + + + + + + + + + + + + 1 + S28 + S28b + + + 3.1 + 2 + + + + + + + + + + + + + + + + + 1 + S29 + S29b + + + + 2 + + 4 + + + + + + + + + + + + + + + + + 1 + S30 + S30b + + + + 2 + + 7.4 + + + + + + + + + + + + + + + + + 1 + S31 + S31b + + + 2.1 + + + + + + + + + + + + + + + + + 1 + S32 + S32b + + + 0 + + + + + + + + + + + + + + + + + 1 + S33 + S33b + + + -5.9 + + + + + + + + + + + + + + + + + 1 + S34 + S34b + + + 0 + + + + + + + + + + + + + + + + + 1 + S35 + S35b + + + 1.11 + + + + + + + + + + + + + + + + + 1 + S36 + S36b + + + -6 + + + + + + + + + + + + + + + + + 1 + S37 + S37b + + + 0.5 + + + + + + + + + + + + + + + + + 1 + S38 + S38b + + + 4.5 + + + + + + + + + + + + + + + + + 1 + S39 + S39b + + + 0.2 + + + + + + + + + + + + + + + + + 1 + S40 + S40b + + + 0.3 + + + + + + + + + + + + + + + + + 1 + S41 + S41b + + + 1.7 + + + + + + + + + + + + + + + + + 1 + S42 + S42b + + + 2.3 + + + + + + + + + + + + + + + + + 1 + S43 + S43b + + + 1.1 + + + + + + + + + + + + + + + + + 1 + S44 + S44b + + + -0.1 + + + + + + + + + + + + + + + + + 1 + S45 + S45b + + + 99 + + + + + + + + + + + + + + + + + 1 + S46 + S46b + + + 1.34 + + + + + + + + + + + + + + + + + 1 + S47 + S47b + + + -0.7 + + + + + + + + + + + + + + + + + 1 + S48 + S48b + + + 0.42 + + + + + + + + + + + + + + + + + 1 + S49 + S49b + + + 0.01 + + + + + + + + + + + + + + + + + 1 + S50 + S50b + + + + + + + + + + + + + + + + 1 + S51 + S51b + + + + + + + + + + diff --git a/latest/cases/01565/synopsis.txt b/latest/cases/01565/synopsis.txt new file mode 100644 index 000000000..08bce5c06 --- /dev/null +++ b/latest/cases/01565/synopsis.txt @@ -0,0 +1,184 @@ + +category: Test +synopsis: Uncommon MathML in kinetic laws from fast reactions. +componentTags: Compartment, Reaction, Species +testTags: Amount, FastReaction, MultipleFastReactions, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + +The model tests various uncommon mathematical constructs in kinetic laws from fast reactions. + +The model contains: +* 104 species (S0, S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17, S18, S19, S20, S21, S22, S23, S24, S25, S26, S27, S28, S29, S30, S31, S32, S33, S34, S35, S36, S37, S38, S39, S40, S41, S42, S43, S44, S45, S46, S47, S48, S49, S50, S51, S0b, S1b, S2b, S3b, S4b, S5b, S6b, S7b, S8b, S9b, S10b, S11b, S12b, S13b, S14b, S15b, S16b, S17b, S18b, S19b, S20b, S21b, S22b, S23b, S24b, S25b, S26b, S27b, S28b, S29b, S30b, S31b, S32b, S33b, S34b, S35b, S36b, S37b, S38b, S39b, S40b, S41b, S42b, S43b, S44b, S45b, S46b, S47b, S48b, S49b, S50b, S51b) +* 1 compartment (C) + +There are 52 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S0b -> S0 | $1 * S0 * S0b * exponentiale$ | fast | +| J1: S1b -> S1 | $1 * S1 * S1b * exp(exponentiale)$ | fast | +| J2: S2b -> S2 | $1 * S2 * S2b * abs(-1)$ | fast | +| J3: S3b -> S3 | $1 * S3 * S3b * abs(1)$ | fast | +| J4: S4b -> S4 | $1 * S4 * S4b * acos(-1)$ | fast | +| J5: S5b -> S5 | $1 * S5 * S5b * acos(0.5)$ | fast | +| J6: S6b -> S6 | $1 * S6 * S6b * asin(1)$ | fast | +| J7: S7b -> S7 | $1 * S7 * S7b * asin(-0.5)$ | fast | +| J8: S8b -> S8 | $1 * S8 * S8b * atan(2.8)$ | fast | +| J9: S9b -> S9 | $1 * S9 * S9b * atan(-7.09)$ | fast | +| J10: S10b -> S10 | $1 * S10 * S10b * ceil(0.5)$ | fast | +| J11: S11b -> S11 | $1 * S11 * S11b * ceil(3.55)$ | fast | +| J12: S12b -> S12 | $1 * S12 * S12b * ceil(-4.6)$ | fast | +| J13: S13b -> S13 | $1 * S13 * S13b * cos(9.1)$ | fast | +| J14: S14b -> S14 | $1 * S14 * S14b * cos(-0.22)$ | fast | +| J15: S15b -> S15 | $1 * S15 * S15b * exp(0)$ | fast | +| J16: S16b -> S16 | $1 * S16 * S16b * exp(1)$ | fast | +| J17: S17b -> S17 | $1 * S17 * S17b * exp(0.77)$ | fast | +| J18: S18b -> S18 | $1 * S18 * S18b * floor(-4.6)$ | fast | +| J19: S19b -> S19 | $1 * S19 * S19b * floor(9.1)$ | fast | +| J20: S20b -> S20 | $1 * S20 * S20b * ln(0.2)$ | fast | +| J21: S21b -> S21 | $1 * S21 * S21b * ln(1)$ | fast | +| J22: S22b -> S22 | $1 * S22 * S22b * log10(0.2)$ | fast | +| J23: S23b -> S23 | $1 * S23 * S23b * log10(1)$ | fast | +| J24: S24b -> S24 | $1 * S24 * S24b * 1^2$ | fast | +| J25: S25b -> S25 | $1 * S25 * S25b * 2^2$ | fast | +| J26: S26b -> S26 | $1 * S26 * S26b * 1.4^5.1$ | fast | +| J27: S27b -> S27 | $1 * S27 * S27b * 4^2$ | fast | +| J28: S28b -> S28 | $1 * S28 * S28b * 3.1^2$ | fast | +| J29: S29b -> S29 | $1 * S29 * S29b * sqrt(4)$ | fast | +| J30: S30b -> S30 | $1 * S30 * S30b * sqrt(7.4)$ | fast | +| J31: S31b -> S31 | $1 * S31 * S31b * sin(2.1)$ | fast | +| J32: S32b -> S32 | $1 * S32 * S32b * sin(0)$ | fast | +| J33: S33b -> S33 | $1 * S33 * S33b * sin(-5.9)$ | fast | +| J34: S34b -> S34 | $1 * S34 * S34b * tan(0)$ | fast | +| J35: S35b -> S35 | $1 * S35 * S35b * tan(1.11)$ | fast | +| J36: S36b -> S36 | $1 * S36 * S36b * tan(-6)$ | fast | +| J37: S37b -> S37 | $1 * S37 * S37b * sec(0.5)$ | fast | +| J38: S38b -> S38 | $1 * S38 * S38b * csc(4.5)$ | fast | +| J39: S39b -> S39 | $1 * S39 * S39b * cot(0.2)$ | fast | +| J40: S40b -> S40 | $1 * S40 * S40b * sinh(0.3)$ | fast | +| J41: S41b -> S41 | $1 * S41 * S41b * cosh(1.7)$ | fast | +| J42: S42b -> S42 | $1 * S42 * S42b * arcsec(2.3)$ | fast | +| J43: S43b -> S43 | $1 * S43 * S43b * arccsc(1.1)$ | fast | +| J44: S44b -> S44 | $1 * S44 * S44b * arccot(-0.1)$ | fast | +| J45: S45b -> S45 | $1 * S45 * S45b * arcsinh(99)$ | fast | +| J46: S46b -> S46 | $1 * S46 * S46b * arccosh(1.34)$ | fast | +| J47: S47b -> S47 | $1 * S47 * S47b * arctanh(-0.7)$ | fast | +| J48: S48b -> S48 | $1 * S48 * S48b * arcsech(0.42)$ | fast | +| J49: S49b -> S49 | $1 * S49 * S49b * arccsch(0.01)$ | fast | +| J50: S50b -> S50 | $1 * S50 * S50b$ | fast | +| J51: S51b -> S51 | $1 * S51 * S51b * plus()$ | fast |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S0 | $2$ | variable | +| Initial concentration of species S1 | $2$ | variable | +| Initial concentration of species S2 | $2$ | variable | +| Initial concentration of species S3 | $2$ | variable | +| Initial concentration of species S4 | $2$ | variable | +| Initial concentration of species S5 | $2$ | variable | +| Initial concentration of species S6 | $2$ | variable | +| Initial concentration of species S7 | $2$ | variable | +| Initial concentration of species S8 | $2$ | variable | +| Initial concentration of species S9 | $2$ | variable | +| Initial concentration of species S10 | $2$ | variable | +| Initial concentration of species S11 | $2$ | variable | +| Initial concentration of species S12 | $2$ | variable | +| Initial concentration of species S13 | $2$ | variable | +| Initial concentration of species S14 | $2$ | variable | +| Initial concentration of species S15 | $2$ | variable | +| Initial concentration of species S16 | $2$ | variable | +| Initial concentration of species S17 | $2$ | variable | +| Initial concentration of species S18 | $2$ | variable | +| Initial concentration of species S19 | $2$ | variable | +| Initial concentration of species S20 | $2$ | variable | +| Initial concentration of species S21 | $2$ | variable | +| Initial concentration of species S22 | $2$ | variable | +| Initial concentration of species S23 | $2$ | variable | +| Initial concentration of species S24 | $2$ | variable | +| Initial concentration of species S25 | $2$ | variable | +| Initial concentration of species S26 | $2$ | variable | +| Initial concentration of species S27 | $2$ | variable | +| Initial concentration of species S28 | $2$ | variable | +| Initial concentration of species S29 | $2$ | variable | +| Initial concentration of species S30 | $2$ | variable | +| Initial concentration of species S31 | $2$ | variable | +| Initial concentration of species S32 | $2$ | variable | +| Initial concentration of species S33 | $2$ | variable | +| Initial concentration of species S34 | $2$ | variable | +| Initial concentration of species S35 | $2$ | variable | +| Initial concentration of species S36 | $2$ | variable | +| Initial concentration of species S37 | $2$ | variable | +| Initial concentration of species S38 | $2$ | variable | +| Initial concentration of species S39 | $2$ | variable | +| Initial concentration of species S40 | $2$ | variable | +| Initial concentration of species S41 | $2$ | variable | +| Initial concentration of species S42 | $2$ | variable | +| Initial concentration of species S43 | $2$ | variable | +| Initial concentration of species S44 | $2$ | variable | +| Initial concentration of species S45 | $2$ | variable | +| Initial concentration of species S46 | $2$ | variable | +| Initial concentration of species S47 | $2$ | variable | +| Initial concentration of species S48 | $2$ | variable | +| Initial concentration of species S49 | $2$ | variable | +| Initial concentration of species S50 | $2$ | variable | +| Initial concentration of species S51 | $2$ | variable | +| Initial concentration of species S0b | $3$ | variable | +| Initial concentration of species S1b | $3$ | variable | +| Initial concentration of species S2b | $3$ | variable | +| Initial concentration of species S3b | $3$ | variable | +| Initial concentration of species S4b | $3$ | variable | +| Initial concentration of species S5b | $3$ | variable | +| Initial concentration of species S6b | $3$ | variable | +| Initial concentration of species S7b | $3$ | variable | +| Initial concentration of species S8b | $3$ | variable | +| Initial concentration of species S9b | $3$ | variable | +| Initial concentration of species S10b | $3$ | variable | +| Initial concentration of species S11b | $3$ | variable | +| Initial concentration of species S12b | $3$ | variable | +| Initial concentration of species S13b | $3$ | variable | +| Initial concentration of species S14b | $3$ | variable | +| Initial concentration of species S15b | $3$ | variable | +| Initial concentration of species S16b | $3$ | variable | +| Initial concentration of species S17b | $3$ | variable | +| Initial concentration of species S18b | $3$ | variable | +| Initial concentration of species S19b | $3$ | variable | +| Initial concentration of species S20b | $3$ | variable | +| Initial concentration of species S21b | $3$ | variable | +| Initial concentration of species S22b | $3$ | variable | +| Initial concentration of species S23b | $3$ | variable | +| Initial concentration of species S24b | $3$ | variable | +| Initial concentration of species S25b | $3$ | variable | +| Initial concentration of species S26b | $3$ | variable | +| Initial concentration of species S27b | $3$ | variable | +| Initial concentration of species S28b | $3$ | variable | +| Initial concentration of species S29b | $3$ | variable | +| Initial concentration of species S30b | $3$ | variable | +| Initial concentration of species S31b | $3$ | variable | +| Initial concentration of species S32b | $3$ | variable | +| Initial concentration of species S33b | $3$ | variable | +| Initial concentration of species S34b | $3$ | variable | +| Initial concentration of species S35b | $3$ | variable | +| Initial concentration of species S36b | $3$ | variable | +| Initial concentration of species S37b | $3$ | variable | +| Initial concentration of species S38b | $3$ | variable | +| Initial concentration of species S39b | $3$ | variable | +| Initial concentration of species S40b | $3$ | variable | +| Initial concentration of species S41b | $3$ | variable | +| Initial concentration of species S42b | $3$ | variable | +| Initial concentration of species S43b | $3$ | variable | +| Initial concentration of species S44b | $3$ | variable | +| Initial concentration of species S45b | $3$ | variable | +| Initial concentration of species S46b | $3$ | variable | +| Initial concentration of species S47b | $3$ | variable | +| Initial concentration of species S48b | $3$ | variable | +| Initial concentration of species S49b | $3$ | variable | +| Initial concentration of species S50b | $3$ | variable | +| Initial concentration of species S51b | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01566/l2v5/index.heta b/latest/cases/01566/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01566/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01566/l3v2/build.log b/latest/cases/01566/l3v2/build.log new file mode 100644 index 000000000..f91b69357 --- /dev/null +++ b/latest/cases/01566/l3v2/build.log @@ -0,0 +1,66 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01566/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01566/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01566/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 131 +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P1 [ode_]= exp(S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P2 [ode_]= abs((-S1_stoich)); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P3 [ode_]= abs(S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P4 [ode_]= acos((-S1_stoich) + 1); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P5 [ode_]= acos(S1_stoich / 4); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P6 [ode_]= asin(S1_stoich - 1); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P7 [ode_]= asin((-S1_stoich) / 4); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P8 [ode_]= atan(S1_stoich + 0.8); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P9 [ode_]= atan((-S1_stoich) * 3 - 1.09); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P10 [ode_]= ceil(S1_stoich / 4); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P11 [ode_]= ceil(S1_stoich * 4 - 0.45); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P12 [ode_]= ceil((-S1_stoich) * 2 - 0.6); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P13 [ode_]= cos(S1_stoich * 4 + 1.1); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P14 [ode_]= cos((-S1_stoich) / 10 - 0.02); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P15 [ode_]= exp(0 * S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P16 [ode_]= exp(S1_stoich / 2); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P17 [ode_]= exp(S1_stoich / 2 - 0.33); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P18 [ode_]= floor((-S1_stoich) * 2 - 0.6); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P19 [ode_]= floor(S1_stoich * 4 + 1.1); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P20 [ode_]= ln(S1_stoich / 10); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P21 [ode_]= ln(S1_stoich / 2); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P22 [ode_]= logbase(S1_stoich / 10, 10); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P23 [ode_]= logbase(S1_stoich / 2, 10); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P24 [ode_]= pow(1, S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P25 [ode_]= pow(S1_stoich, S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P25 [ode_]= pow(S1_stoich, S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P27 [ode_]= pow(S1_stoich * S1_stoich, S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P27 [ode_]= pow(S1_stoich * S1_stoich, S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P27 [ode_]= pow(S1_stoich * S1_stoich, S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P28 [ode_]= pow(3.1, S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P29 [ode_]= pow(S1_stoich * 2, 1 / 2); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P30 [ode_]= pow(7 + S1_stoich / 5, 1 / 2); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P31 [ode_]= sin(S1_stoich + 0.1); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P32 [ode_]= sin(0 * S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P33 [ode_]= sin((-S1_stoich) * 2 - 1.9); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P34 [ode_]= tan(0 * S1_stoich); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P35 [ode_]= tan(S1_stoich / 2 + 0.11); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P36 [ode_]= tan((-S1_stoich) * 3); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P37 [ode_]= sec(S1_stoich / 4); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P38 [ode_]= csc(S1_stoich * 2.25); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P39 [ode_]= cot(S1_stoich / 10); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P40 [ode_]= sinh(S1_stoich / 10 + 0.1); +[error] FunctionDef "sinh" is not found as expected here: P40 { math: undefined }; +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P41 [ode_]= cosh(S1_stoich - 0.3); +[error] FunctionDef "cosh" is not found as expected here: P41 { math: undefined }; +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P42 [ode_]= asec(S1_stoich + 0.3); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P43 [ode_]= acsc(S1_stoich - 0.9); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P44 [ode_]= acot(S1_stoich - 2.1); +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P45 [ode_]= asinh(S1_stoich * 50 - 1); +[error] FunctionDef "asinh" is not found as expected here: P45 { math: undefined }; +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P46 [ode_]= acosh(S1_stoich / 2 + 0.34); +[error] FunctionDef "acosh" is not found as expected here: P46 { math: undefined }; +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P47 [ode_]= atanh(S1_stoich - 2.7); +[error] FunctionDef "atanh" is not found as expected here: P47 { math: undefined }; +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P48 [ode_]= asech(S1_stoich * 0.21); +[error] FunctionDef "asech" is not found as expected here: P48 { math: undefined }; +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: P49 [ode_]= acsch(S1_stoich * 0.005); +[error] FunctionDef "acsch" is not found as expected here: P49 { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01566/l3v2/index.heta b/latest/cases/01566/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01566/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01566/model-sbml-l3v2.xml b/latest/cases/01566/model-sbml-l3v2.xml new file mode 100644 index 000000000..93960eace --- /dev/null +++ b/latest/cases/01566/model-sbml-l3v2.xml @@ -0,0 +1,737 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + S1_stoich + + + + + + + + + + S1_stoich + + + + + + + + + S1_stoich + + + + + + + + + + + + S1_stoich + + 1 + + + + + + + + + + + S1_stoich + 4 + + + + + + + + + + + S1_stoich + 1 + + + + + + + + + + + + + S1_stoich + + 4 + + + + + + + + + + + S1_stoich + 0.8 + + + + + + + + + + + + + + + S1_stoich + + 3 + + 1.09 + + + + + + + + + + + S1_stoich + 4 + + + + + + + + + + + + + S1_stoich + 4 + + 0.45 + + + + + + + + + + + + + + + S1_stoich + + 2 + + 0.6 + + + + + + + + + + + + + S1_stoich + 4 + + 1.1 + + + + + + + + + + + + + + + S1_stoich + + 10 + + 0.02 + + + + + + + + + + + 0 + S1_stoich + + + + + + + + + + + S1_stoich + 2 + + + + + + + + + + + + + S1_stoich + 2 + + 0.33 + + + + + + + + + + + + + + + S1_stoich + + 2 + + 0.6 + + + + + + + + + + + + + S1_stoich + 4 + + 1.1 + + + + + + + + + + + S1_stoich + 10 + + + + + + + + + + + S1_stoich + 2 + + + + + + + + + + 10 + + + + S1_stoich + 10 + + + + + + + + + + 10 + + + + S1_stoich + 2 + + + + + + + + + 1 + S1_stoich + + + + + + + + S1_stoich + S1_stoich + + + + + + + + 1.4 + 5.1 + + + + + + + + + + S1_stoich + S1_stoich + + S1_stoich + + + + + + + + 3.1 + S1_stoich + + + + + + + + + 2 + + + + S1_stoich + 2 + + + + + + + + + + 2 + + + + 7 + + + S1_stoich + 5 + + + + + + + + + + + + S1_stoich + 0.1 + + + + + + + + + + + 0 + S1_stoich + + + + + + + + + + + + + + + S1_stoich + + 2 + + 1.9 + + + + + + + + + + + 0 + S1_stoich + + + + + + + + + + + + + S1_stoich + 2 + + 0.11 + + + + + + + + + + + + + S1_stoich + + 3 + + + + + + + + + + + S1_stoich + 4 + + + + + + + + + + + S1_stoich + 2.25 + + + + + + + + + + + S1_stoich + 10 + + + + + + + + + + + + + S1_stoich + 10 + + 0.1 + + + + + + + + + + + S1_stoich + 0.3 + + + + + + + + + + + S1_stoich + 0.3 + + + + + + + + + + + S1_stoich + 0.9 + + + + + + + + + + + S1_stoich + 2.1 + + + + + + + + + + + + + S1_stoich + 50 + + 1 + + + + + + + + + + + + + S1_stoich + 2 + + 0.34 + + + + + + + + + + + S1_stoich + 2.7 + + + + + + + + + + + S1_stoich + 0.21 + + + + + + + + + + + S1_stoich + 0.005 + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01566/synopsis.txt b/latest/cases/01566/synopsis.txt new file mode 100644 index 000000000..2d979d58a --- /dev/null +++ b/latest/cases/01566/synopsis.txt @@ -0,0 +1,141 @@ + +category: Test +synopsis: Uncommon MathML that uses species references. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests various uncommon mathematical constructs using a species reference. + +The model contains: +* 1 species (S1) +* 49 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40, P41, P42, P43, P44, P45, P46, P47, P48, P49) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> 2S1 | $1$ |] + + +There are 49 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $exp(S1_stoich)$ | +| Assignment | P2 | $abs(-S1_stoich)$ | +| Assignment | P3 | $abs(S1_stoich)$ | +| Assignment | P4 | $acos(-S1_stoich + 1)$ | +| Assignment | P5 | $acos(S1_stoich / 4)$ | +| Assignment | P6 | $asin(S1_stoich - 1)$ | +| Assignment | P7 | $asin(-S1_stoich / 4)$ | +| Assignment | P8 | $atan(S1_stoich + 0.8)$ | +| Assignment | P9 | $atan(-S1_stoich * 3 - 1.09)$ | +| Assignment | P10 | $ceil(S1_stoich / 4)$ | +| Assignment | P11 | $ceil(S1_stoich * 4 - 0.45)$ | +| Assignment | P12 | $ceil(-S1_stoich * 2 - 0.6)$ | +| Assignment | P13 | $cos(S1_stoich * 4 + 1.1)$ | +| Assignment | P14 | $cos(-S1_stoich / 10 - 0.02)$ | +| Assignment | P15 | $exp(0 * S1_stoich)$ | +| Assignment | P16 | $exp(S1_stoich / 2)$ | +| Assignment | P17 | $exp(S1_stoich / 2 - 0.33)$ | +| Assignment | P18 | $floor(-S1_stoich * 2 - 0.6)$ | +| Assignment | P19 | $floor(S1_stoich * 4 + 1.1)$ | +| Assignment | P20 | $ln(S1_stoich / 10)$ | +| Assignment | P21 | $ln(S1_stoich / 2)$ | +| Assignment | P22 | $log10(S1_stoich / 10)$ | +| Assignment | P23 | $log10(S1_stoich / 2)$ | +| Assignment | P24 | $1^S1_stoich$ | +| Assignment | P25 | $S1_stoich^S1_stoich$ | +| Assignment | P26 | $1.4^5.1$ | +| Assignment | P27 | $(S1_stoich * S1_stoich)^S1_stoich$ | +| Assignment | P28 | $3.1^S1_stoich$ | +| Assignment | P29 | $sqrt(S1_stoich * 2)$ | +| Assignment | P30 | $sqrt(7 + S1_stoich / 5)$ | +| Assignment | P31 | $sin(S1_stoich + 0.1)$ | +| Assignment | P32 | $sin(0 * S1_stoich)$ | +| Assignment | P33 | $sin(-S1_stoich * 2 - 1.9)$ | +| Assignment | P34 | $tan(0 * S1_stoich)$ | +| Assignment | P35 | $tan(S1_stoich / 2 + 0.11)$ | +| Assignment | P36 | $tan(-S1_stoich * 3)$ | +| Assignment | P37 | $sec(S1_stoich / 4)$ | +| Assignment | P38 | $csc(S1_stoich * 2.25)$ | +| Assignment | P39 | $cot(S1_stoich / 10)$ | +| Assignment | P40 | $sinh(S1_stoich / 10 + 0.1)$ | +| Assignment | P41 | $cosh(S1_stoich - 0.3)$ | +| Assignment | P42 | $arcsec(S1_stoich + 0.3)$ | +| Assignment | P43 | $arccsc(S1_stoich - 0.9)$ | +| Assignment | P44 | $arccot(S1_stoich - 2.1)$ | +| Assignment | P45 | $arcsinh(S1_stoich * 50 - 1)$ | +| Assignment | P46 | $arccosh(S1_stoich / 2 + 0.34)$ | +| Assignment | P47 | $arctanh(S1_stoich - 2.7)$ | +| Assignment | P48 | $arcsech(S1_stoich * 0.21)$ | +| Assignment | P49 | $arccsch(S1_stoich * 0.005)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $0$ | variable | +| Initial value of parameter P1 | $exp(S1_stoich)$ | variable | +| Initial value of parameter P2 | $abs(-S1_stoich)$ | variable | +| Initial value of parameter P3 | $abs(S1_stoich)$ | variable | +| Initial value of parameter P4 | $acos(-S1_stoich + 1)$ | variable | +| Initial value of parameter P5 | $acos(S1_stoich / 4)$ | variable | +| Initial value of parameter P6 | $asin(S1_stoich - 1)$ | variable | +| Initial value of parameter P7 | $asin(-S1_stoich / 4)$ | variable | +| Initial value of parameter P8 | $atan(S1_stoich + 0.8)$ | variable | +| Initial value of parameter P9 | $atan(-S1_stoich * 3 - 1.09)$ | variable | +| Initial value of parameter P10 | $ceil(S1_stoich / 4)$ | variable | +| Initial value of parameter P11 | $ceil(S1_stoich * 4 - 0.45)$ | variable | +| Initial value of parameter P12 | $ceil(-S1_stoich * 2 - 0.6)$ | variable | +| Initial value of parameter P13 | $cos(S1_stoich * 4 + 1.1)$ | variable | +| Initial value of parameter P14 | $cos(-S1_stoich / 10 - 0.02)$ | variable | +| Initial value of parameter P15 | $exp(0 * S1_stoich)$ | variable | +| Initial value of parameter P16 | $exp(S1_stoich / 2)$ | variable | +| Initial value of parameter P17 | $exp(S1_stoich / 2 - 0.33)$ | variable | +| Initial value of parameter P18 | $floor(-S1_stoich * 2 - 0.6)$ | variable | +| Initial value of parameter P19 | $floor(S1_stoich * 4 + 1.1)$ | variable | +| Initial value of parameter P20 | $ln(S1_stoich / 10)$ | variable | +| Initial value of parameter P21 | $ln(S1_stoich / 2)$ | variable | +| Initial value of parameter P22 | $log10(S1_stoich / 10)$ | variable | +| Initial value of parameter P23 | $log10(S1_stoich / 2)$ | variable | +| Initial value of parameter P24 | $1^S1_stoich$ | variable | +| Initial value of parameter P25 | $S1_stoich^S1_stoich$ | variable | +| Initial value of parameter P26 | $1.4^5.1$ | variable | +| Initial value of parameter P27 | $(S1_stoich * S1_stoich)^S1_stoich$ | variable | +| Initial value of parameter P28 | $3.1^S1_stoich$ | variable | +| Initial value of parameter P29 | $sqrt(S1_stoich * 2)$ | variable | +| Initial value of parameter P30 | $sqrt(7 + S1_stoich / 5)$ | variable | +| Initial value of parameter P31 | $sin(S1_stoich + 0.1)$ | variable | +| Initial value of parameter P32 | $sin(0 * S1_stoich)$ | variable | +| Initial value of parameter P33 | $sin(-S1_stoich * 2 - 1.9)$ | variable | +| Initial value of parameter P34 | $tan(0 * S1_stoich)$ | variable | +| Initial value of parameter P35 | $tan(S1_stoich / 2 + 0.11)$ | variable | +| Initial value of parameter P36 | $tan(-S1_stoich * 3)$ | variable | +| Initial value of parameter P37 | $sec(S1_stoich / 4)$ | variable | +| Initial value of parameter P38 | $csc(S1_stoich * 2.25)$ | variable | +| Initial value of parameter P39 | $cot(S1_stoich / 10)$ | variable | +| Initial value of parameter P40 | $sinh(S1_stoich / 10 + 0.1)$ | variable | +| Initial value of parameter P41 | $cosh(S1_stoich - 0.3)$ | variable | +| Initial value of parameter P42 | $arcsec(S1_stoich + 0.3)$ | variable | +| Initial value of parameter P43 | $arccsc(S1_stoich - 0.9)$ | variable | +| Initial value of parameter P44 | $arccot(S1_stoich - 2.1)$ | variable | +| Initial value of parameter P45 | $arcsinh(S1_stoich * 50 - 1)$ | variable | +| Initial value of parameter P46 | $arccosh(S1_stoich / 2 + 0.34)$ | variable | +| Initial value of parameter P47 | $arctanh(S1_stoich - 2.7)$ | variable | +| Initial value of parameter P48 | $arcsech(S1_stoich * 0.21)$ | variable | +| Initial value of parameter P49 | $arccsch(S1_stoich * 0.005)$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01567/l2v5/build.log b/latest/cases/01567/l2v5/build.log new file mode 100644 index 000000000..a592ab415 --- /dev/null +++ b/latest/cases/01567/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01567/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01567/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01567/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01567/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01567/l2v5/index.heta b/latest/cases/01567/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01567/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01567/l3v2/index.heta b/latest/cases/01567/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01567/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01567/model-sbml-l2v5.xml b/latest/cases/01567/model-sbml-l2v5.xml new file mode 100644 index 000000000..4afb66243 --- /dev/null +++ b/latest/cases/01567/model-sbml-l2v5.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + + + k + 3 + + + + + + + + + + + + + + + + + S2 + k + + + + + + + diff --git a/latest/cases/01567/synopsis.txt b/latest/cases/01567/synopsis.txt new file mode 100644 index 000000000..b4b866664 --- /dev/null +++ b/latest/cases/01567/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A fast reaction whose rate depends on an algebraic rule. +componentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species +testTags: Amount, FastReaction, InitialValueReassigned, NonConstantParameter, ReversibleReaction +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + +The model tests a fast reaction which is negative because of an algebraic rule. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $S2 * k$ | fast |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $k + 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial value of parameter k | $unknown$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01568/l2v5/build.log b/latest/cases/01568/l2v5/build.log new file mode 100644 index 000000000..b114977a2 --- /dev/null +++ b/latest/cases/01568/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01568/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01568/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01568/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01568/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01568/l2v5/index.heta b/latest/cases/01568/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01568/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01568/l3v2/index.heta b/latest/cases/01568/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01568/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01568/model-sbml-l2v5.xml b/latest/cases/01568/model-sbml-l2v5.xml new file mode 100644 index 000000000..4361a00b5 --- /dev/null +++ b/latest/cases/01568/model-sbml-l2v5.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + 5.5 + time + + + + + + + + + + + + + + + + + + + S1 + k + + + + k + 0 + + + + + + S2 + k + + + + + + + + + diff --git a/latest/cases/01568/synopsis.txt b/latest/cases/01568/synopsis.txt new file mode 100644 index 000000000..ab6201807 --- /dev/null +++ b/latest/cases/01568/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A fast reaction whose rate depends on an assignment rule. +componentTags: AssignmentRule, CSymbolTime, Compartment, Parameter, Reaction, Species +testTags: Amount, FastReaction, InitialValueReassigned, NonConstantParameter, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + +The model tests a fast reaction which is positive or negative depending on the results of an assignment rule. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $piecewise(S1 * k, k > 0, S2 * k)$ | fast |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | k | $5.5 - time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial value of parameter k | $5.5 - time$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01569/l2v5/build.log b/latest/cases/01569/l2v5/build.log new file mode 100644 index 000000000..280a77904 --- /dev/null +++ b/latest/cases/01569/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01569/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01569/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01569/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01569/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01569/l2v5/index.heta b/latest/cases/01569/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01569/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01569/l3v2/index.heta b/latest/cases/01569/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01569/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01569/model-sbml-l2v5.xml b/latest/cases/01569/model-sbml-l2v5.xml new file mode 100644 index 000000000..23eccea7c --- /dev/null +++ b/latest/cases/01569/model-sbml-l2v5.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + 0.5 + time + + + + + + + + time + 0.5 + + + + + + + + + + + + + + + + + S1 + S2 + k1 + + + + + + + + + + + + + + + + S3 + S4 + k2 + + + + + + + diff --git a/latest/cases/01569/synopsis.txt b/latest/cases/01569/synopsis.txt new file mode 100644 index 000000000..7014c6b5d --- /dev/null +++ b/latest/cases/01569/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Two fast reactions whose rates depend on initial assignments. +componentTags: CSymbolTime, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, FastReaction, InitialValueReassigned, MultipleFastReactions +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + +The model tests fast reactions which are positive or negative depending on the results of initial assignments. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 2 parameters (k1, k2) +* 1 compartment (C) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $S1 * S2 * k1$ | fast | +| J1: S3 -> S4 | $S3 * S4 * k2$ | fast |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial concentration of species S3 | $4$ | variable | +| Initial concentration of species S4 | $4$ | variable | +| Initial value of parameter k1 | $0.5 - time$ | variable | +| Initial value of parameter k2 | $time - 0.5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01570/l2v5/build.log b/latest/cases/01570/l2v5/build.log new file mode 100644 index 000000000..a4cd6b121 --- /dev/null +++ b/latest/cases/01570/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01570/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01570/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01570/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01570/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01570/l2v5/index.heta b/latest/cases/01570/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01570/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01570/l3v2/index.heta b/latest/cases/01570/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01570/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01570/model-sbml-l2v5.xml b/latest/cases/01570/model-sbml-l2v5.xml new file mode 100644 index 000000000..c4bcd304e --- /dev/null +++ b/latest/cases/01570/model-sbml-l2v5.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + -1 + + + + + + + + + + + + + + + + + + S1 + k + + + + k + 0 + + + + + + S2 + k + + + + + + + + + diff --git a/latest/cases/01570/synopsis.txt b/latest/cases/01570/synopsis.txt new file mode 100644 index 000000000..3fd0babc8 --- /dev/null +++ b/latest/cases/01570/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A fast reaction whose rate depends on a rate rule. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, FastReaction, NonConstantParameter, ReversibleReaction +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + +The model tests a fast reaction which is positive or negative depending on the results of a rate rule. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1 -> S2 | $piecewise(S1 * k, k > 0, S2 * k)$ | fast |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial value of parameter k | $4.5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01571/l2v5/index.heta b/latest/cases/01571/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01571/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01571/l3v2/index.heta b/latest/cases/01571/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01571/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01571/synopsis.txt b/latest/cases/01571/synopsis.txt new file mode 100644 index 000000000..f50f55338 --- /dev/null +++ b/latest/cases/01571/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A fast reaction with assigned stoichiometry. +componentTags: AssignmentRule, Compartment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, FastReaction, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + +The model tests a fast reaction with assigned stoichiometry. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1_stoich S1 -> S2 | $S1 * S2 * 0.1$ | fast |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1_stoich | $2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01572/l2v5/build.log b/latest/cases/01572/l2v5/build.log new file mode 100644 index 000000000..8a9c3295c --- /dev/null +++ b/latest/cases/01572/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01572/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01572/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01572/model-sbml-l2v5.xml"... +[error] "fast" reactions "J0" is not supported in SBML module. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01572/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01572/l2v5/index.heta b/latest/cases/01572/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01572/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01572/l3v2/index.heta b/latest/cases/01572/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01572/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01572/model-sbml-l2v5.xml b/latest/cases/01572/model-sbml-l2v5.xml new file mode 100644 index 000000000..e2fc0a187 --- /dev/null +++ b/latest/cases/01572/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + S1 + S2 + 0.1 + + + + + + + diff --git a/latest/cases/01572/synopsis.txt b/latest/cases/01572/synopsis.txt new file mode 100644 index 000000000..afe9d4b52 --- /dev/null +++ b/latest/cases/01572/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A fast reaction with assigned stoichiometry. +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, FastReaction, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + The model tests a fast reaction with assigned stoichiometry. This is the same model as 1571, but with L2's stoichiometry math construct. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* | +| J0: S1_stoich S1 -> S2 | $S1 * S2 * 0.1$ | fast |] +Note: the following stoichiometries are set separately: S1_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01573/l2v5/build.log b/latest/cases/01573/l2v5/build.log new file mode 100644 index 000000000..371b16c10 --- /dev/null +++ b/latest/cases/01573/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01573/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01573/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01573/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01573/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01573/l2v5/index.heta b/latest/cases/01573/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01573/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01573/l3v2/index.heta b/latest/cases/01573/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01573/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01573/model-sbml-l2v5.xml b/latest/cases/01573/model-sbml-l2v5.xml new file mode 100644 index 000000000..0936dd0c8 --- /dev/null +++ b/latest/cases/01573/model-sbml-l2v5.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + S1 + 0.1 + + + + + + + diff --git a/latest/cases/01573/synopsis.txt b/latest/cases/01573/synopsis.txt new file mode 100644 index 000000000..d4f306e1c --- /dev/null +++ b/latest/cases/01573/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A reaction with assigned stoichiometry for a boundary species. +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, BoundaryCondition, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + The model has an assigned stoichiometry for a boundary species, using stoichiometry math. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> S2 | $S1 * 0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01574/l2v5/index.heta b/latest/cases/01574/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01574/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01574/l3v2/build.log b/latest/cases/01574/l3v2/build.log new file mode 100644 index 000000000..0c4c14afb --- /dev/null +++ b/latest/cases/01574/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01574/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01574/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01574/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01574/l3v2/index.heta b/latest/cases/01574/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01574/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01574/model-sbml-l3v2.xml b/latest/cases/01574/model-sbml-l3v2.xml new file mode 100644 index 000000000..f24ce8848 --- /dev/null +++ b/latest/cases/01574/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + S1 + 0.1 + + + + + + + diff --git a/latest/cases/01574/synopsis.txt b/latest/cases/01574/synopsis.txt new file mode 100644 index 000000000..9364643a5 --- /dev/null +++ b/latest/cases/01574/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: A reaction with assigned stoichiometry for a boundary species. +componentTags: AssignmentRule, Compartment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, BoundaryCondition, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model has an assigned stoichiometry for a boundary species, using an assignment rule. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> S2 | $S1 * 0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1_stoich | $2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $3$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01575/l2v5/build.log b/latest/cases/01575/l2v5/build.log new file mode 100644 index 000000000..39d3598a8 --- /dev/null +++ b/latest/cases/01575/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01575/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01575/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01575/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01575/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01575/l2v5/index.heta b/latest/cases/01575/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01575/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01575/l3v2/build.log b/latest/cases/01575/l3v2/build.log new file mode 100644 index 000000000..38c195d1b --- /dev/null +++ b/latest/cases/01575/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01575/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01575/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01575/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01575/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01575/l3v2/index.heta b/latest/cases/01575/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01575/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01575/model-sbml-l2v5.xml b/latest/cases/01575/model-sbml-l2v5.xml new file mode 100644 index 000000000..abc2181ae --- /dev/null +++ b/latest/cases/01575/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + k1 + k2 + + + + + + 1 + + + + + + + + + + + + k2 + 3.5 + + + + k2 + 4 + + + + + + + 1.1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/01575/model-sbml-l3v2.xml b/latest/cases/01575/model-sbml-l3v2.xml new file mode 100644 index 000000000..3b9df17c0 --- /dev/null +++ b/latest/cases/01575/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + k1 + k2 + + + + + + 1 + + + + + + + + + + + + k2 + 3.5 + + + + k2 + 4 + + + + + + + 1.1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/01575/synopsis.txt b/latest/cases/01575/synopsis.txt new file mode 100644 index 000000000..1fe525f0e --- /dev/null +++ b/latest/cases/01575/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A persistent event influenced by an algebraic rule. +componentTags: AlgebraicRule, EventWithDelay, Parameter, RateRule +testTags: EventIsPersistent, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a persistent event has a delay that lasts longer than the trigger is true, so it fires anyway. It affects the value of a different parameter through an algebraic rule. + +The model contains: +* 2 parameters (k1, k2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(k2 > 3.5) && (k2 < 4)$ | $1.1$ | $k1 = 1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $k1 - k2$ | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter k1 | $1$ | variable | +| Initial value of parameter k2 | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01576/l2v5/index.heta b/latest/cases/01576/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01576/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01576/l3v2/build.log b/latest/cases/01576/l3v2/build.log new file mode 100644 index 000000000..53a08984a --- /dev/null +++ b/latest/cases/01576/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01576/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01576/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01576/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01576/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01576/l3v2/index.heta b/latest/cases/01576/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01576/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01576/model-sbml-l3v2.xml b/latest/cases/01576/model-sbml-l3v2.xml new file mode 100644 index 000000000..4d3ec9503 --- /dev/null +++ b/latest/cases/01576/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + k1 + k2 + + + + + + 1 + + + + + + + + + + + + k2 + 3.5 + + + + k2 + 4 + + + + + + + 1 + + + + + + 1 + + + + + + + diff --git a/latest/cases/01576/synopsis.txt b/latest/cases/01576/synopsis.txt new file mode 100644 index 000000000..eb1fa9812 --- /dev/null +++ b/latest/cases/01576/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A non-persistent event influenced by an algebraic rule. +componentTags: AlgebraicRule, EventWithDelay, Parameter, RateRule +testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model has a non-persistent event whose trigger is controlled by an algebraic rule such that it does not actually fire, being 'true' for less time than its delay. This is the same as model 1575, but with a non-persistent event. + +The model contains: +* 2 parameters (k1, k2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E0 | $(k2 > 3.5) && (k2 < 4)$ | false | $1$ | $k1 = 1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $k1 - k2$ | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter k1 | $1$ | variable | +| Initial value of parameter k2 | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01577/l2v5/index.heta b/latest/cases/01577/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01577/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01577/l3v2/build.log b/latest/cases/01577/l3v2/build.log new file mode 100644 index 000000000..c143d46b7 --- /dev/null +++ b/latest/cases/01577/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01577/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01577/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01577/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01577/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01577/l3v2/index.heta b/latest/cases/01577/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01577/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01577/model-sbml-l3v2.xml b/latest/cases/01577/model-sbml-l3v2.xml new file mode 100644 index 000000000..9652a66eb --- /dev/null +++ b/latest/cases/01577/model-sbml-l3v2.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + 10 + k1 + + k2 + + + + + + 1 + + + + + + + + + + time + 4.5 + + + + + + k1 + + + + + + 3 + + + + + + + + + + time + 4.5 + + + + + + k2 + + + + + + 5 + + + + + + + diff --git a/latest/cases/01577/synopsis.txt b/latest/cases/01577/synopsis.txt new file mode 100644 index 000000000..2f529a7c2 --- /dev/null +++ b/latest/cases/01577/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Two event priorities affected by an algebraic rule. +componentTags: AlgebraicRule, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model has two competing events whose priorities are set via an algebraic rule. + +The model contains: +* 3 parameters (k1, P1, k2) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 4.5$ | $k1$ | $P1 = 3$ | +| E1 | $time > 4.5$ | $k2$ | $P1 = 5$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $10 - k1 - k2$ | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial value of parameter k2 | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01578/l2v5/index.heta b/latest/cases/01578/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01578/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01578/l3v2/build.log b/latest/cases/01578/l3v2/build.log new file mode 100644 index 000000000..55a132ccb --- /dev/null +++ b/latest/cases/01578/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01578/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01578/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01578/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01578/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01578/l3v2/index.heta b/latest/cases/01578/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01578/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01578/model-sbml-l3v2.xml b/latest/cases/01578/model-sbml-l3v2.xml new file mode 100644 index 000000000..a826381a9 --- /dev/null +++ b/latest/cases/01578/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + 10 + k1 + + + + + + + + + + + k1 + 4.5 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01578/synopsis.txt b/latest/cases/01578/synopsis.txt new file mode 100644 index 000000000..37d1114ea --- /dev/null +++ b/latest/cases/01578/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: An event that fires at t0 because of an algebraic rule. +componentTags: AlgebraicRule, EventNoDelay, Parameter +testTags: EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model has an event set 'initialValue=false', allowing it to fire at t0. The variable in the trigger is set via an algebraic rule. + +The model contains: +* 2 parameters (k1, P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $k1 > 4.5$ | false | $P1 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $10 - k1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01579/l2v5/build.log b/latest/cases/01579/l2v5/build.log new file mode 100644 index 000000000..576304003 --- /dev/null +++ b/latest/cases/01579/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01579/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01579/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01579/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01579/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01579/l2v5/index.heta b/latest/cases/01579/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01579/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01579/l3v2/build.log b/latest/cases/01579/l3v2/build.log new file mode 100644 index 000000000..bcaafd520 --- /dev/null +++ b/latest/cases/01579/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01579/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01579/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01579/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01579/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01579/l3v2/index.heta b/latest/cases/01579/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01579/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01579/model-sbml-l2v5.xml b/latest/cases/01579/model-sbml-l2v5.xml new file mode 100644 index 000000000..2da0d6772 --- /dev/null +++ b/latest/cases/01579/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + 1 + + + + + + + k1 + k2 + + + + + + + + + + + k1 + 4.5 + + + + + + 2 + + + + + + k2 + + + + + + + diff --git a/latest/cases/01579/model-sbml-l3v2.xml b/latest/cases/01579/model-sbml-l3v2.xml new file mode 100644 index 000000000..4ec6b34c7 --- /dev/null +++ b/latest/cases/01579/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + 1 + + + + + + + k1 + k2 + + + + + + + + + + + k1 + 4.5 + + + + + + 2 + + + + + + k2 + + + + + + + diff --git a/latest/cases/01579/synopsis.txt b/latest/cases/01579/synopsis.txt new file mode 100644 index 000000000..ca3e36dd4 --- /dev/null +++ b/latest/cases/01579/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: An event whose delayed assignment is dependent on an algebraic rule. +componentTags: AlgebraicRule, EventWithDelay, Parameter, RateRule +testTags: EventUsesAssignmentTimeValues, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The model has a delayed event which assigns the assignment-time value of one parameter to another. The first is under control of an algebraic rule. + +The model contains: +* 3 parameters (k1, P1, k2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $k1 > 4.5$ | Assignment time | $2$ | $P1 = k2$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ | +| Algebraic | $0$ | $k1 - k2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial value of parameter k2 | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01580/l2v5/index.heta b/latest/cases/01580/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01580/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01580/l3v2/build.log b/latest/cases/01580/l3v2/build.log new file mode 100644 index 000000000..1ae805f32 --- /dev/null +++ b/latest/cases/01580/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01580/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01580/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01580/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01580/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01580/l3v2/index.heta b/latest/cases/01580/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01580/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01580/model-sbml-l3v2.xml b/latest/cases/01580/model-sbml-l3v2.xml new file mode 100644 index 000000000..b6d422511 --- /dev/null +++ b/latest/cases/01580/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + P1 + + + + + + + + + + + 0.1 + + + + + + + + + + + + + k1 + 4.5 + + + + k1 + 5.1 + + + + + + + 2 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01580/synopsis.txt b/latest/cases/01580/synopsis.txt new file mode 100644 index 000000000..efb66e931 --- /dev/null +++ b/latest/cases/01580/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: A persistent event whose delayed assignment affects a reaction's stoichiometry. +componentTags: AssignmentRule, Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, EventIsPersistent, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The event in this model is persistent, and fires even though its trigger reverts to 'false' before executing. It assigns a value to a parameter, which in turn assigns to the stoichiometry of the reaction. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(k1 > 4.5) && (k1 < 5.1)$ | $2$ | $P1 = 3$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ | +| Assignment | S1_stoich | $P1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $P1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01581/l2v5/build.log b/latest/cases/01581/l2v5/build.log new file mode 100644 index 000000000..4b37eef74 --- /dev/null +++ b/latest/cases/01581/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01581/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01581/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01581/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01581/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01581/l2v5/index.heta b/latest/cases/01581/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01581/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01581/l3v2/index.heta b/latest/cases/01581/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01581/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01581/model-sbml-l2v5.xml b/latest/cases/01581/model-sbml-l2v5.xml new file mode 100644 index 000000000..59541964b --- /dev/null +++ b/latest/cases/01581/model-sbml-l2v5.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + P1 + + + + + + + 0.1 + + + + + + + + + + + + + k1 + 4.5 + + + + k1 + 5.1 + + + + + + + 2 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01581/synopsis.txt b/latest/cases/01581/synopsis.txt new file mode 100644 index 000000000..b5aed5e9e --- /dev/null +++ b/latest/cases/01581/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: A persistent event whose delayed assignment affects a reaction's stoichiometry. +componentTags: Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, EventIsPersistent, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + The event in this model is persistent, and fires even though its trigger reverts to 'false' before executing. It assigns a value to a parameter, which in turn assigns to the stoichiometry of the reaction. This is the same model as 1580, but uses L2's StoichiometryMath construct to assign the value. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(k1 > 4.5) && (k1 < 5.1)$ | $2$ | $P1 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $P1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01582/l2v5/index.heta b/latest/cases/01582/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01582/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01582/l3v2/build.log b/latest/cases/01582/l3v2/build.log new file mode 100644 index 000000000..b40ac34a8 --- /dev/null +++ b/latest/cases/01582/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01582/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01582/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01582/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01582/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01582/l3v2/index.heta b/latest/cases/01582/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01582/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01582/model-sbml-l3v2.xml b/latest/cases/01582/model-sbml-l3v2.xml new file mode 100644 index 000000000..64401fef5 --- /dev/null +++ b/latest/cases/01582/model-sbml-l3v2.xml @@ -0,0 +1,73 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + P1 + + + + + + + + + + + 0.1 + + + + + + + + + + + + + k1 + 4.5 + + + + k1 + 5.1 + + + + + + + 2 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01582/synopsis.txt b/latest/cases/01582/synopsis.txt new file mode 100644 index 000000000..41240918b --- /dev/null +++ b/latest/cases/01582/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: A non-persistent event whose delayed assignment would affect a reaction's stoichiometry. +componentTags: AssignmentRule, Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The event in this model is not persistent, and therefore does not fire because its trigger reverts to 'false' before executing. It would assign a value to a parameter, which in turn is assigned to the stoichiometry of the reaction; this does not happen. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E0 | $(k1 > 4.5) && (k1 < 5.1)$ | false | $2$ | $P1 = 3$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ | +| Assignment | S1_stoich | $P1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $P1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01583/l2v5/index.heta b/latest/cases/01583/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01583/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01583/l3v2/build.log b/latest/cases/01583/l3v2/build.log new file mode 100644 index 000000000..bebb4551c --- /dev/null +++ b/latest/cases/01583/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01583/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01583/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01583/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01583/l3v2/index.heta b/latest/cases/01583/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01583/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01583/model-sbml-l3v2.xml b/latest/cases/01583/model-sbml-l3v2.xml new file mode 100644 index 000000000..55ce0388e --- /dev/null +++ b/latest/cases/01583/model-sbml-l3v2.xml @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + 0.1 + + + + + + + + + + + k1 + 4.5 + + + + + + 10 + + + + + + 2 + + + + + + + + + + k1 + 4.5 + + + + + + 5 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01583/synopsis.txt b/latest/cases/01583/synopsis.txt new file mode 100644 index 000000000..59252f3db --- /dev/null +++ b/latest/cases/01583/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Two simultaneous events which both assign to a stoichiometry according to their priorities. +componentTags: Compartment, EventNoDelay, EventPriority, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The two events in this model both assign to a stoichiometry at the same time, meaning that the higher-priority event fires first, and is then overridden by the lower-priority event. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $k1 > 4.5$ | $10$ | $S1_stoich = 2$ | +| E1 | $k1 > 4.5$ | $5$ | $S1_stoich = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01584/l2v5/index.heta b/latest/cases/01584/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01584/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01584/l3v2/build.log b/latest/cases/01584/l3v2/build.log new file mode 100644 index 000000000..5f470df18 --- /dev/null +++ b/latest/cases/01584/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01584/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01584/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01584/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01584/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01584/l3v2/index.heta b/latest/cases/01584/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01584/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01584/model-sbml-l3v2.xml b/latest/cases/01584/model-sbml-l3v2.xml new file mode 100644 index 000000000..ba61f8177 --- /dev/null +++ b/latest/cases/01584/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + P1 + + + + + + + + + + + 0.1 + + + + + + + + + + + k1 + 3 + + + + + + 2.5 + + + + + + k1 + + + + + + + diff --git a/latest/cases/01584/synopsis.txt b/latest/cases/01584/synopsis.txt new file mode 100644 index 000000000..2e4c45c60 --- /dev/null +++ b/latest/cases/01584/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: An event whose delayed assignment affects a reaction's stoichiometry. +componentTags: AssignmentRule, Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, EventUsesTriggerTimeValues, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The event in this model assigns values from the event's trigger time, assigning a value to a parameter, which in turn assigns to the stoichiometry of the reaction. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $k1 > 3$ | $2.5$ | $P1 = k1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ | +| Assignment | S1_stoich | $P1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $P1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01585/l2v5/build.log b/latest/cases/01585/l2v5/build.log new file mode 100644 index 000000000..e8120157c --- /dev/null +++ b/latest/cases/01585/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01585/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01585/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01585/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01585/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01585/l2v5/index.heta b/latest/cases/01585/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01585/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01585/l3v2/index.heta b/latest/cases/01585/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01585/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01585/model-sbml-l2v5.xml b/latest/cases/01585/model-sbml-l2v5.xml new file mode 100644 index 000000000..77a86a4f5 --- /dev/null +++ b/latest/cases/01585/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + P1 + + + + + + + 0.1 + + + + + + + + + + + k1 + 3 + + + + + + 2.5 + + + + + + k1 + + + + + + + diff --git a/latest/cases/01585/synopsis.txt b/latest/cases/01585/synopsis.txt new file mode 100644 index 000000000..22749e42f --- /dev/null +++ b/latest/cases/01585/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: An event whose delayed assignment affects a reaction's stoichiometry. +componentTags: Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, EventUsesTriggerTimeValues, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + The event in this model assigns values from the event's trigger time, assigning a value to a parameter, which in turn assigns to the stoichiometry of the reaction. Same as test 1584, with L2's StoichiometryMath construct. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $k1 > 3$ | $2.5$ | $P1 = k1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $P1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01586/l2v5/index.heta b/latest/cases/01586/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01586/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01586/l3v2/build.log b/latest/cases/01586/l3v2/build.log new file mode 100644 index 000000000..3094fde19 --- /dev/null +++ b/latest/cases/01586/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01586/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01586/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01586/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01586/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01586/l3v2/index.heta b/latest/cases/01586/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01586/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01586/model-sbml-l3v2.xml b/latest/cases/01586/model-sbml-l3v2.xml new file mode 100644 index 000000000..d78babaa5 --- /dev/null +++ b/latest/cases/01586/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + 1 + + + + + P1 + + + + + + + + + + + 0.1 + + + + + + + + + + + k1 + 3 + + + + + + 2.5 + + + + + + k1 + + + + + + + diff --git a/latest/cases/01586/synopsis.txt b/latest/cases/01586/synopsis.txt new file mode 100644 index 000000000..0cc7b661e --- /dev/null +++ b/latest/cases/01586/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: An event whose delayed assignment affects a reaction's stoichiometry. +componentTags: AssignmentRule, Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, EventUsesAssignmentTimeValues, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + The event in this model assigns values from the event's assignment time, assigning a value to a parameter, which in turn assigns to the stoichiometry of the reaction. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $k1 > 3$ | Assignment time | $2.5$ | $P1 = k1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ | +| Assignment | S1_stoich | $P1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $P1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01587/l2v5/build.log b/latest/cases/01587/l2v5/build.log new file mode 100644 index 000000000..d86a10f81 --- /dev/null +++ b/latest/cases/01587/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01587/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01587/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01587/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01587/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01587/l2v5/index.heta b/latest/cases/01587/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01587/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01587/l3v2/index.heta b/latest/cases/01587/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01587/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01587/model-sbml-l2v5.xml b/latest/cases/01587/model-sbml-l2v5.xml new file mode 100644 index 000000000..66a975249 --- /dev/null +++ b/latest/cases/01587/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + P1 + + + + + + + 0.1 + + + + + + + + + + + k1 + 3 + + + + + + 2.5 + + + + + + k1 + + + + + + + diff --git a/latest/cases/01587/synopsis.txt b/latest/cases/01587/synopsis.txt new file mode 100644 index 000000000..6c9c684b7 --- /dev/null +++ b/latest/cases/01587/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: An event whose delayed assignment affects a reaction's stoichiometry. +componentTags: Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, EventUsesAssignmentTimeValues, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + The event in this model assigns values from the event's assignment time, assigning a value to a parameter, which in turn assigns to the stoichiometry of the reaction. This test is the same as 1586, with L2's StoichiometryMath construct. + +The model contains: +* 1 species (S1) +* 2 parameters (k1, P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $k1 > 3$ | Assignment time | $2.5$ | $P1 = k1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of parameter P1 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $P1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01588/l2v5/index.heta b/latest/cases/01588/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01588/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01588/l3v2/build.log b/latest/cases/01588/l3v2/build.log new file mode 100644 index 000000000..80272a924 --- /dev/null +++ b/latest/cases/01588/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01588/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01588/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01588/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 92 +[error] No required "num" property for "k1" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01588/l3v2/index.heta b/latest/cases/01588/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01588/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01588/model-sbml-l3v2.xml b/latest/cases/01588/model-sbml-l3v2.xml new file mode 100644 index 000000000..50cd8035b --- /dev/null +++ b/latest/cases/01588/model-sbml-l3v2.xml @@ -0,0 +1,188 @@ + + + + + + + + + + + + + + + + + + + + 1 + 0.01 + + + + + + + + + + Q + R + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + k1 + + + + + + time + + + + + + + Q + k1 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 0.01 + + + + + + time + + + + + + + R + k1 + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01588/synopsis.txt b/latest/cases/01588/synopsis.txt new file mode 100644 index 000000000..304cc2c44 --- /dev/null +++ b/latest/cases/01588/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, InitialAssignment, Parameter + testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle of an initial assignment to a parameter used in one of the two priorities, and in the event assignments. + +The model contains: +* 8 parameters (S, Q, R, reset, k1, maxdiff, errorLow, errorHigh) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $(time - reset) >= 0.01$ | $k1$ | false | $reset = time$ | +| | | | | $Q = Q + k1$ | +| Rinc | $(time - reset) >= 0.01$ | $0.01$ | false | $reset = time$ | +| | | | | $R = R + k1$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter k1 | $1 * 0.01$ | constant | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01589/l2v5/index.heta b/latest/cases/01589/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01589/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01589/l3v2/build.log b/latest/cases/01589/l3v2/build.log new file mode 100644 index 000000000..c96bb5b90 --- /dev/null +++ b/latest/cases/01589/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01589/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01589/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01589/model-sbml-l3v2.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01589/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01589/l3v2/index.heta b/latest/cases/01589/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01589/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01589/model-sbml-l3v2.xml b/latest/cases/01589/model-sbml-l3v2.xml new file mode 100644 index 000000000..4bc93b02a --- /dev/null +++ b/latest/cases/01589/model-sbml-l3v2.xml @@ -0,0 +1,180 @@ + + + + + + + + + + + + + + + + + + + + + Q + R + + S + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 0.01 + + + + + + time + + + + + + + Q + 0.01 + + + + + + + + + + + + + time + reset + + 0.01 + + + + + + 0.01 + + + + + + time + + + + + + + R + 0.01 + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01589/synopsis.txt b/latest/cases/01589/synopsis.txt new file mode 100644 index 000000000..d6fb26b7d --- /dev/null +++ b/latest/cases/01589/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AlgebraicRule, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle of 'S' being set with an algebraic rule instead of via an assignment rule. + +The model contains: +* 7 parameters (reset, Q, R, maxdiff, errorLow, errorHigh, S) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $(time - reset) >= 0.01$ | $0.01$ | false | $reset = time$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $(time - reset) >= 0.01$ | $0.01$ | false | $reset = time$ | +| | | | | $R = R + 0.01$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $Q + R - S$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable | +| Initial value of parameter S | $unknown$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01590/l2v5/index.heta b/latest/cases/01590/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01590/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01590/l3v2/build.log b/latest/cases/01590/l3v2/build.log new file mode 100644 index 000000000..7e8339758 --- /dev/null +++ b/latest/cases/01590/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01590/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01590/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01590/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01590/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01590/l3v2/index.heta b/latest/cases/01590/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01590/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01590/model-sbml-l3v2.xml b/latest/cases/01590/model-sbml-l3v2.xml new file mode 100644 index 000000000..e06ed5911 --- /dev/null +++ b/latest/cases/01590/model-sbml-l3v2.xml @@ -0,0 +1,186 @@ + + + + + + + + + + + + + + + + + + + Q + R + + + + + + + + + + + + + time + reset + + 0.005 + + + + + + 0.005 + + + + + 1 + + + + + + time + + + + + + + Q + 0.01 + + + + + + + + + + + + + time + reset + + 0.005 + + + + + + 0.005 + + + + + 1 + + + + + + time + + + + + + + R + 0.01 + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01590/synopsis.txt b/latest/cases/01590/synopsis.txt new file mode 100644 index 000000000..7fc115be4 --- /dev/null +++ b/latest/cases/01590/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, EventWithDelay, Parameter +testTags: EventIsNotPersistent, EventUsesAssignmentTimeValues, InitialValueReassigned, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle of both simultaneous events executing after a delay. + +The model contains: +* 7 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh) + +There are 5 events: + +[{width:50em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Use values from:* | *Delay* | *Event Assignments* | +| Qinc | $(time - reset) >= 0.005$ | $1$ | false | Assignment time | $0.005$ | $reset = time$ | +| | | | | | | $Q = Q + 0.01$ | +| Rinc | $(time - reset) >= 0.005$ | $1$ | false | Assignment time | $0.005$ | $reset = time$ | +| | | | | | | $R = R + 0.01$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | Trigger time | $0$ | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | Trigger time | $0$ | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | Trigger time | $0$ | $errorHigh = 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01591/l2v5/index.heta b/latest/cases/01591/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01591/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01591/l3v2/heta-code/output.heta b/latest/cases/01591/l3v2/heta-code/output.heta new file mode 100644 index 000000000..7478fe3b0 --- /dev/null +++ b/latest/cases/01591/l3v2/heta-code/output.heta @@ -0,0 +1,29 @@ + + +t @TimeScale { }; + +reset_proc @Process { actors: = reset, }; +reset_proc := 1; + +S @Record { }; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= 0; +reset [Rinc]= 0; +maxdiff @Record { } .= 0; +maxdiff [maxcheck]= abs(Q - R); +errorLow @Record { } .= 0; +errorLow [error_check]= 1; +errorHigh @Record { } .= 0; +errorHigh [error_check2]= 1; + +Qinc @DSwitcher { trigger: reset >= 0.01, }; +Rinc @DSwitcher { trigger: reset >= 0.01, }; +maxcheck @DSwitcher { trigger: abs(Q - R) > maxdiff, }; +error_check @DSwitcher { trigger: t >= 99 and maxdiff < 0.2, }; +error_check2 @DSwitcher { trigger: maxdiff >= 4, }; + diff --git a/latest/cases/01591/l3v2/index.heta b/latest/cases/01591/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01591/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01591/l3v2/json/output.json b/latest/cases/01591/l3v2/json/output.json new file mode 100644 index 000000000..7ffb0f29f --- /dev/null +++ b/latest/cases/01591/l3v2/json/output.json @@ -0,0 +1,99 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "S", + "assignments": { + "ode_": "Q + R" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "0", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "0", + "Rinc": "R + 0.01" + } + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Qinc": "0", + "Rinc": "0" + } + }, + { + "class": "Record", + "id": "maxdiff", + "assignments": { + "start_": "0", + "maxcheck": "abs(Q - R)" + } + }, + { + "class": "Record", + "id": "errorLow", + "assignments": { + "start_": "0", + "error_check": "1" + } + }, + { + "class": "Record", + "id": "errorHigh", + "assignments": { + "start_": "0", + "error_check2": "1" + } + }, + { + "class": "Process", + "id": "reset_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "reset", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "reset >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "reset >= 0.01" + }, + { + "class": "DSwitcher", + "id": "maxcheck", + "trigger": "abs(Q - R) > maxdiff" + }, + { + "class": "DSwitcher", + "id": "error_check", + "trigger": "t >= 99 and maxdiff < 0.2" + }, + { + "class": "DSwitcher", + "id": "error_check2", + "trigger": "maxdiff >= 4" + } +] \ No newline at end of file diff --git a/latest/cases/01591/model-sbml-l3v2.xml b/latest/cases/01591/model-sbml-l3v2.xml new file mode 100644 index 000000000..65d8d0bc3 --- /dev/null +++ b/latest/cases/01591/model-sbml-l3v2.xml @@ -0,0 +1,173 @@ + + + + + + + + + + + + + + + + + + + Q + R + + + + + + 1 + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + Q + 0.01 + + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + R + 0.01 + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01591/output.heta b/latest/cases/01591/output.heta new file mode 100644 index 000000000..de594580c --- /dev/null +++ b/latest/cases/01591/output.heta @@ -0,0 +1,78 @@ +/* +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle of the triggers being set via a variable under control of a rate rule. + +The model contains: +* 7 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $R = R + 0.01$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ | +| Rate | reset | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +reset_proc @Process { actors: = reset, }; +reset_proc := 1; + +S @Record { }; +S := Q + R; +Q @Record { } .= 0; +Q [Qinc]= Q + 0.01; +R @Record { } .= 0; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= 0; +reset [Rinc]= 0; +maxdiff @Record { } .= 0; +maxdiff [maxcheck]= abs(Q - R); +errorLow @Record { } .= 0; +errorLow [error_check]= 1; +errorHigh @Record { } .= 0; +errorHigh [error_check2]= 1; + +Qinc @DSwitcher { trigger: reset >= 0.01, }; +Rinc @DSwitcher { trigger: reset >= 0.01, }; +maxcheck @DSwitcher { trigger: abs(Q - R) > maxdiff, }; +error_check @DSwitcher { trigger: t >= 99 and maxdiff < 0.2, }; +error_check2 @DSwitcher { trigger: maxdiff >= 4, }; + diff --git a/latest/cases/01591/synopsis.txt b/latest/cases/01591/synopsis.txt new file mode 100644 index 000000000..340e60e91 --- /dev/null +++ b/latest/cases/01591/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle of the triggers being set via a variable under control of a rate rule. + +The model contains: +* 7 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $R = R + 0.01$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ | +| Rate | reset | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01592/l2v5/index.heta b/latest/cases/01592/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01592/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01592/l3v2/build.log b/latest/cases/01592/l3v2/build.log new file mode 100644 index 000000000..bb757939d --- /dev/null +++ b/latest/cases/01592/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01592/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01592/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01592/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01592/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01592/l3v2/index.heta b/latest/cases/01592/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01592/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01592/model-sbml-l3v2.xml b/latest/cases/01592/model-sbml-l3v2.xml new file mode 100644 index 000000000..3332f2619 --- /dev/null +++ b/latest/cases/01592/model-sbml-l3v2.xml @@ -0,0 +1,183 @@ + + + + + + + + + + + + + + + + + + + Q + R + + + + + + 1 + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + Q + + delay + reset + 0.005 + + 0.005 + + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + R + + delay + reset + 0.005 + + 0.005 + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01592/synopsis.txt b/latest/cases/01592/synopsis.txt new file mode 100644 index 000000000..f7abc5c72 --- /dev/null +++ b/latest/cases/01592/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: DelayInEventAssignment, EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle that a delay is used in the assignments. + +The model contains: +* 7 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $Q = Q + delay(reset, 0.005) + 0.005$ | +| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $R = R + delay(reset, 0.005) + 0.005$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ | +| Rate | reset | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01593/l2v5/index.heta b/latest/cases/01593/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01593/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01593/l3v2/build.log b/latest/cases/01593/l3v2/build.log new file mode 100644 index 000000000..69e9999d5 --- /dev/null +++ b/latest/cases/01593/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01593/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01593/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01593/model-sbml-l3v2.xml"... +[error] "delay" symbol in expression (SBML module) is not supported when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01593/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01593/l3v2/index.heta b/latest/cases/01593/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01593/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01593/model-sbml-l3v2.xml b/latest/cases/01593/model-sbml-l3v2.xml new file mode 100644 index 000000000..4a0f115ee --- /dev/null +++ b/latest/cases/01593/model-sbml-l3v2.xml @@ -0,0 +1,191 @@ + + + + + + + + + + + + + + + + + + + + Q + R + + + + + + + + + delay + Q + 1 + + + delay + R + 1 + + + + + + + 1 + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + Q + 0.01 + + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + R + 0.01 + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01593/synopsis.txt b/latest/cases/01593/synopsis.txt new file mode 100644 index 000000000..33fbe3773 --- /dev/null +++ b/latest/cases/01593/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolDelay, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, RandomEventExecution +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle that a new 'S2' variable is calcualted from the delay values of Q and R. + +The model contains: +* 8 parameters (S, Q, R, S2, reset, maxdiff, errorLow, errorHigh) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $R = R + 0.01$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ | +| Assignment | S2 | $delay(Q, 1) + delay(R, 1)$ | +| Rate | reset | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter S2 | $delay(Q, 1) + delay(R, 1)$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01594/l2v5/build.log b/latest/cases/01594/l2v5/build.log new file mode 100644 index 000000000..b4f8f2e85 --- /dev/null +++ b/latest/cases/01594/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01594/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01594/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01594/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01594/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01594/l2v5/index.heta b/latest/cases/01594/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01594/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01594/l3v2/build.log b/latest/cases/01594/l3v2/build.log new file mode 100644 index 000000000..c29116b1b --- /dev/null +++ b/latest/cases/01594/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01594/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01594/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01594/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01594/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01594/l3v2/index.heta b/latest/cases/01594/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01594/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01594/model-sbml-l2v5.xml b/latest/cases/01594/model-sbml-l2v5.xml new file mode 100644 index 000000000..1c9f76eea --- /dev/null +++ b/latest/cases/01594/model-sbml-l2v5.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + time + + + + + + + + + + + + + + + time + + 9 + + + + + + time + + 11 + + + + + + + 1 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01594/model-sbml-l3v2.xml b/latest/cases/01594/model-sbml-l3v2.xml new file mode 100644 index 000000000..aaa144b80 --- /dev/null +++ b/latest/cases/01594/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + time + + + + + + + + + + + + + + + time + + 9 + + + + + + time + + 11 + + + + + + + 1 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01594/synopsis.txt b/latest/cases/01594/synopsis.txt new file mode 100644 index 000000000..7df4f732c --- /dev/null +++ b/latest/cases/01594/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Uncommon MathML in a persistent event. +componentTags: AssignmentRule, CSymbolTime, EventWithDelay, Parameter +testTags: EventIsPersistent, InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests the use of an uncommon mathematical construct in a persistent event. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(cosh(time) > 9) && (cosh(time) < 11)$ | $1$ | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $cosh(time)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $cosh(time)$ | variable | +| Initial value of parameter P2 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01595/l2v5/index.heta b/latest/cases/01595/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01595/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01595/l3v2/build.log b/latest/cases/01595/l3v2/build.log new file mode 100644 index 000000000..9c8805dbf --- /dev/null +++ b/latest/cases/01595/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01595/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01595/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01595/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01595/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01595/l3v2/index.heta b/latest/cases/01595/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01595/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01595/model-sbml-l3v2.xml b/latest/cases/01595/model-sbml-l3v2.xml new file mode 100644 index 000000000..26c300626 --- /dev/null +++ b/latest/cases/01595/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + time + + + + + + + + + + + + + + + time + + 9 + + + + + + time + + 11 + + + + + + + 1 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01595/synopsis.txt b/latest/cases/01595/synopsis.txt new file mode 100644 index 000000000..284d94f34 --- /dev/null +++ b/latest/cases/01595/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Uncommon MathML in a non-persistent event. +componentTags: AssignmentRule, CSymbolTime, EventWithDelay, Parameter +testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests the use of an uncommon mathematical construct in a non-persistent event (that ends up not firing). + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E0 | $(cosh(time) > 9) && (cosh(time) < 11)$ | false | $1$ | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $cosh(time)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $cosh(time)$ | variable | +| Initial value of parameter P2 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01596/l2v5/index.heta b/latest/cases/01596/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01596/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01596/l3v2/build.log b/latest/cases/01596/l3v2/build.log new file mode 100644 index 000000000..bbf9facd9 --- /dev/null +++ b/latest/cases/01596/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01596/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01596/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01596/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 82 +[error] FunctionDef "cosh" is not found as expected here: P1 { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: E0 { trigger: cosh(t) > 0.5 }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01596/l3v2/index.heta b/latest/cases/01596/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01596/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01596/model-sbml-l3v2.xml b/latest/cases/01596/model-sbml-l3v2.xml new file mode 100644 index 000000000..08f345f77 --- /dev/null +++ b/latest/cases/01596/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + time + + + + + + + + + + + + + time + + 0.5 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01596/synopsis.txt b/latest/cases/01596/synopsis.txt new file mode 100644 index 000000000..20a69edc4 --- /dev/null +++ b/latest/cases/01596/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Uncommon MathML in an event that fires at t0. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, Parameter +testTags: EventT0Firing, InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests the use of an uncommon mathematical construct in an event that fires at t0. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $cosh(time) > 0.5$ | false | $P2 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $cosh(time)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $cosh(time)$ | variable | +| Initial value of parameter P2 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01597/l2v5/build.log b/latest/cases/01597/l2v5/build.log new file mode 100644 index 000000000..5dca754e9 --- /dev/null +++ b/latest/cases/01597/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01597/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01597/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01597/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01597/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01597/l2v5/index.heta b/latest/cases/01597/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01597/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01597/l3v2/build.log b/latest/cases/01597/l3v2/build.log new file mode 100644 index 000000000..821a9adef --- /dev/null +++ b/latest/cases/01597/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01597/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01597/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01597/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01597/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01597/l3v2/index.heta b/latest/cases/01597/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01597/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01597/model-sbml-l2v5.xml b/latest/cases/01597/model-sbml-l2v5.xml new file mode 100644 index 000000000..36f6a71b8 --- /dev/null +++ b/latest/cases/01597/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + time + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + + + time + + + + + + + + diff --git a/latest/cases/01597/model-sbml-l3v2.xml b/latest/cases/01597/model-sbml-l3v2.xml new file mode 100644 index 000000000..9feb4bdc2 --- /dev/null +++ b/latest/cases/01597/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + time + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + + + time + + + + + + + + diff --git a/latest/cases/01597/synopsis.txt b/latest/cases/01597/synopsis.txt new file mode 100644 index 000000000..474fd3f87 --- /dev/null +++ b/latest/cases/01597/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Uncommon MathML in a delayed event with trigger time values. +componentTags: AssignmentRule, CSymbolTime, EventWithDelay, Parameter +testTags: EventUsesTriggerTimeValues, InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests the use of an uncommon mathematical construct in a delayed event with trigger time values. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time > 4.5$ | $1$ | $P2 = cosh(time)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $cosh(time)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $cosh(time)$ | variable | +| Initial value of parameter P2 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01598/l2v5/build.log b/latest/cases/01598/l2v5/build.log new file mode 100644 index 000000000..7cf789147 --- /dev/null +++ b/latest/cases/01598/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01598/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01598/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01598/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01598/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01598/l2v5/index.heta b/latest/cases/01598/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01598/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01598/l3v2/build.log b/latest/cases/01598/l3v2/build.log new file mode 100644 index 000000000..404d5bae9 --- /dev/null +++ b/latest/cases/01598/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01598/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01598/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01598/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01598/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01598/l3v2/index.heta b/latest/cases/01598/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01598/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01598/model-sbml-l2v5.xml b/latest/cases/01598/model-sbml-l2v5.xml new file mode 100644 index 000000000..ef98e4d6d --- /dev/null +++ b/latest/cases/01598/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + time + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + + + time + + + + + + + + diff --git a/latest/cases/01598/model-sbml-l3v2.xml b/latest/cases/01598/model-sbml-l3v2.xml new file mode 100644 index 000000000..5c6461ac1 --- /dev/null +++ b/latest/cases/01598/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + time + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + + + time + + + + + + + + diff --git a/latest/cases/01598/synopsis.txt b/latest/cases/01598/synopsis.txt new file mode 100644 index 000000000..7bf6327fd --- /dev/null +++ b/latest/cases/01598/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: Uncommon MathML in a delayed event with assignment time values. +componentTags: AssignmentRule, CSymbolTime, EventWithDelay, Parameter +testTags: EventUsesAssignmentTimeValues, InitialValueReassigned, NonConstantParameter, UncommonMathML +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model tests the use of an uncommon mathematical construct in a delayed event uses assignment time values. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $time >= 4.5$ | Assignment time | $1$ | $P2 = cosh(time)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | P1 | $cosh(time)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $cosh(time)$ | variable | +| Initial value of parameter P2 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01599/l2v5/index.heta b/latest/cases/01599/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01599/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01599/l3v2/build.log b/latest/cases/01599/l3v2/build.log new file mode 100644 index 000000000..ccfcf043c --- /dev/null +++ b/latest/cases/01599/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01599/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01599/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01599/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 92 +[error] FunctionDef "cosh" is not found as expected here: Q { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: R { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01599/l3v2/index.heta b/latest/cases/01599/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01599/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01599/model-sbml-l3v2.xml b/latest/cases/01599/model-sbml-l3v2.xml new file mode 100644 index 000000000..91d1994d7 --- /dev/null +++ b/latest/cases/01599/model-sbml-l3v2.xml @@ -0,0 +1,187 @@ + + + + + + + + + + + + + + + + + + + Q + R + + + + + + 1 + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + Q + + + + + 0 + + 100 + + + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + R + + + + + 0 + + 100 + + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01599/synopsis.txt b/latest/cases/01599/synopsis.txt new file mode 100644 index 000000000..96667d9d5 --- /dev/null +++ b/latest/cases/01599/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, RandomEventExecution, UncommonMathML +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle that an uncommon MathML element is used in the event assignments. + +The model contains: +* 7 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $Q = Q + cosh(0) / 100$ | +| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $R = R + cosh(0) / 100$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ | +| Rate | reset | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01600/l2v5/index.heta b/latest/cases/01600/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01600/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01600/l3v2/build.log b/latest/cases/01600/l3v2/build.log new file mode 100644 index 000000000..c7209b86a --- /dev/null +++ b/latest/cases/01600/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01600/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01600/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01600/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01600/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01600/l3v2/index.heta b/latest/cases/01600/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01600/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01600/model-sbml-l3v2.xml b/latest/cases/01600/model-sbml-l3v2.xml new file mode 100644 index 000000000..5a527d13b --- /dev/null +++ b/latest/cases/01600/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + + + + diff --git a/latest/cases/01600/synopsis.txt b/latest/cases/01600/synopsis.txt new file mode 100644 index 000000000..d7f717db7 --- /dev/null +++ b/latest/cases/01600/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Missing MathML in a delayed event assignment with trigger-time values. +componentTags: CSymbolTime, EventWithDelay, Parameter +testTags: EventUsesTriggerTimeValues, NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The model ensures that a delayed even with an assignment with trigger-time values can handle the fact that the assignment actually has no MathML. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time >= 4.5$ | $1$ | $P1 = $ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01601/l2v5/index.heta b/latest/cases/01601/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01601/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01601/l3v2/build.log b/latest/cases/01601/l3v2/build.log new file mode 100644 index 000000000..ea02ca680 --- /dev/null +++ b/latest/cases/01601/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01601/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01601/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01601/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01601/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01601/l3v2/index.heta b/latest/cases/01601/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01601/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01601/model-sbml-l3v2.xml b/latest/cases/01601/model-sbml-l3v2.xml new file mode 100644 index 000000000..d47f3be57 --- /dev/null +++ b/latest/cases/01601/model-sbml-l3v2.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + 3 + + + + + + + + diff --git a/latest/cases/01601/synopsis.txt b/latest/cases/01601/synopsis.txt new file mode 100644 index 000000000..b722b5605 --- /dev/null +++ b/latest/cases/01601/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Missing MathML in a delayed event assignment with trigger-time values. +componentTags: CSymbolTime, EventWithDelay, Parameter +testTags: EventUsesTriggerTimeValues, NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The model ensures that a delayed even with an assignment with trigger-time values can handle the fact that one assignment actually has no MathML, while the other one does. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time >= 4.5$ | $1$ | $P2 = 3$ | +| | | | $P1 = $ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable | +| Initial value of parameter P2 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01602/l2v5/index.heta b/latest/cases/01602/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01602/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01602/l3v2/build.log b/latest/cases/01602/l3v2/build.log new file mode 100644 index 000000000..38aed9a1e --- /dev/null +++ b/latest/cases/01602/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01602/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01602/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01602/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01602/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01602/l3v2/index.heta b/latest/cases/01602/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01602/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01602/model-sbml-l3v2.xml b/latest/cases/01602/model-sbml-l3v2.xml new file mode 100644 index 000000000..4b9c881f2 --- /dev/null +++ b/latest/cases/01602/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + + + + diff --git a/latest/cases/01602/synopsis.txt b/latest/cases/01602/synopsis.txt new file mode 100644 index 000000000..15fd9c39e --- /dev/null +++ b/latest/cases/01602/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Missing MathML in a delayed event assignment with assignment-time values. +componentTags: CSymbolTime, EventWithDelay, Parameter +testTags: EventUsesAssignmentTimeValues, NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The model ensures that a delayed even with an assignment with assignment-time values can handle the fact that the assignment actually has no MathML. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $time >= 4.5$ | Assignment time | $1$ | $P1 = $ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01603/l2v5/index.heta b/latest/cases/01603/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01603/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01603/l3v2/build.log b/latest/cases/01603/l3v2/build.log new file mode 100644 index 000000000..a90a35bc2 --- /dev/null +++ b/latest/cases/01603/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01603/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01603/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01603/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01603/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01603/l3v2/index.heta b/latest/cases/01603/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01603/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01603/model-sbml-l3v2.xml b/latest/cases/01603/model-sbml-l3v2.xml new file mode 100644 index 000000000..650f9fd0d --- /dev/null +++ b/latest/cases/01603/model-sbml-l3v2.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + time + + + + + + + + diff --git a/latest/cases/01603/synopsis.txt b/latest/cases/01603/synopsis.txt new file mode 100644 index 000000000..e8722ba3f --- /dev/null +++ b/latest/cases/01603/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: Missing MathML in a delayed event assignment with assignment-time values. +componentTags: CSymbolTime, EventWithDelay, Parameter +testTags: EventUsesAssignmentTimeValues, NoMathML, NonConstantParameter +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +The model ensures that a delayed even with an assignment with assignment-time values can handle the fact that one assignment actually has no MathML, while the other one does. + +The model contains: +* 2 parameters (P1, P2) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $time >= 4.5$ | Assignment time | $1$ | $P2 = time$ | +| | | | | $P1 = $ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable | +| Initial value of parameter P2 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01604/l2v5/build.log b/latest/cases/01604/l2v5/build.log new file mode 100644 index 000000000..c473a9231 --- /dev/null +++ b/latest/cases/01604/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01604/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01604/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01604/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01604/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01604/l2v5/index.heta b/latest/cases/01604/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01604/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01604/l3v2/build.log b/latest/cases/01604/l3v2/build.log new file mode 100644 index 000000000..581ae8c43 --- /dev/null +++ b/latest/cases/01604/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01604/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01604/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01604/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01604/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01604/l3v2/index.heta b/latest/cases/01604/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01604/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01604/model-sbml-l2v5.xml b/latest/cases/01604/model-sbml-l2v5.xml new file mode 100644 index 000000000..7dbba76da --- /dev/null +++ b/latest/cases/01604/model-sbml-l2v5.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + time + + + + + + + diff --git a/latest/cases/01604/model-sbml-l3v2.xml b/latest/cases/01604/model-sbml-l3v2.xml new file mode 100644 index 000000000..030aac2e3 --- /dev/null +++ b/latest/cases/01604/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + time + 4.5 + + + + + + 1 + + + + + + time + + + + + + + diff --git a/latest/cases/01604/synopsis.txt b/latest/cases/01604/synopsis.txt new file mode 100644 index 000000000..11307da7b --- /dev/null +++ b/latest/cases/01604/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A delayed event assignment with assignment-time values using 'time'. +componentTags: CSymbolTime, EventWithDelay, Parameter +testTags: EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model ensures that a delayed event with an assignment of 'time' with assignment-time values works even when the requested time points are not the exact effective assignment time. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $time >= 4.5$ | Assignment time | $1$ | $P1 = time$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01605/l2v5/index.heta b/latest/cases/01605/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01605/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01605/l3v2/build.log b/latest/cases/01605/l3v2/build.log new file mode 100644 index 000000000..99b1c01b5 --- /dev/null +++ b/latest/cases/01605/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01605/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01605/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01605/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 92 +[error] FunctionDef "cosh" is not found as expected here: Q { math: undefined }; +[error] FunctionDef "cosh" is not found as expected here: R { math: undefined }; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01605/l3v2/index.heta b/latest/cases/01605/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01605/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01605/model-sbml-l3v2.xml b/latest/cases/01605/model-sbml-l3v2.xml new file mode 100644 index 000000000..0ce5e260d --- /dev/null +++ b/latest/cases/01605/model-sbml-l3v2.xml @@ -0,0 +1,189 @@ + + + + + + + + + + + + + + + + + + + Q + R + + + + + + 1 + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + + Q + + + + + 0 + + 100 + + + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + + R + + + + + 0 + + 100 + + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01605/synopsis.txt b/latest/cases/01605/synopsis.txt new file mode 100644 index 000000000..cd06040dd --- /dev/null +++ b/latest/cases/01605/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule +testTags: EventIsNotPersistent, InitialValueReassigned, NoMathML, NonConstantParameter, RandomEventExecution, UncommonMathML +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + +This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle that assignments with no MathML are also incorporated into the events, which should fail to assign anything, leaving Q and R unchanged from their previous values. + +The model contains: +* 7 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh) + +There are 5 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $R = $ | +| | | | | $Q = Q + cosh(0) / 100$ | +| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $Q = $ | +| | | | | $R = R + cosh(0) / 100$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ | +| Rate | reset | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $0$ | variable | +| Initial value of parameter R | $0$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01606/l2v5/index.heta b/latest/cases/01606/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01606/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01606/l3v2/build.log b/latest/cases/01606/l3v2/build.log new file mode 100644 index 000000000..ccc8d7edb --- /dev/null +++ b/latest/cases/01606/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01606/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01606/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01606/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01606/l3v2/index.heta b/latest/cases/01606/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01606/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01606/model-sbml-l3v2.xml b/latest/cases/01606/model-sbml-l3v2.xml new file mode 100644 index 000000000..be31af06b --- /dev/null +++ b/latest/cases/01606/model-sbml-l3v2.xml @@ -0,0 +1,518 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: C2

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subsystem: C1

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subsystem: C1

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subsystem: L

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subsystem: C2

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subsystem: C2

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subsystem: C2

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subsystem: C2

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subsystem: C2

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: L

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subsystem: C4

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subsystem: L

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subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01606/synopsis.txt b/latest/cases/01606/synopsis.txt new file mode 100644 index 000000000..538d062d5 --- /dev/null +++ b/latest/cases/01606/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: Maximize single objective function, hard bounds. +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + +Maximize single objective function, hard bounds. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1, fb_1000, fb_neg_1000) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_neg_1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_neg_1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_neg_1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_neg_1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_neg_1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_neg_1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_neg_1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_neg_1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_neg_1000 | $-1000$ | constant |] + diff --git a/latest/cases/01607/l2v5/index.heta b/latest/cases/01607/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01607/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01607/l3v2/build.log b/latest/cases/01607/l3v2/build.log new file mode 100644 index 000000000..9550eca85 --- /dev/null +++ b/latest/cases/01607/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01607/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01607/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01607/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01607/l3v2/index.heta b/latest/cases/01607/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01607/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01607/model-sbml-l3v2.xml b/latest/cases/01607/model-sbml-l3v2.xml new file mode 100644 index 000000000..290343900 --- /dev/null +++ b/latest/cases/01607/model-sbml-l3v2.xml @@ -0,0 +1,518 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: C1

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subsystem: C2

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subsystem: C2

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subsystem: C2

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subsystem: L

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subsystem: C4

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subsystem: L

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01607/synopsis.txt b/latest/cases/01607/synopsis.txt new file mode 100644 index 000000000..050bae7d4 --- /dev/null +++ b/latest/cases/01607/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: Minimize single objective function, hard bounds. +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MinimizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Minimize single objective function, hard bounds. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1, fb_1000, fb_n1000) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant |] + diff --git a/latest/cases/01608/l2v5/index.heta b/latest/cases/01608/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01608/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01608/l3v2/build.log b/latest/cases/01608/l3v2/build.log new file mode 100644 index 000000000..5f96dfe1c --- /dev/null +++ b/latest/cases/01608/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01608/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01608/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01608/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01608/l3v2/index.heta b/latest/cases/01608/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01608/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01608/model-sbml-l3v2.xml b/latest/cases/01608/model-sbml-l3v2.xml new file mode 100644 index 000000000..08675aa39 --- /dev/null +++ b/latest/cases/01608/model-sbml-l3v2.xml @@ -0,0 +1,518 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01608/synopsis.txt b/latest/cases/01608/synopsis.txt new file mode 100644 index 000000000..3e8d0bc3e --- /dev/null +++ b/latest/cases/01608/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: Maximize single objective function, infinite bounds. +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Maximize single objective function, infinite bounds. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1, fb_inf, fb_ninf) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_inf$$ | +| R14: K -> L | $fb_ninf <= R14 <= fb_inf$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_inf$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_inf$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_inf$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_inf$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_inf$$ | +| R03: A -> C | $fb_ninf <= R03 <= fb_inf$$ | +| R02: A -> B | $fb_ninf <= R02 <= fb_inf$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_inf$$ | +| R04: C -> B | $fb_ninf <= R04 <= fb_inf$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_inf$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_inf$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_inf$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_inf$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_inf$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_inf$$ | +| R19: K -> O | $fb_ninf <= R19 <= fb_inf$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_inf$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_inf$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_inf$$ | +| R23: R -> S | $fb_ninf <= R23 <= fb_inf$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_inf$$ | +| R21: P -> L | $fb_ninf <= R21 <= fb_inf$$ | +| R20: O -> P | $fb_ninf <= R20 <= fb_inf$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_inf | $inf$ | constant | +| Initial value of parameter fb_ninf | $-inf$ | constant |] + diff --git a/latest/cases/01609/l2v5/index.heta b/latest/cases/01609/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01609/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01609/l3v2/build.log b/latest/cases/01609/l3v2/build.log new file mode 100644 index 000000000..f3ac4b414 --- /dev/null +++ b/latest/cases/01609/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01609/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01609/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01609/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01609/l3v2/index.heta b/latest/cases/01609/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01609/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01609/model-sbml-l3v2.xml b/latest/cases/01609/model-sbml-l3v2.xml new file mode 100644 index 000000000..2bd41b523 --- /dev/null +++ b/latest/cases/01609/model-sbml-l3v2.xml @@ -0,0 +1,518 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: C2

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subsystem: C3

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subsystem: L

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subsystem: C3

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subsystem: C1

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subsystem: C1

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subsystem: L

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subsystem: C1

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subsystem: C2

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subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: L

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subsystem: C4

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subsystem: C4

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subsystem: L

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01609/synopsis.txt b/latest/cases/01609/synopsis.txt new file mode 100644 index 000000000..109cd38a8 --- /dev/null +++ b/latest/cases/01609/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: Minimize single objective function, infinite bounds. +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MinimizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Minimize single objective function, infinite bounds. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_inf, fb_negInf, fb_1) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_inf$$ | +| R14: K -> L | $fb_negInf <= R14 <= fb_inf$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_inf$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_inf$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_inf$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_inf$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_inf$$ | +| R03: A -> C | $fb_negInf <= R03 <= fb_inf$$ | +| R02: A -> B | $fb_negInf <= R02 <= fb_inf$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_inf$$ | +| R04: C -> B | $fb_negInf <= R04 <= fb_inf$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_inf$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_inf$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_inf$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_inf$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_inf$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_inf$$ | +| R19: K -> O | $fb_negInf <= R19 <= fb_inf$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_inf$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_inf$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_inf$$ | +| R23: R -> S | $fb_negInf <= R23 <= fb_inf$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_inf$$ | +| R21: P -> L | $fb_negInf <= R21 <= fb_inf$$ | +| R20: O -> P | $fb_negInf <= R20 <= fb_inf$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_inf | $inf$ | constant | +| Initial value of parameter fb_negInf | $-inf$ | constant | +| Initial value of parameter fb_1 | $1$ | constant |] + diff --git a/latest/cases/01610/l2v5/index.heta b/latest/cases/01610/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01610/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01610/l3v2/build.log b/latest/cases/01610/l3v2/build.log new file mode 100644 index 000000000..67dbc33ed --- /dev/null +++ b/latest/cases/01610/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01610/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01610/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01610/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01610/l3v2/index.heta b/latest/cases/01610/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01610/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01610/model-sbml-l3v2.xml b/latest/cases/01610/model-sbml-l3v2.xml new file mode 100644 index 000000000..206435dd6 --- /dev/null +++ b/latest/cases/01610/model-sbml-l3v2.xml @@ -0,0 +1,518 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01610/synopsis.txt b/latest/cases/01610/synopsis.txt new file mode 100644 index 000000000..f0c6c6d3b --- /dev/null +++ b/latest/cases/01610/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: Maximize single objective function, non-unitary objective flux coefficient +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Maximize single objective function, non-unitary objective flux coefficient. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1000, fb_n1000, fb_1) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 0.5 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_1 | $1$ | constant |] + diff --git a/latest/cases/01611/l2v5/index.heta b/latest/cases/01611/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01611/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01611/l3v2/build.log b/latest/cases/01611/l3v2/build.log new file mode 100644 index 000000000..9dc4e0585 --- /dev/null +++ b/latest/cases/01611/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01611/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01611/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01611/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01611/l3v2/index.heta b/latest/cases/01611/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01611/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01611/model-sbml-l3v2.xml b/latest/cases/01611/model-sbml-l3v2.xml new file mode 100644 index 000000000..f8730f562 --- /dev/null +++ b/latest/cases/01611/model-sbml-l3v2.xml @@ -0,0 +1,523 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: C2

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subsystem: C3

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subsystem: L

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subsystem: C3

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subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

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subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

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subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01611/synopsis.txt b/latest/cases/01611/synopsis.txt new file mode 100644 index 000000000..d254748a8 --- /dev/null +++ b/latest/cases/01611/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: Multiple objectives defined, optimize active one (maximize) +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective, fbc:MinimizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Multiple objectives defined, optimize active one (maximize) + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1000, fb_n1000, fb_1) +* 1 compartment (Cell) +* 2 objectives (OBJF, OBJF2) + +The active objective is OBJF2, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_1 | $1$ | constant |] + diff --git a/latest/cases/01612/l2v5/index.heta b/latest/cases/01612/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01612/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01612/l3v2/build.log b/latest/cases/01612/l3v2/build.log new file mode 100644 index 000000000..86ab7f30c --- /dev/null +++ b/latest/cases/01612/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01612/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01612/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01612/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01612/l3v2/index.heta b/latest/cases/01612/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01612/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01612/model-sbml-l3v2.xml b/latest/cases/01612/model-sbml-l3v2.xml new file mode 100644 index 000000000..8b59f3cf1 --- /dev/null +++ b/latest/cases/01612/model-sbml-l3v2.xml @@ -0,0 +1,519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01612/synopsis.txt b/latest/cases/01612/synopsis.txt new file mode 100644 index 000000000..345f4813b --- /dev/null +++ b/latest/cases/01612/synopsis.txt @@ -0,0 +1,60 @@ + +category: Test +synopsis: Single objective, multiple flux objectives +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Single objective, multiple flux objectives. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1000, fb_n1000, fb_1) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + + 1 R10 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_1 | $1$ | constant |] + diff --git a/latest/cases/01613/l2v5/index.heta b/latest/cases/01613/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01613/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01613/l3v2/build.log b/latest/cases/01613/l3v2/build.log new file mode 100644 index 000000000..58fe2fbee --- /dev/null +++ b/latest/cases/01613/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01613/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01613/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01613/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 133 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01613/l3v2/index.heta b/latest/cases/01613/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01613/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01613/model-sbml-l3v2.xml b/latest/cases/01613/model-sbml-l3v2.xml new file mode 100644 index 000000000..afdcf8f4f --- /dev/null +++ b/latest/cases/01613/model-sbml-l3v2.xml @@ -0,0 +1,519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: C2

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subsystem: C3

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subsystem: L

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subsystem: C3

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subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01613/synopsis.txt b/latest/cases/01613/synopsis.txt new file mode 100644 index 000000000..b3724d014 --- /dev/null +++ b/latest/cases/01613/synopsis.txt @@ -0,0 +1,60 @@ + +category: Test +synopsis: Single objective, test R07 GE 0.5, R10 GE 0.5 +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Single objective, test R07 GE 0.5, R10 GE 0.5 + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 5 parameters (fb_0, fb_1000, fb_n1000, fb_0_5, fb_1) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0_5 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0_5 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_0_5 | $0.5$ | constant | +| Initial value of parameter fb_1 | $1$ | constant |] + diff --git a/latest/cases/01614/l2v5/index.heta b/latest/cases/01614/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01614/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01614/l3v2/build.log b/latest/cases/01614/l3v2/build.log new file mode 100644 index 000000000..ab16855e4 --- /dev/null +++ b/latest/cases/01614/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01614/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01614/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01614/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 134 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01614/l3v2/index.heta b/latest/cases/01614/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01614/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01614/model-sbml-l3v2.xml b/latest/cases/01614/model-sbml-l3v2.xml new file mode 100644 index 000000000..abeccc63f --- /dev/null +++ b/latest/cases/01614/model-sbml-l3v2.xml @@ -0,0 +1,520 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01614/synopsis.txt b/latest/cases/01614/synopsis.txt new file mode 100644 index 000000000..06b2fe142 --- /dev/null +++ b/latest/cases/01614/synopsis.txt @@ -0,0 +1,61 @@ + +category: Test +synopsis: Single objective, test R07 LE 0.2, R10 LE 0.3 +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Single objective, test R07 LE 0.2, R10 LE 0.3 + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 6 parameters (fb_0, fb_1000, fb_n1000, fb_0_2, fb_1, fb_0_3) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_0_2$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_0_3$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_0_2 | $0.2$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_0_3 | $0.3$ | constant |] + diff --git a/latest/cases/01615/l2v5/index.heta b/latest/cases/01615/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01615/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01615/l3v2/build.log b/latest/cases/01615/l3v2/build.log new file mode 100644 index 000000000..980058b98 --- /dev/null +++ b/latest/cases/01615/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01615/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01615/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01615/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 135 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01615/l3v2/index.heta b/latest/cases/01615/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01615/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01615/model-sbml-l3v2.xml b/latest/cases/01615/model-sbml-l3v2.xml new file mode 100644 index 000000000..e7a0401d9 --- /dev/null +++ b/latest/cases/01615/model-sbml-l3v2.xml @@ -0,0 +1,521 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: L

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subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01615/synopsis.txt b/latest/cases/01615/synopsis.txt new file mode 100644 index 000000000..9e0d24e9d --- /dev/null +++ b/latest/cases/01615/synopsis.txt @@ -0,0 +1,62 @@ + +category: Test +synopsis: Single objective, test: R07 EQ 0.2, R10 EQ 0.2, R25 EQ 0.6 +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Single objective, test: R07 EQ 0.2, R10 EQ 0.2, R25 EQ 0.6 + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 7 parameters (fb_0, fb_1000, fb_n1000, fb_1, fb_0_2, fb_0_3, fb_0_4) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0_2 <= R07 <= fb_0_2$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0_3 <= R10 <= fb_0_3$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0_4 <= R25 <= fb_0_4$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_0_2 | $0.2$ | constant | +| Initial value of parameter fb_0_3 | $0.3$ | constant | +| Initial value of parameter fb_0_4 | $0.4$ | constant |] + diff --git a/latest/cases/01616/l2v5/index.heta b/latest/cases/01616/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01616/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01616/l3v2/build.log b/latest/cases/01616/l3v2/build.log new file mode 100644 index 000000000..56d1ecbd4 --- /dev/null +++ b/latest/cases/01616/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01616/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01616/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01616/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 133 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01616/l3v2/index.heta b/latest/cases/01616/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01616/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01616/model-sbml-l3v2.xml b/latest/cases/01616/model-sbml-l3v2.xml new file mode 100644 index 000000000..32a0a6ab8 --- /dev/null +++ b/latest/cases/01616/model-sbml-l3v2.xml @@ -0,0 +1,519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01616/synopsis.txt b/latest/cases/01616/synopsis.txt new file mode 100644 index 000000000..fb4c34837 --- /dev/null +++ b/latest/cases/01616/synopsis.txt @@ -0,0 +1,60 @@ + +category: Test +synopsis: Infeasible solution, should return a nan +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + Infeasible solution, should return a nan + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 5 parameters (fb_0, fb_1000, fb_n1000, fb_2, fb_1) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_2 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_2 | $2$ | constant | +| Initial value of parameter fb_1 | $1$ | constant |] + diff --git a/latest/cases/01617/l2v5/index.heta b/latest/cases/01617/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01617/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01617/l3v2/build.log b/latest/cases/01617/l3v2/build.log new file mode 100644 index 000000000..0db0ea2e3 --- /dev/null +++ b/latest/cases/01617/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01617/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01617/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01617/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01617/l3v2/index.heta b/latest/cases/01617/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01617/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01617/model-sbml-l3v2.xml b/latest/cases/01617/model-sbml-l3v2.xml new file mode 100644 index 000000000..422f2725f --- /dev/null +++ b/latest/cases/01617/model-sbml-l3v2.xml @@ -0,0 +1,525 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01617/synopsis.txt b/latest/cases/01617/synopsis.txt new file mode 100644 index 000000000..3bd94bbc7 --- /dev/null +++ b/latest/cases/01617/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: FBC test with initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, InitialValueReassigned, NonUnityStoichiometry, fbc:MaximizeObjective, fbc:NonStrict +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + In this test, fb_0 is set to zero by an initial assignment, which contradicts its 'value' attribute. A non-strict test. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1, fb_1000, fb_neg_1000) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_neg_1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_neg_1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_neg_1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_neg_1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_neg_1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_neg_1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_neg_1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_neg_1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_neg_1000 | $-1000$ | constant |] + diff --git a/latest/cases/01618/l2v5/index.heta b/latest/cases/01618/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01618/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01618/l3v2/build.log b/latest/cases/01618/l3v2/build.log new file mode 100644 index 000000000..6983352aa --- /dev/null +++ b/latest/cases/01618/l3v2/build.log @@ -0,0 +1,39 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01618/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01618/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01618/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] No required "num" property for "fb_1000" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01618/l3v2/index.heta b/latest/cases/01618/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01618/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01618/model-sbml-l3v2.xml b/latest/cases/01618/model-sbml-l3v2.xml new file mode 100644 index 000000000..18b9e9dd2 --- /dev/null +++ b/latest/cases/01618/model-sbml-l3v2.xml @@ -0,0 +1,529 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 100 + 10 + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01618/synopsis.txt b/latest/cases/01618/synopsis.txt new file mode 100644 index 000000000..c01a29cef --- /dev/null +++ b/latest/cases/01618/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: FBC with initial assignment. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, InitialValueReassigned, NonUnityStoichiometry, fbc:MinimizeObjective, fbc:NonStrict +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + In this test, an initial assignment sets the value for fb_1000, giving it a value where it did not have one before. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1, fb_1000, fb_n1000) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_1000 | $100 * 10$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant |] + diff --git a/latest/cases/01619/l2v5/index.heta b/latest/cases/01619/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01619/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01619/l3v2/build.log b/latest/cases/01619/l3v2/build.log new file mode 100644 index 000000000..4b587a3f9 --- /dev/null +++ b/latest/cases/01619/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01619/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01619/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01619/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01619/l3v2/index.heta b/latest/cases/01619/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01619/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01619/model-sbml-l3v2.xml b/latest/cases/01619/model-sbml-l3v2.xml new file mode 100644 index 000000000..59a18f837 --- /dev/null +++ b/latest/cases/01619/model-sbml-l3v2.xml @@ -0,0 +1,525 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: C2

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subsystem: C3

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subsystem: L

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subsystem: C1

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subsystem: L

+ + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + +

subsystem: L

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subsystem: L

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subsystem: C4

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subsystem: C4

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subsystem: L

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01619/synopsis.txt b/latest/cases/01619/synopsis.txt new file mode 100644 index 000000000..9f3ee8157 --- /dev/null +++ b/latest/cases/01619/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: FBC test with initial assignment of infinity. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, InitialValueReassigned, NonUnityStoichiometry, fbc:MaximizeObjective, fbc:NonStrict +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + In this test, an initial assignment to a flux bound sets a value of infinity. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1, fb_inf, fb_ninf) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_inf$$ | +| R14: K -> L | $fb_ninf <= R14 <= fb_inf$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_inf$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_inf$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_inf$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_inf$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_inf$$ | +| R03: A -> C | $fb_ninf <= R03 <= fb_inf$$ | +| R02: A -> B | $fb_ninf <= R02 <= fb_inf$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_inf$$ | +| R04: C -> B | $fb_ninf <= R04 <= fb_inf$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_inf$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_inf$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_inf$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_inf$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_inf$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_inf$$ | +| R19: K -> O | $fb_ninf <= R19 <= fb_inf$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_inf$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_inf$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_inf$$ | +| R23: R -> S | $fb_ninf <= R23 <= fb_inf$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_inf$$ | +| R21: P -> L | $fb_ninf <= R21 <= fb_inf$$ | +| R20: O -> P | $fb_ninf <= R20 <= fb_inf$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_inf | $INF$ | constant | +| Initial value of parameter fb_ninf | $-inf$ | constant |] + diff --git a/latest/cases/01620/l2v5/index.heta b/latest/cases/01620/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01620/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01620/l3v2/build.log b/latest/cases/01620/l3v2/build.log new file mode 100644 index 000000000..099c064cb --- /dev/null +++ b/latest/cases/01620/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01620/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01620/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01620/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01620/l3v2/index.heta b/latest/cases/01620/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01620/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01620/model-sbml-l3v2.xml b/latest/cases/01620/model-sbml-l3v2.xml new file mode 100644 index 000000000..9a9528adf --- /dev/null +++ b/latest/cases/01620/model-sbml-l3v2.xml @@ -0,0 +1,525 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + + + + + +

subsystem: C3

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01620/synopsis.txt b/latest/cases/01620/synopsis.txt new file mode 100644 index 000000000..521c17834 --- /dev/null +++ b/latest/cases/01620/synopsis.txt @@ -0,0 +1,65 @@ + +category: Test +synopsis: FBC with constant assignment rule to flux bound. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, InitialValueReassigned, NonUnityStoichiometry, fbc:MinimizeObjective, fbc:NonStrict +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + In this test, an assignment rule is used to set a flux bound to a constant value. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_inf, fb_negInf, fb_1) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_inf$$ | +| R14: K -> L | $fb_negInf <= R14 <= fb_inf$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_inf$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_inf$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_inf$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_inf$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_inf$$ | +| R03: A -> C | $fb_negInf <= R03 <= fb_inf$$ | +| R02: A -> B | $fb_negInf <= R02 <= fb_inf$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_inf$$ | +| R04: C -> B | $fb_negInf <= R04 <= fb_inf$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_inf$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_inf$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_inf$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_inf$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_inf$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_inf$$ | +| R19: K -> O | $fb_negInf <= R19 <= fb_inf$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_inf$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_inf$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_inf$$ | +| R23: R -> S | $fb_negInf <= R23 <= fb_inf$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_inf$$ | +| R21: P -> L | $fb_negInf <= R21 <= fb_inf$$ | +| R20: O -> P | $fb_negInf <= R20 <= fb_inf$$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | fb_0 | $0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_inf | $inf$ | constant | +| Initial value of parameter fb_negInf | $-inf$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_0 | $0$ | variable |] + diff --git a/latest/cases/01621/l2v5/index.heta b/latest/cases/01621/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01621/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01621/l3v2/build.log b/latest/cases/01621/l3v2/build.log new file mode 100644 index 000000000..31156c7dc --- /dev/null +++ b/latest/cases/01621/l3v2/build.log @@ -0,0 +1,39 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01621/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01621/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01621/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] R25_S_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01621/l3v2/index.heta b/latest/cases/01621/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01621/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01621/model-sbml-l3v2.xml b/latest/cases/01621/model-sbml-l3v2.xml new file mode 100644 index 000000000..e74a1c675 --- /dev/null +++ b/latest/cases/01621/model-sbml-l3v2.xml @@ -0,0 +1,525 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: C2

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subsystem: C3

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subsystem: L

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subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

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subsystem: L

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subsystem: C1

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subsystem: C2

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subsystem: C2

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subsystem: C2

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subsystem: C3

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subsystem: L

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subsystem: L

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subsystem: C4

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subsystem: C4

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subsystem: L

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01621/synopsis.txt b/latest/cases/01621/synopsis.txt new file mode 100644 index 000000000..bdc08781f --- /dev/null +++ b/latest/cases/01621/synopsis.txt @@ -0,0 +1,62 @@ + +category: Test +synopsis: Initial assignment of an FBC stoichiometry. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: AssignedConstantStoichiometry, BoundaryCondition, InitialValueReassigned, NonUnityStoichiometry, fbc:MaximizeObjective, fbc:NonStrict +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + In this test, an initial assignment is used to set the stoichiometry of a product in reaction R25. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1000, fb_n1000, fb_1) +* 1 compartment (Cell) +* 1 species reference (R25_S_stoich) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 0.5 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> R25_S_stoich S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] +Note: the following stoichiometries are set separately: R25_S_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of species reference 'R25_S_stoich' | $0.5$ | constant |] + diff --git a/latest/cases/01622/l2v5/index.heta b/latest/cases/01622/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01622/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01622/l3v2/build.log b/latest/cases/01622/l3v2/build.log new file mode 100644 index 000000000..dd3a11e4e --- /dev/null +++ b/latest/cases/01622/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01622/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01622/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01622/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01622/l3v2/index.heta b/latest/cases/01622/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01622/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01622/model-sbml-l3v2.xml b/latest/cases/01622/model-sbml-l3v2.xml new file mode 100644 index 000000000..f2ae5826c --- /dev/null +++ b/latest/cases/01622/model-sbml-l3v2.xml @@ -0,0 +1,523 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

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subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01622/synopsis.txt b/latest/cases/01622/synopsis.txt new file mode 100644 index 000000000..ab5f24240 --- /dev/null +++ b/latest/cases/01622/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: FBC test with negative stoichiometries +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MaximizeObjective, fbc:MinimizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + In this test, reaction R25 has negative stoichiometries. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1000, fb_n1000, fb_1) +* 1 compartment (Cell) +* 2 objectives (OBJF, OBJF2) + +The active objective is OBJF2, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: -0.5S + -1U -> -1A + -1T | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_1 | $1$ | constant |] + diff --git a/latest/cases/01623/l2v5/index.heta b/latest/cases/01623/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01623/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01623/l3v2/build.log b/latest/cases/01623/l3v2/build.log new file mode 100644 index 000000000..224f475a4 --- /dev/null +++ b/latest/cases/01623/l3v2/build.log @@ -0,0 +1,39 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01623/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01623/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01623/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] R14_K_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 133 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01623/l3v2/index.heta b/latest/cases/01623/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01623/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01623/model-sbml-l3v2.xml b/latest/cases/01623/model-sbml-l3v2.xml new file mode 100644 index 000000000..1d70e493b --- /dev/null +++ b/latest/cases/01623/model-sbml-l3v2.xml @@ -0,0 +1,526 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: C2

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subsystem: C3

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subsystem: L

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subsystem: C3

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subsystem: C1

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subsystem: C1

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subsystem: L

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subsystem: C1

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subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

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subsystem: C2

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subsystem: C2

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subsystem: L

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subsystem: L

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subsystem: C4

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subsystem: C4

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subsystem: L

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01623/synopsis.txt b/latest/cases/01623/synopsis.txt new file mode 100644 index 000000000..a8343c082 --- /dev/null +++ b/latest/cases/01623/synopsis.txt @@ -0,0 +1,63 @@ + +category: Test +synopsis: FBC test with initial assignment to stoichiometry. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: AssignedConstantStoichiometry, BoundaryCondition, InitialValueReassigned, NonUnityStoichiometry, fbc:MinimizeObjective, fbc:NonStrict +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + +A test with minimization that is dependent on an initial assignment to a stoichiometry. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 5 parameters (fb_0, fb_1000, fb_n1000, fb_n100, fb_1) +* 1 compartment (Cell) +* 1 species reference (R14_K_stoich) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: R14_K_stoich K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_n1000 <= R25 <= fb_n100$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] +Note: the following stoichiometries are set separately: R14_K_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_n100 | $-100$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of species reference 'R14_K_stoich' | $1$ | constant |] + diff --git a/latest/cases/01624/l2v5/index.heta b/latest/cases/01624/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01624/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01624/l3v2/build.log b/latest/cases/01624/l3v2/build.log new file mode 100644 index 000000000..097bcda2e --- /dev/null +++ b/latest/cases/01624/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01624/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01624/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01624/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 133 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01624/l3v2/index.heta b/latest/cases/01624/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01624/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01624/model-sbml-l3v2.xml b/latest/cases/01624/model-sbml-l3v2.xml new file mode 100644 index 000000000..52010f7a2 --- /dev/null +++ b/latest/cases/01624/model-sbml-l3v2.xml @@ -0,0 +1,519 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01624/synopsis.txt b/latest/cases/01624/synopsis.txt new file mode 100644 index 000000000..fe9bcb315 --- /dev/null +++ b/latest/cases/01624/synopsis.txt @@ -0,0 +1,60 @@ + +category: Test +synopsis: FBC minimization test with a flux set to equal a particular value. +componentTags: Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:MinimizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + +A test with minimization that uses a reaction whose upper and lower bounds are set to be equal. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 5 parameters (fb_0, fb_1000, fb_n1000, fb_n100, fb_1) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_0 <= R14 <= fb_0$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_n1000 <= R25 <= fb_n100$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_n100 | $-100$ | constant | +| Initial value of parameter fb_1 | $1$ | constant |] + diff --git a/latest/cases/01625/l2v5/index.heta b/latest/cases/01625/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01625/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01625/l3v2/build.log b/latest/cases/01625/l3v2/build.log new file mode 100644 index 000000000..d26724bac --- /dev/null +++ b/latest/cases/01625/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01625/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01625/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01625/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 128 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01625/l3v2/index.heta b/latest/cases/01625/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01625/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01625/model-sbml-l3v2.xml b/latest/cases/01625/model-sbml-l3v2.xml new file mode 100644 index 000000000..56bc86340 --- /dev/null +++ b/latest/cases/01625/model-sbml-l3v2.xml @@ -0,0 +1,565 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

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subsystem: L

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subsystem: C2

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subsystem: C3

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subsystem: L

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subsystem: C1

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subsystem: L

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subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

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+ + + + + + + + + + + + + + + + + +

subsystem: C2

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subsystem: C4

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subsystem: C4

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subsystem: L

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subsystem: C3

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subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01625/synopsis.txt b/latest/cases/01625/synopsis.txt new file mode 100644 index 000000000..3ceeae218 --- /dev/null +++ b/latest/cases/01625/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: FBC minimization test with a flux set to equal a particular value. +componentTags: Compartment, Reaction, Species, fbc:FluxBound, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, NonUnityStoichiometry, fbc:BoundEqual, fbc:BoundGreaterEqual, fbc:BoundLessEqual, fbc:MinimizeObjective +testType: FluxBalanceSteadyState +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v1 + +A test with minimization that uses a reaction whose bound is set to be equal to zero, instead of having an upper and lower bound. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions, and 51 flux bounds: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $R16 >= 0 && R16 <= 1000$ | +| R14: K -> L | $R14 == 0$ | +| R15: L -> Q | $R15 >= 0 && R15 <= 1000$ | +| R12: I -> J | $R12 >= 0 && R12 <= 1000$ | +| R07: E -> F | $R07 >= 0 && R07 <= 1000$ | +| R13: J -> K | $R13 >= 0 && R13 <= 1000$ | +| R01: X -> A | $R01 >= 0 && R01 <= 1$ | +| R17: M -> N | $R17 >= 0 && R17 <= 1000$ | +| R03: A -> C | $R03 >= -1000 && R03 <= 1000$ | +| R02: A -> B | $R02 >= -1000 && R02 <= 1000$ | +| R05: B -> D | $R05 >= 0 && R05 <= 1000$ | +| R04: C -> B | $R04 >= -1000 && R04 <= 1000$ | +| R10: G -> H | $R10 >= 0 && R10 <= 1000$ | +| R06: D -> E | $R06 >= 0 && R06 <= 1000$ | +| R09: D -> G | $R09 >= 0 && R09 <= 1000$ | +| R08: F -> I | $R08 >= 0 && R08 <= 1000$ | +| R11: H -> I | $R11 >= 0 && R11 <= 1000$ | +| R18: N -> Q | $R18 >= 0 && R18 <= 1000$ | +| R19: K -> O | $R19 >= -1000 && R19 <= 1000$ | +| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ | +| R25: A + T -> 0.5S + U | $R25 >= -1000 && R25 <= -100$ | +| R24: R -> S | $R24 >= 0 && R24 <= 1000$ | +| R23: R -> S | $R23 >= -1000 && R23 <= 1000$ | +| R22: Q -> R | $R22 >= 0 && R22 <= 1000$ | +| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ | +| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ |] + + diff --git a/latest/cases/01626/l2v5/index.heta b/latest/cases/01626/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01626/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01626/l3v2/build.log b/latest/cases/01626/l3v2/build.log new file mode 100644 index 000000000..0b93a7456 --- /dev/null +++ b/latest/cases/01626/l3v2/build.log @@ -0,0 +1,18 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01626/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01626/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01626/model-sbml-l3v2.xml"... +[error] Q component does not exist which is not allowed for the "update" action. +[error] R component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 97 +[error] Component "Q" is not found in space "nameless" as expected in expression: S [ode_]= Q + R; +[error] Component "R" is not found in space "nameless" as expected in expression: S [ode_]= Q + R; +[error] Component "Q" is not found in space "nameless" as expected in expression: maxdiff [maxcheck]= abs(Q - R); +[error] Component "R" is not found in space "nameless" as expected in expression: maxdiff [maxcheck]= abs(Q - R); +[error] Component "Q" is not found in space "nameless" as expected in DSwitcher: "maxcheck" + abs(Q - R) > maxdiff; +[error] Component "R" is not found in space "nameless" as expected in DSwitcher: "maxcheck" + abs(Q - R) > maxdiff; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01626/l3v2/index.heta b/latest/cases/01626/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01626/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01626/model-sbml-l3v2.xml b/latest/cases/01626/model-sbml-l3v2.xml new file mode 100644 index 000000000..cc6b8bba2 --- /dev/null +++ b/latest/cases/01626/model-sbml-l3v2.xml @@ -0,0 +1,216 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + Q + R + + + + + + 1 + + + + + + + + + + + + + + 0.1 + + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + Q + 0.01 + + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + R + 0.01 + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + + + + + + S2 + + 25 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01626/synopsis.txt b/latest/cases/01626/synopsis.txt new file mode 100644 index 000000000..e103a98d6 --- /dev/null +++ b/latest/cases/01626/synopsis.txt @@ -0,0 +1,63 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, RateRule, Reaction, Species +testTags: AssignedVariableStoichiometry, EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, NonUnityStoichiometry, RandomEventExecution, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the stoichiometries Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. Three other parameters (errorHigh, errorLow, and errorS2), check to make sure neither Q nor R are chosen more or less frequently than the other, and that the species S2 doesn't get too extreme (the reaction in which it appears should be balanced, on average). Note: The error parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. + +The model contains: +* 1 species (S2) +* 8 parameters (S, reset, maxdiff, errorLow, errorHigh, errorS2, S2_det, maxS2diff) +* 1 compartment (C) +* 2 species references (Q, R) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: Q S2 -> R S2 | $0.1$ |] +Note: the following stoichiometries are set separately: Q, R + + +There are 6 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $R = R + 0.01$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ | +| error_check3 | $abs(S2) >= 25$ | (unset) | true | $errorS2 = 1$ |] + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S | $Q + R$ | +| Rate | reset | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S2 | $0$ | variable | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable | +| Initial value of parameter errorS2 | $0$ | variable | +| Initial value of parameter S2_det | $0$ | variable | +| Initial value of parameter maxS2diff | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'Q' | $1$ | variable | +| Initial value of species reference 'R' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01627/l2v5/index.heta b/latest/cases/01627/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01627/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01627/l3v2/heta-code/output.heta b/latest/cases/01627/l3v2/heta-code/output.heta new file mode 100644 index 000000000..102035aa6 --- /dev/null +++ b/latest/cases/01627/l3v2/heta-code/output.heta @@ -0,0 +1,41 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 1; + +S2 @Species { compartment: C1, } .= 0; + +S2_proc @Process { actors: = S2, }; +S2_proc := Q - R; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.002; +reset_proc @Process { actors: = reset, }; +reset_proc := 1; + +S @Record { }; +S := Q + R; +Q @Record { } .= 1; +Q [Qinc]= Q + 0.01; +R @Record { } .= 1; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= 0; +reset [Rinc]= 0; +maxdiff @Record { } .= 0; +maxdiff [maxcheck]= abs(Q - R); +errorLow @Record { } .= 0; +errorLow [error_check]= 1; +errorHigh @Record { } .= 0; +errorHigh [error_check2]= 1; +errorS2 @Record { } .= 0; +errorS2 [error_check3]= 1; +S2_det @Record { } .= 0; + +Qinc @DSwitcher { trigger: reset >= 0.01, }; +Rinc @DSwitcher { trigger: reset >= 0.01, }; +maxcheck @DSwitcher { trigger: abs(Q - R) > maxdiff, }; +error_check @DSwitcher { trigger: t >= 99 and maxdiff < 0.2, }; +error_check2 @DSwitcher { trigger: maxdiff >= 4, }; +error_check3 @DSwitcher { trigger: abs(S2) >= 250, }; + diff --git a/latest/cases/01627/l3v2/index.heta b/latest/cases/01627/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01627/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01627/l3v2/json/output.json b/latest/cases/01627/l3v2/json/output.json new file mode 100644 index 000000000..a4fe45f51 --- /dev/null +++ b/latest/cases/01627/l3v2/json/output.json @@ -0,0 +1,160 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0" + }, + "compartment": "C1" + }, + { + "class": "Record", + "id": "S", + "assignments": { + "ode_": "Q + R" + } + }, + { + "class": "Record", + "id": "Q", + "assignments": { + "start_": "1", + "Qinc": "Q + 0.01" + } + }, + { + "class": "Record", + "id": "R", + "assignments": { + "start_": "1", + "Rinc": "R + 0.01" + } + }, + { + "class": "Record", + "id": "reset", + "assignments": { + "start_": "0", + "Qinc": "0", + "Rinc": "0" + } + }, + { + "class": "Record", + "id": "maxdiff", + "assignments": { + "start_": "0", + "maxcheck": "abs(Q - R)" + } + }, + { + "class": "Record", + "id": "errorLow", + "assignments": { + "start_": "0", + "error_check": "1" + } + }, + { + "class": "Record", + "id": "errorHigh", + "assignments": { + "start_": "0", + "error_check2": "1" + } + }, + { + "class": "Record", + "id": "errorS2", + "assignments": { + "start_": "0", + "error_check3": "1" + } + }, + { + "class": "Record", + "id": "S2_det", + "assignments": { + "start_": "0" + } + }, + { + "class": "Process", + "id": "S2_proc", + "assignments": { + "ode_": "Q - R" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "C1_proc", + "assignments": { + "ode_": "0.002" + }, + "actors": [ + { + "target": "C1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "reset_proc", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "reset", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "Qinc", + "trigger": "reset >= 0.01" + }, + { + "class": "DSwitcher", + "id": "Rinc", + "trigger": "reset >= 0.01" + }, + { + "class": "DSwitcher", + "id": "maxcheck", + "trigger": "abs(Q - R) > maxdiff" + }, + { + "class": "DSwitcher", + "id": "error_check", + "trigger": "t >= 99 and maxdiff < 0.2" + }, + { + "class": "DSwitcher", + "id": "error_check2", + "trigger": "maxdiff >= 4" + }, + { + "class": "DSwitcher", + "id": "error_check3", + "trigger": "abs(S2) >= 250" + } +] \ No newline at end of file diff --git a/latest/cases/01627/model-sbml-l3v2.xml b/latest/cases/01627/model-sbml-l3v2.xml new file mode 100644 index 000000000..3736e2ad2 --- /dev/null +++ b/latest/cases/01627/model-sbml-l3v2.xml @@ -0,0 +1,216 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + Q + R + + + + + + 0.002 + + + + + + + Q + R + + + + + + 1 + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + Q + 0.01 + + + + + + + + + + + reset + 0.01 + + + + + + 1 + + + + + + 0 + + + + + + + R + 0.01 + + + + + + + + + + + + + + + Q + R + + + maxdiff + + + + + + + + + + + Q + R + + + + + + + + + + + + + + time + 99 + + + + maxdiff + 0.2 + + + + + + + + 1 + + + + + + + + + + maxdiff + 4 + + + + + + + 1 + + + + + + + + + + + + S2 + + 250 + + + + + + + 1 + + + + + + + diff --git a/latest/cases/01627/output.heta b/latest/cases/01627/output.heta new file mode 100644 index 000000000..2b3096e73 --- /dev/null +++ b/latest/cases/01627/output.heta @@ -0,0 +1,99 @@ +/* +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, RateRule, Species +testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, RandomEventExecution, VolumeConcentrationRates +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the stoichiometries Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A species S2 is controlled by a rate rule for its concentration based on Q-R, which should be close to zero for the duration of the simulation. Its compartment is also under control of a rate rule, making the amount of S2 dependent on those two different rate rules. Three other parameters (errorHigh, errorLow, and errorS2), check to make sure neither Q nor R are chosen more or less frequently than the other, and that the species S2 doesn't get too extreme (the reaction in which it appears should be balanced, on average). Note: The error parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. + +The model contains: +* 1 species (S2) +* 9 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh, errorS2, S2_det) +* 1 compartment (C1) + +There are 6 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $R = R + 0.01$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ | +| error_check3 | $abs(S2) >= 250$ | (unset) | true | $errorS2 = 1$ |] + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S2 | $Q - R$ | +| Rate | C1 | $0.002$ | +| Assignment | S | $Q + R$ | +| Rate | reset | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S2 | $0$ | variable | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $1$ | variable | +| Initial value of parameter R | $1$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable | +| Initial value of parameter errorS2 | $0$ | variable | +| Initial value of parameter S2_det | $0$ | variable | +| Initial volume of compartment 'C1' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 1; + +S2 @Species { compartment: C1, } .= 0; + +S2_proc @Process { actors: = S2, }; +S2_proc := Q - R; +C1_proc @Process { actors: = C1, }; +C1_proc := 0.002; +reset_proc @Process { actors: = reset, }; +reset_proc := 1; + +S @Record { }; +S := Q + R; +Q @Record { } .= 1; +Q [Qinc]= Q + 0.01; +R @Record { } .= 1; +R [Rinc]= R + 0.01; +reset @Record { } .= 0; +reset [Qinc]= 0; +reset [Rinc]= 0; +maxdiff @Record { } .= 0; +maxdiff [maxcheck]= abs(Q - R); +errorLow @Record { } .= 0; +errorLow [error_check]= 1; +errorHigh @Record { } .= 0; +errorHigh [error_check2]= 1; +errorS2 @Record { } .= 0; +errorS2 [error_check3]= 1; +S2_det @Record { } .= 0; + +Qinc @DSwitcher { trigger: reset >= 0.01, }; +Rinc @DSwitcher { trigger: reset >= 0.01, }; +maxcheck @DSwitcher { trigger: abs(Q - R) > maxdiff, }; +error_check @DSwitcher { trigger: t >= 99 and maxdiff < 0.2, }; +error_check2 @DSwitcher { trigger: maxdiff >= 4, }; +error_check3 @DSwitcher { trigger: abs(S2) >= 250, }; + diff --git a/latest/cases/01627/synopsis.txt b/latest/cases/01627/synopsis.txt new file mode 100644 index 000000000..fb8edd122 --- /dev/null +++ b/latest/cases/01627/synopsis.txt @@ -0,0 +1,56 @@ + +category: Test +synopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, RateRule, Species +testTags: EventIsNotPersistent, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, RandomEventExecution, VolumeConcentrationRates +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the stoichiometries Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A species S2 is controlled by a rate rule for its concentration based on Q-R, which should be close to zero for the duration of the simulation. Its compartment is also under control of a rate rule, making the amount of S2 dependent on those two different rate rules. Three other parameters (errorHigh, errorLow, and errorS2), check to make sure neither Q nor R are chosen more or less frequently than the other, and that the species S2 doesn't get too extreme (the reaction in which it appears should be balanced, on average). Note: The error parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. + +The model contains: +* 1 species (S2) +* 9 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh, errorS2, S2_det) +* 1 compartment (C1) + +There are 6 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* | +| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $Q = Q + 0.01$ | +| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ | +| | | | | $R = R + 0.01$ | +| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ | +| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ | +| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ | +| error_check3 | $abs(S2) >= 250$ | (unset) | true | $errorS2 = 1$ |] + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S2 | $Q - R$ | +| Rate | C1 | $0.002$ | +| Assignment | S | $Q + R$ | +| Rate | reset | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S2 | $0$ | variable | +| Initial value of parameter S | $Q + R$ | variable | +| Initial value of parameter Q | $1$ | variable | +| Initial value of parameter R | $1$ | variable | +| Initial value of parameter reset | $0$ | variable | +| Initial value of parameter maxdiff | $0$ | variable | +| Initial value of parameter errorLow | $0$ | variable | +| Initial value of parameter errorHigh | $0$ | variable | +| Initial value of parameter errorS2 | $0$ | variable | +| Initial value of parameter S2_det | $0$ | variable | +| Initial volume of compartment 'C1' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01628/l2v5/index.heta b/latest/cases/01628/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01628/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01628/l3v2/build.log b/latest/cases/01628/l3v2/build.log new file mode 100644 index 000000000..9bc1f48a6 --- /dev/null +++ b/latest/cases/01628/l3v2/build.log @@ -0,0 +1,39 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01628/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01628/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01628/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] R14_K_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 133 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01628/l3v2/index.heta b/latest/cases/01628/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01628/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01628/model-sbml-l3v2.xml b/latest/cases/01628/model-sbml-l3v2.xml new file mode 100644 index 000000000..9395a31a9 --- /dev/null +++ b/latest/cases/01628/model-sbml-l3v2.xml @@ -0,0 +1,522 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01628/synopsis.txt b/latest/cases/01628/synopsis.txt new file mode 100644 index 000000000..c3a710639 --- /dev/null +++ b/latest/cases/01628/synopsis.txt @@ -0,0 +1,63 @@ + +category: Test +synopsis: FBC test with initial assignment with no MathML to a stoichiometry. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: AssignedConstantStoichiometry, BoundaryCondition, InitialValueReassigned, NoMathML, NonUnityStoichiometry, fbc:MinimizeObjective, fbc:NonStrict +testType: FluxBalanceSteadyState +levels: 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + +A test with minimization that has an initial assignment to a stoichiometry, but that assignment has no math, meaning that the original value of the stoichiometry takes precedence. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 5 parameters (fb_0, fb_1000, fb_n1000, fb_n100, fb_1) +* 1 compartment (Cell) +* 1 species reference (R14_K_stoich) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: R14_K_stoich K -> L | $fb_n1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_n1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_n1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_n1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_n1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_n1000 <= R25 <= fb_n100$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_n1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_n1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_n1000 <= R20 <= fb_1000$$ |] +Note: the following stoichiometries are set separately: R14_K_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_n1000 | $-1000$ | constant | +| Initial value of parameter fb_n100 | $-100$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of species reference 'R14_K_stoich' | $1$ | constant |] + diff --git a/latest/cases/01629/l2v5/index.heta b/latest/cases/01629/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01629/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01629/l3v2/build.log b/latest/cases/01629/l3v2/build.log new file mode 100644 index 000000000..07dcf64c2 --- /dev/null +++ b/latest/cases/01629/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01629/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01629/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01629/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01629/l3v2/index.heta b/latest/cases/01629/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01629/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01629/model-sbml-l3v2.xml b/latest/cases/01629/model-sbml-l3v2.xml new file mode 100644 index 000000000..63a0054f1 --- /dev/null +++ b/latest/cases/01629/model-sbml-l3v2.xml @@ -0,0 +1,521 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01629/synopsis.txt b/latest/cases/01629/synopsis.txt new file mode 100644 index 000000000..8bc2200e1 --- /dev/null +++ b/latest/cases/01629/synopsis.txt @@ -0,0 +1,59 @@ + +category: Test +synopsis: FBC test with initial assignment with no MathML to a flux bound. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, InitialValueReassigned, NoMathML, NonUnityStoichiometry, fbc:MaximizeObjective, fbc:NonStrict +testType: FluxBalanceSteadyState +levels: 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + + In this test, fb_0 is initially zero, and has an initial assignment with no MathML, leaving its value at zero. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_1, fb_1000, fb_neg_1000) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be maximized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_1000$$ | +| R14: K -> L | $fb_neg_1000 <= R14 <= fb_1000$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_1000$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_1000$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_1000$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_1000$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_1000$$ | +| R03: A -> C | $fb_neg_1000 <= R03 <= fb_1000$$ | +| R02: A -> B | $fb_neg_1000 <= R02 <= fb_1000$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_1000$$ | +| R04: C -> B | $fb_neg_1000 <= R04 <= fb_1000$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_1000$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_1000$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_1000$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_1000$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_1000$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_1000$$ | +| R19: K -> O | $fb_neg_1000 <= R19 <= fb_1000$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_1000$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_1000$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_1000$$ | +| R23: R -> S | $fb_neg_1000 <= R23 <= fb_1000$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_1000$$ | +| R21: P -> L | $fb_neg_1000 <= R21 <= fb_1000$$ | +| R20: O -> P | $fb_neg_1000 <= R20 <= fb_1000$$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_0 | $0$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_1000 | $1000$ | constant | +| Initial value of parameter fb_neg_1000 | $-1000$ | constant |] + diff --git a/latest/cases/01630/l2v5/index.heta b/latest/cases/01630/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01630/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01630/l3v2/build.log b/latest/cases/01630/l3v2/build.log new file mode 100644 index 000000000..cf5206628 --- /dev/null +++ b/latest/cases/01630/l3v2/build.log @@ -0,0 +1,38 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01630/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01630/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01630/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "E". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 132 +[error] Record "R16" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R14" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R15" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R12" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R07 Property "actors[1].target" has lost reference "E". +[error] Record "R07" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R13" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R01" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R17" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R03" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R02" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R05" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R04" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R10" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] R06 Property "actors[0].target" has lost reference "E". +[error] Record "R06" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R09" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R08" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R11" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R18" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R19" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R26" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R25" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R24" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R23" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R22" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R21" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[error] Record "R20" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01630/l3v2/index.heta b/latest/cases/01630/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01630/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01630/model-sbml-l3v2.xml b/latest/cases/01630/model-sbml-l3v2.xml new file mode 100644 index 000000000..de11b613a --- /dev/null +++ b/latest/cases/01630/model-sbml-l3v2.xml @@ -0,0 +1,521 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01630/synopsis.txt b/latest/cases/01630/synopsis.txt new file mode 100644 index 000000000..eb05000a9 --- /dev/null +++ b/latest/cases/01630/synopsis.txt @@ -0,0 +1,65 @@ + +category: Test +synopsis: FBC with empty assignment rule to flux bound. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, fbc:FluxObjective, fbc:Objective +testTags: BoundaryCondition, InitialValueReassigned, NoMathML, NonUnityStoichiometry, fbc:MinimizeObjective, fbc:NonStrict +testType: FluxBalanceSteadyState +levels: 3.2 +generatedBy: Numeric +packagesPresent: fbc, fbc_v2 + +In this test, a blank assignment rule points at a flux bound, but has no mathML, so the flux bound retains its original value. + +The model contains: +* 23 species (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, X, Y) +* 4 parameters (fb_0, fb_inf, fb_negInf, fb_1) +* 1 compartment (Cell) +* 1 objective (OBJF) + +The active objective is OBJF, which is to be minimized: + + 1 R26 + +There are 26 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| R16: J -> M | $fb_0 <= R16 <= fb_inf$$ | +| R14: K -> L | $fb_negInf <= R14 <= fb_inf$$ | +| R15: L -> Q | $fb_0 <= R15 <= fb_inf$$ | +| R12: I -> J | $fb_0 <= R12 <= fb_inf$$ | +| R07: E -> F | $fb_0 <= R07 <= fb_inf$$ | +| R13: J -> K | $fb_0 <= R13 <= fb_inf$$ | +| R01: X -> A | $fb_0 <= R01 <= fb_1$$ | +| R17: M -> N | $fb_0 <= R17 <= fb_inf$$ | +| R03: A -> C | $fb_negInf <= R03 <= fb_inf$$ | +| R02: A -> B | $fb_negInf <= R02 <= fb_inf$$ | +| R05: B -> D | $fb_0 <= R05 <= fb_inf$$ | +| R04: C -> B | $fb_negInf <= R04 <= fb_inf$$ | +| R10: G -> H | $fb_0 <= R10 <= fb_inf$$ | +| R06: D -> E | $fb_0 <= R06 <= fb_inf$$ | +| R09: D -> G | $fb_0 <= R09 <= fb_inf$$ | +| R08: F -> I | $fb_0 <= R08 <= fb_inf$$ | +| R11: H -> I | $fb_0 <= R11 <= fb_inf$$ | +| R18: N -> Q | $fb_0 <= R18 <= fb_inf$$ | +| R19: K -> O | $fb_negInf <= R19 <= fb_inf$$ | +| R26: S -> Y | $fb_0 <= R26 <= fb_inf$$ | +| R25: A + T -> 0.5S + U | $fb_0 <= R25 <= fb_inf$$ | +| R24: R -> S | $fb_0 <= R24 <= fb_inf$$ | +| R23: R -> S | $fb_negInf <= R23 <= fb_inf$$ | +| R22: Q -> R | $fb_0 <= R22 <= fb_inf$$ | +| R21: P -> L | $fb_negInf <= R21 <= fb_inf$$ | +| R20: O -> P | $fb_negInf <= R20 <= fb_inf$$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | fb_0 | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter fb_inf | $inf$ | constant | +| Initial value of parameter fb_negInf | $-inf$ | constant | +| Initial value of parameter fb_1 | $1$ | constant | +| Initial value of parameter fb_0 | $0$ | variable |] + diff --git a/latest/cases/01631/l2v5/index.heta b/latest/cases/01631/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01631/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01631/l3v2/build.log b/latest/cases/01631/l3v2/build.log new file mode 100644 index 000000000..4ca420532 --- /dev/null +++ b/latest/cases/01631/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01631/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01631/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01631/model-sbml-l3v2.xml"... +[error] S1_degrade component does not exist which is not allowed for the "update" action. +[error] S1_create component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] S1_create_proc Property "actors[0].target" has lost reference "S1_create". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01631/l3v2/index.heta b/latest/cases/01631/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01631/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01631/model-sbml-l3v2.xml b/latest/cases/01631/model-sbml-l3v2.xml new file mode 100644 index 000000000..9cf2cb2fc --- /dev/null +++ b/latest/cases/01631/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + 3 + + + + + + + 1 + + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01631/synopsis.txt b/latest/cases/01631/synopsis.txt new file mode 100644 index 000000000..6027f7f35 --- /dev/null +++ b/latest/cases/01631/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Assigned stoichiometries, both constant and variable. +componentTags: Compartment, InitialAssignment, RateRule, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model has two reactions that affect one species; one with an assigned constant stoichiometry, and one with an assigned variable stoichiometry. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 2 species references (S1_degrade, S1_create) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_degrade S1 -> | $1$ | +| J1: -> S1_create S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_degrade, S1_create + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_create | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_degrade' | $3$ | constant | +| Initial value of species reference 'S1_create' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01632/l2v5/build.log b/latest/cases/01632/l2v5/build.log new file mode 100644 index 000000000..cf25ed1b8 --- /dev/null +++ b/latest/cases/01632/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01632/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01632/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01632/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01632/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01632/l2v5/index.heta b/latest/cases/01632/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01632/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01632/l3v2/index.heta b/latest/cases/01632/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01632/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01632/model-sbml-l2v5.xml b/latest/cases/01632/model-sbml-l2v5.xml new file mode 100644 index 000000000..32ea7874c --- /dev/null +++ b/latest/cases/01632/model-sbml-l2v5.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + + + 3 + + + + + + + 1 + + + + + + + + + parameterId_0 + + + + + + + 1 + + + + + + diff --git a/latest/cases/01632/synopsis.txt b/latest/cases/01632/synopsis.txt new file mode 100644 index 000000000..1c114170c --- /dev/null +++ b/latest/cases/01632/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Assigned stoichiometries, both constant and variable. +componentTags: Compartment, Parameter, RateRule, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, AssignedVariableStoichiometry, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + The model has two reactions that affect one species; one with an assigned constant stoichiometry, and one with an assigned variable stoichiometry. (L2 version of 01631, using stoichiometry math.) + +The model contains: +* 1 species (S1) +* 1 parameter (parameterId_0) +* 1 compartment (C) +* 2 species references (S1_degrade, S1_create) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_degrade S1 -> | $1$ | +| J1: -> S1_create S1 | $1$ |] +Note: the following stoichiometries are set separately: S1_degrade, S1_create + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | parameterId_0 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of parameter parameterId_0 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_degrade' | $3$ | variable | +| Initial value of species reference 'S1_create' | $parameterId_0$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01633/l2v5/index.heta b/latest/cases/01633/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01633/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01633/l3v2/build.log b/latest/cases/01633/l3v2/build.log new file mode 100644 index 000000000..50bd6faa5 --- /dev/null +++ b/latest/cases/01633/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01633/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01633/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01633/model-sbml-l3v2.xml"... +[error] S1_degrade component does not exist which is not allowed for the "update" action. +[error] S2_create component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] S2_create_proc Property "actors[0].target" has lost reference "S2_create". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01633/l3v2/index.heta b/latest/cases/01633/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01633/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01633/model-sbml-l3v2.xml b/latest/cases/01633/model-sbml-l3v2.xml new file mode 100644 index 000000000..64f9e2737 --- /dev/null +++ b/latest/cases/01633/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + 3 + + + + + + + 1 + + + + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01633/synopsis.txt b/latest/cases/01633/synopsis.txt new file mode 100644 index 000000000..a5a6ffc25 --- /dev/null +++ b/latest/cases/01633/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Assigned stoichiometries, both constant and variable. +componentTags: Compartment, InitialAssignment, RateRule, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model has a reaction with both an assigned constant stoichiometry, and an assigned variable stoichiometry. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) +* 2 species references (S1_degrade, S2_create) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_degrade S1 -> S2_create S2 | $1$ |] +Note: the following stoichiometries are set separately: S1_degrade, S2_create + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S2_create | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $30$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_degrade' | $3$ | constant | +| Initial value of species reference 'S2_create' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01634/l2v5/build.log b/latest/cases/01634/l2v5/build.log new file mode 100644 index 000000000..9c33fb2b0 --- /dev/null +++ b/latest/cases/01634/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01634/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01634/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01634/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01634/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01634/l2v5/index.heta b/latest/cases/01634/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01634/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01634/l3v2/index.heta b/latest/cases/01634/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01634/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01634/model-sbml-l2v5.xml b/latest/cases/01634/model-sbml-l2v5.xml new file mode 100644 index 000000000..6782e4a7d --- /dev/null +++ b/latest/cases/01634/model-sbml-l2v5.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + 3 + + + + + + + + + parameterId_0 + + + + + + + 1 + + + + + + diff --git a/latest/cases/01634/synopsis.txt b/latest/cases/01634/synopsis.txt new file mode 100644 index 000000000..7dd33c11d --- /dev/null +++ b/latest/cases/01634/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Assigned stoichiometries, both constant and variable. +componentTags: Compartment, Parameter, RateRule, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, AssignedVariableStoichiometry, DefaultValue, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +The model has a reaction with both an assigned constant stoichiometry, and an assigned variable stoichiometry. The L2 version of 01633, with stoichiometry math. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (parameterId_0) +* 1 compartment (C) +* 2 species references (S1_degrade, S2_create) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_degrade S1 -> S2_create S2 | $1$ |] +Note: the following stoichiometries are set separately: S1_degrade, S2_create + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | parameterId_0 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $30$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of parameter parameterId_0 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_degrade' | $3$ | variable | +| Initial value of species reference 'S2_create' | $parameterId_0$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01635/l2v5/index.heta b/latest/cases/01635/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01635/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01635/l3v2/build.log b/latest/cases/01635/l3v2/build.log new file mode 100644 index 000000000..7bdfca509 --- /dev/null +++ b/latest/cases/01635/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01635/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01635/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01635/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01635/l3v2/index.heta b/latest/cases/01635/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01635/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01635/model-sbml-l3v2.xml b/latest/cases/01635/model-sbml-l3v2.xml new file mode 100644 index 000000000..4ca9bfe57 --- /dev/null +++ b/latest/cases/01635/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + 1 + + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01635/synopsis.txt b/latest/cases/01635/synopsis.txt new file mode 100644 index 000000000..177e5555b --- /dev/null +++ b/latest/cases/01635/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Assigned stoichiometries, both constant and variable. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, BoundaryCondition, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +The model has a reaction whose sole participant is a boundary species, whose stoichiometry changes in time... which obviously does nothing at all. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> | $1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01636/l2v5/build.log b/latest/cases/01636/l2v5/build.log new file mode 100644 index 000000000..5ecf5b190 --- /dev/null +++ b/latest/cases/01636/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01636/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01636/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01636/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01636/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01636/l2v5/index.heta b/latest/cases/01636/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01636/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01636/l3v2/index.heta b/latest/cases/01636/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01636/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01636/model-sbml-l2v5.xml b/latest/cases/01636/model-sbml-l2v5.xml new file mode 100644 index 000000000..e108465c1 --- /dev/null +++ b/latest/cases/01636/model-sbml-l2v5.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + + + parameterId_0 + + + + + + + 1 + + + + + + diff --git a/latest/cases/01636/synopsis.txt b/latest/cases/01636/synopsis.txt new file mode 100644 index 000000000..b830a4536 --- /dev/null +++ b/latest/cases/01636/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Assigned stoichiometries, both constant and variable. +componentTags: Compartment, Parameter, RateRule, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedVariableStoichiometry, BoundaryCondition, DefaultValue, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +The model has a reaction whose sole participant is a boundary species, whose stoichiometry changes in time... which obviously does nothing at all. + +The model contains: +* 1 species (S1) +* 1 parameter (parameterId_0) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> | $1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | parameterId_0 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of parameter parameterId_0 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $parameterId_0$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01637/l2v5/index.heta b/latest/cases/01637/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01637/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01637/l3v2/index.heta b/latest/cases/01637/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01637/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01637/synopsis.txt b/latest/cases/01637/synopsis.txt new file mode 100644 index 000000000..ff18d54ad --- /dev/null +++ b/latest/cases/01637/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A rate rule for a species reference that has the same ID as a local parameter. +componentTags: Compartment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, LocalParameters, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter has the same ID as a species reference, which itself has a rate rule for it. + +The model contains: +* 1 species (S1) +* 1 local parameter (J0.k0) +* 1 compartment (C) +* 1 species reference (k0) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> k0 S1 | $1 / k0$ |] +Note: the following stoichiometries are set separately: k0 + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k0 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of local parameter 'J0.k0' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'k0' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01638/l2v5/index.heta b/latest/cases/01638/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01638/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01638/l3v2/index.heta b/latest/cases/01638/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01638/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01638/synopsis.txt b/latest/cases/01638/synopsis.txt new file mode 100644 index 000000000..72e1594f4 --- /dev/null +++ b/latest/cases/01638/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A species reference for a boundary species that has the same ID as a local parameter. +componentTags: Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, LocalParameters +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter has the same ID as a species reference for a boundary species. + +The model contains: +* 1 species (S1) +* 1 local parameter (J0.k0) +* 1 compartment (C) +* 1 species reference (k0) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1 / k0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of local parameter 'J0.k0' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'k0' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01639/l2v5/index.heta b/latest/cases/01639/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01639/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01639/l3v2/index.heta b/latest/cases/01639/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01639/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01639/synopsis.txt b/latest/cases/01639/synopsis.txt new file mode 100644 index 000000000..d9952e7e1 --- /dev/null +++ b/latest/cases/01639/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A species reference for a boundary species that has the same ID as a local parameter. +componentTags: Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, LocalParameters +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter has the same ID as a species reference for a boundary species (but another . + +The model contains: +* 2 species (S1, S2) +* 1 local parameter (J0.k0) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $1 / k0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of local parameter 'J0.k0' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01640/l2v5/heta-code/output.heta b/latest/cases/01640/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e19337ca0 --- /dev/null +++ b/latest/cases/01640/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +k0 @Species { boundary: true, compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 0 / C; + +J0 @Reaction { actors: k0 = S2, }; +J0 := 1 / k0__J0_local; + +k0__J0_local @Const { } = 3; + diff --git a/latest/cases/01640/l2v5/index.heta b/latest/cases/01640/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01640/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01640/l2v5/json/output.json b/latest/cases/01640/l2v5/json/output.json new file mode 100644 index 000000000..56ce8cba1 --- /dev/null +++ b/latest/cases/01640/l2v5/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "k0", + "assignments": { + "start_": "2 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k0__J0_local", + "num": 3 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1 / k0__J0_local" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "k0", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01640/l3v2/index.heta b/latest/cases/01640/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01640/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01640/model-sbml-l2v5.xml b/latest/cases/01640/model-sbml-l2v5.xml new file mode 100644 index 000000000..d2e84333d --- /dev/null +++ b/latest/cases/01640/model-sbml-l2v5.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + 1 + k0 + + + + + + + + + + diff --git a/latest/cases/01640/output.heta b/latest/cases/01640/output.heta new file mode 100644 index 000000000..52692f62d --- /dev/null +++ b/latest/cases/01640/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: A species reference for a boundary species that has the same ID as a local parameter. +componentTags: Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter has the same ID as a boundary species (but another species is present in the model as well). + +The model contains: +* 2 species (k0, S2) +* 1 local parameter (J0.k0) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: k0 -> S2 | $1 / k0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species k0 | $2$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of local parameter 'J0.k0' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +k0 @Species { boundary: true, compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 0 / C; + +J0 @Reaction { actors: k0 = S2, }; +J0 := 1 / k0__J0_local; + +k0__J0_local @Const { } = 3; + diff --git a/latest/cases/01640/synopsis.txt b/latest/cases/01640/synopsis.txt new file mode 100644 index 000000000..779ffbfc4 --- /dev/null +++ b/latest/cases/01640/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A species reference for a boundary species that has the same ID as a local parameter. +componentTags: Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter has the same ID as a boundary species (but another species is present in the model as well). + +The model contains: +* 2 species (k0, S2) +* 1 local parameter (J0.k0) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: k0 -> S2 | $1 / k0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species k0 | $2$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of local parameter 'J0.k0' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01641/l2v5/index.heta b/latest/cases/01641/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01641/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01641/l3v2/build.log b/latest/cases/01641/l3v2/build.log new file mode 100644 index 000000000..ae4be8827 --- /dev/null +++ b/latest/cases/01641/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01641/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01641/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01641/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 81 +[error] No required "num" property for "k1" of Const. +[error] No required "num" property for "k2" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01641/l3v2/index.heta b/latest/cases/01641/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01641/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01641/model-sbml-l3v2.xml b/latest/cases/01641/model-sbml-l3v2.xml new file mode 100644 index 000000000..d3fb272da --- /dev/null +++ b/latest/cases/01641/model-sbml-l3v2.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + avogadro + + + + + time + + + + + diff --git a/latest/cases/01641/synopsis.txt b/latest/cases/01641/synopsis.txt new file mode 100644 index 000000000..0157c0e66 --- /dev/null +++ b/latest/cases/01641/synopsis.txt @@ -0,0 +1,23 @@ + +category: Test +synopsis: The csymbols avogadro and time with each other's names. +componentTags: CSymbolAvogadro, CSymbolTime, InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the csymbol avogadro is given the name 'time', and the csymbol time is given the name 'avogadro'. Just to be confusing. + +The model contains: +* 2 parameters (k1, k2) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter k1 | $time$ | constant | +| Initial value of parameter k2 | $avogadro$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01642/l2v5/index.heta b/latest/cases/01642/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01642/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01642/l3v2/build.log b/latest/cases/01642/l3v2/build.log new file mode 100644 index 000000000..997177c06 --- /dev/null +++ b/latest/cases/01642/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01642/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01642/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01642/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 87 +[error] No required "num" property for "m_cf" of Const. +[error] No required "num" property for "s1_cf" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01642/l3v2/index.heta b/latest/cases/01642/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01642/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01642/model-sbml-l3v2.xml b/latest/cases/01642/model-sbml-l3v2.xml new file mode 100644 index 000000000..c30f2473e --- /dev/null +++ b/latest/cases/01642/model-sbml-l3v2.xml @@ -0,0 +1,63 @@ + + + + + + + + 3 + + + + + + + 5 + + + + + + + + + + + + + + + + + + + + getThree + + + + + + + getFive + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01642/synopsis.txt b/latest/cases/01642/synopsis.txt new file mode 100644 index 000000000..05b2c2479 --- /dev/null +++ b/latest/cases/01642/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Model and species conversion factors set by a function. +componentTags: Compartment, FunctionDefinition, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set by function definitions. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The model contains the following function definitions: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getThree | | $3$ | + | getFive | | $5$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $getThree()$ | constant | +| Initial value of parameter s1_cf | $getFive()$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01643/l2v5/index.heta b/latest/cases/01643/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01643/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01643/l3v2/build.log b/latest/cases/01643/l3v2/build.log new file mode 100644 index 000000000..8cbd6048a --- /dev/null +++ b/latest/cases/01643/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01643/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01643/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01643/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 85 +[error] No required "num" property for "s1_cf" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01643/l3v2/index.heta b/latest/cases/01643/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01643/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01643/model-sbml-l3v2.xml b/latest/cases/01643/model-sbml-l3v2.xml new file mode 100644 index 000000000..9ff387244 --- /dev/null +++ b/latest/cases/01643/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + 5 + + + + + + + + + + + + + + + + + + + getFive + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01643/synopsis.txt b/latest/cases/01643/synopsis.txt new file mode 100644 index 000000000..a2957a289 --- /dev/null +++ b/latest/cases/01643/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Species conversion factors set by a function. +componentTags: Compartment, FunctionDefinition, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set by a function definition. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getFive | | $5$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $getFive()$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01644/l2v5/index.heta b/latest/cases/01644/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01644/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01644/l3v2/build.log b/latest/cases/01644/l3v2/build.log new file mode 100644 index 000000000..779147c25 --- /dev/null +++ b/latest/cases/01644/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01644/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01644/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01644/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 85 +[error] No required "num" property for "m_cf" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01644/l3v2/index.heta b/latest/cases/01644/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01644/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01644/model-sbml-l3v2.xml b/latest/cases/01644/model-sbml-l3v2.xml new file mode 100644 index 000000000..56e01e83f --- /dev/null +++ b/latest/cases/01644/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + 3 + + + + + + + + + + + + + + + + + + + getThree + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01644/synopsis.txt b/latest/cases/01644/synopsis.txt new file mode 100644 index 000000000..77f7cde9e --- /dev/null +++ b/latest/cases/01644/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Model conversion factor set by a function. +componentTags: Compartment, FunctionDefinition, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor is set by a function definition. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getThree | | $3$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $getThree()$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01645/l2v5/index.heta b/latest/cases/01645/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01645/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01645/l3v2/heta-code/output.heta b/latest/cases/01645/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8347df741 --- /dev/null +++ b/latest/cases/01645/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01645/l3v2/index.heta b/latest/cases/01645/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01645/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01645/l3v2/json/output.json b/latest/cases/01645/l3v2/json/output.json new file mode 100644 index 000000000..bd0521f04 --- /dev/null +++ b/latest/cases/01645/l3v2/json/output.json @@ -0,0 +1,58 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01645/model-sbml-l3v2.xml b/latest/cases/01645/model-sbml-l3v2.xml new file mode 100644 index 000000000..c741c28d0 --- /dev/null +++ b/latest/cases/01645/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01645/output.heta b/latest/cases/01645/output.heta new file mode 100644 index 000000000..1e06ebab2 --- /dev/null +++ b/latest/cases/01645/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: Model and species conversion factors for substance-only species. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species set to be substance-only (hasOnlySubstanceUnits=true). + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01645/synopsis.txt b/latest/cases/01645/synopsis.txt new file mode 100644 index 000000000..a7b095693 --- /dev/null +++ b/latest/cases/01645/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Model and species conversion factors for substance-only species. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species set to be substance-only (hasOnlySubstanceUnits=true). + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01646/l2v5/index.heta b/latest/cases/01646/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01646/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01646/l3v2/heta-code/output.heta b/latest/cases/01646/l3v2/heta-code/output.heta new file mode 100644 index 000000000..69b7fe5da --- /dev/null +++ b/latest/cases/01646/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + diff --git a/latest/cases/01646/l3v2/index.heta b/latest/cases/01646/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01646/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01646/l3v2/json/output.json b/latest/cases/01646/l3v2/json/output.json new file mode 100644 index 000000000..5e023f492 --- /dev/null +++ b/latest/cases/01646/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01646/model-sbml-l3v2.xml b/latest/cases/01646/model-sbml-l3v2.xml new file mode 100644 index 000000000..41d56a57b --- /dev/null +++ b/latest/cases/01646/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01646/output.heta b/latest/cases/01646/output.heta new file mode 100644 index 000000000..f374d1fb7 --- /dev/null +++ b/latest/cases/01646/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A species conversion factor for substance-only species. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species set to be substance-only (hasOnlySubstanceUnits=true). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + diff --git a/latest/cases/01646/synopsis.txt b/latest/cases/01646/synopsis.txt new file mode 100644 index 000000000..d33b39b10 --- /dev/null +++ b/latest/cases/01646/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A species conversion factor for substance-only species. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species set to be substance-only (hasOnlySubstanceUnits=true). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01647/l2v5/index.heta b/latest/cases/01647/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01647/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01647/l3v2/heta-code/output.heta b/latest/cases/01647/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6cb9739d7 --- /dev/null +++ b/latest/cases/01647/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; + diff --git a/latest/cases/01647/l3v2/index.heta b/latest/cases/01647/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01647/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01647/l3v2/json/output.json b/latest/cases/01647/l3v2/json/output.json new file mode 100644 index 000000000..7a1e3c0e6 --- /dev/null +++ b/latest/cases/01647/l3v2/json/output.json @@ -0,0 +1,53 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + } +] \ No newline at end of file diff --git a/latest/cases/01647/model-sbml-l3v2.xml b/latest/cases/01647/model-sbml-l3v2.xml new file mode 100644 index 000000000..1f960e12b --- /dev/null +++ b/latest/cases/01647/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01647/output.heta b/latest/cases/01647/output.heta new file mode 100644 index 000000000..81e93fb95 --- /dev/null +++ b/latest/cases/01647/output.heta @@ -0,0 +1,51 @@ +/* +category: Test +synopsis: A model conversion factor for substance-only species. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model has a model conversion factor for species set to be substance-only (hasOnlySubstanceUnits=true). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; + diff --git a/latest/cases/01647/synopsis.txt b/latest/cases/01647/synopsis.txt new file mode 100644 index 000000000..8a183849b --- /dev/null +++ b/latest/cases/01647/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A model conversion factor for substance-only species. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model has a model conversion factor for species set to be substance-only (hasOnlySubstanceUnits=true). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01648/l2v5/index.heta b/latest/cases/01648/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01648/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01648/l3v2/heta-code/output.heta b/latest/cases/01648/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2fc58a562 --- /dev/null +++ b/latest/cases/01648/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local + s1_cf__J0_local; + +m_cf__J0_local @Const { } = 0.003; +s1_cf__J0_local @Const { } = 0.007; +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01648/l3v2/index.heta b/latest/cases/01648/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01648/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01648/l3v2/json/output.json b/latest/cases/01648/l3v2/json/output.json new file mode 100644 index 000000000..8630a7697 --- /dev/null +++ b/latest/cases/01648/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "m_cf__J0_local", + "num": 0.003 + }, + { + "class": "Const", + "id": "s1_cf__J0_local", + "num": 0.007 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "m_cf__J0_local + s1_cf__J0_local" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01648/model-sbml-l3v2.xml b/latest/cases/01648/model-sbml-l3v2.xml new file mode 100644 index 000000000..2d92cb07f --- /dev/null +++ b/latest/cases/01648/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + m_cf + s1_cf + + + + + + + + + + + diff --git a/latest/cases/01648/output.heta b/latest/cases/01648/output.heta new file mode 100644 index 000000000..93040bb43 --- /dev/null +++ b/latest/cases/01648/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Model and species conversion factors whose IDs are duplicated by local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors IDs are duplicated by local parameters. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf + s1_cf$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial value of local parameter 'J0.m_cf' | $0.003$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $0.007$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local + s1_cf__J0_local; + +m_cf__J0_local @Const { } = 0.003; +s1_cf__J0_local @Const { } = 0.007; +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01648/synopsis.txt b/latest/cases/01648/synopsis.txt new file mode 100644 index 000000000..4d164c66d --- /dev/null +++ b/latest/cases/01648/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Model and species conversion factors whose IDs are duplicated by local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors IDs are duplicated by local parameters. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf + s1_cf$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial value of local parameter 'J0.m_cf' | $0.003$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $0.007$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01649/l2v5/index.heta b/latest/cases/01649/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01649/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01649/l3v2/heta-code/output.heta b/latest/cases/01649/l3v2/heta-code/output.heta new file mode 100644 index 000000000..007c87af5 --- /dev/null +++ b/latest/cases/01649/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local + s1_cf__J0_local; + +m_cf__J0_local @Const { } = 0.003; +s1_cf__J0_local @Const { } = 0.007; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01649/l3v2/index.heta b/latest/cases/01649/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01649/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01649/l3v2/json/output.json b/latest/cases/01649/l3v2/json/output.json new file mode 100644 index 000000000..5c6464f29 --- /dev/null +++ b/latest/cases/01649/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "m_cf__J0_local", + "num": 0.003 + }, + { + "class": "Const", + "id": "s1_cf__J0_local", + "num": 0.007 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "m_cf__J0_local + s1_cf__J0_local" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01649/model-sbml-l3v2.xml b/latest/cases/01649/model-sbml-l3v2.xml new file mode 100644 index 000000000..05a56f6b4 --- /dev/null +++ b/latest/cases/01649/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + m_cf + s1_cf + + + + + + + + + + + diff --git a/latest/cases/01649/output.heta b/latest/cases/01649/output.heta new file mode 100644 index 000000000..7955b4468 --- /dev/null +++ b/latest/cases/01649/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: A species conversion factor whose ID is duplicated by local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factors ID is duplicated by a local parameter. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf + s1_cf$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial value of local parameter 'J0.m_cf' | $0.003$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $0.007$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local + s1_cf__J0_local; + +m_cf__J0_local @Const { } = 0.003; +s1_cf__J0_local @Const { } = 0.007; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01649/synopsis.txt b/latest/cases/01649/synopsis.txt new file mode 100644 index 000000000..bf4d117e5 --- /dev/null +++ b/latest/cases/01649/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A species conversion factor whose ID is duplicated by local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factors ID is duplicated by a local parameter. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf + s1_cf$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial value of local parameter 'J0.m_cf' | $0.003$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $0.007$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01650/l2v5/index.heta b/latest/cases/01650/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01650/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01650/l3v2/heta-code/output.heta b/latest/cases/01650/l3v2/heta-code/output.heta new file mode 100644 index 000000000..929013e68 --- /dev/null +++ b/latest/cases/01650/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local + s1_cf__J0_local; + +m_cf__J0_local @Const { } = 0.003; +s1_cf__J0_local @Const { } = 0.007; +m_cf @Const { } = 3; + diff --git a/latest/cases/01650/l3v2/index.heta b/latest/cases/01650/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01650/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01650/l3v2/json/output.json b/latest/cases/01650/l3v2/json/output.json new file mode 100644 index 000000000..3d5bf154c --- /dev/null +++ b/latest/cases/01650/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "m_cf__J0_local", + "num": 0.003 + }, + { + "class": "Const", + "id": "s1_cf__J0_local", + "num": 0.007 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "m_cf__J0_local + s1_cf__J0_local" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + } +] \ No newline at end of file diff --git a/latest/cases/01650/model-sbml-l3v2.xml b/latest/cases/01650/model-sbml-l3v2.xml new file mode 100644 index 000000000..4f5e647c7 --- /dev/null +++ b/latest/cases/01650/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + m_cf + s1_cf + + + + + + + + + + + diff --git a/latest/cases/01650/output.heta b/latest/cases/01650/output.heta new file mode 100644 index 000000000..897ad0368 --- /dev/null +++ b/latest/cases/01650/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: A model conversion factor whose ID is duplicated by a local parameter. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor ID is duplicated by a local parameter. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf + s1_cf$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of local parameter 'J0.m_cf' | $0.003$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $0.007$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local + s1_cf__J0_local; + +m_cf__J0_local @Const { } = 0.003; +s1_cf__J0_local @Const { } = 0.007; +m_cf @Const { } = 3; + diff --git a/latest/cases/01650/synopsis.txt b/latest/cases/01650/synopsis.txt new file mode 100644 index 000000000..af1cc4b47 --- /dev/null +++ b/latest/cases/01650/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A model conversion factor whose ID is duplicated by a local parameter. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor ID is duplicated by a local parameter. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf + s1_cf$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of local parameter 'J0.m_cf' | $0.003$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $0.007$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01651/l2v5/index.heta b/latest/cases/01651/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01651/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01651/l3v2/build.log b/latest/cases/01651/l3v2/build.log new file mode 100644 index 000000000..2086a0e45 --- /dev/null +++ b/latest/cases/01651/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01651/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01651/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01651/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 85 +[error] No required "num" property for "m_cf" of Const. +[error] No required "num" property for "s1_cf" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01651/l3v2/index.heta b/latest/cases/01651/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01651/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01651/model-sbml-l3v2.xml b/latest/cases/01651/model-sbml-l3v2.xml new file mode 100644 index 000000000..4d6d86a05 --- /dev/null +++ b/latest/cases/01651/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + S1_stoich + 3 + + + + + + + + S1_stoich + 5 + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01651/synopsis.txt b/latest/cases/01651/synopsis.txt new file mode 100644 index 000000000..1b041436b --- /dev/null +++ b/latest/cases/01651/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Model and species conversion factors set with species references. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set with species reference values. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $S1_stoich * 3$ | constant | +| Initial value of parameter s1_cf | $S1_stoich * 5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01652/l2v5/index.heta b/latest/cases/01652/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01652/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01652/l3v2/build.log b/latest/cases/01652/l3v2/build.log new file mode 100644 index 000000000..036462463 --- /dev/null +++ b/latest/cases/01652/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01652/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01652/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01652/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 84 +[error] No required "num" property for "s1_cf" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01652/l3v2/index.heta b/latest/cases/01652/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01652/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01652/model-sbml-l3v2.xml b/latest/cases/01652/model-sbml-l3v2.xml new file mode 100644 index 000000000..e21af7e80 --- /dev/null +++ b/latest/cases/01652/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + S1_stoich + 5 + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01652/synopsis.txt b/latest/cases/01652/synopsis.txt new file mode 100644 index 000000000..d1af31db6 --- /dev/null +++ b/latest/cases/01652/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: A species conversion factor set with a species reference. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set with species reference values. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $S1_stoich * 5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01653/l2v5/index.heta b/latest/cases/01653/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01653/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01653/l3v2/build.log b/latest/cases/01653/l3v2/build.log new file mode 100644 index 000000000..3c41d67fa --- /dev/null +++ b/latest/cases/01653/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01653/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01653/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01653/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 84 +[error] No required "num" property for "m_cf" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01653/l3v2/index.heta b/latest/cases/01653/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01653/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01653/model-sbml-l3v2.xml b/latest/cases/01653/model-sbml-l3v2.xml new file mode 100644 index 000000000..2803812b3 --- /dev/null +++ b/latest/cases/01653/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + S1_stoich + 3 + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01653/synopsis.txt b/latest/cases/01653/synopsis.txt new file mode 100644 index 000000000..9c820e2f2 --- /dev/null +++ b/latest/cases/01653/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: A model conversion factor set with a species reference. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor is set with a species reference value. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $S1_stoich * 3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01654/l2v5/index.heta b/latest/cases/01654/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01654/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01654/l3v2/build.log b/latest/cases/01654/l3v2/build.log new file mode 100644 index 000000000..c86ce8faa --- /dev/null +++ b/latest/cases/01654/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01654/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01654/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01654/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 85 +[error] No required "num" property for "k0" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01654/l3v2/index.heta b/latest/cases/01654/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01654/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01654/model-sbml-l3v2.xml b/latest/cases/01654/model-sbml-l3v2.xml new file mode 100644 index 000000000..a437805df --- /dev/null +++ b/latest/cases/01654/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + x + + + + x + 2 + + + + + + + + + + + + + + + + + + + + addTwo + S1_stoich + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01654/synopsis.txt b/latest/cases/01654/synopsis.txt new file mode 100644 index 000000000..295b96621 --- /dev/null +++ b/latest/cases/01654/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: A function calling a species reference. +componentTags: Compartment, FunctionDefinition, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an initial assignment calls a function with a species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> S2 | $0.01$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addTwo | x | $x + 2$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $addTwo(S1_stoich)$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01655/l2v5/index.heta b/latest/cases/01655/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01655/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01655/l3v2/build.log b/latest/cases/01655/l3v2/build.log new file mode 100644 index 000000000..896bfa7aa --- /dev/null +++ b/latest/cases/01655/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01655/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01655/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01655/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 84 +[error] No required "num" property for "k0" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01655/l3v2/index.heta b/latest/cases/01655/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01655/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01655/model-sbml-l3v2.xml b/latest/cases/01655/model-sbml-l3v2.xml new file mode 100644 index 000000000..f83c9000b --- /dev/null +++ b/latest/cases/01655/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + S1_stoich + 2 + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01655/synopsis.txt b/latest/cases/01655/synopsis.txt new file mode 100644 index 000000000..4d5ba7f8a --- /dev/null +++ b/latest/cases/01655/synopsis.txt @@ -0,0 +1,35 @@ + +category: Test +synopsis: A species reference to a substance-only species. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an initial assignment uses a species reference for a substance-only species. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> S2 | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $S1_stoich * 2$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01656/l2v5/index.heta b/latest/cases/01656/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01656/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01656/l3v2/index.heta b/latest/cases/01656/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01656/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01656/synopsis.txt b/latest/cases/01656/synopsis.txt new file mode 100644 index 000000000..230865836 --- /dev/null +++ b/latest/cases/01656/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A local parameter shadowing a species reference. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, LocalParameters, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in an initial assignment, and refers to the species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J0.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> S2 | $S1_stoich$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $S1_stoich * 2$ | constant | +| Initial value of local parameter 'J0.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01657/l2v5/index.heta b/latest/cases/01657/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01657/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01657/l3v2/build.log b/latest/cases/01657/l3v2/build.log new file mode 100644 index 000000000..013f270c8 --- /dev/null +++ b/latest/cases/01657/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01657/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01657/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01657/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] No required "num" property for "k0" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01657/l3v2/index.heta b/latest/cases/01657/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01657/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01657/model-sbml-l3v2.xml b/latest/cases/01657/model-sbml-l3v2.xml new file mode 100644 index 000000000..8a00c04d1 --- /dev/null +++ b/latest/cases/01657/model-sbml-l3v2.xml @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + + + + S1_stoich + 2 + + + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01657/synopsis.txt b/latest/cases/01657/synopsis.txt new file mode 100644 index 000000000..eeb219462 --- /dev/null +++ b/latest/cases/01657/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: A species reference with an empty assignment rule. +componentTags: AssignmentRule, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NoMathML, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an initial assignment uses a species reference which has an assignment rule, but that assignment rule has no MathML, leaving it with its original value. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> S2 | $0.01$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1_stoich | $$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $S1_stoich * 2$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01658/l2v5/index.heta b/latest/cases/01658/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01658/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01658/l3v2/heta-code/output.heta b/latest/cases/01658/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0d6dc7ab6 --- /dev/null +++ b/latest/cases/01658/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [_E0]= 3; + +_E0 @DSwitcher { trigger: t > 6.02214076e+23 / (6.022e+23), }; + diff --git a/latest/cases/01658/l3v2/index.heta b/latest/cases/01658/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01658/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01658/l3v2/json/output.json b/latest/cases/01658/l3v2/json/output.json new file mode 100644 index 000000000..a87ad681b --- /dev/null +++ b/latest/cases/01658/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "1", + "_E0": "3" + } + }, + { + "class": "DSwitcher", + "id": "_E0", + "trigger": "t > 6.02214076e+23 / (6.022e+23)" + } +] \ No newline at end of file diff --git a/latest/cases/01658/model-sbml-l3v2.xml b/latest/cases/01658/model-sbml-l3v2.xml new file mode 100644 index 000000000..43baded04 --- /dev/null +++ b/latest/cases/01658/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + time + + + avogadro + 6.022 23 + + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01658/output.heta b/latest/cases/01658/output.heta new file mode 100644 index 000000000..ce1063dbe --- /dev/null +++ b/latest/cases/01658/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: An event with avogadro in the trigger. +componentTags: CSymbolAvogadro, CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used in an event trigger. + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > (avogadro / 6.022e23)$ | $p1 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [_E0]= 3; + +_E0 @DSwitcher { trigger: t > 6.02214076e+23 / (6.022e+23), }; + diff --git a/latest/cases/01658/synopsis.txt b/latest/cases/01658/synopsis.txt new file mode 100644 index 000000000..3b7d2e839 --- /dev/null +++ b/latest/cases/01658/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event with avogadro in the trigger. +componentTags: CSymbolAvogadro, CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used in an event trigger. + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| _E0 | $time > (avogadro / 6.022e23)$ | $p1 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01659/l2v5/index.heta b/latest/cases/01659/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01659/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01659/l3v2/build.log b/latest/cases/01659/l3v2/build.log new file mode 100644 index 000000000..4678bba27 --- /dev/null +++ b/latest/cases/01659/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01659/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01659/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01659/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01659/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01659/l3v2/index.heta b/latest/cases/01659/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01659/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01659/model-sbml-l3v2.xml b/latest/cases/01659/model-sbml-l3v2.xml new file mode 100644 index 000000000..39ca69f6f --- /dev/null +++ b/latest/cases/01659/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + time + 1 + + + + + + + + avogadro + 6.022 23 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01659/synopsis.txt b/latest/cases/01659/synopsis.txt new file mode 100644 index 000000000..1f2d1d0ed --- /dev/null +++ b/latest/cases/01659/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event with avogadro in the delay. +componentTags: CSymbolAvogadro, CSymbolTime, EventWithDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used in an event delay. + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| _E0 | $time >= 1$ | $avogadro / 6.022e23$ | $p1 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01660/l2v5/index.heta b/latest/cases/01660/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01660/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01660/l3v2/build.log b/latest/cases/01660/l3v2/build.log new file mode 100644 index 000000000..ddac01006 --- /dev/null +++ b/latest/cases/01660/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01660/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01660/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01660/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01660/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01660/l3v2/index.heta b/latest/cases/01660/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01660/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01660/model-sbml-l3v2.xml b/latest/cases/01660/model-sbml-l3v2.xml new file mode 100644 index 000000000..17213312c --- /dev/null +++ b/latest/cases/01660/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + time + 0.5 + + + + time + + + avogadro + 6.022 23 + + + + + + + + 1 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01660/synopsis.txt b/latest/cases/01660/synopsis.txt new file mode 100644 index 000000000..749128569 --- /dev/null +++ b/latest/cases/01660/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event with avogadro in the trigger. +componentTags: CSymbolAvogadro, CSymbolTime, EventWithDelay, Parameter +testTags: EventIsPersistent, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used in an event trigger, and is used in a comparison where it makes a difference whether the event is persistent or not (in this version, it is). + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| _E0 | $(time >= 0.5) && (time <= (avogadro / 6.022e23))$ | $1$ | $p1 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01661/l2v5/index.heta b/latest/cases/01661/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01661/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01661/l3v2/build.log b/latest/cases/01661/l3v2/build.log new file mode 100644 index 000000000..dfed15e37 --- /dev/null +++ b/latest/cases/01661/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01661/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01661/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01661/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01661/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01661/l3v2/index.heta b/latest/cases/01661/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01661/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01661/model-sbml-l3v2.xml b/latest/cases/01661/model-sbml-l3v2.xml new file mode 100644 index 000000000..e7912e572 --- /dev/null +++ b/latest/cases/01661/model-sbml-l3v2.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + time + 0.5 + + + + time + + + avogadro + 6.022 23 + + + + + + + + 1 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01661/synopsis.txt b/latest/cases/01661/synopsis.txt new file mode 100644 index 000000000..a5dd12294 --- /dev/null +++ b/latest/cases/01661/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event with avogadro in the trigger. +componentTags: CSymbolAvogadro, CSymbolTime, EventWithDelay, Parameter +testTags: EventIsNotPersistent, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used in an event trigger, and is used in a comparison where it makes a difference whether the event is persistent or not (in this version, it is not). + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| _E0 | $(time >= 0.5) && (time <= (avogadro / 6.022e23))$ | false | $1$ | $p1 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01662/l2v5/index.heta b/latest/cases/01662/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01662/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01662/l3v2/heta-code/output.heta b/latest/cases/01662/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6ce0f0046 --- /dev/null +++ b/latest/cases/01662/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [E0]= 3; +p1 [E1]= 5; + +E0 @DSwitcher { trigger: t >= 2.5, }; +E1 @DSwitcher { trigger: t >= 2.5, }; + diff --git a/latest/cases/01662/l3v2/index.heta b/latest/cases/01662/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01662/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01662/l3v2/json/output.json b/latest/cases/01662/l3v2/json/output.json new file mode 100644 index 000000000..d59e2d10d --- /dev/null +++ b/latest/cases/01662/l3v2/json/output.json @@ -0,0 +1,24 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "1", + "E0": "3", + "E1": "5" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 2.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t >= 2.5" + } +] \ No newline at end of file diff --git a/latest/cases/01662/model-sbml-l3v2.xml b/latest/cases/01662/model-sbml-l3v2.xml new file mode 100644 index 000000000..20be04913 --- /dev/null +++ b/latest/cases/01662/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + time + 2.5 + + + + + + 1 + + + + + + 3 + + + + + + + + + + time + 2.5 + + + + + + + + avogadro + 6.022 23 + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01662/output.heta b/latest/cases/01662/output.heta new file mode 100644 index 000000000..e5d8e7dff --- /dev/null +++ b/latest/cases/01662/output.heta @@ -0,0 +1,42 @@ +/* +category: Test +synopsis: An event with avogadro in the priority. +componentTags: CSymbolAvogadro, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used in an event priority, determining which of two simultaneous events fires first. + +The model contains: +* 1 parameter (p1) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time >= 2.5$ | $1$ | $p1 = 3$ | +| E1 | $time >= 2.5$ | $avogadro / 6.022e23$ | $p1 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [E0]= 3; +p1 [E1]= 5; + +E0 @DSwitcher { trigger: t >= 2.5, }; +E1 @DSwitcher { trigger: t >= 2.5, }; + diff --git a/latest/cases/01662/synopsis.txt b/latest/cases/01662/synopsis.txt new file mode 100644 index 000000000..c074fe70f --- /dev/null +++ b/latest/cases/01662/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: An event with avogadro in the priority. +componentTags: CSymbolAvogadro, CSymbolTime, EventNoDelay, EventPriority, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used in an event priority, determining which of two simultaneous events fires first. + +The model contains: +* 1 parameter (p1) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time >= 2.5$ | $1$ | $p1 = 3$ | +| E1 | $time >= 2.5$ | $avogadro / 6.022e23$ | $p1 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01663/l2v5/index.heta b/latest/cases/01663/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01663/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01663/l3v2/heta-code/output.heta b/latest/cases/01663/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e3602acf9 --- /dev/null +++ b/latest/cases/01663/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [E0]= 5; + +E0 @DSwitcher { trigger: 6.02214076e+23 > (6.022e+23), }; + diff --git a/latest/cases/01663/l3v2/index.heta b/latest/cases/01663/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01663/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01663/l3v2/json/output.json b/latest/cases/01663/l3v2/json/output.json new file mode 100644 index 000000000..8ad22dcbf --- /dev/null +++ b/latest/cases/01663/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "1", + "E0": "5" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "6.02214076e+23 > (6.022e+23)" + } +] \ No newline at end of file diff --git a/latest/cases/01663/model-sbml-l3v2.xml b/latest/cases/01663/model-sbml-l3v2.xml new file mode 100644 index 000000000..b2d5fb334 --- /dev/null +++ b/latest/cases/01663/model-sbml-l3v2.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + avogadro + 6.022 23 + + + + + + + 5 + + + + + + + diff --git a/latest/cases/01663/output.heta b/latest/cases/01663/output.heta new file mode 100644 index 000000000..e21d4d4e1 --- /dev/null +++ b/latest/cases/01663/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: An event with avogadro in the trigger. +componentTags: CSymbolAvogadro, EventNoDelay, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used in an event trigger, which evaluates to 'true' at t0, and firing only because it's set initialValue=false. + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $avogadro > 6.022e23$ | false | $p1 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [E0]= 5; + +E0 @DSwitcher { trigger: 6.02214076e+23 > (6.022e+23), }; + diff --git a/latest/cases/01663/synopsis.txt b/latest/cases/01663/synopsis.txt new file mode 100644 index 000000000..abbc33605 --- /dev/null +++ b/latest/cases/01663/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event with avogadro in the trigger. +componentTags: CSymbolAvogadro, EventNoDelay, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used in an event trigger, which evaluates to 'true' at t0, and firing only because it's set initialValue=false. + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $avogadro > 6.022e23$ | false | $p1 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01664/l2v5/index.heta b/latest/cases/01664/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01664/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01664/l3v2/heta-code/output.heta b/latest/cases/01664/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4466e35e0 --- /dev/null +++ b/latest/cases/01664/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [E0]= 6.02214076e+23; + +E0 @DSwitcher { trigger: t > 1.5, }; + diff --git a/latest/cases/01664/l3v2/index.heta b/latest/cases/01664/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01664/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01664/l3v2/json/output.json b/latest/cases/01664/l3v2/json/output.json new file mode 100644 index 000000000..9cbbbb458 --- /dev/null +++ b/latest/cases/01664/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "1", + "E0": "6.02214076e+23" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 1.5" + } +] \ No newline at end of file diff --git a/latest/cases/01664/model-sbml-l3v2.xml b/latest/cases/01664/model-sbml-l3v2.xml new file mode 100644 index 000000000..5b81132df --- /dev/null +++ b/latest/cases/01664/model-sbml-l3v2.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + time + 1.5 + + + + + + + avogadro + + + + + + + diff --git a/latest/cases/01664/output.heta b/latest/cases/01664/output.heta new file mode 100644 index 000000000..1f91b91e8 --- /dev/null +++ b/latest/cases/01664/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: An event with avogadro in an event assignment. +componentTags: CSymbolAvogadro, CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used as the assignment value in an event. + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 1.5$ | $p1 = avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p1 @Record { } .= 1; +p1 [E0]= 6.02214076e+23; + +E0 @DSwitcher { trigger: t > 1.5, }; + diff --git a/latest/cases/01664/synopsis.txt b/latest/cases/01664/synopsis.txt new file mode 100644 index 000000000..00ef4e22e --- /dev/null +++ b/latest/cases/01664/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event with avogadro in an event assignment. +componentTags: CSymbolAvogadro, CSymbolTime, EventNoDelay, Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the avogadro csymbol is used as the assignment value in an event. + +The model contains: +* 1 parameter (p1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time > 1.5$ | $p1 = avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01665/l2v5/index.heta b/latest/cases/01665/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01665/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01665/l3v2/heta-code/output.heta b/latest/cases/01665/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3b9871ae0 --- /dev/null +++ b/latest/cases/01665/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +p1_proc @Process { actors: = p1, }; +p1_proc := 6.02214076e+23 / (1e+23); + +p1 @Record { } .= 1; + diff --git a/latest/cases/01665/l3v2/index.heta b/latest/cases/01665/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01665/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01665/l3v2/json/output.json b/latest/cases/01665/l3v2/json/output.json new file mode 100644 index 000000000..b654cb17b --- /dev/null +++ b/latest/cases/01665/l3v2/json/output.json @@ -0,0 +1,25 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "p1", + "assignments": { + "start_": "1" + } + }, + { + "class": "Process", + "id": "p1_proc", + "assignments": { + "ode_": "6.02214076e+23 / (1e+23)" + }, + "actors": [ + { + "target": "p1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01665/model-sbml-l3v2.xml b/latest/cases/01665/model-sbml-l3v2.xml new file mode 100644 index 000000000..983765daf --- /dev/null +++ b/latest/cases/01665/model-sbml-l3v2.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + avogadro + 1 23 + + + + + + diff --git a/latest/cases/01665/output.heta b/latest/cases/01665/output.heta new file mode 100644 index 000000000..9230ab23f --- /dev/null +++ b/latest/cases/01665/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A rate rule that uses avogadro. +componentTags: CSymbolAvogadro, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In this model, the avogadro csymbol is used in a rate rule. + +The model contains: +* 1 parameter (p1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $avogadro / 1e23$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +p1_proc @Process { actors: = p1, }; +p1_proc := 6.02214076e+23 / (1e+23); + +p1 @Record { } .= 1; + diff --git a/latest/cases/01665/synopsis.txt b/latest/cases/01665/synopsis.txt new file mode 100644 index 000000000..71defc13f --- /dev/null +++ b/latest/cases/01665/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A rate rule that uses avogadro. +componentTags: CSymbolAvogadro, Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +In this model, the avogadro csymbol is used in a rate rule. + +The model contains: +* 1 parameter (p1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | p1 | $avogadro / 1e23$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter p1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01666/l2v5/index.heta b/latest/cases/01666/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01666/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01666/l3v2/heta-code/output.heta b/latest/cases/01666/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1a9167782 --- /dev/null +++ b/latest/cases/01666/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +S1_proc @Process { actors: = S1, }; +S1_proc := (-0.01); +S2_proc @Process { actors: = S2, }; +S2_proc := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01666/l3v2/index.heta b/latest/cases/01666/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01666/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01666/l3v2/json/output.json b/latest/cases/01666/l3v2/json/output.json new file mode 100644 index 000000000..1f9bfab7c --- /dev/null +++ b/latest/cases/01666/l3v2/json/output.json @@ -0,0 +1,65 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "(-0.01)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01666/model-sbml-l3v2.xml b/latest/cases/01666/model-sbml-l3v2.xml new file mode 100644 index 000000000..2de3dbe29 --- /dev/null +++ b/latest/cases/01666/model-sbml-l3v2.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + -0.01 + + + + + 0.01 + + + + + diff --git a/latest/cases/01666/output.heta b/latest/cases/01666/output.heta new file mode 100644 index 000000000..9d099f334 --- /dev/null +++ b/latest/cases/01666/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Model and species conversion factors for species only affected by rate rules. +componentTags: Compartment, Parameter, RateRule, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species, but those species only change due to rate rules, which means the conversion factors are not used (as they only affect reactions). + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-0.01$ | +| Rate | S2 | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +S1_proc @Process { actors: = S1, }; +S1_proc := (-0.01); +S2_proc @Process { actors: = S2, }; +S2_proc := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01666/synopsis.txt b/latest/cases/01666/synopsis.txt new file mode 100644 index 000000000..0d84428aa --- /dev/null +++ b/latest/cases/01666/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Model and species conversion factors for species only affected by rate rules. +componentTags: Compartment, Parameter, RateRule, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species, but those species only change due to rate rules, which means the conversion factors are not used (as they only affect reactions). + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-0.01$ | +| Rate | S2 | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01667/l2v5/index.heta b/latest/cases/01667/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01667/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01667/l3v2/heta-code/output.heta b/latest/cases/01667/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b50a34e3d --- /dev/null +++ b/latest/cases/01667/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +S1_proc @Process { actors: = S1, }; +S1_proc := (-0.01); +S2_proc @Process { actors: = S2, }; +S2_proc := 0.01; + +s1_cf @Const { } = 5; + diff --git a/latest/cases/01667/l3v2/index.heta b/latest/cases/01667/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01667/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01667/l3v2/json/output.json b/latest/cases/01667/l3v2/json/output.json new file mode 100644 index 000000000..1b6447b15 --- /dev/null +++ b/latest/cases/01667/l3v2/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "(-0.01)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01667/model-sbml-l3v2.xml b/latest/cases/01667/model-sbml-l3v2.xml new file mode 100644 index 000000000..5dbfb50e7 --- /dev/null +++ b/latest/cases/01667/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + -0.01 + + + + + 0.01 + + + + + diff --git a/latest/cases/01667/output.heta b/latest/cases/01667/output.heta new file mode 100644 index 000000000..7cdb29007 --- /dev/null +++ b/latest/cases/01667/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: A species conversion factor for species only affected by rate rules. +componentTags: Compartment, Parameter, RateRule, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species, but those species only change due to rate rules, which means the conversion factor is not used (as they only affect reactions). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-0.01$ | +| Rate | S2 | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +S1_proc @Process { actors: = S1, }; +S1_proc := (-0.01); +S2_proc @Process { actors: = S2, }; +S2_proc := 0.01; + +s1_cf @Const { } = 5; + diff --git a/latest/cases/01667/synopsis.txt b/latest/cases/01667/synopsis.txt new file mode 100644 index 000000000..ba1a406ae --- /dev/null +++ b/latest/cases/01667/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A species conversion factor for species only affected by rate rules. +componentTags: Compartment, Parameter, RateRule, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species, but those species only change due to rate rules, which means the conversion factor is not used (as they only affect reactions). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-0.01$ | +| Rate | S2 | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01668/l2v5/index.heta b/latest/cases/01668/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01668/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01668/l3v2/heta-code/output.heta b/latest/cases/01668/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1a9167782 --- /dev/null +++ b/latest/cases/01668/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +S1_proc @Process { actors: = S1, }; +S1_proc := (-0.01); +S2_proc @Process { actors: = S2, }; +S2_proc := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01668/l3v2/index.heta b/latest/cases/01668/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01668/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01668/l3v2/json/output.json b/latest/cases/01668/l3v2/json/output.json new file mode 100644 index 000000000..1f9bfab7c --- /dev/null +++ b/latest/cases/01668/l3v2/json/output.json @@ -0,0 +1,65 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "(-0.01)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Process", + "id": "S2_proc", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01668/model-sbml-l3v2.xml b/latest/cases/01668/model-sbml-l3v2.xml new file mode 100644 index 000000000..df5cee80b --- /dev/null +++ b/latest/cases/01668/model-sbml-l3v2.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + -0.01 + + + + + 0.01 + + + + + diff --git a/latest/cases/01668/output.heta b/latest/cases/01668/output.heta new file mode 100644 index 000000000..0200b8d6d --- /dev/null +++ b/latest/cases/01668/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Model conversion factor for species only affected by rate rules. +componentTags: Compartment, Parameter, RateRule, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor is set for species, but those species only change due to rate rules, which means the conversion factor is not used (as they only affect reactions). + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-0.01$ | +| Rate | S2 | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +S1_proc @Process { actors: = S1, }; +S1_proc := (-0.01); +S2_proc @Process { actors: = S2, }; +S2_proc := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01668/synopsis.txt b/latest/cases/01668/synopsis.txt new file mode 100644 index 000000000..0a1f11b90 --- /dev/null +++ b/latest/cases/01668/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Model conversion factor for species only affected by rate rules. +componentTags: Compartment, Parameter, RateRule, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor is set for species, but those species only change due to rate rules, which means the conversion factor is not used (as they only affect reactions). + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-0.01$ | +| Rate | S2 | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01669/l2v5/index.heta b/latest/cases/01669/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01669/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01669/l3v2/heta-code/output.heta b/latest/cases/01669/l3v2/heta-code/output.heta new file mode 100644 index 000000000..27ac08956 --- /dev/null +++ b/latest/cases/01669/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t >= 4.5, }; + diff --git a/latest/cases/01669/l3v2/index.heta b/latest/cases/01669/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01669/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01669/l3v2/json/output.json b/latest/cases/01669/l3v2/json/output.json new file mode 100644 index 000000000..ed7e26d16 --- /dev/null +++ b/latest/cases/01669/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C", + "E0": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C", + "E0": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 4.5" + } +] \ No newline at end of file diff --git a/latest/cases/01669/model-sbml-l3v2.xml b/latest/cases/01669/model-sbml-l3v2.xml new file mode 100644 index 000000000..7e960c6e0 --- /dev/null +++ b/latest/cases/01669/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + time + 4.5 + + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/01669/output.heta b/latest/cases/01669/output.heta new file mode 100644 index 000000000..ca8d0d221 --- /dev/null +++ b/latest/cases/01669/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Model and species conversion factors for event-modified species. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset partway through the simulation by an event. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 4.5$ | $S2 = 3$ | +| | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t >= 4.5, }; + diff --git a/latest/cases/01669/synopsis.txt b/latest/cases/01669/synopsis.txt new file mode 100644 index 000000000..bf2804109 --- /dev/null +++ b/latest/cases/01669/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Model and species conversion factors for event-modified species. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset partway through the simulation by an event. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 4.5$ | $S2 = 3$ | +| | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01670/l2v5/index.heta b/latest/cases/01670/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01670/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01670/l3v2/heta-code/output.heta b/latest/cases/01670/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cdb7e26cd --- /dev/null +++ b/latest/cases/01670/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t >= 4.5, }; + diff --git a/latest/cases/01670/l3v2/index.heta b/latest/cases/01670/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01670/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01670/l3v2/json/output.json b/latest/cases/01670/l3v2/json/output.json new file mode 100644 index 000000000..6371fd41f --- /dev/null +++ b/latest/cases/01670/l3v2/json/output.json @@ -0,0 +1,58 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C", + "E0": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C", + "E0": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 4.5" + } +] \ No newline at end of file diff --git a/latest/cases/01670/model-sbml-l3v2.xml b/latest/cases/01670/model-sbml-l3v2.xml new file mode 100644 index 000000000..3db335a61 --- /dev/null +++ b/latest/cases/01670/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + time + 4.5 + + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/01670/output.heta b/latest/cases/01670/output.heta new file mode 100644 index 000000000..7d50f7b1a --- /dev/null +++ b/latest/cases/01670/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Species conversion factor for event-modified species. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, species conversion factor set for species reset partway through the simulation by an event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 4.5$ | $S2 = 3$ | +| | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t >= 4.5, }; + diff --git a/latest/cases/01670/synopsis.txt b/latest/cases/01670/synopsis.txt new file mode 100644 index 000000000..6af81a80b --- /dev/null +++ b/latest/cases/01670/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Species conversion factor for event-modified species. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, species conversion factor set for species reset partway through the simulation by an event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 4.5$ | $S2 = 3$ | +| | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01671/l2v5/index.heta b/latest/cases/01671/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01671/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01671/l3v2/heta-code/output.heta b/latest/cases/01671/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c932cb05e --- /dev/null +++ b/latest/cases/01671/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; + +E0 @DSwitcher { trigger: t >= 4.5, }; + diff --git a/latest/cases/01671/l3v2/index.heta b/latest/cases/01671/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01671/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01671/l3v2/json/output.json b/latest/cases/01671/l3v2/json/output.json new file mode 100644 index 000000000..ad37dde4d --- /dev/null +++ b/latest/cases/01671/l3v2/json/output.json @@ -0,0 +1,58 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C", + "E0": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C", + "E0": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 4.5" + } +] \ No newline at end of file diff --git a/latest/cases/01671/model-sbml-l3v2.xml b/latest/cases/01671/model-sbml-l3v2.xml new file mode 100644 index 000000000..3a37e3c16 --- /dev/null +++ b/latest/cases/01671/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + time + 4.5 + + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/01671/output.heta b/latest/cases/01671/output.heta new file mode 100644 index 000000000..4a10f8ca9 --- /dev/null +++ b/latest/cases/01671/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Model conversion factors for event-modified species. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model conversion factor set for species reset partway through the simulation by an event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 4.5$ | $S2 = 3$ | +| | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; + +E0 @DSwitcher { trigger: t >= 4.5, }; + diff --git a/latest/cases/01671/synopsis.txt b/latest/cases/01671/synopsis.txt new file mode 100644 index 000000000..42ccf7318 --- /dev/null +++ b/latest/cases/01671/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Model conversion factors for event-modified species. +componentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model conversion factor set for species reset partway through the simulation by an event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 4.5$ | $S2 = 3$ | +| | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01672/l2v5/index.heta b/latest/cases/01672/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01672/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01672/l3v2/build.log b/latest/cases/01672/l3v2/build.log new file mode 100644 index 000000000..9afe8ec50 --- /dev/null +++ b/latest/cases/01672/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01672/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01672/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01672/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01672/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01672/l3v2/index.heta b/latest/cases/01672/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01672/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01672/model-sbml-l3v2.xml b/latest/cases/01672/model-sbml-l3v2.xml new file mode 100644 index 000000000..fcc242b37 --- /dev/null +++ b/latest/cases/01672/model-sbml-l3v2.xml @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + time + 4.5 + + + + + + S1 + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/01672/synopsis.txt b/latest/cases/01672/synopsis.txt new file mode 100644 index 000000000..3488b0d94 --- /dev/null +++ b/latest/cases/01672/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Model and species conversion factors for event-modified species. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset partway through the simulation by a delayed event. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time >= 4.5$ | $S1$ | $S2 = 3$ | +| | | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01673/l2v5/index.heta b/latest/cases/01673/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01673/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01673/l3v2/build.log b/latest/cases/01673/l3v2/build.log new file mode 100644 index 000000000..a6d973d56 --- /dev/null +++ b/latest/cases/01673/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01673/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01673/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01673/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01673/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01673/l3v2/index.heta b/latest/cases/01673/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01673/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01673/model-sbml-l3v2.xml b/latest/cases/01673/model-sbml-l3v2.xml new file mode 100644 index 000000000..4f159db8c --- /dev/null +++ b/latest/cases/01673/model-sbml-l3v2.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + time + 4.5 + + + + + + S1 + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/01673/synopsis.txt b/latest/cases/01673/synopsis.txt new file mode 100644 index 000000000..a5e18ad5f --- /dev/null +++ b/latest/cases/01673/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Model and species conversion factors for event-modified species. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, species conversion factor set for species reset partway through the simulation by a delayed event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time >= 4.5$ | $S1$ | $S2 = 3$ | +| | | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01674/l2v5/index.heta b/latest/cases/01674/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01674/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01674/l3v2/build.log b/latest/cases/01674/l3v2/build.log new file mode 100644 index 000000000..de4694488 --- /dev/null +++ b/latest/cases/01674/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01674/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01674/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01674/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01674/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01674/l3v2/index.heta b/latest/cases/01674/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01674/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01674/model-sbml-l3v2.xml b/latest/cases/01674/model-sbml-l3v2.xml new file mode 100644 index 000000000..e4b34327d --- /dev/null +++ b/latest/cases/01674/model-sbml-l3v2.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + time + 4.5 + + + + + + S1 + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/01674/synopsis.txt b/latest/cases/01674/synopsis.txt new file mode 100644 index 000000000..695d3ce19 --- /dev/null +++ b/latest/cases/01674/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Model and species conversion factors for event-modified species. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model conversion factor set for species reset partway through the simulation by a delayed event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $time >= 4.5$ | $S1$ | $S2 = 3$ | +| | | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01675/l2v5/index.heta b/latest/cases/01675/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01675/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01675/l3v2/build.log b/latest/cases/01675/l3v2/build.log new file mode 100644 index 000000000..e18958ff5 --- /dev/null +++ b/latest/cases/01675/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01675/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01675/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01675/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01675/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01675/l3v2/index.heta b/latest/cases/01675/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01675/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01675/model-sbml-l3v2.xml b/latest/cases/01675/model-sbml-l3v2.xml new file mode 100644 index 000000000..dec1fc992 --- /dev/null +++ b/latest/cases/01675/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + + + S1 + 1.88 + + + + S1 + 1.84 + + + + + + + 1 + + + + + + 3 + + + + + 6 + + + + + + + diff --git a/latest/cases/01675/synopsis.txt b/latest/cases/01675/synopsis.txt new file mode 100644 index 000000000..58a703136 --- /dev/null +++ b/latest/cases/01675/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Model and species conversion factors for a persistent event. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventIsPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset partway through the simulation by a persistent event. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(S1 <= 1.88) && (S1 > 1.84)$ | $1$ | $S2 = 3$ | +| | | | $S1 = 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01676/l2v5/index.heta b/latest/cases/01676/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01676/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01676/l3v2/build.log b/latest/cases/01676/l3v2/build.log new file mode 100644 index 000000000..a4a2afcaa --- /dev/null +++ b/latest/cases/01676/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01676/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01676/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01676/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01676/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01676/l3v2/index.heta b/latest/cases/01676/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01676/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01676/model-sbml-l3v2.xml b/latest/cases/01676/model-sbml-l3v2.xml new file mode 100644 index 000000000..3513f8928 --- /dev/null +++ b/latest/cases/01676/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + + + S1 + 1.88 + + + + S1 + 1.84 + + + + + + + 1 + + + + + + 3 + + + + + 6 + + + + + + + diff --git a/latest/cases/01676/synopsis.txt b/latest/cases/01676/synopsis.txt new file mode 100644 index 000000000..5683407d0 --- /dev/null +++ b/latest/cases/01676/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: A species conversion factor for persistent event. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventIsPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factors is set for a species reset partway through the simulation by a persistent event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(S1 <= 1.88) && (S1 > 1.84)$ | $1$ | $S2 = 3$ | +| | | | $S1 = 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01677/l2v5/index.heta b/latest/cases/01677/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01677/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01677/l3v2/build.log b/latest/cases/01677/l3v2/build.log new file mode 100644 index 000000000..ee15e2b52 --- /dev/null +++ b/latest/cases/01677/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01677/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01677/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01677/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01677/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01677/l3v2/index.heta b/latest/cases/01677/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01677/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01677/model-sbml-l3v2.xml b/latest/cases/01677/model-sbml-l3v2.xml new file mode 100644 index 000000000..2cec9453e --- /dev/null +++ b/latest/cases/01677/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + + + S2 + 3.07 + + + + S2 + 3.095 + + + + + + + 1 + + + + + + 4 + + + + + 6 + + + + + + + diff --git a/latest/cases/01677/synopsis.txt b/latest/cases/01677/synopsis.txt new file mode 100644 index 000000000..9e6fac178 --- /dev/null +++ b/latest/cases/01677/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Model and species conversion factors for a persistent event. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventIsPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset partway through the simulation by a persistent event. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(S2 >= 3.07) && (S2 <= 3.095)$ | $1$ | $S2 = 4$ | +| | | | $S1 = 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $4$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01678/l2v5/index.heta b/latest/cases/01678/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01678/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01678/l3v2/build.log b/latest/cases/01678/l3v2/build.log new file mode 100644 index 000000000..18d7ab9bf --- /dev/null +++ b/latest/cases/01678/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01678/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01678/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01678/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01678/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01678/l3v2/index.heta b/latest/cases/01678/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01678/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01678/model-sbml-l3v2.xml b/latest/cases/01678/model-sbml-l3v2.xml new file mode 100644 index 000000000..d1081c9a7 --- /dev/null +++ b/latest/cases/01678/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + + + S1 + 1.88 + + + + S1 + 1.84 + + + + + + + 1 + + + + + + 3 + + + + + 6 + + + + + + + diff --git a/latest/cases/01678/synopsis.txt b/latest/cases/01678/synopsis.txt new file mode 100644 index 000000000..265323020 --- /dev/null +++ b/latest/cases/01678/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Model and species conversion factors for a non-persistent event. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventIsNotPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species triggered but not reset partway through the simulation by a non-persistent event. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E0 | $(S1 <= 1.88) && (S1 > 1.84)$ | false | $1$ | $S2 = 3$ | +| | | | | $S1 = 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01679/l2v5/index.heta b/latest/cases/01679/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01679/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01679/l3v2/build.log b/latest/cases/01679/l3v2/build.log new file mode 100644 index 000000000..960b58258 --- /dev/null +++ b/latest/cases/01679/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01679/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01679/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01679/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01679/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01679/l3v2/index.heta b/latest/cases/01679/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01679/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01679/model-sbml-l3v2.xml b/latest/cases/01679/model-sbml-l3v2.xml new file mode 100644 index 000000000..dc7d2f09a --- /dev/null +++ b/latest/cases/01679/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + + + S1 + 1.88 + + + + S1 + 1.84 + + + + + + + 1 + + + + + + 3 + + + + + 6 + + + + + + + diff --git a/latest/cases/01679/synopsis.txt b/latest/cases/01679/synopsis.txt new file mode 100644 index 000000000..b36b7297c --- /dev/null +++ b/latest/cases/01679/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: A species conversion factor for non-persistent event. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventIsNotPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factors is set for a species not reset partway through the simulation by a non-persistent event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E0 | $(S1 <= 1.88) && (S1 > 1.84)$ | false | $1$ | $S2 = 3$ | +| | | | | $S1 = 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01680/l2v5/index.heta b/latest/cases/01680/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01680/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01680/l3v2/build.log b/latest/cases/01680/l3v2/build.log new file mode 100644 index 000000000..9577f5894 --- /dev/null +++ b/latest/cases/01680/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01680/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01680/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01680/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01680/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01680/l3v2/index.heta b/latest/cases/01680/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01680/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01680/model-sbml-l3v2.xml b/latest/cases/01680/model-sbml-l3v2.xml new file mode 100644 index 000000000..4f7f025fe --- /dev/null +++ b/latest/cases/01680/model-sbml-l3v2.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + + + S2 + 3.07 + + + + S2 + 3.095 + + + + + + + 1 + + + + + + 4 + + + + + 6 + + + + + + + diff --git a/latest/cases/01680/synopsis.txt b/latest/cases/01680/synopsis.txt new file mode 100644 index 000000000..a2a3bd926 --- /dev/null +++ b/latest/cases/01680/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Model and species conversion factors for a non-persistent event. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventIsNotPersistent +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species not reset partway through the simulation by a non-persistent event. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E0 | $(S2 >= 3.07) && (S2 <= 3.095)$ | false | $1$ | $S2 = 4$ | +| | | | | $S1 = 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $4$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01681/l2v5/index.heta b/latest/cases/01681/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01681/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01681/l3v2/heta-code/output.heta b/latest/cases/01681/l3v2/heta-code/output.heta new file mode 100644 index 000000000..43c6b16fe --- /dev/null +++ b/latest/cases/01681/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 1; +S1 [E1]= 4; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; +S2 [E1]= 4; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t > 3.5, }; +E1 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01681/l3v2/index.heta b/latest/cases/01681/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01681/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01681/l3v2/json/output.json b/latest/cases/01681/l3v2/json/output.json new file mode 100644 index 000000000..c486d4870 --- /dev/null +++ b/latest/cases/01681/l3v2/json/output.json @@ -0,0 +1,70 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C", + "E0": "1", + "E1": "4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C", + "E0": "3", + "E1": "4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 3.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 3.5" + } +] \ No newline at end of file diff --git a/latest/cases/01681/model-sbml-l3v2.xml b/latest/cases/01681/model-sbml-l3v2.xml new file mode 100644 index 000000000..ba49b923d --- /dev/null +++ b/latest/cases/01681/model-sbml-l3v2.xml @@ -0,0 +1,89 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + time + 3.5 + + + + + + S1 + + + + + + 3 + + + + + 1 + + + + + + + + + + time + 3.5 + + + + + + 1.82 + + + + + + 4 + + + + + 4 + + + + + + + diff --git a/latest/cases/01681/output.heta b/latest/cases/01681/output.heta new file mode 100644 index 000000000..e29b989bc --- /dev/null +++ b/latest/cases/01681/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Model and species conversion factors for simultaneous events. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset partway through the simulation by two simultaneous events, whose priorities involve the species. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 3.5$ | $S1$ | $S2 = 3$ | +| | | | $S1 = 1$ | +| E1 | $time > 3.5$ | $1.82$ | $S2 = 4$ | +| | | | $S1 = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 1; +S1 [E1]= 4; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; +S2 [E1]= 4; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t > 3.5, }; +E1 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01681/synopsis.txt b/latest/cases/01681/synopsis.txt new file mode 100644 index 000000000..b158b0204 --- /dev/null +++ b/latest/cases/01681/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Model and species conversion factors for simultaneous events. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset partway through the simulation by two simultaneous events, whose priorities involve the species. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 3.5$ | $S1$ | $S2 = 3$ | +| | | | $S1 = 1$ | +| E1 | $time > 3.5$ | $1.82$ | $S2 = 4$ | +| | | | $S1 = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01682/l2v5/index.heta b/latest/cases/01682/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01682/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01682/l3v2/heta-code/output.heta b/latest/cases/01682/l3v2/heta-code/output.heta new file mode 100644 index 000000000..08ff31720 --- /dev/null +++ b/latest/cases/01682/l3v2/heta-code/output.heta @@ -0,0 +1,21 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 1; +S1 [E1]= 4; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; +S2 [E1]= 4; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t > 3.5, }; +E1 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01682/l3v2/index.heta b/latest/cases/01682/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01682/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01682/l3v2/json/output.json b/latest/cases/01682/l3v2/json/output.json new file mode 100644 index 000000000..71d2ff1b5 --- /dev/null +++ b/latest/cases/01682/l3v2/json/output.json @@ -0,0 +1,65 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C", + "E0": "1", + "E1": "4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C", + "E0": "3", + "E1": "4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 3.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 3.5" + } +] \ No newline at end of file diff --git a/latest/cases/01682/model-sbml-l3v2.xml b/latest/cases/01682/model-sbml-l3v2.xml new file mode 100644 index 000000000..eadf9e100 --- /dev/null +++ b/latest/cases/01682/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + time + 3.5 + + + + + + S1 + + + + + + 3 + + + + + 1 + + + + + + + + + + time + 3.5 + + + + + + 1.82 + + + + + + 4 + + + + + 4 + + + + + + + diff --git a/latest/cases/01682/output.heta b/latest/cases/01682/output.heta new file mode 100644 index 000000000..5e33ba3c4 --- /dev/null +++ b/latest/cases/01682/output.heta @@ -0,0 +1,72 @@ +/* +category: Test +synopsis: A species conversion factor for simultaneous events. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species reset partway through the simulation by two simultaneous events, whose priorities involve the species. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 3.5$ | $S1$ | $S2 = 3$ | +| | | | $S1 = 1$ | +| E1 | $time > 3.5$ | $1.82$ | $S2 = 4$ | +| | | | $S1 = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 1; +S1 [E1]= 4; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; +S2 [E1]= 4; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t > 3.5, }; +E1 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01682/synopsis.txt b/latest/cases/01682/synopsis.txt new file mode 100644 index 000000000..d02928f50 --- /dev/null +++ b/latest/cases/01682/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: A species conversion factor for simultaneous events. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species reset partway through the simulation by two simultaneous events, whose priorities involve the species. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 3.5$ | $S1$ | $S2 = 3$ | +| | | | $S1 = 1$ | +| E1 | $time > 3.5$ | $1.82$ | $S2 = 4$ | +| | | | $S1 = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01683/l2v5/index.heta b/latest/cases/01683/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01683/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01683/l3v2/heta-code/output.heta b/latest/cases/01683/l3v2/heta-code/output.heta new file mode 100644 index 000000000..43c6b16fe --- /dev/null +++ b/latest/cases/01683/l3v2/heta-code/output.heta @@ -0,0 +1,22 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 1; +S1 [E1]= 4; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; +S2 [E1]= 4; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t > 3.5, }; +E1 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01683/l3v2/index.heta b/latest/cases/01683/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01683/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01683/l3v2/json/output.json b/latest/cases/01683/l3v2/json/output.json new file mode 100644 index 000000000..c486d4870 --- /dev/null +++ b/latest/cases/01683/l3v2/json/output.json @@ -0,0 +1,70 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C", + "E0": "1", + "E1": "4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C", + "E0": "3", + "E1": "4" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 3.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 3.5" + } +] \ No newline at end of file diff --git a/latest/cases/01683/model-sbml-l3v2.xml b/latest/cases/01683/model-sbml-l3v2.xml new file mode 100644 index 000000000..e8e3f94c8 --- /dev/null +++ b/latest/cases/01683/model-sbml-l3v2.xml @@ -0,0 +1,89 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + time + 3.5 + + + + + + S2 + + + + + + 3 + + + + + 1 + + + + + + + + + + time + 3.5 + + + + + + 3.013 + + + + + + 4 + + + + + 4 + + + + + + + diff --git a/latest/cases/01683/output.heta b/latest/cases/01683/output.heta new file mode 100644 index 000000000..adfa1f5a5 --- /dev/null +++ b/latest/cases/01683/output.heta @@ -0,0 +1,75 @@ +/* +category: Test +synopsis: Model and species conversion factors for simultaneous events. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset partway through the simulation by two simultaneous events, whose priorities involve the species. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 3.5$ | $S2$ | $S2 = 3$ | +| | | | $S1 = 1$ | +| E1 | $time > 3.5$ | $3.013$ | $S2 = 4$ | +| | | | $S1 = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S1 [E0]= 1; +S1 [E1]= 4; +S2 @Species { compartment: C, } .= 3 / C; +S2 [E0]= 3; +S2 [E1]= 4; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: t > 3.5, }; +E1 @DSwitcher { trigger: t > 3.5, }; + diff --git a/latest/cases/01683/synopsis.txt b/latest/cases/01683/synopsis.txt new file mode 100644 index 000000000..93ac8c044 --- /dev/null +++ b/latest/cases/01683/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Model and species conversion factors for simultaneous events. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset partway through the simulation by two simultaneous events, whose priorities involve the species. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 3.5$ | $S2$ | $S2 = 3$ | +| | | | $S1 = 1$ | +| E1 | $time > 3.5$ | $3.013$ | $S2 = 4$ | +| | | | $S1 = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01684/l2v5/index.heta b/latest/cases/01684/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01684/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01684/l3v2/heta-code/output.heta b/latest/cases/01684/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d00811f68 --- /dev/null +++ b/latest/cases/01684/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 0 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: S1 > 0.9, }; + diff --git a/latest/cases/01684/l3v2/index.heta b/latest/cases/01684/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01684/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01684/l3v2/json/output.json b/latest/cases/01684/l3v2/json/output.json new file mode 100644 index 000000000..66e731e2a --- /dev/null +++ b/latest/cases/01684/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C", + "E0": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0 / C", + "E0": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "S1 > 0.9" + } +] \ No newline at end of file diff --git a/latest/cases/01684/model-sbml-l3v2.xml b/latest/cases/01684/model-sbml-l3v2.xml new file mode 100644 index 000000000..34f0afd73 --- /dev/null +++ b/latest/cases/01684/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + S1 + 0.9 + + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/01684/output.heta b/latest/cases/01684/output.heta new file mode 100644 index 000000000..326e88be6 --- /dev/null +++ b/latest/cases/01684/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: Model and species conversion factors for events that fire at t0. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset at t0 by an event. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $S1 > 0.9$ | false | $S2 = 3$ | +| | | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 0 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: S1 > 0.9, }; + diff --git a/latest/cases/01684/synopsis.txt b/latest/cases/01684/synopsis.txt new file mode 100644 index 000000000..f4bef690a --- /dev/null +++ b/latest/cases/01684/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: Model and species conversion factors for events that fire at t0. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species reset at t0 by an event. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $S1 > 0.9$ | false | $S2 = 3$ | +| | | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01685/l2v5/index.heta b/latest/cases/01685/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01685/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01685/l3v2/heta-code/output.heta b/latest/cases/01685/l3v2/heta-code/output.heta new file mode 100644 index 000000000..11634cad8 --- /dev/null +++ b/latest/cases/01685/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 0 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: S1 > 0.9, }; + diff --git a/latest/cases/01685/l3v2/index.heta b/latest/cases/01685/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01685/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01685/l3v2/json/output.json b/latest/cases/01685/l3v2/json/output.json new file mode 100644 index 000000000..a2281cdce --- /dev/null +++ b/latest/cases/01685/l3v2/json/output.json @@ -0,0 +1,58 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C", + "E0": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0 / C", + "E0": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "S1 > 0.9" + } +] \ No newline at end of file diff --git a/latest/cases/01685/model-sbml-l3v2.xml b/latest/cases/01685/model-sbml-l3v2.xml new file mode 100644 index 000000000..5d4a2c652 --- /dev/null +++ b/latest/cases/01685/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + S1 + 0.9 + + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/01685/output.heta b/latest/cases/01685/output.heta new file mode 100644 index 000000000..123658e97 --- /dev/null +++ b/latest/cases/01685/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: A species conversion factor for events that fire at t0. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species reset at t0 by an event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $S1 > 0.9$ | false | $S2 = 3$ | +| | | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 0 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + +E0 @DSwitcher { trigger: S1 > 0.9, }; + diff --git a/latest/cases/01685/synopsis.txt b/latest/cases/01685/synopsis.txt new file mode 100644 index 000000000..6aee71192 --- /dev/null +++ b/latest/cases/01685/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: A species conversion factor for events that fire at t0. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species reset at t0 by an event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $S1 > 0.9$ | false | $S2 = 3$ | +| | | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01686/l2v5/index.heta b/latest/cases/01686/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01686/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01686/l3v2/heta-code/output.heta b/latest/cases/01686/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5f8282a18 --- /dev/null +++ b/latest/cases/01686/l3v2/heta-code/output.heta @@ -0,0 +1,18 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 0 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; + +E0 @DSwitcher { trigger: S1 > 0.9, }; + diff --git a/latest/cases/01686/l3v2/index.heta b/latest/cases/01686/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01686/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01686/l3v2/json/output.json b/latest/cases/01686/l3v2/json/output.json new file mode 100644 index 000000000..c12ec7ed0 --- /dev/null +++ b/latest/cases/01686/l3v2/json/output.json @@ -0,0 +1,58 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 / C", + "E0": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "0 / C", + "E0": "3" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "S1 > 0.9" + } +] \ No newline at end of file diff --git a/latest/cases/01686/model-sbml-l3v2.xml b/latest/cases/01686/model-sbml-l3v2.xml new file mode 100644 index 000000000..162885d60 --- /dev/null +++ b/latest/cases/01686/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + S1 + 0.9 + + + + + + + 3 + + + + + 2 + + + + + + + diff --git a/latest/cases/01686/output.heta b/latest/cases/01686/output.heta new file mode 100644 index 000000000..edd59ab3b --- /dev/null +++ b/latest/cases/01686/output.heta @@ -0,0 +1,67 @@ +/* +category: Test +synopsis: Model conversion factor for events that fire at t0. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor is set for species reset at t0 by an event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $S1 > 0.9$ | false | $S2 = 3$ | +| | | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1 / C; +S1 [E0]= 2; +S2 @Species { compartment: C, } .= 0 / C; +S2 [E0]= 3; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; + +E0 @DSwitcher { trigger: S1 > 0.9, }; + diff --git a/latest/cases/01686/synopsis.txt b/latest/cases/01686/synopsis.txt new file mode 100644 index 000000000..e659b5d29 --- /dev/null +++ b/latest/cases/01686/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: Model conversion factor for events that fire at t0. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventT0Firing +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor is set for species reset at t0 by an event. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $S1 > 0.9$ | false | $S2 = 3$ | +| | | | $S1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $1$ | variable | +| Initial amount of species S2 | $0$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01687/l2v5/index.heta b/latest/cases/01687/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01687/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01687/l3v2/build.log b/latest/cases/01687/l3v2/build.log new file mode 100644 index 000000000..e3a3f4880 --- /dev/null +++ b/latest/cases/01687/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01687/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01687/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01687/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01687/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01687/l3v2/index.heta b/latest/cases/01687/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01687/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01687/model-sbml-l3v2.xml b/latest/cases/01687/model-sbml-l3v2.xml new file mode 100644 index 000000000..692a27fa1 --- /dev/null +++ b/latest/cases/01687/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + S1 + 1.83 + + + + + + 2 + + + + + + S1 + + + + + + + diff --git a/latest/cases/01687/synopsis.txt b/latest/cases/01687/synopsis.txt new file mode 100644 index 000000000..dc97ed90f --- /dev/null +++ b/latest/cases/01687/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Model and species conversion factors affecting events with trigger-time assignment. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species that are involved in an event which, after a delay, assigns values of one of the species to the other, based on its trigger-time value. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $S1 <= 1.83$ | $2$ | $S2 = S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01688/l2v5/index.heta b/latest/cases/01688/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01688/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01688/l3v2/build.log b/latest/cases/01688/l3v2/build.log new file mode 100644 index 000000000..087b22ca0 --- /dev/null +++ b/latest/cases/01688/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01688/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01688/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01688/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01688/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01688/l3v2/index.heta b/latest/cases/01688/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01688/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01688/model-sbml-l3v2.xml b/latest/cases/01688/model-sbml-l3v2.xml new file mode 100644 index 000000000..a67f399d6 --- /dev/null +++ b/latest/cases/01688/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + S1 + 1.83 + + + + + + 2 + + + + + + S1 + + + + + + + diff --git a/latest/cases/01688/synopsis.txt b/latest/cases/01688/synopsis.txt new file mode 100644 index 000000000..18f0ebf76 --- /dev/null +++ b/latest/cases/01688/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A species conversion factor affecting events with trigger-time assignment. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species that are involved in an event which, after a delay, assigns values of one of the species to the other, based on its trigger-time value. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $S1 <= 1.83$ | $2$ | $S2 = S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01689/l2v5/index.heta b/latest/cases/01689/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01689/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01689/l3v2/build.log b/latest/cases/01689/l3v2/build.log new file mode 100644 index 000000000..f2660f81b --- /dev/null +++ b/latest/cases/01689/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01689/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01689/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01689/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01689/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01689/l3v2/index.heta b/latest/cases/01689/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01689/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01689/model-sbml-l3v2.xml b/latest/cases/01689/model-sbml-l3v2.xml new file mode 100644 index 000000000..93098bf68 --- /dev/null +++ b/latest/cases/01689/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + S1 + 1.83 + + + + + + 2 + + + + + + S2 + + + + + + + diff --git a/latest/cases/01689/synopsis.txt b/latest/cases/01689/synopsis.txt new file mode 100644 index 000000000..404ea3ed6 --- /dev/null +++ b/latest/cases/01689/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Model and species conversion factors affecting events with trigger-time assignment. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventUsesTriggerTimeValues +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species that are involved in an event which, after a delay, assigns values of one of the species to the other, based on its trigger-time value. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $S1 <= 1.83$ | $2$ | $S1 = S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01690/l2v5/index.heta b/latest/cases/01690/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01690/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01690/l3v2/build.log b/latest/cases/01690/l3v2/build.log new file mode 100644 index 000000000..b3bd3aff9 --- /dev/null +++ b/latest/cases/01690/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01690/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01690/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01690/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01690/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01690/l3v2/index.heta b/latest/cases/01690/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01690/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01690/model-sbml-l3v2.xml b/latest/cases/01690/model-sbml-l3v2.xml new file mode 100644 index 000000000..52ab217ca --- /dev/null +++ b/latest/cases/01690/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + S1 + 1.83 + + + + + + 2 + + + + + + S1 + + + + + + + diff --git a/latest/cases/01690/synopsis.txt b/latest/cases/01690/synopsis.txt new file mode 100644 index 000000000..e72639f91 --- /dev/null +++ b/latest/cases/01690/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Model and species conversion factors affecting events with assignment-time value assignment. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventUsesAssignmentTimeValues +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species that are involved in an event which, after a delay, assigns values of one of the species to the other, based on its assignment-time value. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $S1 <= 1.83$ | Assignment time | $2$ | $S2 = S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01691/l2v5/index.heta b/latest/cases/01691/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01691/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01691/l3v2/build.log b/latest/cases/01691/l3v2/build.log new file mode 100644 index 000000000..cdf4c1e49 --- /dev/null +++ b/latest/cases/01691/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01691/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01691/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01691/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01691/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01691/l3v2/index.heta b/latest/cases/01691/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01691/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01691/model-sbml-l3v2.xml b/latest/cases/01691/model-sbml-l3v2.xml new file mode 100644 index 000000000..b34c33e2d --- /dev/null +++ b/latest/cases/01691/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + S1 + 1.83 + + + + + + 2 + + + + + + S1 + + + + + + + diff --git a/latest/cases/01691/synopsis.txt b/latest/cases/01691/synopsis.txt new file mode 100644 index 000000000..4f7cbe5b5 --- /dev/null +++ b/latest/cases/01691/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A species conversion factor affecting events with assignment-time value assignment. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventUsesAssignmentTimeValues +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor is set for species that are involved in an event which, after a delay, assigns values of one of the species to the other, based on its assignment-time value. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $S1 <= 1.83$ | Assignment time | $2$ | $S2 = S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01692/l2v5/index.heta b/latest/cases/01692/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01692/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01692/l3v2/build.log b/latest/cases/01692/l3v2/build.log new file mode 100644 index 000000000..695c92e1b --- /dev/null +++ b/latest/cases/01692/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01692/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01692/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01692/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01692/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01692/l3v2/index.heta b/latest/cases/01692/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01692/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01692/model-sbml-l3v2.xml b/latest/cases/01692/model-sbml-l3v2.xml new file mode 100644 index 000000000..81da11719 --- /dev/null +++ b/latest/cases/01692/model-sbml-l3v2.xml @@ -0,0 +1,56 @@ + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + + S1 + 1.83 + + + + + + 2 + + + + + + S2 + + + + + + + diff --git a/latest/cases/01692/synopsis.txt b/latest/cases/01692/synopsis.txt new file mode 100644 index 000000000..522d6018e --- /dev/null +++ b/latest/cases/01692/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Model and species conversion factors affecting events with assignment-time value assignment. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, EventUsesAssignmentTimeValues +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set for species that are involved in an event which, after a delay, assigns values of one of the species to the other, based on its assignment-time value. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $S1 <= 1.83$ | Assignment time | $2$ | $S1 = S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01693/l2v5/index.heta b/latest/cases/01693/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01693/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01693/l3v2/heta-code/output.heta b/latest/cases/01693/l3v2/heta-code/output.heta new file mode 100644 index 000000000..485f8e811 --- /dev/null +++ b/latest/cases/01693/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + +getThree #defineFunction { arguments: [], math: 3, }; + +t @TimeScale { }; + +P1 @Record { } .= 1; +P1 [E0]= getThree(); + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01693/l3v2/index.heta b/latest/cases/01693/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01693/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01693/l3v2/json/output.json b/latest/cases/01693/l3v2/json/output.json new file mode 100644 index 000000000..f9bfe245f --- /dev/null +++ b/latest/cases/01693/l3v2/json/output.json @@ -0,0 +1,23 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "1", + "E0": "getThree()" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "P1 > 0.9" + }, + { + "id": "getThree", + "math": "3", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01693/model-sbml-l3v2.xml b/latest/cases/01693/model-sbml-l3v2.xml new file mode 100644 index 000000000..20d359d0f --- /dev/null +++ b/latest/cases/01693/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + 3 + + + + + + + + + + + + + + P1 + 0.9 + + + + + + + + getThree + + + + + + + + diff --git a/latest/cases/01693/output.heta b/latest/cases/01693/output.heta new file mode 100644 index 000000000..d5bb612c3 --- /dev/null +++ b/latest/cases/01693/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: A function definition in an event that fires at t0. +componentTags: EventNoDelay, FunctionDefinition, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the event assignment of an event that fires at t0 uses a function defintion. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = getThree()$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getThree | | $3$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +getThree #defineFunction { arguments: [], math: 3, }; + +t @TimeScale { }; + +P1 @Record { } .= 1; +P1 [E0]= getThree(); + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01693/synopsis.txt b/latest/cases/01693/synopsis.txt new file mode 100644 index 000000000..d424fc9e2 --- /dev/null +++ b/latest/cases/01693/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A function definition in an event that fires at t0. +componentTags: EventNoDelay, FunctionDefinition, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the event assignment of an event that fires at t0 uses a function defintion. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = getThree()$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getThree | | $3$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01694/l2v5/index.heta b/latest/cases/01694/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01694/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01694/l3v2/heta-code/output.heta b/latest/cases/01694/l3v2/heta-code/output.heta new file mode 100644 index 000000000..125ab9e9a --- /dev/null +++ b/latest/cases/01694/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + +getPointNine #defineFunction { arguments: [], math: 0.9, }; + +t @TimeScale { }; + +P1 @Record { } .= 1; +P1 [E0]= 3; + +E0 @DSwitcher { trigger: P1 > getPointNine(), }; + diff --git a/latest/cases/01694/l3v2/index.heta b/latest/cases/01694/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01694/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01694/l3v2/json/output.json b/latest/cases/01694/l3v2/json/output.json new file mode 100644 index 000000000..c03dd00cc --- /dev/null +++ b/latest/cases/01694/l3v2/json/output.json @@ -0,0 +1,23 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "1", + "E0": "3" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "P1 > getPointNine()" + }, + { + "id": "getPointNine", + "math": "0.9", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01694/model-sbml-l3v2.xml b/latest/cases/01694/model-sbml-l3v2.xml new file mode 100644 index 000000000..0a4bea994 --- /dev/null +++ b/latest/cases/01694/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + 0.9 + + + + + + + + + + + + + + P1 + + getPointNine + + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01694/output.heta b/latest/cases/01694/output.heta new file mode 100644 index 000000000..c2b349980 --- /dev/null +++ b/latest/cases/01694/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: A function definition in an event that fires at t0. +componentTags: EventNoDelay, FunctionDefinition, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the trigger of an event that fires at t0 uses a function defintion. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > getPointNine()$ | false | $P1 = 3$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getPointNine | | $0.9$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +getPointNine #defineFunction { arguments: [], math: 0.9, }; + +t @TimeScale { }; + +P1 @Record { } .= 1; +P1 [E0]= 3; + +E0 @DSwitcher { trigger: P1 > getPointNine(), }; + diff --git a/latest/cases/01694/synopsis.txt b/latest/cases/01694/synopsis.txt new file mode 100644 index 000000000..34478d40d --- /dev/null +++ b/latest/cases/01694/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A function definition in an event that fires at t0. +componentTags: EventNoDelay, FunctionDefinition, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the trigger of an event that fires at t0 uses a function defintion. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > getPointNine()$ | false | $P1 = 3$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getPointNine | | $0.9$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01695/l2v5/index.heta b/latest/cases/01695/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01695/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01695/l3v2/build.log b/latest/cases/01695/l3v2/build.log new file mode 100644 index 000000000..9097b1ab0 --- /dev/null +++ b/latest/cases/01695/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01695/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01695/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01695/model-sbml-l3v2.xml"... +[error] Function math "comparePointNine" should be a numeric expression. +[error] DSwitcher trigger "E0" should be a boolean expression. +[info] Setting references in elements, total length 81 +[error] No required "trigger" property for "E0" of DSwitcher. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01695/l3v2/index.heta b/latest/cases/01695/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01695/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01695/model-sbml-l3v2.xml b/latest/cases/01695/model-sbml-l3v2.xml new file mode 100644 index 000000000..a2a6eb122 --- /dev/null +++ b/latest/cases/01695/model-sbml-l3v2.xml @@ -0,0 +1,44 @@ + + + + + + + + + + x + + + + x + 0.9 + + + + + + + + + + + + + + comparePointNine + P1 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01695/synopsis.txt b/latest/cases/01695/synopsis.txt new file mode 100644 index 000000000..354a938ed --- /dev/null +++ b/latest/cases/01695/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A function definition in an event that fires at t0. +componentTags: EventNoDelay, FunctionDefinition, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the trigger of an event that fires at t0 uses a function defintion. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $comparePointNine(P1)$ | false | $P1 = 3$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | comparePointNine | x | $x > 0.9$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01696/l2v5/index.heta b/latest/cases/01696/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01696/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01696/l3v2/heta-code/output.heta b/latest/cases/01696/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5a39c5be4 --- /dev/null +++ b/latest/cases/01696/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + +addTo #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +P1 @Record { } .= 1; +P1 [E0]= addTo(P1, 2); + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01696/l3v2/index.heta b/latest/cases/01696/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01696/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01696/l3v2/json/output.json b/latest/cases/01696/l3v2/json/output.json new file mode 100644 index 000000000..46e671bc2 --- /dev/null +++ b/latest/cases/01696/l3v2/json/output.json @@ -0,0 +1,27 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "1", + "E0": "addTo(P1, 2)" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "P1 > 0.9" + }, + { + "id": "addTo", + "arguments": [ + "x", + "y" + ], + "math": "x + y", + "action": "defineFunction" + } +] \ No newline at end of file diff --git a/latest/cases/01696/model-sbml-l3v2.xml b/latest/cases/01696/model-sbml-l3v2.xml new file mode 100644 index 000000000..0a8b5e31f --- /dev/null +++ b/latest/cases/01696/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + + + + P1 + 0.9 + + + + + + + + addTo + P1 + 2 + + + + + + + + diff --git a/latest/cases/01696/output.heta b/latest/cases/01696/output.heta new file mode 100644 index 000000000..35dc4c3cf --- /dev/null +++ b/latest/cases/01696/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: A function definition in an event that fires at t0. +componentTags: EventNoDelay, FunctionDefinition, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the assignment of an event that fires at t0 uses a function defintion. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = addTo(P1, 2)$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addTo | x, y | $x + y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +addTo #defineFunction { arguments: [x, y], math: x + y, }; + +t @TimeScale { }; + +P1 @Record { } .= 1; +P1 [E0]= addTo(P1, 2); + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01696/synopsis.txt b/latest/cases/01696/synopsis.txt new file mode 100644 index 000000000..3800afae6 --- /dev/null +++ b/latest/cases/01696/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A function definition in an event that fires at t0. +componentTags: EventNoDelay, FunctionDefinition, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the assignment of an event that fires at t0 uses a function defintion. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = addTo(P1, 2)$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addTo | x, y | $x + y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01697/l2v5/index.heta b/latest/cases/01697/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01697/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01697/l3v2/heta-code/output.heta b/latest/cases/01697/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c5a3f612d --- /dev/null +++ b/latest/cases/01697/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +P1 @Record { } .= 1; +P1 [E0]= P1 + 2; + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01697/l3v2/index.heta b/latest/cases/01697/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01697/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01697/l3v2/json/output.json b/latest/cases/01697/l3v2/json/output.json new file mode 100644 index 000000000..f5ac877db --- /dev/null +++ b/latest/cases/01697/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "1", + "E0": "P1 + 2" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "P1 > 0.9" + } +] \ No newline at end of file diff --git a/latest/cases/01697/model-sbml-l3v2.xml b/latest/cases/01697/model-sbml-l3v2.xml new file mode 100644 index 000000000..af07d6123 --- /dev/null +++ b/latest/cases/01697/model-sbml-l3v2.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + P1 + 0.9 + + + + + + + + + P1 + 2 + + + + + + + + diff --git a/latest/cases/01697/output.heta b/latest/cases/01697/output.heta new file mode 100644 index 000000000..da2d456e6 --- /dev/null +++ b/latest/cases/01697/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: An event that fires at t0 that uses a parameter in its own assignment. +componentTags: EventNoDelay, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event that fires at t0 uses a parameter in its own assignment. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P1 @Record { } .= 1; +P1 [E0]= P1 + 2; + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01697/synopsis.txt b/latest/cases/01697/synopsis.txt new file mode 100644 index 000000000..698c5ec53 --- /dev/null +++ b/latest/cases/01697/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event that fires at t0 that uses a parameter in its own assignment. +componentTags: EventNoDelay, Parameter +testTags: EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event that fires at t0 uses a parameter in its own assignment. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01698/l2v5/index.heta b/latest/cases/01698/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01698/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01698/l3v2/heta-code/output.heta b/latest/cases/01698/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1fd0d2b71 --- /dev/null +++ b/latest/cases/01698/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +P1 @Record { } .= 2; +P1 [E0]= P1 + 2; + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01698/l3v2/index.heta b/latest/cases/01698/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01698/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01698/l3v2/json/output.json b/latest/cases/01698/l3v2/json/output.json new file mode 100644 index 000000000..43e3ca328 --- /dev/null +++ b/latest/cases/01698/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "2", + "E0": "P1 + 2" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "P1 > 0.9" + } +] \ No newline at end of file diff --git a/latest/cases/01698/model-sbml-l3v2.xml b/latest/cases/01698/model-sbml-l3v2.xml new file mode 100644 index 000000000..8c53fac9d --- /dev/null +++ b/latest/cases/01698/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + 2 + + + + + + + + + + P1 + 0.9 + + + + + + + + + P1 + 2 + + + + + + + + diff --git a/latest/cases/01698/output.heta b/latest/cases/01698/output.heta new file mode 100644 index 000000000..14512f8b4 --- /dev/null +++ b/latest/cases/01698/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: An event that fires at t0 that uses a parameter in its own assignment. +componentTags: EventNoDelay, InitialAssignment, Parameter +testTags: EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event that fires at t0 uses a parameter in its own assignment. Also, its 'value' attribute would not trigger the event, but its initial assignment will. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P1 @Record { } .= 2; +P1 [E0]= P1 + 2; + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01698/synopsis.txt b/latest/cases/01698/synopsis.txt new file mode 100644 index 000000000..3f20c705d --- /dev/null +++ b/latest/cases/01698/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event that fires at t0 that uses a parameter in its own assignment. +componentTags: EventNoDelay, InitialAssignment, Parameter +testTags: EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event that fires at t0 uses a parameter in its own assignment. Also, its 'value' attribute would not trigger the event, but its initial assignment will. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01699/l2v5/index.heta b/latest/cases/01699/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01699/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01699/l3v2/heta-code/output.heta b/latest/cases/01699/l3v2/heta-code/output.heta new file mode 100644 index 000000000..1fd0d2b71 --- /dev/null +++ b/latest/cases/01699/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +P1 @Record { } .= 2; +P1 [E0]= P1 + 2; + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01699/l3v2/index.heta b/latest/cases/01699/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01699/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01699/l3v2/json/output.json b/latest/cases/01699/l3v2/json/output.json new file mode 100644 index 000000000..43e3ca328 --- /dev/null +++ b/latest/cases/01699/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "2", + "E0": "P1 + 2" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "P1 > 0.9" + } +] \ No newline at end of file diff --git a/latest/cases/01699/model-sbml-l3v2.xml b/latest/cases/01699/model-sbml-l3v2.xml new file mode 100644 index 000000000..a511bd595 --- /dev/null +++ b/latest/cases/01699/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + 2 + + + + + + + + + + P1 + 0.9 + + + + + + + + + P1 + 2 + + + + + + + + diff --git a/latest/cases/01699/output.heta b/latest/cases/01699/output.heta new file mode 100644 index 000000000..84b177b6b --- /dev/null +++ b/latest/cases/01699/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: An event that fires at t0 that uses a parameter in its own assignment. +componentTags: EventNoDelay, InitialAssignment, Parameter +testTags: EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event that fires at t0 uses a parameter in its own assignment. Also, its 'value' attribute and its initial assignment will trigger the event, but both are different values. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P1 @Record { } .= 2; +P1 [E0]= P1 + 2; + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01699/synopsis.txt b/latest/cases/01699/synopsis.txt new file mode 100644 index 000000000..4d20b8f44 --- /dev/null +++ b/latest/cases/01699/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event that fires at t0 that uses a parameter in its own assignment. +componentTags: EventNoDelay, InitialAssignment, Parameter +testTags: EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event that fires at t0 uses a parameter in its own assignment. Also, its 'value' attribute and its initial assignment will trigger the event, but both are different values. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01700/l2v5/index.heta b/latest/cases/01700/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01700/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01700/l3v2/heta-code/output.heta b/latest/cases/01700/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6df3a451b --- /dev/null +++ b/latest/cases/01700/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +P1 @Record { } .= 0; +P1 [E0]= P1 + 2; + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01700/l3v2/index.heta b/latest/cases/01700/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01700/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01700/l3v2/json/output.json b/latest/cases/01700/l3v2/json/output.json new file mode 100644 index 000000000..2f7d72c00 --- /dev/null +++ b/latest/cases/01700/l3v2/json/output.json @@ -0,0 +1,18 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "P1", + "assignments": { + "start_": "0", + "E0": "P1 + 2" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "P1 > 0.9" + } +] \ No newline at end of file diff --git a/latest/cases/01700/model-sbml-l3v2.xml b/latest/cases/01700/model-sbml-l3v2.xml new file mode 100644 index 000000000..ff25d2dcc --- /dev/null +++ b/latest/cases/01700/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + 0 + + + + + + + + + + P1 + 0.9 + + + + + + + + + P1 + 2 + + + + + + + + diff --git a/latest/cases/01700/output.heta b/latest/cases/01700/output.heta new file mode 100644 index 000000000..b5fb88398 --- /dev/null +++ b/latest/cases/01700/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: An event that fires at t0 that uses a parameter in its own assignment. +componentTags: EventNoDelay, InitialAssignment, Parameter +testTags: EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event that would fire at t0, and use a parameter in its own assignment. However, though its 'value' attribute would trigger the event, its initial assignment will not, meaning the event should not be triggered. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +P1 @Record { } .= 0; +P1 [E0]= P1 + 2; + +E0 @DSwitcher { trigger: P1 > 0.9, }; + diff --git a/latest/cases/01700/synopsis.txt b/latest/cases/01700/synopsis.txt new file mode 100644 index 000000000..113c7bd91 --- /dev/null +++ b/latest/cases/01700/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An event that fires at t0 that uses a parameter in its own assignment. +componentTags: EventNoDelay, InitialAssignment, Parameter +testTags: EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event that would fire at t0, and use a parameter in its own assignment. However, though its 'value' attribute would trigger the event, its initial assignment will not, meaning the event should not be triggered. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01701/l2v5/build.log b/latest/cases/01701/l2v5/build.log new file mode 100644 index 000000000..c88709917 --- /dev/null +++ b/latest/cases/01701/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01701/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01701/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01701/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01701/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01701/l2v5/index.heta b/latest/cases/01701/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01701/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01701/l3v2/build.log b/latest/cases/01701/l3v2/build.log new file mode 100644 index 000000000..ab386e9f7 --- /dev/null +++ b/latest/cases/01701/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01701/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01701/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01701/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01701/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01701/l3v2/index.heta b/latest/cases/01701/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01701/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01701/model-sbml-l2v5.xml b/latest/cases/01701/model-sbml-l2v5.xml new file mode 100644 index 000000000..1fcdd6932 --- /dev/null +++ b/latest/cases/01701/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + -1 + + + + + + + + + + P1 + 8.9 + + + + + + 2 + + + + + + + addEm + P1 + 3 + + + + + + + + diff --git a/latest/cases/01701/model-sbml-l3v2.xml b/latest/cases/01701/model-sbml-l3v2.xml new file mode 100644 index 000000000..89b940fe6 --- /dev/null +++ b/latest/cases/01701/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + -1 + + + + + + + + + + P1 + 8.9 + + + + + + 2 + + + + + + + addEm + P1 + 3 + + + + + + + + diff --git a/latest/cases/01701/synopsis.txt b/latest/cases/01701/synopsis.txt new file mode 100644 index 000000000..7aeb87528 --- /dev/null +++ b/latest/cases/01701/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A trigger-time event with a function definition. +componentTags: EventWithDelay, FunctionDefinition, Parameter, RateRule +testTags: EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event uses the trigger-time value of its parameters in a function definition. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $P1 <= 8.9$ | $2$ | $P1 = addEm(P1, 3)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $-1$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addEm | x, y | $x + y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01702/l2v5/build.log b/latest/cases/01702/l2v5/build.log new file mode 100644 index 000000000..789669250 --- /dev/null +++ b/latest/cases/01702/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01702/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01702/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01702/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01702/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01702/l2v5/index.heta b/latest/cases/01702/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01702/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01702/l3v2/build.log b/latest/cases/01702/l3v2/build.log new file mode 100644 index 000000000..4ae89d072 --- /dev/null +++ b/latest/cases/01702/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01702/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01702/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01702/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01702/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01702/l3v2/index.heta b/latest/cases/01702/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01702/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01702/model-sbml-l2v5.xml b/latest/cases/01702/model-sbml-l2v5.xml new file mode 100644 index 000000000..928fb11b2 --- /dev/null +++ b/latest/cases/01702/model-sbml-l2v5.xml @@ -0,0 +1,63 @@ + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + -1 + + + + + + + + + + P1 + 8.9 + + + + + + 2 + + + + + + + addEm + P1 + 3 + + + + + + + + diff --git a/latest/cases/01702/model-sbml-l3v2.xml b/latest/cases/01702/model-sbml-l3v2.xml new file mode 100644 index 000000000..b8106f981 --- /dev/null +++ b/latest/cases/01702/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + x + + + y + + + + x + y + + + + + + + + + + + + -1 + + + + + + + + + + P1 + 8.9 + + + + + + 2 + + + + + + + addEm + P1 + 3 + + + + + + + + diff --git a/latest/cases/01702/synopsis.txt b/latest/cases/01702/synopsis.txt new file mode 100644 index 000000000..688eac26f --- /dev/null +++ b/latest/cases/01702/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: An assignment-time event with a function definition. +componentTags: EventWithDelay, FunctionDefinition, Parameter, RateRule +testTags: EventUsesAssignmentTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event uses the assignment-time value of its parameters in a function definition. + +The model contains: +* 1 parameter (P1) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $P1 <= 8.9$ | Assignment time | $2$ | $P1 = addEm(P1, 3)$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $-1$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | addEm | x, y | $x + y$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01703/l2v5/build.log b/latest/cases/01703/l2v5/build.log new file mode 100644 index 000000000..786aa2a31 --- /dev/null +++ b/latest/cases/01703/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01703/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01703/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01703/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01703/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01703/l2v5/index.heta b/latest/cases/01703/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01703/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01703/l3v2/build.log b/latest/cases/01703/l3v2/build.log new file mode 100644 index 000000000..ebad50635 --- /dev/null +++ b/latest/cases/01703/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01703/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01703/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01703/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01703/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01703/l3v2/index.heta b/latest/cases/01703/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01703/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01703/model-sbml-l2v5.xml b/latest/cases/01703/model-sbml-l2v5.xml new file mode 100644 index 000000000..4c288a1b9 --- /dev/null +++ b/latest/cases/01703/model-sbml-l2v5.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + -1 + + + + + + + + + + + + S1 + 4.3 + + + + S1 + 3 + + + + + + + 2 + + + + + + 10 + + + + + + + diff --git a/latest/cases/01703/model-sbml-l3v2.xml b/latest/cases/01703/model-sbml-l3v2.xml new file mode 100644 index 000000000..7835c1b21 --- /dev/null +++ b/latest/cases/01703/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + -1 + + + + + + + + + + + + S1 + 4.3 + + + + S1 + 3 + + + + + + + 2 + + + + + + 10 + + + + + + + diff --git a/latest/cases/01703/synopsis.txt b/latest/cases/01703/synopsis.txt new file mode 100644 index 000000000..7ad866453 --- /dev/null +++ b/latest/cases/01703/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A persistent event involving a substance-only species. +componentTags: Compartment, EventWithDelay, RateRule, Species +testTags: Amount, EventIsPersistent, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event is triggered by a substance-only species entering a window of values which will be different if the species is mis-interpreted in that section as a concentration. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $(S1 <= 4.3) && (S1 >= 3)$ | $2$ | $S1 = 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01704/l2v5/index.heta b/latest/cases/01704/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01704/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01704/l3v2/build.log b/latest/cases/01704/l3v2/build.log new file mode 100644 index 000000000..412db027e --- /dev/null +++ b/latest/cases/01704/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01704/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01704/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01704/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01704/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01704/l3v2/index.heta b/latest/cases/01704/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01704/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01704/model-sbml-l3v2.xml b/latest/cases/01704/model-sbml-l3v2.xml new file mode 100644 index 000000000..e3c0cc188 --- /dev/null +++ b/latest/cases/01704/model-sbml-l3v2.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + -1 + + + + + + + + + + + + S1 + 4.3 + + + + S1 + 3 + + + + + + + 2 + + + + + + 10 + + + + + + + diff --git a/latest/cases/01704/synopsis.txt b/latest/cases/01704/synopsis.txt new file mode 100644 index 000000000..efc3afddd --- /dev/null +++ b/latest/cases/01704/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A non-persistent event involving a substance-only species. +componentTags: Compartment, EventWithDelay, RateRule, Species +testTags: Amount, EventIsNotPersistent, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event is triggered by a substance-only species entering a window of values which will be different if the species is mis-interpreted in that section as a concentration. The event is not persistent, so when the trigger reverts to 'false' before being executed, the execution is cancelled. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one event: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $(S1 <= 4.3) && (S1 >= 3)$ | false | Assignment time | $2$ | $S1 = 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01705/l2v5/index.heta b/latest/cases/01705/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01705/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01705/l3v2/heta-code/output.heta b/latest/cases/01705/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0a14d225a --- /dev/null +++ b/latest/cases/01705/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 10; +S1 [E0]= 5; +S1 [E1]= 10; + +S1_proc @Process { actors: = S1, }; +S1_proc := (-1); + +E0 @DSwitcher { trigger: t >= 2.5, }; +E1 @DSwitcher { trigger: t >= 2.5, }; + diff --git a/latest/cases/01705/l3v2/index.heta b/latest/cases/01705/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01705/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01705/l3v2/json/output.json b/latest/cases/01705/l3v2/json/output.json new file mode 100644 index 000000000..4dff23c05 --- /dev/null +++ b/latest/cases/01705/l3v2/json/output.json @@ -0,0 +1,47 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "10", + "E0": "5", + "E1": "10" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Process", + "id": "S1_proc", + "assignments": { + "ode_": "(-1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 2.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t >= 2.5" + } +] \ No newline at end of file diff --git a/latest/cases/01705/model-sbml-l3v2.xml b/latest/cases/01705/model-sbml-l3v2.xml new file mode 100644 index 000000000..b144b3fb5 --- /dev/null +++ b/latest/cases/01705/model-sbml-l3v2.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + -1 + + + + + + + + + + time + 2.5 + + + + + + S1 + + + + + + 5 + + + + + + + + + + time + 2.5 + + + + + + 7.4 + + + + + + 10 + + + + + + + diff --git a/latest/cases/01705/output.heta b/latest/cases/01705/output.heta new file mode 100644 index 000000000..d1190824b --- /dev/null +++ b/latest/cases/01705/output.heta @@ -0,0 +1,55 @@ +/* +category: Test +synopsis: Two simultaneous events whose priorities involve a substance-only species. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two simultaneous events have similar priorities, with one being greater than the other because of the actual value of the substance-only speces. If misinterpreted, the two events will fire in the wrong order.. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time >= 2.5$ | $S1$ | $S1 = 5$ | +| E1 | $time >= 2.5$ | $7.4$ | $S1 = 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 10; +S1 [E0]= 5; +S1 [E1]= 10; + +S1_proc @Process { actors: = S1, }; +S1_proc := (-1); + +E0 @DSwitcher { trigger: t >= 2.5, }; +E1 @DSwitcher { trigger: t >= 2.5, }; + diff --git a/latest/cases/01705/synopsis.txt b/latest/cases/01705/synopsis.txt new file mode 100644 index 000000000..18e385540 --- /dev/null +++ b/latest/cases/01705/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Two simultaneous events whose priorities involve a substance-only species. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, RateRule, Species +testTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two simultaneous events have similar priorities, with one being greater than the other because of the actual value of the substance-only speces. If misinterpreted, the two events will fire in the wrong order.. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time >= 2.5$ | $S1$ | $S1 = 5$ | +| E1 | $time >= 2.5$ | $7.4$ | $S1 = 10$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01706/l2v5/build.log b/latest/cases/01706/l2v5/build.log new file mode 100644 index 000000000..501b56a32 --- /dev/null +++ b/latest/cases/01706/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01706/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01706/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01706/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01706/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01706/l2v5/index.heta b/latest/cases/01706/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01706/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01706/l3v2/build.log b/latest/cases/01706/l3v2/build.log new file mode 100644 index 000000000..f73d2628a --- /dev/null +++ b/latest/cases/01706/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01706/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01706/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01706/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01706/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01706/l3v2/index.heta b/latest/cases/01706/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01706/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01706/model-sbml-l2v5.xml b/latest/cases/01706/model-sbml-l2v5.xml new file mode 100644 index 000000000..f17cc56b7 --- /dev/null +++ b/latest/cases/01706/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + -1 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + + + S1 + 1 + + + + + + + + diff --git a/latest/cases/01706/model-sbml-l3v2.xml b/latest/cases/01706/model-sbml-l3v2.xml new file mode 100644 index 000000000..d0437f936 --- /dev/null +++ b/latest/cases/01706/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + -1 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + + + S1 + 1 + + + + + + + + diff --git a/latest/cases/01706/synopsis.txt b/latest/cases/01706/synopsis.txt new file mode 100644 index 000000000..73cf5b991 --- /dev/null +++ b/latest/cases/01706/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: An event assignment using the trigger-time value of a substance-only species. +componentTags: CSymbolTime, Compartment, EventWithDelay, RateRule, Species +testTags: Amount, EventUsesTriggerTimeValues, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event assignment uses the ID of a substance-only speces, using the value from when the trigger time. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E1 | $time >= 2.5$ | $2$ | $S1 = S1 + 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01707/l2v5/build.log b/latest/cases/01707/l2v5/build.log new file mode 100644 index 000000000..80c87b1b0 --- /dev/null +++ b/latest/cases/01707/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01707/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01707/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01707/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01707/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01707/l2v5/index.heta b/latest/cases/01707/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01707/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01707/l3v2/build.log b/latest/cases/01707/l3v2/build.log new file mode 100644 index 000000000..41ad7e107 --- /dev/null +++ b/latest/cases/01707/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01707/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01707/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01707/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01707/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01707/l3v2/index.heta b/latest/cases/01707/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01707/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01707/model-sbml-l2v5.xml b/latest/cases/01707/model-sbml-l2v5.xml new file mode 100644 index 000000000..2ba24005c --- /dev/null +++ b/latest/cases/01707/model-sbml-l2v5.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + -1 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + + + S1 + 1 + + + + + + + + diff --git a/latest/cases/01707/model-sbml-l3v2.xml b/latest/cases/01707/model-sbml-l3v2.xml new file mode 100644 index 000000000..bd285ee6f --- /dev/null +++ b/latest/cases/01707/model-sbml-l3v2.xml @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + -1 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + + + S1 + 1 + + + + + + + + diff --git a/latest/cases/01707/synopsis.txt b/latest/cases/01707/synopsis.txt new file mode 100644 index 000000000..d537a26ce --- /dev/null +++ b/latest/cases/01707/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: An event assignment using the assignment-time value of a substance-only species. +componentTags: CSymbolTime, Compartment, EventWithDelay, RateRule, Species +testTags: Amount, EventUsesAssignmentTimeValues, HasOnlySubstanceUnits, NonUnityCompartment +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event assignment uses the ID of a substance-only speces, using the value from the assignment time. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E1 | $time >= 2.5$ | Assignment time | $2$ | $S1 = S1 + 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01708/l2v5/build.log b/latest/cases/01708/l2v5/build.log new file mode 100644 index 000000000..98ffecf89 --- /dev/null +++ b/latest/cases/01708/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01708/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01708/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01708/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01708/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01708/l2v5/index.heta b/latest/cases/01708/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01708/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01708/l3v2/build.log b/latest/cases/01708/l3v2/build.log new file mode 100644 index 000000000..bce441e58 --- /dev/null +++ b/latest/cases/01708/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01708/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01708/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01708/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01708/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01708/l3v2/index.heta b/latest/cases/01708/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01708/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01708/model-sbml-l2v5.xml b/latest/cases/01708/model-sbml-l2v5.xml new file mode 100644 index 000000000..afdd464c1 --- /dev/null +++ b/latest/cases/01708/model-sbml-l2v5.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + -1 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + + + S1 + 1 + + + + + + + + diff --git a/latest/cases/01708/model-sbml-l3v2.xml b/latest/cases/01708/model-sbml-l3v2.xml new file mode 100644 index 000000000..2e005ee47 --- /dev/null +++ b/latest/cases/01708/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + -1 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + + + S1 + 1 + + + + + + + + diff --git a/latest/cases/01708/synopsis.txt b/latest/cases/01708/synopsis.txt new file mode 100644 index 000000000..0638ec179 --- /dev/null +++ b/latest/cases/01708/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: An event assignment using the trigger-time value of a substance-only species. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, RateRule, Species +testTags: Amount, EventUsesTriggerTimeValues, HasOnlySubstanceUnits, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event assignment uses the ID of a substance-only speces, using the value from when the trigger time. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 compartment (C) + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E1 | $time >= 2.5$ | $2$ | $P1 = S1 + 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01709/l2v5/build.log b/latest/cases/01709/l2v5/build.log new file mode 100644 index 000000000..3497d5c78 --- /dev/null +++ b/latest/cases/01709/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01709/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01709/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01709/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01709/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01709/l2v5/index.heta b/latest/cases/01709/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01709/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01709/l3v2/build.log b/latest/cases/01709/l3v2/build.log new file mode 100644 index 000000000..d2284c28f --- /dev/null +++ b/latest/cases/01709/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01709/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01709/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01709/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01709/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01709/l3v2/index.heta b/latest/cases/01709/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01709/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01709/model-sbml-l2v5.xml b/latest/cases/01709/model-sbml-l2v5.xml new file mode 100644 index 000000000..59c5e382f --- /dev/null +++ b/latest/cases/01709/model-sbml-l2v5.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + -1 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + + + S1 + 1 + + + + + + + + diff --git a/latest/cases/01709/model-sbml-l3v2.xml b/latest/cases/01709/model-sbml-l3v2.xml new file mode 100644 index 000000000..eed42f92e --- /dev/null +++ b/latest/cases/01709/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + -1 + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + + + S1 + 1 + + + + + + + + diff --git a/latest/cases/01709/synopsis.txt b/latest/cases/01709/synopsis.txt new file mode 100644 index 000000000..97c013981 --- /dev/null +++ b/latest/cases/01709/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: An event assignment using the assignment-time value of a substance-only species. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, RateRule, Species +testTags: Amount, EventUsesAssignmentTimeValues, HasOnlySubstanceUnits, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event assignment uses the ID of a substance-only speces, using the value from the assignment time. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 compartment (C) + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E1 | $time >= 2.5$ | Assignment time | $2$ | $P1 = S1 + 1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1 | $-1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $10$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01710/l2v5/build.log b/latest/cases/01710/l2v5/build.log new file mode 100644 index 000000000..ed1ae4897 --- /dev/null +++ b/latest/cases/01710/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01710/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01710/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01710/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01710/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01710/l2v5/index.heta b/latest/cases/01710/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01710/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01710/l3v2/build.log b/latest/cases/01710/l3v2/build.log new file mode 100644 index 000000000..101156e8b --- /dev/null +++ b/latest/cases/01710/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01710/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01710/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01710/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01710/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01710/l3v2/index.heta b/latest/cases/01710/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01710/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01710/model-sbml-l2v5.xml b/latest/cases/01710/model-sbml-l2v5.xml new file mode 100644 index 000000000..2c7d5c0da --- /dev/null +++ b/latest/cases/01710/model-sbml-l2v5.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + k1 + + + + + + + + + + + + + + + + k1 + 2.25 + + + + k1 + 3.5 + + + + + + + 2 + + + + + + 0 + + + + + + + diff --git a/latest/cases/01710/model-sbml-l3v2.xml b/latest/cases/01710/model-sbml-l3v2.xml new file mode 100644 index 000000000..41492bdfc --- /dev/null +++ b/latest/cases/01710/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + k1 + + + + + + + + + + + + + + + + k1 + 2.25 + + + + k1 + 3.5 + + + + + + + 2 + + + + + + 0 + + + + + + + diff --git a/latest/cases/01710/synopsis.txt b/latest/cases/01710/synopsis.txt new file mode 100644 index 000000000..805561821 --- /dev/null +++ b/latest/cases/01710/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A persistent event that uses a parameter with the same ID as a local parameter. +componentTags: Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, EventIsPersistent, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses a parameter whose ID is shadowed by a local parameter in an unrelated reaction. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E1 | $(k1 >= 2.25) && (k1 <= 3.5)$ | $2$ | $k1 = 0$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $0$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01711/l2v5/index.heta b/latest/cases/01711/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01711/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01711/l3v2/build.log b/latest/cases/01711/l3v2/build.log new file mode 100644 index 000000000..95605e694 --- /dev/null +++ b/latest/cases/01711/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01711/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01711/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01711/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01711/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01711/l3v2/index.heta b/latest/cases/01711/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01711/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01711/model-sbml-l3v2.xml b/latest/cases/01711/model-sbml-l3v2.xml new file mode 100644 index 000000000..b20dbb963 --- /dev/null +++ b/latest/cases/01711/model-sbml-l3v2.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + k1 + + + + + + + + + + + + + + + + k1 + 2.25 + + + + k1 + 3.5 + + + + + + + 2 + + + + + + 0 + + + + + + + diff --git a/latest/cases/01711/synopsis.txt b/latest/cases/01711/synopsis.txt new file mode 100644 index 000000000..6a069b18d --- /dev/null +++ b/latest/cases/01711/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A non-persistent event that uses a parameter with the same ID as a local parameter. +componentTags: Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, EventIsNotPersistent, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event uses a parameter whose ID is shadowed by a local parameter in an unrelated reaction. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E1 | $(k1 >= 2.25) && (k1 <= 3.5)$ | false | $2$ | $k1 = 0$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $0$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01712/l2v5/index.heta b/latest/cases/01712/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01712/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01712/l3v2/build.log b/latest/cases/01712/l3v2/build.log new file mode 100644 index 000000000..74f17371f --- /dev/null +++ b/latest/cases/01712/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01712/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01712/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01712/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01712/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01712/l3v2/index.heta b/latest/cases/01712/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01712/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01712/model-sbml-l3v2.xml b/latest/cases/01712/model-sbml-l3v2.xml new file mode 100644 index 000000000..a5a38846f --- /dev/null +++ b/latest/cases/01712/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + + + + k1 + 2.25 + + + + + + 2 + + + + + + 2 + + + + + + + diff --git a/latest/cases/01712/synopsis.txt b/latest/cases/01712/synopsis.txt new file mode 100644 index 000000000..a85dd9fdc --- /dev/null +++ b/latest/cases/01712/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: An event triggered at t0 that uses a parameter with the same ID as a local parameter. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, EventT0Firing, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event would be triggered at t0 if it was testing the local parameter instead of the global parameter. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Delay* | *Event Assignments* | +| E1 | $k1 >= 2.25$ | false | $2$ | $k1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01713/l2v5/index.heta b/latest/cases/01713/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01713/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01713/l3v2/build.log b/latest/cases/01713/l3v2/build.log new file mode 100644 index 000000000..948da421e --- /dev/null +++ b/latest/cases/01713/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01713/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01713/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01713/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01713/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01713/l3v2/index.heta b/latest/cases/01713/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01713/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01713/model-sbml-l3v2.xml b/latest/cases/01713/model-sbml-l3v2.xml new file mode 100644 index 000000000..dbf4f5caa --- /dev/null +++ b/latest/cases/01713/model-sbml-l3v2.xml @@ -0,0 +1,55 @@ + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + + + + k1 + 2.25 + + + + + + 2.3 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01713/synopsis.txt b/latest/cases/01713/synopsis.txt new file mode 100644 index 000000000..e841838dd --- /dev/null +++ b/latest/cases/01713/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: An event triggered at t0 that uses a parameter with the same ID as a local parameter. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, EventT0Firing, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, an event would not be triggered at t0 if it was testing the local parameter instead of the global parameter. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Delay* | *Event Assignments* | +| E1 | $k1 <= 2.25$ | false | $2.3$ | $k1 = 3$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $0$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01714/l2v5/index.heta b/latest/cases/01714/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01714/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01714/l3v2/heta-code/output.heta b/latest/cases/01714/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0c9bbd3c5 --- /dev/null +++ b/latest/cases/01714/l3v2/heta-code/output.heta @@ -0,0 +1,20 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1__J0_local; + +k1 @Record { } .= 2; +k1 [E0]= 5; +k1 [E1]= 10; + +k1__J0_local @Const { } = 3; + +E0 @DSwitcher { trigger: t > 2.5, }; +E1 @DSwitcher { trigger: t > 2.5, }; + diff --git a/latest/cases/01714/l3v2/index.heta b/latest/cases/01714/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01714/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01714/l3v2/json/output.json b/latest/cases/01714/l3v2/json/output.json new file mode 100644 index 000000000..6dbc973ee --- /dev/null +++ b/latest/cases/01714/l3v2/json/output.json @@ -0,0 +1,58 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "k1__J0_local", + "num": 3 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "k1__J0_local" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k1", + "assignments": { + "start_": "2", + "E0": "5", + "E1": "10" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t > 2.5" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "t > 2.5" + } +] \ No newline at end of file diff --git a/latest/cases/01714/model-sbml-l3v2.xml b/latest/cases/01714/model-sbml-l3v2.xml new file mode 100644 index 000000000..a669ab804 --- /dev/null +++ b/latest/cases/01714/model-sbml-l3v2.xml @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + + + + + + + + time + 2.5 + + + + + + k1 + + + + + + 5 + + + + + + + + + + time + 2.5 + + + + + + 2.5 + + + + + + 10 + + + + + + + diff --git a/latest/cases/01714/output.heta b/latest/cases/01714/output.heta new file mode 100644 index 000000000..8772fef71 --- /dev/null +++ b/latest/cases/01714/output.heta @@ -0,0 +1,63 @@ +/* +category: Test +synopsis: Two simultaneous events with a priority with the same ID as a local parameter. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the two simultaneous events fire in one order because of the priorities, but would fire in the wrong order if a local parameter was confused for the global parameter. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 2.5$ | $k1$ | $k1 = 5$ | +| E1 | $time > 2.5$ | $2.5$ | $k1 = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $2$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := k1__J0_local; + +k1 @Record { } .= 2; +k1 [E0]= 5; +k1 [E1]= 10; + +k1__J0_local @Const { } = 3; + +E0 @DSwitcher { trigger: t > 2.5, }; +E1 @DSwitcher { trigger: t > 2.5, }; + diff --git a/latest/cases/01714/synopsis.txt b/latest/cases/01714/synopsis.txt new file mode 100644 index 000000000..e38697a5b --- /dev/null +++ b/latest/cases/01714/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: Two simultaneous events with a priority with the same ID as a local parameter. +componentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the two simultaneous events fire in one order because of the priorities, but would fire in the wrong order if a local parameter was confused for the global parameter. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $time > 2.5$ | $k1$ | $k1 = 5$ | +| E1 | $time > 2.5$ | $2.5$ | $k1 = 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $2$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01715/l2v5/build.log b/latest/cases/01715/l2v5/build.log new file mode 100644 index 000000000..ae0c85003 --- /dev/null +++ b/latest/cases/01715/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01715/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01715/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01715/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01715/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01715/l2v5/index.heta b/latest/cases/01715/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01715/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01715/l3v2/build.log b/latest/cases/01715/l3v2/build.log new file mode 100644 index 000000000..a3e1397a7 --- /dev/null +++ b/latest/cases/01715/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01715/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01715/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01715/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01715/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01715/l3v2/index.heta b/latest/cases/01715/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01715/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01715/model-sbml-l2v5.xml b/latest/cases/01715/model-sbml-l2v5.xml new file mode 100644 index 000000000..79c5cbcd8 --- /dev/null +++ b/latest/cases/01715/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + k1 + + + + + + + + + + + + + + k1 + 2.3 + + + + + + 2 + + + + + + + + S1 + k1 + + + + + + + + diff --git a/latest/cases/01715/model-sbml-l3v2.xml b/latest/cases/01715/model-sbml-l3v2.xml new file mode 100644 index 000000000..8b83e17d0 --- /dev/null +++ b/latest/cases/01715/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + k1 + + + + + + + + + + + + + + k1 + 2.3 + + + + + + 2 + + + + + + + + S1 + k1 + + + + + + + + diff --git a/latest/cases/01715/synopsis.txt b/latest/cases/01715/synopsis.txt new file mode 100644 index 000000000..0abc18d5e --- /dev/null +++ b/latest/cases/01715/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: An event using trigger-time variables that are shadowed by a local parameter. +componentTags: Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, EventUsesTriggerTimeValues, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event uses trigger-time values of a parameter that is shadowed by a local parameter. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E1 | $k1 >= 2.3$ | $2$ | $k1 = S1 + k1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $2$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01716/l2v5/build.log b/latest/cases/01716/l2v5/build.log new file mode 100644 index 000000000..d5f568cba --- /dev/null +++ b/latest/cases/01716/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01716/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01716/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01716/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01716/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01716/l2v5/index.heta b/latest/cases/01716/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01716/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01716/l3v2/build.log b/latest/cases/01716/l3v2/build.log new file mode 100644 index 000000000..03bbbff71 --- /dev/null +++ b/latest/cases/01716/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01716/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01716/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01716/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01716/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01716/l3v2/index.heta b/latest/cases/01716/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01716/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01716/model-sbml-l2v5.xml b/latest/cases/01716/model-sbml-l2v5.xml new file mode 100644 index 000000000..7831f615a --- /dev/null +++ b/latest/cases/01716/model-sbml-l2v5.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + k1 + + + + + + + + + + + + + + k1 + 2.3 + + + + + + 2 + + + + + + + + S1 + k1 + + + + + + + + diff --git a/latest/cases/01716/model-sbml-l3v2.xml b/latest/cases/01716/model-sbml-l3v2.xml new file mode 100644 index 000000000..2093ba8e7 --- /dev/null +++ b/latest/cases/01716/model-sbml-l3v2.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + k1 + + + + + + + + + + + + + + k1 + 2.3 + + + + + + 2 + + + + + + + + S1 + k1 + + + + + + + + diff --git a/latest/cases/01716/synopsis.txt b/latest/cases/01716/synopsis.txt new file mode 100644 index 000000000..cda6fe036 --- /dev/null +++ b/latest/cases/01716/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: An event using assignment-time variables that are shadowed by a local parameter. +componentTags: Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, EventUsesAssignmentTimeValues, LocalParameters, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event uses assignment-time values of a parameter that is shadowed by a local parameter. + +The model contains: +* 1 species (S1) +* 1 parameter (k1) +* 1 local parameter (J0.k1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $k1$ |] + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E1 | $k1 >= 2.3$ | Assignment time | $2$ | $k1 = S1 + k1$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k1 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $2$ | variable | +| Initial value of local parameter 'J0.k1' | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01717/l2v5/index.heta b/latest/cases/01717/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01717/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01717/l3v2/build.log b/latest/cases/01717/l3v2/build.log new file mode 100644 index 000000000..5ca25e7de --- /dev/null +++ b/latest/cases/01717/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01717/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01717/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01717/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01717/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01717/l3v2/index.heta b/latest/cases/01717/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01717/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01717/model-sbml-l3v2.xml b/latest/cases/01717/model-sbml-l3v2.xml new file mode 100644 index 000000000..9947e3932 --- /dev/null +++ b/latest/cases/01717/model-sbml-l3v2.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + 0.1 + + + + + + + + + + + + + S1_stoich + 2.3 + + + + S1_stoich + 3.3 + + + + + + + 2 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01717/synopsis.txt b/latest/cases/01717/synopsis.txt new file mode 100644 index 000000000..0ae91db39 --- /dev/null +++ b/latest/cases/01717/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: A persistent event that references a stoichiometry. +componentTags: Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, EventIsPersistent, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a persistent event is triggered by changes in a stoichiometry. + +The model contains: +* 1 species (S1) +* 2 parameters (P1, k1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E1 | $(S1_stoich >= 2.3) && (S1_stoich <= 3.3)$ | $2$ | $P1 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $2$ | constant | +| Initial value of parameter P1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01718/l2v5/index.heta b/latest/cases/01718/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01718/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01718/l3v2/build.log b/latest/cases/01718/l3v2/build.log new file mode 100644 index 000000000..0f8f6e965 --- /dev/null +++ b/latest/cases/01718/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01718/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01718/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01718/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01718/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01718/l3v2/index.heta b/latest/cases/01718/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01718/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01718/model-sbml-l3v2.xml b/latest/cases/01718/model-sbml-l3v2.xml new file mode 100644 index 000000000..96489950d --- /dev/null +++ b/latest/cases/01718/model-sbml-l3v2.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + 0.1 + + + + + + + + + + + + + S1_stoich + 2.3 + + + + S1_stoich + 3.3 + + + + + + + 2 + + + + + + 3 + + + + + + + diff --git a/latest/cases/01718/synopsis.txt b/latest/cases/01718/synopsis.txt new file mode 100644 index 000000000..b23086bd7 --- /dev/null +++ b/latest/cases/01718/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: A non-persistent event that references a stoichiometry. +componentTags: Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, EventIsNotPersistent, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a non-persistent event is triggered by changes in a stoichiometry, but not for long enough, and it doesn't execute. + +The model contains: +* 1 species (S1) +* 2 parameters (P1, k1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Delay* | *Event Assignments* | +| E1 | $(S1_stoich >= 2.3) && (S1_stoich <= 3.3)$ | false | $2$ | $P1 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $2$ | constant | +| Initial value of parameter P1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01719/l2v5/index.heta b/latest/cases/01719/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01719/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01719/l3v2/build.log b/latest/cases/01719/l3v2/build.log new file mode 100644 index 000000000..68f156bae --- /dev/null +++ b/latest/cases/01719/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01719/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01719/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01719/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[error] Component "S1_stoich" is not found in space "nameless" as expected in DSwitcher: "E1" + S1_stoich <= 3.3; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01719/l3v2/index.heta b/latest/cases/01719/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01719/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01719/model-sbml-l3v2.xml b/latest/cases/01719/model-sbml-l3v2.xml new file mode 100644 index 000000000..861c11909 --- /dev/null +++ b/latest/cases/01719/model-sbml-l3v2.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + 0.1 + + + + + + + + + + + S1_stoich + 3.3 + + + + + + + 3 + + + + + + + diff --git a/latest/cases/01719/synopsis.txt b/latest/cases/01719/synopsis.txt new file mode 100644 index 000000000..4efbf4ebd --- /dev/null +++ b/latest/cases/01719/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: A non-persistent event that references a stoichiometry. +componentTags: Compartment, EventNoDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, EventT0Firing, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a non-persistent event is triggered by changes in a stoichiometry, but not for long enough, and it doesn't execute. + +The model contains: +* 1 species (S1) +* 2 parameters (P1, k1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* | +| E1 | $S1_stoich <= 3.3$ | false | $P1 = 3$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter k1 | $2$ | constant | +| Initial value of parameter P1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01720/l2v5/index.heta b/latest/cases/01720/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01720/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01720/l3v2/build.log b/latest/cases/01720/l3v2/build.log new file mode 100644 index 000000000..bcaece3a9 --- /dev/null +++ b/latest/cases/01720/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01720/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01720/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01720/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01720/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01720/l3v2/index.heta b/latest/cases/01720/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01720/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01720/model-sbml-l3v2.xml b/latest/cases/01720/model-sbml-l3v2.xml new file mode 100644 index 000000000..b9e9b540d --- /dev/null +++ b/latest/cases/01720/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + 0.1 + + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + S1_stoich + + + + + + + diff --git a/latest/cases/01720/synopsis.txt b/latest/cases/01720/synopsis.txt new file mode 100644 index 000000000..a70ebe92a --- /dev/null +++ b/latest/cases/01720/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: An event using trigger-time values that references a stoichiometry. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, EventUsesTriggerTimeValues, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event assigns the value of a stoichiometry obtained at the trigger time of the event. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E1 | $time > 2.5$ | $2$ | $P1 = S1_stoich$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01721/l2v5/index.heta b/latest/cases/01721/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01721/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01721/l3v2/build.log b/latest/cases/01721/l3v2/build.log new file mode 100644 index 000000000..4d890ca9e --- /dev/null +++ b/latest/cases/01721/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01721/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01721/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01721/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01721/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01721/l3v2/index.heta b/latest/cases/01721/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01721/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01721/model-sbml-l3v2.xml b/latest/cases/01721/model-sbml-l3v2.xml new file mode 100644 index 000000000..cb91fb244 --- /dev/null +++ b/latest/cases/01721/model-sbml-l3v2.xml @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + 0.1 + + + + + + + + + + + time + 2.5 + + + + + + 2 + + + + + + S1_stoich + + + + + + + diff --git a/latest/cases/01721/synopsis.txt b/latest/cases/01721/synopsis.txt new file mode 100644 index 000000000..ebdc54a19 --- /dev/null +++ b/latest/cases/01721/synopsis.txt @@ -0,0 +1,47 @@ + +category: Test +synopsis: An event using assignment-time values that references a stoichiometry. +componentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, EventUsesAssignmentTimeValues, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a delayed event assigns the value of a stoichiometry obtained at the assignment time of the event. + +The model contains: +* 1 species (S1) +* 1 parameter (P1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one event: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E1 | $time > 2.5$ | Assignment time | $2$ | $P1 = S1_stoich$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial value of parameter P1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01722/l2v5/index.heta b/latest/cases/01722/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01722/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01722/l3v2/build.log b/latest/cases/01722/l3v2/build.log new file mode 100644 index 000000000..c72a2b8fd --- /dev/null +++ b/latest/cases/01722/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01722/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01722/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01722/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 82 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01722/l3v2/index.heta b/latest/cases/01722/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01722/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01722/model-sbml-l3v2.xml b/latest/cases/01722/model-sbml-l3v2.xml new file mode 100644 index 000000000..b7484dd5b --- /dev/null +++ b/latest/cases/01722/model-sbml-l3v2.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + avogadro + 1 23 + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01722/synopsis.txt b/latest/cases/01722/synopsis.txt new file mode 100644 index 000000000..99e05a88b --- /dev/null +++ b/latest/cases/01722/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A stoichiometry set with reference to avogadro. +componentTags: CSymbolAvogadro, Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the stoichiometry of a reaction is set to be equal to avogadro/10^23. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $avogadro / 1e23$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01723/l2v5/index.heta b/latest/cases/01723/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01723/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01723/l3v2/build.log b/latest/cases/01723/l3v2/build.log new file mode 100644 index 000000000..743ab93ee --- /dev/null +++ b/latest/cases/01723/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01723/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01723/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01723/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01723/l3v2/index.heta b/latest/cases/01723/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01723/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01723/model-sbml-l3v2.xml b/latest/cases/01723/model-sbml-l3v2.xml new file mode 100644 index 000000000..f4e94523d --- /dev/null +++ b/latest/cases/01723/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + avogadro + 1 24 + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01723/synopsis.txt b/latest/cases/01723/synopsis.txt new file mode 100644 index 000000000..84ca8ba93 --- /dev/null +++ b/latest/cases/01723/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A stoichiometry change rate set with reference to avogadro. +componentTags: CSymbolAvogadro, Compartment, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, the rate rule for a reaction stoichiometry is set to be equal to avogadro/10^24. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $avogadro / 1e24$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01724/l2v5/index.heta b/latest/cases/01724/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01724/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01724/l3v2/build.log b/latest/cases/01724/l3v2/build.log new file mode 100644 index 000000000..83cb4f85e --- /dev/null +++ b/latest/cases/01724/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01724/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01724/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01724/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 85 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01724/l3v2/index.heta b/latest/cases/01724/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01724/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01724/model-sbml-l3v2.xml b/latest/cases/01724/model-sbml-l3v2.xml new file mode 100644 index 000000000..3c137783d --- /dev/null +++ b/latest/cases/01724/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + 1.5 + + + + + 1.5 + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01724/synopsis.txt b/latest/cases/01724/synopsis.txt new file mode 100644 index 000000000..1af9f7de5 --- /dev/null +++ b/latest/cases/01724/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: Model and species conversion factors affecting a reaction with assigned stoichiometries. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, ConversionFactors, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors affect a reaction with assigned stoichiometries, changing the levels of S1 and S2. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> S2_stoich S2 | $0.01$ |] +Note: the following stoichiometries are set separately: S1_stoich, S2_stoich + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1.5$ | constant | +| Initial value of species reference 'S2_stoich' | $1.5$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01725/l2v5/index.heta b/latest/cases/01725/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01725/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01725/l3v2/build.log b/latest/cases/01725/l3v2/build.log new file mode 100644 index 000000000..32f398864 --- /dev/null +++ b/latest/cases/01725/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01725/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01725/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01725/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01725/l3v2/index.heta b/latest/cases/01725/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01725/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01725/model-sbml-l3v2.xml b/latest/cases/01725/model-sbml-l3v2.xml new file mode 100644 index 000000000..3b3245fc9 --- /dev/null +++ b/latest/cases/01725/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + 1.5 + + + + + 1.5 + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01725/synopsis.txt b/latest/cases/01725/synopsis.txt new file mode 100644 index 000000000..5e40bd397 --- /dev/null +++ b/latest/cases/01725/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Species conversion factor affecting a reaction with assigned stoichiometries. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, ConversionFactors, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor affects a reaction with assigned stoichiometries, changing the levels of S1 and S2. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> S2_stoich S2 | $0.01$ |] +Note: the following stoichiometries are set separately: S1_stoich, S2_stoich + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1.5$ | constant | +| Initial value of species reference 'S2_stoich' | $1.5$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01726/l2v5/index.heta b/latest/cases/01726/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01726/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01726/l3v2/build.log b/latest/cases/01726/l3v2/build.log new file mode 100644 index 000000000..56106aa33 --- /dev/null +++ b/latest/cases/01726/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01726/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01726/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01726/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01726/l3v2/index.heta b/latest/cases/01726/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01726/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01726/model-sbml-l3v2.xml b/latest/cases/01726/model-sbml-l3v2.xml new file mode 100644 index 000000000..e4ae57eea --- /dev/null +++ b/latest/cases/01726/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + 1.5 + + + + + 1.5 + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01726/synopsis.txt b/latest/cases/01726/synopsis.txt new file mode 100644 index 000000000..6a1061c97 --- /dev/null +++ b/latest/cases/01726/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: Model conversion factor affecting a reaction with assigned stoichiometries. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, ConversionFactors, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor affects a reaction with assigned stoichiometries, changing the levels of S1 and S2. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> S2_stoich S2 | $0.01$ |] +Note: the following stoichiometries are set separately: S1_stoich, S2_stoich + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1.5$ | constant | +| Initial value of species reference 'S2_stoich' | $1.5$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01727/l2v5/index.heta b/latest/cases/01727/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01727/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01727/l3v2/build.log b/latest/cases/01727/l3v2/build.log new file mode 100644 index 000000000..ac91086df --- /dev/null +++ b/latest/cases/01727/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01727/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01727/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01727/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 87 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[error] S2_stoich_proc Property "actors[0].target" has lost reference "S2_stoich". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01727/l3v2/index.heta b/latest/cases/01727/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01727/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01727/model-sbml-l3v2.xml b/latest/cases/01727/model-sbml-l3v2.xml new file mode 100644 index 000000000..2be2f8df7 --- /dev/null +++ b/latest/cases/01727/model-sbml-l3v2.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + 0.01 + + + + + 0.01 + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01727/synopsis.txt b/latest/cases/01727/synopsis.txt new file mode 100644 index 000000000..405961736 --- /dev/null +++ b/latest/cases/01727/synopsis.txt @@ -0,0 +1,53 @@ + +category: Test +synopsis: Model and species conversion factors affecting a reaction with assigned variable stoichiometries. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors affect a reaction with assigned variable stoichiometries, changing the levels of S1 and S2. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> S2_stoich S2 | $0.01$ |] +Note: the following stoichiometries are set separately: S1_stoich, S2_stoich + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $0.01$ | +| Rate | S2_stoich | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable | +| Initial value of species reference 'S2_stoich' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01728/l2v5/index.heta b/latest/cases/01728/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01728/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01728/l3v2/build.log b/latest/cases/01728/l3v2/build.log new file mode 100644 index 000000000..27a5c9fa5 --- /dev/null +++ b/latest/cases/01728/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01728/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01728/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01728/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[error] S2_stoich_proc Property "actors[0].target" has lost reference "S2_stoich". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01728/l3v2/index.heta b/latest/cases/01728/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01728/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01728/model-sbml-l3v2.xml b/latest/cases/01728/model-sbml-l3v2.xml new file mode 100644 index 000000000..ad5fe1e33 --- /dev/null +++ b/latest/cases/01728/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + 0.01 + + + + + 0.01 + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01728/synopsis.txt b/latest/cases/01728/synopsis.txt new file mode 100644 index 000000000..8803871d6 --- /dev/null +++ b/latest/cases/01728/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: A species conversion factor affecting a reaction with assigned variable stoichiometries. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor affects a reaction with assigned variable stoichiometries, changing the levels of S1 and S2. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> S2_stoich S2 | $0.01$ |] +Note: the following stoichiometries are set separately: S1_stoich, S2_stoich + +The conversion factor for the species 'S1' is 's1_cf' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $0.01$ | +| Rate | S2_stoich | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable | +| Initial value of species reference 'S2_stoich' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01729/l2v5/index.heta b/latest/cases/01729/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01729/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01729/l3v2/build.log b/latest/cases/01729/l3v2/build.log new file mode 100644 index 000000000..09a174e46 --- /dev/null +++ b/latest/cases/01729/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01729/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01729/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01729/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[error] S2_stoich_proc Property "actors[0].target" has lost reference "S2_stoich". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01729/l3v2/index.heta b/latest/cases/01729/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01729/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01729/model-sbml-l3v2.xml b/latest/cases/01729/model-sbml-l3v2.xml new file mode 100644 index 000000000..cae8872bf --- /dev/null +++ b/latest/cases/01729/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + 0.01 + + + + + 0.01 + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01729/synopsis.txt b/latest/cases/01729/synopsis.txt new file mode 100644 index 000000000..34c04f19d --- /dev/null +++ b/latest/cases/01729/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Model conversion factor affecting a reaction with assigned variable stoichiometries. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor affects a reaction with assigned variable stoichiometries, changing the levels of S1 and S2. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1_stoich S1 -> S2_stoich S2 | $0.01$ |] +Note: the following stoichiometries are set separately: S1_stoich, S2_stoich + +The conversion factor for the model is 'm_cf' + + +There are 2 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $0.01$ | +| Rate | S2_stoich | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable | +| Initial value of species reference 'S2_stoich' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01730/l2v5/index.heta b/latest/cases/01730/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01730/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01730/l3v2/heta-code/output.heta b/latest/cases/01730/l3v2/heta-code/output.heta new file mode 100644 index 000000000..ca1a70e95 --- /dev/null +++ b/latest/cases/01730/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; +S3 @Species { boundary: true, compartment: C, } .= 2 / C; +S4 @Species { boundary: true, compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S3 + S1 = S2 + S4, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01730/l3v2/index.heta b/latest/cases/01730/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01730/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01730/l3v2/json/output.json b/latest/cases/01730/l3v2/json/output.json new file mode 100644 index 000000000..7cf645fd6 --- /dev/null +++ b/latest/cases/01730/l3v2/json/output.json @@ -0,0 +1,82 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "2 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "assignments": { + "start_": "3 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01730/model-sbml-l3v2.xml b/latest/cases/01730/model-sbml-l3v2.xml new file mode 100644 index 000000000..62f67958b --- /dev/null +++ b/latest/cases/01730/model-sbml-l3v2.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01730/output.heta b/latest/cases/01730/output.heta new file mode 100644 index 000000000..72b5d1042 --- /dev/null +++ b/latest/cases/01730/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Model and species conversion factors affecting a reaction with boundary conditions. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, BoundaryCondition, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors affect a reaction with boundary species. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3 + S1 -> S2 + S4 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' +The conversion factor for the species 'S3' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; +S3 @Species { boundary: true, compartment: C, } .= 2 / C; +S4 @Species { boundary: true, compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S3 + S1 = S2 + S4, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01730/synopsis.txt b/latest/cases/01730/synopsis.txt new file mode 100644 index 000000000..218ed8f1d --- /dev/null +++ b/latest/cases/01730/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Model and species conversion factors affecting a reaction with boundary conditions. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, BoundaryCondition, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors affect a reaction with boundary species. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3 + S1 -> S2 + S4 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' +The conversion factor for the species 'S3' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01731/l2v5/index.heta b/latest/cases/01731/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01731/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01731/l3v2/heta-code/output.heta b/latest/cases/01731/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d01893c39 --- /dev/null +++ b/latest/cases/01731/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; +S3 @Species { boundary: true, compartment: C, } .= 2 / C; +S4 @Species { boundary: true, compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S3 + S1 = S2 + S4, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + diff --git a/latest/cases/01731/l3v2/index.heta b/latest/cases/01731/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01731/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01731/l3v2/json/output.json b/latest/cases/01731/l3v2/json/output.json new file mode 100644 index 000000000..98e87563b --- /dev/null +++ b/latest/cases/01731/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "2 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "assignments": { + "start_": "3 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01731/model-sbml-l3v2.xml b/latest/cases/01731/model-sbml-l3v2.xml new file mode 100644 index 000000000..6ac0b5955 --- /dev/null +++ b/latest/cases/01731/model-sbml-l3v2.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01731/output.heta b/latest/cases/01731/output.heta new file mode 100644 index 000000000..06e6d5ede --- /dev/null +++ b/latest/cases/01731/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: A species conversion factor affecting a reaction with boundary conditions. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, BoundaryCondition, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor affects a reaction with boundary species. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3 + S1 -> S2 + S4 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' +The conversion factor for the species 'S3' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; +S3 @Species { boundary: true, compartment: C, } .= 2 / C; +S4 @Species { boundary: true, compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S3 + S1 = S2 + S4, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + diff --git a/latest/cases/01731/synopsis.txt b/latest/cases/01731/synopsis.txt new file mode 100644 index 000000000..ab0531826 --- /dev/null +++ b/latest/cases/01731/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A species conversion factor affecting a reaction with boundary conditions. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, BoundaryCondition, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor affects a reaction with boundary species. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3 + S1 -> S2 + S4 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' +The conversion factor for the species 'S3' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01732/l2v5/index.heta b/latest/cases/01732/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01732/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01732/l3v2/heta-code/output.heta b/latest/cases/01732/l3v2/heta-code/output.heta new file mode 100644 index 000000000..948bdda44 --- /dev/null +++ b/latest/cases/01732/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; +S3 @Species { boundary: true, compartment: C, } .= 2 / C; +S4 @Species { boundary: true, compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S3 + S1 = S2 + S4, }; +J0 := 0.01; + +m_cf @Const { } = 3; + diff --git a/latest/cases/01732/l3v2/index.heta b/latest/cases/01732/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01732/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01732/l3v2/json/output.json b/latest/cases/01732/l3v2/json/output.json new file mode 100644 index 000000000..f9899da87 --- /dev/null +++ b/latest/cases/01732/l3v2/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "2 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S4", + "assignments": { + "start_": "3 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S4", + "stoichiometry": 1 + }, + { + "target": "S3", + "stoichiometry": -1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + } +] \ No newline at end of file diff --git a/latest/cases/01732/model-sbml-l3v2.xml b/latest/cases/01732/model-sbml-l3v2.xml new file mode 100644 index 000000000..30a92803e --- /dev/null +++ b/latest/cases/01732/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01732/output.heta b/latest/cases/01732/output.heta new file mode 100644 index 000000000..6ab68e39c --- /dev/null +++ b/latest/cases/01732/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: Model conversion factor affecting a reaction with boundary conditions. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, BoundaryCondition, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor affects a reaction with boundary species. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3 + S1 -> S2 + S4 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; +S3 @Species { boundary: true, compartment: C, } .= 2 / C; +S4 @Species { boundary: true, compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S3 + S1 = S2 + S4, }; +J0 := 0.01; + +m_cf @Const { } = 3; + diff --git a/latest/cases/01732/synopsis.txt b/latest/cases/01732/synopsis.txt new file mode 100644 index 000000000..92e174b05 --- /dev/null +++ b/latest/cases/01732/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Model conversion factor affecting a reaction with boundary conditions. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, BoundaryCondition, ConversionFactors +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor affects a reaction with boundary species. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3 + S1 -> S2 + S4 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01733/l2v5/index.heta b/latest/cases/01733/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01733/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01733/l3v2/build.log b/latest/cases/01733/l3v2/build.log new file mode 100644 index 000000000..b04884239 --- /dev/null +++ b/latest/cases/01733/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01733/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01733/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01733/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[error] S3_stoich component does not exist which is not allowed for the "update" action. +[error] S4_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 87 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01733/l3v2/index.heta b/latest/cases/01733/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01733/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01733/model-sbml-l3v2.xml b/latest/cases/01733/model-sbml-l3v2.xml new file mode 100644 index 000000000..6f916c92d --- /dev/null +++ b/latest/cases/01733/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + 1.5 + + + + + 1.5 + + + + + 1.5 + + + + + 1.5 + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01733/synopsis.txt b/latest/cases/01733/synopsis.txt new file mode 100644 index 000000000..74dce2a0b --- /dev/null +++ b/latest/cases/01733/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: Model and species conversion factors affecting a reaction with assigned stoichiometries and boundary conditions. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, BoundaryCondition, ConversionFactors, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors affect a reaction with assigned stoichiometries and boundary conditions, changing the levels of S1 and S2, but not S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) +* 4 species references (S3_stoich, S1_stoich, S2_stoich, S4_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3_stoich S3 + S1_stoich S1 -> S2_stoich S2 + S4_stoich S4 | $0.01$ |] +Note: the following stoichiometries are set separately: S3_stoich, S1_stoich, S2_stoich, S4_stoich + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' +The conversion factor for the species 'S3' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S3_stoich' | $1.5$ | constant | +| Initial value of species reference 'S1_stoich' | $1.5$ | constant | +| Initial value of species reference 'S2_stoich' | $1.5$ | constant | +| Initial value of species reference 'S4_stoich' | $1.5$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01734/l2v5/index.heta b/latest/cases/01734/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01734/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01734/l3v2/build.log b/latest/cases/01734/l3v2/build.log new file mode 100644 index 000000000..884dc8534 --- /dev/null +++ b/latest/cases/01734/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01734/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01734/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01734/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[error] S3_stoich component does not exist which is not allowed for the "update" action. +[error] S4_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01734/l3v2/index.heta b/latest/cases/01734/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01734/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01734/model-sbml-l3v2.xml b/latest/cases/01734/model-sbml-l3v2.xml new file mode 100644 index 000000000..ddf004c78 --- /dev/null +++ b/latest/cases/01734/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + 1.5 + + + + + 1.5 + + + + + 1.5 + + + + + 1.5 + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01734/synopsis.txt b/latest/cases/01734/synopsis.txt new file mode 100644 index 000000000..f5d57e040 --- /dev/null +++ b/latest/cases/01734/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: A species conversion factor affecting a reaction with assigned stoichiometries and boundary conditions. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, BoundaryCondition, ConversionFactors, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor affects a reaction with assigned stoichiometries and boundary conditions, changing the levels of S1 and S2, but not S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 1 parameter (s1_cf) +* 1 compartment (C) +* 4 species references (S3_stoich, S1_stoich, S2_stoich, S4_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3_stoich S3 + S1_stoich S1 -> S2_stoich S2 + S4_stoich S4 | $0.01$ |] +Note: the following stoichiometries are set separately: S3_stoich, S1_stoich, S2_stoich, S4_stoich + +The conversion factor for the species 'S1' is 's1_cf' +The conversion factor for the species 'S3' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S3_stoich' | $1.5$ | constant | +| Initial value of species reference 'S1_stoich' | $1.5$ | constant | +| Initial value of species reference 'S2_stoich' | $1.5$ | constant | +| Initial value of species reference 'S4_stoich' | $1.5$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01735/l2v5/index.heta b/latest/cases/01735/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01735/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01735/l3v2/build.log b/latest/cases/01735/l3v2/build.log new file mode 100644 index 000000000..ceafe6522 --- /dev/null +++ b/latest/cases/01735/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01735/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01735/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01735/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[error] S3_stoich component does not exist which is not allowed for the "update" action. +[error] S4_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01735/l3v2/index.heta b/latest/cases/01735/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01735/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01735/model-sbml-l3v2.xml b/latest/cases/01735/model-sbml-l3v2.xml new file mode 100644 index 000000000..24a67a15f --- /dev/null +++ b/latest/cases/01735/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + 1.5 + + + + + 1.5 + + + + + 1.5 + + + + + 1.5 + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01735/synopsis.txt b/latest/cases/01735/synopsis.txt new file mode 100644 index 000000000..c1f899a4e --- /dev/null +++ b/latest/cases/01735/synopsis.txt @@ -0,0 +1,48 @@ + +category: Test +synopsis: Model conversion factor affecting a reaction with assigned stoichiometries and boundary conditions. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, BoundaryCondition, ConversionFactors, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor affects a reaction with assigned stoichiometries and boundary conditions, changing the levels of S1 and S2, but not S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 1 parameter (m_cf) +* 1 compartment (C) +* 4 species references (S3_stoich, S1_stoich, S2_stoich, S4_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3_stoich S3 + S1_stoich S1 -> S2_stoich S2 + S4_stoich S4 | $0.01$ |] +Note: the following stoichiometries are set separately: S3_stoich, S1_stoich, S2_stoich, S4_stoich + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S3_stoich' | $1.5$ | constant | +| Initial value of species reference 'S1_stoich' | $1.5$ | constant | +| Initial value of species reference 'S2_stoich' | $1.5$ | constant | +| Initial value of species reference 'S4_stoich' | $1.5$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01736/l2v5/index.heta b/latest/cases/01736/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01736/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01736/l3v2/build.log b/latest/cases/01736/l3v2/build.log new file mode 100644 index 000000000..640396284 --- /dev/null +++ b/latest/cases/01736/l3v2/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01736/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01736/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01736/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[error] S3_stoich component does not exist which is not allowed for the "update" action. +[error] S4_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 91 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[error] S2_stoich_proc Property "actors[0].target" has lost reference "S2_stoich". +[error] S3_stoich_proc Property "actors[0].target" has lost reference "S3_stoich". +[error] S4_stoich_proc Property "actors[0].target" has lost reference "S4_stoich". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01736/l3v2/index.heta b/latest/cases/01736/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01736/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01736/model-sbml-l3v2.xml b/latest/cases/01736/model-sbml-l3v2.xml new file mode 100644 index 000000000..530c6c007 --- /dev/null +++ b/latest/cases/01736/model-sbml-l3v2.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + 0.01 + + + + + 0.01 + + + + + 0.01 + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01736/synopsis.txt b/latest/cases/01736/synopsis.txt new file mode 100644 index 000000000..a155c2cf5 --- /dev/null +++ b/latest/cases/01736/synopsis.txt @@ -0,0 +1,60 @@ + +category: Test +synopsis: Model and species conversion factors affecting a reaction with assigned variable stoichiometries and boundary conditions. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, BoundaryCondition, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors affect a reaction with assigned variable stoichiometries and boundary conditions, changing the levels of S1 and S2, but not S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) +* 4 species references (S3_stoich, S1_stoich, S2_stoich, S4_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3_stoich S3 + S1_stoich S1 -> S2_stoich S2 + S4_stoich S4 | $0.01$ |] +Note: the following stoichiometries are set separately: S3_stoich, S1_stoich, S2_stoich, S4_stoich + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' +The conversion factor for the species 'S3' is 's1_cf' + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $0.01$ | +| Rate | S2_stoich | $0.01$ | +| Rate | S3_stoich | $0.01$ | +| Rate | S4_stoich | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S3_stoich' | $1$ | variable | +| Initial value of species reference 'S1_stoich' | $1$ | variable | +| Initial value of species reference 'S2_stoich' | $1$ | variable | +| Initial value of species reference 'S4_stoich' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01737/l2v5/index.heta b/latest/cases/01737/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01737/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01737/l3v2/build.log b/latest/cases/01737/l3v2/build.log new file mode 100644 index 000000000..d7d548f1c --- /dev/null +++ b/latest/cases/01737/l3v2/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01737/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01737/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01737/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[error] S3_stoich component does not exist which is not allowed for the "update" action. +[error] S4_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 90 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[error] S2_stoich_proc Property "actors[0].target" has lost reference "S2_stoich". +[error] S3_stoich_proc Property "actors[0].target" has lost reference "S3_stoich". +[error] S4_stoich_proc Property "actors[0].target" has lost reference "S4_stoich". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01737/l3v2/index.heta b/latest/cases/01737/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01737/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01737/model-sbml-l3v2.xml b/latest/cases/01737/model-sbml-l3v2.xml new file mode 100644 index 000000000..2fb865e2f --- /dev/null +++ b/latest/cases/01737/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + 0.01 + + + + + 0.01 + + + + + 0.01 + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01737/synopsis.txt b/latest/cases/01737/synopsis.txt new file mode 100644 index 000000000..deafc6859 --- /dev/null +++ b/latest/cases/01737/synopsis.txt @@ -0,0 +1,58 @@ + +category: Test +synopsis: A species conversion factor affecting a reaction with assigned variable stoichiometries and boundary conditions. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, BoundaryCondition, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor affects a reaction with assigned variable stoichiometries and boundary conditions, changing the levels of S1 and S2, but not S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 1 parameter (s1_cf) +* 1 compartment (C) +* 4 species references (S3_stoich, S1_stoich, S2_stoich, S4_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3_stoich S3 + S1_stoich S1 -> S2_stoich S2 + S4_stoich S4 | $0.01$ |] +Note: the following stoichiometries are set separately: S3_stoich, S1_stoich, S2_stoich, S4_stoich + +The conversion factor for the species 'S1' is 's1_cf' +The conversion factor for the species 'S3' is 's1_cf' + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $0.01$ | +| Rate | S2_stoich | $0.01$ | +| Rate | S3_stoich | $0.01$ | +| Rate | S4_stoich | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S3_stoich' | $1$ | variable | +| Initial value of species reference 'S1_stoich' | $1$ | variable | +| Initial value of species reference 'S2_stoich' | $1$ | variable | +| Initial value of species reference 'S4_stoich' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01738/l2v5/index.heta b/latest/cases/01738/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01738/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01738/l3v2/build.log b/latest/cases/01738/l3v2/build.log new file mode 100644 index 000000000..a4b2c8b13 --- /dev/null +++ b/latest/cases/01738/l3v2/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01738/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01738/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01738/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[error] S2_stoich component does not exist which is not allowed for the "update" action. +[error] S3_stoich component does not exist which is not allowed for the "update" action. +[error] S4_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 90 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[error] S2_stoich_proc Property "actors[0].target" has lost reference "S2_stoich". +[error] S3_stoich_proc Property "actors[0].target" has lost reference "S3_stoich". +[error] S4_stoich_proc Property "actors[0].target" has lost reference "S4_stoich". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01738/l3v2/index.heta b/latest/cases/01738/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01738/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01738/model-sbml-l3v2.xml b/latest/cases/01738/model-sbml-l3v2.xml new file mode 100644 index 000000000..b3014df62 --- /dev/null +++ b/latest/cases/01738/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + 0.01 + + + + + 0.01 + + + + + 0.01 + + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01738/synopsis.txt b/latest/cases/01738/synopsis.txt new file mode 100644 index 000000000..f94bbaf83 --- /dev/null +++ b/latest/cases/01738/synopsis.txt @@ -0,0 +1,57 @@ + +category: Test +synopsis: Model conversion factor affecting a reaction with assigned variable stoichiometries and boundary conditions. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, BoundaryCondition, ConversionFactors, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor affects a reaction with assigned variable stoichiometries and boundary conditions, changing the levels of S1 and S2, but not S3 and S4. + +The model contains: +* 4 species (S1, S2, S3, S4) +* 1 parameter (m_cf) +* 1 compartment (C) +* 4 species references (S3_stoich, S1_stoich, S2_stoich, S4_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S3_stoich S3 + S1_stoich S1 -> S2_stoich S2 + S4_stoich S4 | $0.01$ |] +Note: the following stoichiometries are set separately: S3_stoich, S1_stoich, S2_stoich, S4_stoich + +The conversion factor for the model is 'm_cf' + + +There are 4 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $0.01$ | +| Rate | S2_stoich | $0.01$ | +| Rate | S3_stoich | $0.01$ | +| Rate | S4_stoich | $0.01$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial amount of species S4 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S3_stoich' | $1$ | variable | +| Initial value of species reference 'S1_stoich' | $1$ | variable | +| Initial value of species reference 'S2_stoich' | $1$ | variable | +| Initial value of species reference 'S4_stoich' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01739/l2v5/index.heta b/latest/cases/01739/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01739/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01739/l3v2/heta-code/output.heta b/latest/cases/01739/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5a839b084 --- /dev/null +++ b/latest/cases/01739/l3v2/heta-code/output.heta @@ -0,0 +1,17 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local * s1_cf__J0_local * 0.01; + +m_cf__J0_local @Const { } = 1; +s1_cf__J0_local @Const { } = 1; +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01739/l3v2/index.heta b/latest/cases/01739/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01739/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01739/l3v2/json/output.json b/latest/cases/01739/l3v2/json/output.json new file mode 100644 index 000000000..d7d505f9c --- /dev/null +++ b/latest/cases/01739/l3v2/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "m_cf__J0_local", + "num": 1 + }, + { + "class": "Const", + "id": "s1_cf__J0_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "m_cf__J0_local * s1_cf__J0_local * 0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01739/model-sbml-l3v2.xml b/latest/cases/01739/model-sbml-l3v2.xml new file mode 100644 index 000000000..1df55b1db --- /dev/null +++ b/latest/cases/01739/model-sbml-l3v2.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + m_cf + s1_cf + 0.01 + + + + + + + + + + + diff --git a/latest/cases/01739/output.heta b/latest/cases/01739/output.heta new file mode 100644 index 000000000..f591eeda6 --- /dev/null +++ b/latest/cases/01739/output.heta @@ -0,0 +1,64 @@ +/* +category: Test +synopsis: Model and species conversion factors affecting a reaction with local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors affect a reaction with local parameters that shadow the conversion factor IDs. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf * s1_cf * 0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial value of local parameter 'J0.m_cf' | $1$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local * s1_cf__J0_local * 0.01; + +m_cf__J0_local @Const { } = 1; +s1_cf__J0_local @Const { } = 1; +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01739/synopsis.txt b/latest/cases/01739/synopsis.txt new file mode 100644 index 000000000..fda87ea97 --- /dev/null +++ b/latest/cases/01739/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: Model and species conversion factors affecting a reaction with local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors affect a reaction with local parameters that shadow the conversion factor IDs. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf * s1_cf * 0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial value of local parameter 'J0.m_cf' | $1$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01740/l2v5/index.heta b/latest/cases/01740/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01740/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01740/l3v2/heta-code/output.heta b/latest/cases/01740/l3v2/heta-code/output.heta new file mode 100644 index 000000000..09355a02f --- /dev/null +++ b/latest/cases/01740/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local * s1_cf__J0_local * 0.01; + +m_cf__J0_local @Const { } = 1; +s1_cf__J0_local @Const { } = 1; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01740/l3v2/index.heta b/latest/cases/01740/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01740/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01740/l3v2/json/output.json b/latest/cases/01740/l3v2/json/output.json new file mode 100644 index 000000000..56df18c0f --- /dev/null +++ b/latest/cases/01740/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "m_cf__J0_local", + "num": 1 + }, + { + "class": "Const", + "id": "s1_cf__J0_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "m_cf__J0_local * s1_cf__J0_local * 0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01740/model-sbml-l3v2.xml b/latest/cases/01740/model-sbml-l3v2.xml new file mode 100644 index 000000000..59231d415 --- /dev/null +++ b/latest/cases/01740/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + m_cf + s1_cf + 0.01 + + + + + + + + + + + diff --git a/latest/cases/01740/output.heta b/latest/cases/01740/output.heta new file mode 100644 index 000000000..925a39f59 --- /dev/null +++ b/latest/cases/01740/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: A species conversion factor affecting a reaction with local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor affects a reaction with local parameters that shadow the conversion factor ID. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf * s1_cf * 0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial value of local parameter 'J0.m_cf' | $1$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local * s1_cf__J0_local * 0.01; + +m_cf__J0_local @Const { } = 1; +s1_cf__J0_local @Const { } = 1; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01740/synopsis.txt b/latest/cases/01740/synopsis.txt new file mode 100644 index 000000000..86e3a00d4 --- /dev/null +++ b/latest/cases/01740/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A species conversion factor affecting a reaction with local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a species conversion factor affects a reaction with local parameters that shadow the conversion factor ID. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf * s1_cf * 0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $5$ | constant | +| Initial value of local parameter 'J0.m_cf' | $1$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01741/l2v5/index.heta b/latest/cases/01741/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01741/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01741/l3v2/heta-code/output.heta b/latest/cases/01741/l3v2/heta-code/output.heta new file mode 100644 index 000000000..f55609701 --- /dev/null +++ b/latest/cases/01741/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local * s1_cf__J0_local * 0.01; + +m_cf__J0_local @Const { } = 1; +s1_cf__J0_local @Const { } = 1; +m_cf @Const { } = 3; + diff --git a/latest/cases/01741/l3v2/index.heta b/latest/cases/01741/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01741/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01741/l3v2/json/output.json b/latest/cases/01741/l3v2/json/output.json new file mode 100644 index 000000000..0d3fa08f2 --- /dev/null +++ b/latest/cases/01741/l3v2/json/output.json @@ -0,0 +1,61 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "m_cf__J0_local", + "num": 1 + }, + { + "class": "Const", + "id": "s1_cf__J0_local", + "num": 1 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "m_cf__J0_local * s1_cf__J0_local * 0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + } +] \ No newline at end of file diff --git a/latest/cases/01741/model-sbml-l3v2.xml b/latest/cases/01741/model-sbml-l3v2.xml new file mode 100644 index 000000000..efb74df2e --- /dev/null +++ b/latest/cases/01741/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + m_cf + s1_cf + 0.01 + + + + + + + + + + + diff --git a/latest/cases/01741/output.heta b/latest/cases/01741/output.heta new file mode 100644 index 000000000..071c7da70 --- /dev/null +++ b/latest/cases/01741/output.heta @@ -0,0 +1,61 @@ +/* +category: Test +synopsis: Model conversion factor affecting a reaction with local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor affects a reaction with local parameters that shadow the conversion factor ID. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf * s1_cf * 0.01$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of local parameter 'J0.m_cf' | $1$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := m_cf__J0_local * s1_cf__J0_local * 0.01; + +m_cf__J0_local @Const { } = 1; +s1_cf__J0_local @Const { } = 1; +m_cf @Const { } = 3; + diff --git a/latest/cases/01741/synopsis.txt b/latest/cases/01741/synopsis.txt new file mode 100644 index 000000000..6f13925a6 --- /dev/null +++ b/latest/cases/01741/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: Model conversion factor affecting a reaction with local parameters. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor affects a reaction with local parameters that shadow the conversion factor ID. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 2 local parameters (J0.m_cf, J0.s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $m_cf * s1_cf * 0.01$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $3$ | constant | +| Initial value of local parameter 'J0.m_cf' | $1$ | constant | +| Initial value of local parameter 'J0.s1_cf' | $1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01742/l2v5/index.heta b/latest/cases/01742/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01742/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01742/l3v2/build.log b/latest/cases/01742/l3v2/build.log new file mode 100644 index 000000000..9758f8ed2 --- /dev/null +++ b/latest/cases/01742/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01742/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01742/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01742/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 84 +[error] S1_stoich_proc Property "actors[0].target" has lost reference "S1_stoich". +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01742/l3v2/index.heta b/latest/cases/01742/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01742/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01742/model-sbml-l3v2.xml b/latest/cases/01742/model-sbml-l3v2.xml new file mode 100644 index 000000000..981f4785b --- /dev/null +++ b/latest/cases/01742/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + 1.5 + + + + + + + + + + + + + + + getOnePointFive + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01742/synopsis.txt b/latest/cases/01742/synopsis.txt new file mode 100644 index 000000000..59cfb4554 --- /dev/null +++ b/latest/cases/01742/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: A stoichiometry that changes due to a function definition. +componentTags: Compartment, FunctionDefinition, RateRule, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a stoichiometry is changed due to a rate rule that calls a function definition. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | S1_stoich | $getOnePointFive()$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getOnePointFive | | $1.5$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01743/l2v5/build.log b/latest/cases/01743/l2v5/build.log new file mode 100644 index 000000000..981654bdc --- /dev/null +++ b/latest/cases/01743/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01743/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01743/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01743/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01743/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01743/l2v5/index.heta b/latest/cases/01743/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01743/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01743/l3v2/index.heta b/latest/cases/01743/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01743/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01743/model-sbml-l2v5.xml b/latest/cases/01743/model-sbml-l2v5.xml new file mode 100644 index 000000000..1e13839db --- /dev/null +++ b/latest/cases/01743/model-sbml-l2v5.xml @@ -0,0 +1,50 @@ + + + + + + + + 1.5 + + + + + + + + + + + + + + + + + + getOnePointFive + + + + + + + + + + + parameterId_0 + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01743/synopsis.txt b/latest/cases/01743/synopsis.txt new file mode 100644 index 000000000..6623ecbba --- /dev/null +++ b/latest/cases/01743/synopsis.txt @@ -0,0 +1,51 @@ + +category: Test +synopsis: A stoichiometry that changes due to a function definition. +componentTags: Compartment, FunctionDefinition, Parameter, RateRule, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, NonConstantParameter, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In this model, a stoichiometry is changed due to a rate rule that calls a function definition. This model is the same as 1742, but uses the StoichiometryMath of level 2 SBML. + +The model contains: +* 1 species (S1) +* 1 parameter (parameterId_0) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | parameterId_0 | $getOnePointFive()$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getOnePointFive | | $1.5$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of parameter parameterId_0 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $parameterId_0$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01744/l2v5/index.heta b/latest/cases/01744/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01744/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01744/l3v2/build.log b/latest/cases/01744/l3v2/build.log new file mode 100644 index 000000000..2ea6f78f5 --- /dev/null +++ b/latest/cases/01744/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01744/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01744/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01744/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 83 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01744/l3v2/index.heta b/latest/cases/01744/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01744/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01744/model-sbml-l3v2.xml b/latest/cases/01744/model-sbml-l3v2.xml new file mode 100644 index 000000000..c642991fe --- /dev/null +++ b/latest/cases/01744/model-sbml-l3v2.xml @@ -0,0 +1,50 @@ + + + + + + + + + + x + + + + x + 10 + + + + + + + + + + + + + + + + getOneTenth + time + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01744/synopsis.txt b/latest/cases/01744/synopsis.txt new file mode 100644 index 000000000..09b9fc6be --- /dev/null +++ b/latest/cases/01744/synopsis.txt @@ -0,0 +1,49 @@ + +category: Test +synopsis: A stoichiometry that changes due to a function definition. +componentTags: AssignmentRule, CSymbolTime, Compartment, FunctionDefinition, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a stoichiometry is changed due to an assignment rule that calls a function definition. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1_stoich | $getOneTenth(time)$ |] + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getOneTenth | x | $x / 10$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $getOneTenth(time)$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01745/l2v5/build.log b/latest/cases/01745/l2v5/build.log new file mode 100644 index 000000000..100545821 --- /dev/null +++ b/latest/cases/01745/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01745/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01745/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01745/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01745/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01745/l2v5/index.heta b/latest/cases/01745/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01745/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01745/l3v2/index.heta b/latest/cases/01745/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01745/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01745/model-sbml-l2v5.xml b/latest/cases/01745/model-sbml-l2v5.xml new file mode 100644 index 000000000..e9f1e9820 --- /dev/null +++ b/latest/cases/01745/model-sbml-l2v5.xml @@ -0,0 +1,48 @@ + + + + + + + + + x + + + + x + 10 + + + + + + + + + + + + + + + + + + + getOneTenth + time + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01745/synopsis.txt b/latest/cases/01745/synopsis.txt new file mode 100644 index 000000000..665ad1fae --- /dev/null +++ b/latest/cases/01745/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A stoichiometry that changes due to a function definition. +componentTags: CSymbolTime, Compartment, FunctionDefinition, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In this model, a stoichiometry is changed due to StoichiometryMath that calls a function definition. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + +The model contains the following function definition: + +[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* | + | getOneTenth | x | $x / 10$ | +] +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $getOneTenth(time)$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01746/l2v5/index.heta b/latest/cases/01746/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01746/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01746/l3v2/build.log b/latest/cases/01746/l3v2/build.log new file mode 100644 index 000000000..7fbc74db1 --- /dev/null +++ b/latest/cases/01746/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01746/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01746/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01746/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 82 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01746/l3v2/index.heta b/latest/cases/01746/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01746/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01746/model-sbml-l3v2.xml b/latest/cases/01746/model-sbml-l3v2.xml new file mode 100644 index 000000000..f250beda2 --- /dev/null +++ b/latest/cases/01746/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + 1.5 + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01746/synopsis.txt b/latest/cases/01746/synopsis.txt new file mode 100644 index 000000000..4af861f63 --- /dev/null +++ b/latest/cases/01746/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A set stoichiometry for a substance-only species. +componentTags: Compartment, InitialAssignment, Reaction, Species +testTags: Amount, AssignedConstantStoichiometry, HasOnlySubstanceUnits, InitialValueReassigned, NonUnityCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a stoichiometry is externally set for a species set hasOnlySubstanceUnits=true. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $1.5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01747/l2v5/build.log b/latest/cases/01747/l2v5/build.log new file mode 100644 index 000000000..29bb23669 --- /dev/null +++ b/latest/cases/01747/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01747/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01747/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01747/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01747/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01747/l2v5/index.heta b/latest/cases/01747/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01747/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01747/l3v2/index.heta b/latest/cases/01747/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01747/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01747/model-sbml-l2v5.xml b/latest/cases/01747/model-sbml-l2v5.xml new file mode 100644 index 000000000..b3611ec5c --- /dev/null +++ b/latest/cases/01747/model-sbml-l2v5.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + 1.5 + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01747/synopsis.txt b/latest/cases/01747/synopsis.txt new file mode 100644 index 000000000..ac2385424 --- /dev/null +++ b/latest/cases/01747/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A set stoichiometry for a substance-only species. +componentTags: Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedConstantStoichiometry, DefaultValue, HasOnlySubstanceUnits, NonUnityCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In this model, a stoichiometry is set via StoichiometryMath for a species set hasOnlySubstanceUnits=true. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $1.5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01748/l2v5/index.heta b/latest/cases/01748/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01748/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01748/l3v2/build.log b/latest/cases/01748/l3v2/build.log new file mode 100644 index 000000000..27528577d --- /dev/null +++ b/latest/cases/01748/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01748/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01748/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01748/model-sbml-l3v2.xml"... +[error] S1_stoich component does not exist which is not allowed for the "update" action. +[info] Setting references in elements, total length 82 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01748/l3v2/index.heta b/latest/cases/01748/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01748/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01748/model-sbml-l3v2.xml b/latest/cases/01748/model-sbml-l3v2.xml new file mode 100644 index 000000000..f5928184c --- /dev/null +++ b/latest/cases/01748/model-sbml-l3v2.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + time + 10 + + + + + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01748/synopsis.txt b/latest/cases/01748/synopsis.txt new file mode 100644 index 000000000..2185c9cf6 --- /dev/null +++ b/latest/cases/01748/synopsis.txt @@ -0,0 +1,39 @@ + +category: Test +synopsis: A variable stoichiometry for a substance-only species. +componentTags: AssignmentRule, CSymbolTime, Compartment, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, HasOnlySubstanceUnits, InitialValueReassigned, NonUnityCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a variable stoichiometry is externally set for a species set hasOnlySubstanceUnits=true. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1_stoich | $time / 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $time / 10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01749/l2v5/build.log b/latest/cases/01749/l2v5/build.log new file mode 100644 index 000000000..7369d8a49 --- /dev/null +++ b/latest/cases/01749/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01749/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01749/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01749/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01749/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01749/l2v5/index.heta b/latest/cases/01749/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01749/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01749/l3v2/index.heta b/latest/cases/01749/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01749/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01749/model-sbml-l2v5.xml b/latest/cases/01749/model-sbml-l2v5.xml new file mode 100644 index 000000000..8571e915a --- /dev/null +++ b/latest/cases/01749/model-sbml-l2v5.xml @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + + + time + 10 + + + + + + + + 0.1 + + + + + + diff --git a/latest/cases/01749/synopsis.txt b/latest/cases/01749/synopsis.txt new file mode 100644 index 000000000..f65e24867 --- /dev/null +++ b/latest/cases/01749/synopsis.txt @@ -0,0 +1,33 @@ + +category: Test +synopsis: A variable stoichiometry for a substance-only species. +componentTags: CSymbolTime, Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, HasOnlySubstanceUnits, NonUnityCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In this model, a variable stoichiometry is set with StoichiometryMath for a species set hasOnlySubstanceUnits=true. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $0.1$ |] +Note: the following stoichiometries are set separately: S1_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $time / 10$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01750/l2v5/index.heta b/latest/cases/01750/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01750/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01750/l3v2/index.heta b/latest/cases/01750/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01750/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01750/synopsis.txt b/latest/cases/01750/synopsis.txt new file mode 100644 index 000000000..5a351b493 --- /dev/null +++ b/latest/cases/01750/synopsis.txt @@ -0,0 +1,46 @@ + +category: Test +synopsis: A variable stoichiometry with a shadowing local parameter. +componentTags: AssignmentRule, CSymbolTime, Compartment, Reaction, Species +testTags: Amount, AssignedVariableStoichiometry, InitialValueReassigned, LocalParameters, NonUnityStoichiometry +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a variable stoichiometry has a local parameter that shadows its ID. + +The model contains: +* 1 species (S1) +* 1 local parameter (J0.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $S1_stoich$ |] +Note: the following stoichiometries are set separately: S1_stoich + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | S1_stoich | $time / 10$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of local parameter 'J0.S1_stoich' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $time / 10$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01751/l2v5/build.log b/latest/cases/01751/l2v5/build.log new file mode 100644 index 000000000..e4b7bae0c --- /dev/null +++ b/latest/cases/01751/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01751/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01751/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01751/model-sbml-l2v5.xml"... +[error] "stoichiometryMath" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01751/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01751/l2v5/index.heta b/latest/cases/01751/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01751/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01751/l3v2/index.heta b/latest/cases/01751/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01751/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01751/model-sbml-l2v5.xml b/latest/cases/01751/model-sbml-l2v5.xml new file mode 100644 index 000000000..b890c54a6 --- /dev/null +++ b/latest/cases/01751/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + time + 10 + + + + + + + + S1_stoich + + + + + + + + + diff --git a/latest/cases/01751/synopsis.txt b/latest/cases/01751/synopsis.txt new file mode 100644 index 000000000..fbc22ed18 --- /dev/null +++ b/latest/cases/01751/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A variable stoichiometry with a shadowing local parameter. +componentTags: CSymbolTime, Compartment, Reaction, Species, StoichiometryMath +testTags: Amount, AssignedVariableStoichiometry, DefaultValue, LocalParameters, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In this model, a variable stoichiometry has a local parameter that shadows its ID. + +The model contains: +* 1 species (S1) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1_stoich S1 | $S1_stoich$ |] +Note: the following stoichiometries are set separately: S1_stoich + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $time / 10$ | variable |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01752/l2v5/heta-code/output.heta b/latest/cases/01752/l2v5/heta-code/output.heta new file mode 100644 index 000000000..dfecc5fb6 --- /dev/null +++ b/latest/cases/01752/l2v5/heta-code/output.heta @@ -0,0 +1,19 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := S1__J0_local; + +S1__J0_local @Const { } = 0.1; + diff --git a/latest/cases/01752/l2v5/index.heta b/latest/cases/01752/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01752/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01752/l2v5/json/output.json b/latest/cases/01752/l2v5/json/output.json new file mode 100644 index 000000000..417372646 --- /dev/null +++ b/latest/cases/01752/l2v5/json/output.json @@ -0,0 +1,77 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "S1__J0_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "S1__J0_local" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01752/l3v2/index.heta b/latest/cases/01752/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01752/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01752/model-sbml-l2v5.xml b/latest/cases/01752/model-sbml-l2v5.xml new file mode 100644 index 000000000..fe8cbba07 --- /dev/null +++ b/latest/cases/01752/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + S1 + + + + + + + + + diff --git a/latest/cases/01752/output.heta b/latest/cases/01752/output.heta new file mode 100644 index 000000000..a911c8a9b --- /dev/null +++ b/latest/cases/01752/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: A local parameter that shadows a boundary species. +componentTags: Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a boundary species in that reaction. + +The model contains: +* 2 species (S1, S2) +* 1 local parameter (J0.S1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of local parameter 'J0.S1' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { boundary: true, compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := S1__J0_local; + +S1__J0_local @Const { } = 0.1; + diff --git a/latest/cases/01752/synopsis.txt b/latest/cases/01752/synopsis.txt new file mode 100644 index 000000000..b10dfdfda --- /dev/null +++ b/latest/cases/01752/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A local parameter that shadows a boundary species. +componentTags: Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a boundary species in that reaction. + +The model contains: +* 2 species (S1, S2) +* 1 local parameter (J0.S1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of local parameter 'J0.S1' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01753/l2v5/index.heta b/latest/cases/01753/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01753/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01753/l3v2/index.heta b/latest/cases/01753/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01753/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01753/synopsis.txt b/latest/cases/01753/synopsis.txt new file mode 100644 index 000000000..2303cae4e --- /dev/null +++ b/latest/cases/01753/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A local parameter that shadows a species reference, next to another species reference. +componentTags: Compartment, Reaction, Species +testTags: Amount, LocalParameters, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference, in a formula that also includes a different species reference. + +The model contains: +* 2 species (S1, S2) +* 1 local parameter (J0.S2_stoich) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $S1_stoich * S2_stoich$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of local parameter 'J0.S2_stoich' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | constant | +| Initial value of species reference 'S2_stoich' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01754/l2v5/index.heta b/latest/cases/01754/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01754/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01754/l3v2/build.log b/latest/cases/01754/l3v2/build.log new file mode 100644 index 000000000..a6b5308bd --- /dev/null +++ b/latest/cases/01754/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01754/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01754/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01754/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01754/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01754/l3v2/index.heta b/latest/cases/01754/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01754/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01754/model-sbml-l3v2.xml b/latest/cases/01754/model-sbml-l3v2.xml new file mode 100644 index 000000000..0de93d0ba --- /dev/null +++ b/latest/cases/01754/model-sbml-l3v2.xml @@ -0,0 +1,67 @@ + + + + + + + + + + + + 3 + 2 + + + + + + + + + + + P1 + 1 + + + + + + 2.3 + + + + + + 3 + + + + + + + + + + P1 + 1 + + + + + + 1.5 + + + + + + 0 + + + + + + + diff --git a/latest/cases/01754/synopsis.txt b/latest/cases/01754/synopsis.txt new file mode 100644 index 000000000..1c8a435e5 --- /dev/null +++ b/latest/cases/01754/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A persistent event triggered by a parameter with an initial assignment. +componentTags: EventWithDelay, InitialAssignment, Parameter +testTags: EventIsPersistent, EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events fire at t0 based on a parameter set with an initial assignment. One would cancel the other, were it not persistent. + +The model contains: +* 1 parameter (P1) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Delay* | *Event Assignments* | +| E0 | $P1 > 1$ | false | $2.3$ | $P1 = 3$ | +| E1 | $P1 > 1$ | false | $1.5$ | $P1 = 0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $3 / 2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01755/l2v5/index.heta b/latest/cases/01755/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01755/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01755/l3v2/build.log b/latest/cases/01755/l3v2/build.log new file mode 100644 index 000000000..b2b9dd018 --- /dev/null +++ b/latest/cases/01755/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01755/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01755/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01755/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01755/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01755/l3v2/index.heta b/latest/cases/01755/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01755/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01755/model-sbml-l3v2.xml b/latest/cases/01755/model-sbml-l3v2.xml new file mode 100644 index 000000000..b9ce4a987 --- /dev/null +++ b/latest/cases/01755/model-sbml-l3v2.xml @@ -0,0 +1,68 @@ + + + + + + + + + + + + + 3 + 2 + + + + + + + + + + + P1 + 1 + + + + + + 2.5 + + + + + + 3 + + + + + + + + + + P1 + 1 + + + + + + 1.5 + + + + + + 0 + + + + + + + diff --git a/latest/cases/01755/synopsis.txt b/latest/cases/01755/synopsis.txt new file mode 100644 index 000000000..959001886 --- /dev/null +++ b/latest/cases/01755/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A non-persistent event triggered by a parameter with an initial assignment. +componentTags: EventWithDelay, InitialAssignment, Parameter +testTags: EventIsNotPersistent, EventT0Firing, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events fire at t0 based on a parameter set with an initial assignment. One cancels the other, because it is not persistent. + +The model contains: +* 1 parameter (P1) + +There are 2 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *initialValue* | *Delay* | *Event Assignments* | +| E0 | $P1 > 1$ | false | false | $2.5$ | $P1 = 3$ | +| E1 | $P1 > 1$ | true | false | $1.5$ | $P1 = 0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $3 / 2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01756/l2v5/index.heta b/latest/cases/01756/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01756/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01756/l3v2/build.log b/latest/cases/01756/l3v2/build.log new file mode 100644 index 000000000..4b4621b4a --- /dev/null +++ b/latest/cases/01756/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01756/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01756/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01756/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01756/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01756/l3v2/index.heta b/latest/cases/01756/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01756/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01756/model-sbml-l3v2.xml b/latest/cases/01756/model-sbml-l3v2.xml new file mode 100644 index 000000000..ba8d616fe --- /dev/null +++ b/latest/cases/01756/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + 3 + 2 + + + + + + + + + + + P1 + 1 + + + + + + 2.5 + + + + + + + + P1 + 2 + + + + + + + + + + + P1 + 1 + + + + + + 1.3 + + + + + + 5 + + + + + + + diff --git a/latest/cases/01756/synopsis.txt b/latest/cases/01756/synopsis.txt new file mode 100644 index 000000000..a5e2a3bb9 --- /dev/null +++ b/latest/cases/01756/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A trigger-time event triggered by a parameter with an initial assignment. +componentTags: EventWithDelay, InitialAssignment, Parameter +testTags: EventT0Firing, EventUsesTriggerTimeValues, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events fire at t0 based on a parameter set with an initial assignment. One resets a value used by the second, but this is ignored because the first event uses trigger-time values. + +The model contains: +* 1 parameter (P1) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Delay* | *Event Assignments* | +| E0 | $P1 > 1$ | false | $2.5$ | $P1 = P1^2$ | +| E1 | $P1 > 1$ | false | $1.3$ | $P1 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $3 / 2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01757/l2v5/index.heta b/latest/cases/01757/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01757/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01757/l3v2/build.log b/latest/cases/01757/l3v2/build.log new file mode 100644 index 000000000..05d5bb772 --- /dev/null +++ b/latest/cases/01757/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01757/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01757/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01757/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01757/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01757/l3v2/index.heta b/latest/cases/01757/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01757/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01757/model-sbml-l3v2.xml b/latest/cases/01757/model-sbml-l3v2.xml new file mode 100644 index 000000000..d1142cd9b --- /dev/null +++ b/latest/cases/01757/model-sbml-l3v2.xml @@ -0,0 +1,72 @@ + + + + + + + + + + + + + 3 + 2 + + + + + + + + + + + P1 + 1 + + + + + + 2.5 + + + + + + + + P1 + 2 + + + + + + + + + + + P1 + 1 + + + + + + 1.3 + + + + + + 5 + + + + + + + diff --git a/latest/cases/01757/synopsis.txt b/latest/cases/01757/synopsis.txt new file mode 100644 index 000000000..742f1496a --- /dev/null +++ b/latest/cases/01757/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: An assignment-time event triggered by a parameter with an initial assignment. +componentTags: EventWithDelay, InitialAssignment, Parameter +testTags: EventT0Firing, EventUsesAssignmentTimeValues, InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events fire at t0 based on a parameter set with an initial assignment. One resets a value used by the second, which is incorporated because of its assignment-time setting. + +The model contains: +* 1 parameter (P1) + +There are 2 events: + +[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Use values from:* | *Delay* | *Event Assignments* | +| E0 | $P1 > 1$ | false | Assignment time | $2.5$ | $P1 = P1^2$ | +| E1 | $P1 > 1$ | false | Trigger time | $1.3$ | $P1 = 5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $3 / 2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01758/l2v5/index.heta b/latest/cases/01758/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01758/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01758/l3v2/build.log b/latest/cases/01758/l3v2/build.log new file mode 100644 index 000000000..9659ab2ab --- /dev/null +++ b/latest/cases/01758/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01758/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01758/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01758/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01758/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01758/l3v2/index.heta b/latest/cases/01758/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01758/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01758/model-sbml-l3v2.xml b/latest/cases/01758/model-sbml-l3v2.xml new file mode 100644 index 000000000..a0609c10e --- /dev/null +++ b/latest/cases/01758/model-sbml-l3v2.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + P1 + 1 + + + + + + 2.3 + + + + + + 3 + + + + + + + + + + P1 + 1 + + + + + + 1.5 + + + + + + 0 + + + + + + + diff --git a/latest/cases/01758/synopsis.txt b/latest/cases/01758/synopsis.txt new file mode 100644 index 000000000..39fe329c8 --- /dev/null +++ b/latest/cases/01758/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A persistent event triggered by a parameter with an initial assignment. +componentTags: EventWithDelay, Parameter +testTags: EventIsPersistent, EventT0Firing, NonConstantParameter +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events fire at t0 based on a parameter. One would cancel the other, were it not persistent. The second event actually triggers itself, as its trigger has lapsed to being false in the meantime. This model is a duplicate of 1754, without the initial assignment. + +The model contains: +* 1 parameter (P1) + +There are 2 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Delay* | *Event Assignments* | +| E0 | $P1 > 1$ | false | $2.3$ | $P1 = 3$ | +| E1 | $P1 > 1$ | false | $1.5$ | $P1 = 0$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $1.5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01759/l2v5/build.log b/latest/cases/01759/l2v5/build.log new file mode 100644 index 000000000..22c9845a2 --- /dev/null +++ b/latest/cases/01759/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01759/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01759/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01759/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01759/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01759/l2v5/index.heta b/latest/cases/01759/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01759/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01759/l3v2/build.log b/latest/cases/01759/l3v2/build.log new file mode 100644 index 000000000..2e1cab296 --- /dev/null +++ b/latest/cases/01759/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01759/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01759/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01759/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01759/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01759/l3v2/index.heta b/latest/cases/01759/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01759/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01759/model-sbml-l2v5.xml b/latest/cases/01759/model-sbml-l2v5.xml new file mode 100644 index 000000000..c210c359b --- /dev/null +++ b/latest/cases/01759/model-sbml-l2v5.xml @@ -0,0 +1,74 @@ + + + + + + + + + + + + + P1 + 1 + + + + + + 2 + + + + + + 3 + + + + + + + + + + P1 + 1 + + + + + + 1 + + + + + + 0 + + + + + + + + + + time + 0.65 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01759/model-sbml-l3v2.xml b/latest/cases/01759/model-sbml-l3v2.xml new file mode 100644 index 000000000..fef047417 --- /dev/null +++ b/latest/cases/01759/model-sbml-l3v2.xml @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + P1 + 1 + + + + + + 2 + + + + + + 3 + + + + + + + + + + P1 + 1 + + + + + + 1 + + + + + + 0 + + + + + + + + + + time + 0.65 + + + + + + + 2 + + + + + + + diff --git a/latest/cases/01759/synopsis.txt b/latest/cases/01759/synopsis.txt new file mode 100644 index 000000000..ace351386 --- /dev/null +++ b/latest/cases/01759/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A persistent event triggered by a parameter with an initial assignment. +componentTags: CSymbolTime, EventNoDelay, EventWithDelay, Parameter +testTags: EventIsPersistent, NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two events have the same trigger, but different delays. The one to execute first sets the trigger to 'false', and the one that fires second sets the trigger to 'true' again, causing both the fire repeatedly. A version of tests 1754 and 1758, but without t0 firing or initial assignments. + +The model contains: +* 1 parameter (P1) + +There are 3 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $P1 > 1$ | $2$ | $P1 = 3$ | +| E1 | $P1 > 1$ | $1$ | $P1 = 0$ | +| E2 | $time > 0.65$ | $0$ | $P1 = 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0.5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01760/l2v5/heta-code/output.heta b/latest/cases/01760/l2v5/heta-code/output.heta new file mode 100644 index 000000000..fe562c865 --- /dev/null +++ b/latest/cases/01760/l2v5/heta-code/output.heta @@ -0,0 +1,18 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := avogadro__J0_local; + +avogadro__J0_local @Const { } = 0.1; + diff --git a/latest/cases/01760/l2v5/index.heta b/latest/cases/01760/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01760/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01760/l2v5/json/output.json b/latest/cases/01760/l2v5/json/output.json new file mode 100644 index 000000000..b5f9449c7 --- /dev/null +++ b/latest/cases/01760/l2v5/json/output.json @@ -0,0 +1,64 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "avogadro__J0_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "avogadro__J0_local" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01760/l3v2/heta-code/output.heta b/latest/cases/01760/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c72f92a08 --- /dev/null +++ b/latest/cases/01760/l3v2/heta-code/output.heta @@ -0,0 +1,13 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := avogadro__J0_local; + +avogadro__J0_local @Const { } = 0.1; + diff --git a/latest/cases/01760/l3v2/index.heta b/latest/cases/01760/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01760/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01760/l3v2/json/output.json b/latest/cases/01760/l3v2/json/output.json new file mode 100644 index 000000000..e395b4992 --- /dev/null +++ b/latest/cases/01760/l3v2/json/output.json @@ -0,0 +1,39 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "avogadro__J0_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "avogadro__J0_local" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01760/model-sbml-l2v5.xml b/latest/cases/01760/model-sbml-l2v5.xml new file mode 100644 index 000000000..70b00efa7 --- /dev/null +++ b/latest/cases/01760/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + avogadro + + + + + + + + + diff --git a/latest/cases/01760/model-sbml-l3v2.xml b/latest/cases/01760/model-sbml-l3v2.xml new file mode 100644 index 000000000..ffd9a2b5e --- /dev/null +++ b/latest/cases/01760/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + avogadro + + + + + + + + + diff --git a/latest/cases/01760/output.heta b/latest/cases/01760/output.heta new file mode 100644 index 000000000..deffcb06e --- /dev/null +++ b/latest/cases/01760/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: A reaction with a local parameter named 'avogadro'. +componentTags: Compartment, Reaction, Species +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter is given the id 'avogadro', which the kinetic law references. + +The model contains: +* 1 species (S1) +* 1 local parameter (J0.avogadro) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of local parameter 'J0.avogadro' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := avogadro__J0_local; + +avogadro__J0_local @Const { } = 0.1; + diff --git a/latest/cases/01760/synopsis.txt b/latest/cases/01760/synopsis.txt new file mode 100644 index 000000000..b7dafa3ce --- /dev/null +++ b/latest/cases/01760/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A reaction with a local parameter named 'avogadro'. +componentTags: Compartment, Reaction, Species +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter is given the id 'avogadro', which the kinetic law references. + +The model contains: +* 1 species (S1) +* 1 local parameter (J0.avogadro) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of local parameter 'J0.avogadro' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01761/l2v5/heta-code/output.heta b/latest/cases/01761/l2v5/heta-code/output.heta new file mode 100644 index 000000000..72b13ddc6 --- /dev/null +++ b/latest/cases/01761/l2v5/heta-code/output.heta @@ -0,0 +1,18 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := avogadro; + +avogadro @Record { } .= 0.1; + diff --git a/latest/cases/01761/l2v5/index.heta b/latest/cases/01761/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01761/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01761/l2v5/json/output.json b/latest/cases/01761/l2v5/json/output.json new file mode 100644 index 000000000..cff87fe5f --- /dev/null +++ b/latest/cases/01761/l2v5/json/output.json @@ -0,0 +1,66 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "avogadro" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "avogadro", + "assignments": { + "start_": "0.1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01761/l3v2/heta-code/output.heta b/latest/cases/01761/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a5e2f3cf6 --- /dev/null +++ b/latest/cases/01761/l3v2/heta-code/output.heta @@ -0,0 +1,13 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := avogadro; + +avogadro @Const { } = 0.1; + diff --git a/latest/cases/01761/l3v2/index.heta b/latest/cases/01761/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01761/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01761/l3v2/json/output.json b/latest/cases/01761/l3v2/json/output.json new file mode 100644 index 000000000..fd0cb8125 --- /dev/null +++ b/latest/cases/01761/l3v2/json/output.json @@ -0,0 +1,39 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "avogadro" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Const", + "id": "avogadro", + "num": 0.1 + } +] \ No newline at end of file diff --git a/latest/cases/01761/model-sbml-l2v5.xml b/latest/cases/01761/model-sbml-l2v5.xml new file mode 100644 index 000000000..c62576fa3 --- /dev/null +++ b/latest/cases/01761/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + avogadro + + + + + + diff --git a/latest/cases/01761/model-sbml-l3v2.xml b/latest/cases/01761/model-sbml-l3v2.xml new file mode 100644 index 000000000..49ccbc094 --- /dev/null +++ b/latest/cases/01761/model-sbml-l3v2.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + avogadro + + + + + + diff --git a/latest/cases/01761/output.heta b/latest/cases/01761/output.heta new file mode 100644 index 000000000..c3dabd4b6 --- /dev/null +++ b/latest/cases/01761/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: A parameter with the id 'avogadro' +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a parameter named 'avogadro' is used in a kinetic law. + +The model contains: +* 1 species (S1) +* 1 parameter (avogadro) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter avogadro | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := avogadro; + +avogadro @Const { } = 0.1; + diff --git a/latest/cases/01761/synopsis.txt b/latest/cases/01761/synopsis.txt new file mode 100644 index 000000000..eb6103ee9 --- /dev/null +++ b/latest/cases/01761/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A parameter with the id 'avogadro' +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a parameter named 'avogadro' is used in a kinetic law. + +The model contains: +* 1 species (S1) +* 1 parameter (avogadro) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter avogadro | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01762/l2v5/index.heta b/latest/cases/01762/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01762/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01762/l3v2/heta-code/output.heta b/latest/cases/01762/l3v2/heta-code/output.heta new file mode 100644 index 000000000..b49b5d8a9 --- /dev/null +++ b/latest/cases/01762/l3v2/heta-code/output.heta @@ -0,0 +1,13 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := 6.02214076e+23 / avogadro__J0_local; + +avogadro__J0_local @Const { } = 1e+24; + diff --git a/latest/cases/01762/l3v2/index.heta b/latest/cases/01762/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01762/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01762/l3v2/json/output.json b/latest/cases/01762/l3v2/json/output.json new file mode 100644 index 000000000..025ecbb23 --- /dev/null +++ b/latest/cases/01762/l3v2/json/output.json @@ -0,0 +1,39 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "avogadro__J0_local", + "num": 1e+24 + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "6.02214076e+23 / avogadro__J0_local" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01762/model-sbml-l3v2.xml b/latest/cases/01762/model-sbml-l3v2.xml new file mode 100644 index 000000000..510c382e2 --- /dev/null +++ b/latest/cases/01762/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + avogadro + avogadro + + + + + + + + + + diff --git a/latest/cases/01762/output.heta b/latest/cases/01762/output.heta new file mode 100644 index 000000000..1bc5516cf --- /dev/null +++ b/latest/cases/01762/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: A reaction with a local parameter named 'avogadro'. +componentTags: CSymbolAvogadro, Compartment, Reaction, Species +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter is given the id 'avogadro', and the kinetic law references both it and the avogadro csymbol. + +The model contains: +* 1 species (S1) +* 1 local parameter (J0.avogadro) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $avogadro / avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of local parameter 'J0.avogadro' | $1e+24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := 6.02214076e+23 / avogadro__J0_local; + +avogadro__J0_local @Const { } = 1e+24; + diff --git a/latest/cases/01762/synopsis.txt b/latest/cases/01762/synopsis.txt new file mode 100644 index 000000000..c1f4c2883 --- /dev/null +++ b/latest/cases/01762/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A reaction with a local parameter named 'avogadro'. +componentTags: CSymbolAvogadro, Compartment, Reaction, Species +testTags: Amount, LocalParameters +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter is given the id 'avogadro', and the kinetic law references both it and the avogadro csymbol. + +The model contains: +* 1 species (S1) +* 1 local parameter (J0.avogadro) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $avogadro / avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of local parameter 'J0.avogadro' | $1e+24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01763/l2v5/index.heta b/latest/cases/01763/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01763/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01763/l3v2/heta-code/output.heta b/latest/cases/01763/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a18c901bc --- /dev/null +++ b/latest/cases/01763/l3v2/heta-code/output.heta @@ -0,0 +1,13 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := 6.02214076e+23 / avogadro; + +avogadro @Const { } = 1e+24; + diff --git a/latest/cases/01763/l3v2/index.heta b/latest/cases/01763/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01763/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01763/l3v2/json/output.json b/latest/cases/01763/l3v2/json/output.json new file mode 100644 index 000000000..b19137f14 --- /dev/null +++ b/latest/cases/01763/l3v2/json/output.json @@ -0,0 +1,39 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "6.02214076e+23 / avogadro" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Const", + "id": "avogadro", + "num": 1e+24 + } +] \ No newline at end of file diff --git a/latest/cases/01763/model-sbml-l3v2.xml b/latest/cases/01763/model-sbml-l3v2.xml new file mode 100644 index 000000000..562622971 --- /dev/null +++ b/latest/cases/01763/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + avogadro + avogadro + + + + + + + diff --git a/latest/cases/01763/output.heta b/latest/cases/01763/output.heta new file mode 100644 index 000000000..4e0b66186 --- /dev/null +++ b/latest/cases/01763/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: A parameter named 'avogadro' as well as the csymbol avogadro. +componentTags: CSymbolAvogadro, Compartment, Parameter, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a parameter is given the id 'avogadro', and the kinetic law references both it and the avogadro csymbol. + +The model contains: +* 1 species (S1) +* 1 parameter (avogadro) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $avogadro / avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter avogadro | $1e+24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := 6.02214076e+23 / avogadro; + +avogadro @Const { } = 1e+24; + diff --git a/latest/cases/01763/synopsis.txt b/latest/cases/01763/synopsis.txt new file mode 100644 index 000000000..65a4657eb --- /dev/null +++ b/latest/cases/01763/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A parameter named 'avogadro' as well as the csymbol avogadro. +componentTags: CSymbolAvogadro, Compartment, Parameter, Reaction, Species +testTags: Amount +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a parameter is given the id 'avogadro', and the kinetic law references both it and the avogadro csymbol. + +The model contains: +* 1 species (S1) +* 1 parameter (avogadro) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $avogadro / avogadro$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial value of parameter avogadro | $1e+24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01764/l2v5/index.heta b/latest/cases/01764/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01764/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01764/l3v2/index.heta b/latest/cases/01764/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01764/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01764/synopsis.txt b/latest/cases/01764/synopsis.txt new file mode 100644 index 000000000..fd42a597a --- /dev/null +++ b/latest/cases/01764/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A local parameter shadowing a species reference. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, LocalParameters, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in an assignment rule, and refers to the species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J0.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> S2 | $S1_stoich$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | k0 | $S1_stoich * 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $S1_stoich * 2$ | variable | +| Initial value of local parameter 'J0.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01765/l2v5/index.heta b/latest/cases/01765/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01765/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01765/l3v2/index.heta b/latest/cases/01765/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01765/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01765/synopsis.txt b/latest/cases/01765/synopsis.txt new file mode 100644 index 000000000..2f295f1aa --- /dev/null +++ b/latest/cases/01765/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A local parameter shadowing a species reference. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in a rate rule, and refers to the species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J0.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> S2 | $S1_stoich$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k0 | $S1_stoich * 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $0$ | variable | +| Initial value of local parameter 'J0.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01766/l2v5/index.heta b/latest/cases/01766/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01766/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01766/l3v2/build.log b/latest/cases/01766/l3v2/build.log new file mode 100644 index 000000000..44475e875 --- /dev/null +++ b/latest/cases/01766/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01766/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01766/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01766/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 86 +[error] No required "num" property for "k0" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01766/l3v2/index.heta b/latest/cases/01766/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01766/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01766/model-sbml-l3v2.xml b/latest/cases/01766/model-sbml-l3v2.xml new file mode 100644 index 000000000..11d2e0fc2 --- /dev/null +++ b/latest/cases/01766/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + S1_stoich + 2 + + + + + + + + + + + + 0.01 + + + + + + + + + + S1_stoich + + + + + + + + + diff --git a/latest/cases/01766/synopsis.txt b/latest/cases/01766/synopsis.txt new file mode 100644 index 000000000..59f09a2ce --- /dev/null +++ b/latest/cases/01766/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A local parameter shadowing a species reference. +componentTags: Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, LocalParameters, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in an initial assignment, and refers to the species reference. A modified version of 1656 that is legal in l3v2 (which doesn't allow local parameters to have the ID of a species reference in the same reaction). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $0.01$ | +| J1: -> S2 | $S1_stoich$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $S1_stoich * 2$ | constant | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01767/l2v5/index.heta b/latest/cases/01767/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01767/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01767/l3v2/build.log b/latest/cases/01767/l3v2/build.log new file mode 100644 index 000000000..e8fe8ed0f --- /dev/null +++ b/latest/cases/01767/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01767/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01767/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01767/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 86 +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: k0 [ode_]= S1_stoich * 2; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01767/l3v2/index.heta b/latest/cases/01767/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01767/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01767/model-sbml-l3v2.xml b/latest/cases/01767/model-sbml-l3v2.xml new file mode 100644 index 000000000..9a75b9b21 --- /dev/null +++ b/latest/cases/01767/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + S1_stoich + 2 + + + + + + + + + + + + 0.01 + + + + + + + + + + S1_stoich + + + + + + + + + diff --git a/latest/cases/01767/synopsis.txt b/latest/cases/01767/synopsis.txt new file mode 100644 index 000000000..0c506fd3f --- /dev/null +++ b/latest/cases/01767/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: A local parameter shadowing a species reference. +componentTags: AssignmentRule, Compartment, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, LocalParameters, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in an assignment rule, and refers to the species reference. A modified version of 1764 that is legal in l3v2 (which doesn't allow local parameters to have the ID of a species reference in the same reaction). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $0.01$ | +| J1: -> S2 | $S1_stoich$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | k0 | $S1_stoich * 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $S1_stoich * 2$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01768/l2v5/index.heta b/latest/cases/01768/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01768/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01768/l3v2/build.log b/latest/cases/01768/l3v2/build.log new file mode 100644 index 000000000..07661bc0f --- /dev/null +++ b/latest/cases/01768/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01768/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01768/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01768/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 87 +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: k0_proc [ode_]= S1_stoich * 2; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01768/l3v2/index.heta b/latest/cases/01768/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01768/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01768/model-sbml-l3v2.xml b/latest/cases/01768/model-sbml-l3v2.xml new file mode 100644 index 000000000..a80efb7c0 --- /dev/null +++ b/latest/cases/01768/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + S1_stoich + 2 + + + + + + + + + + + + 0.01 + + + + + + + + + + S1_stoich + + + + + + + + + diff --git a/latest/cases/01768/synopsis.txt b/latest/cases/01768/synopsis.txt new file mode 100644 index 000000000..66b0ef6b4 --- /dev/null +++ b/latest/cases/01768/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: A local parameter shadowing a species reference. +componentTags: Compartment, Parameter, RateRule, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in a rate rule, and refers to the species reference. A modified version of 1765 that is legal in l3v2 (which doesn't allow local parameters to have the ID of a species reference in the same reaction). + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $0.01$ | +| J1: -> S2 | $S1_stoich$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | k0 | $S1_stoich * 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $0$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01769/l2v5/index.heta b/latest/cases/01769/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01769/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01769/l3v2/build.log b/latest/cases/01769/l3v2/build.log new file mode 100644 index 000000000..36855227f --- /dev/null +++ b/latest/cases/01769/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01769/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01769/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01769/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 87 +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: k0 [E0]= S1_stoich * 2; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01769/l3v2/index.heta b/latest/cases/01769/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01769/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01769/model-sbml-l3v2.xml b/latest/cases/01769/model-sbml-l3v2.xml new file mode 100644 index 000000000..fb2894775 --- /dev/null +++ b/latest/cases/01769/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + S1_stoich + + + + + + + + + + + + + + S1 + 1.885 + + + + + + + + + S1_stoich + 2 + + + + + + + + diff --git a/latest/cases/01769/synopsis.txt b/latest/cases/01769/synopsis.txt new file mode 100644 index 000000000..2be8fa080 --- /dev/null +++ b/latest/cases/01769/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: A local parameter shadowing a species reference used in an event assignment. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in an event assignment, and refers to the species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $0.01$ | +| J1: -> S2 | $S1_stoich$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $S1 < 1.885$ | $k0 = S1_stoich * 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $0$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01770/l2v5/index.heta b/latest/cases/01770/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01770/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01770/l3v2/build.log b/latest/cases/01770/l3v2/build.log new file mode 100644 index 000000000..bc8af1ef3 --- /dev/null +++ b/latest/cases/01770/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01770/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01770/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01770/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 87 +[error] Component "S1_stoich" is not found in space "nameless" as expected in DSwitcher: "E0" + S1 < (S1_stoich - 0.115); +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01770/l3v2/index.heta b/latest/cases/01770/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01770/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01770/model-sbml-l3v2.xml b/latest/cases/01770/model-sbml-l3v2.xml new file mode 100644 index 000000000..6a00c79ef --- /dev/null +++ b/latest/cases/01770/model-sbml-l3v2.xml @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + S1_stoich + + + + + + + + + + + + + + S1 + + + S1_stoich + 0.115 + + + + + + + + 4 + + + + + + + diff --git a/latest/cases/01770/synopsis.txt b/latest/cases/01770/synopsis.txt new file mode 100644 index 000000000..642088acd --- /dev/null +++ b/latest/cases/01770/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: A local parameter shadowing a species reference in an event trigger. +componentTags: Compartment, EventNoDelay, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in an event trigger, and refers to the species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $0.01$ | +| J1: -> S2 | $S1_stoich$ |] + + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $S1 < (S1_stoich - 0.115)$ | $k0 = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $0$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01771/l2v5/index.heta b/latest/cases/01771/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01771/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01771/l3v2/build.log b/latest/cases/01771/l3v2/build.log new file mode 100644 index 000000000..15d34b00a --- /dev/null +++ b/latest/cases/01771/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01771/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01771/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01771/model-sbml-l3v2.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01771/model-sbml-l3v2.xml" +[info] Setting references in elements, total length 79 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01771/l3v2/index.heta b/latest/cases/01771/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01771/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01771/model-sbml-l3v2.xml b/latest/cases/01771/model-sbml-l3v2.xml new file mode 100644 index 000000000..e94f173a3 --- /dev/null +++ b/latest/cases/01771/model-sbml-l3v2.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + S1_stoich + + + + + + + + + + + + + + S1 + 1.885 + + + + + + S1_stoich + + + + + + 4 + + + + + + + diff --git a/latest/cases/01771/synopsis.txt b/latest/cases/01771/synopsis.txt new file mode 100644 index 000000000..2ce4811e2 --- /dev/null +++ b/latest/cases/01771/synopsis.txt @@ -0,0 +1,44 @@ + +category: Test +synopsis: A local parameter shadowing a species reference in an event delay. +componentTags: Compartment, EventWithDelay, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in an event delay, and refers to the species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $0.01$ | +| J1: -> S2 | $S1_stoich$ |] + + +There is one event: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* | +| E0 | $S1 < 1.885$ | $S1_stoich$ | $k0 = 4$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $0$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01772/l2v5/index.heta b/latest/cases/01772/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01772/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01772/l3v2/heta-code/output.heta b/latest/cases/01772/l3v2/heta-code/output.heta new file mode 100644 index 000000000..11c4823c0 --- /dev/null +++ b/latest/cases/01772/l3v2/heta-code/output.heta @@ -0,0 +1,23 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J0 @Reaction { actors: 2*S1 = , }; +J0 := 0.01; +J1 @Reaction { actors: = S2, }; +J1 := S1_stoich__J1_local; + +k0 @Record { } .= 0; +k0 [E0]= 4; +k0 [E1]= 6; + +S1_stoich__J1_local @Const { } = 0.01; + +E0 @DSwitcher { trigger: S1 < 1.885, }; +E1 @DSwitcher { trigger: S1 < 1.885, }; + diff --git a/latest/cases/01772/l3v2/index.heta b/latest/cases/01772/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01772/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01772/l3v2/json/output.json b/latest/cases/01772/l3v2/json/output.json new file mode 100644 index 000000000..036acb267 --- /dev/null +++ b/latest/cases/01772/l3v2/json/output.json @@ -0,0 +1,81 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": -2 + } + ] + }, + { + "class": "Const", + "id": "S1_stoich__J1_local", + "num": 0.01 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "S1_stoich__J1_local" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Record", + "id": "k0", + "assignments": { + "start_": "0", + "E0": "4", + "E1": "6" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "S1 < 1.885" + }, + { + "class": "DSwitcher", + "id": "E1", + "trigger": "S1 < 1.885" + } +] \ No newline at end of file diff --git a/latest/cases/01772/model-sbml-l3v2.xml b/latest/cases/01772/model-sbml-l3v2.xml new file mode 100644 index 000000000..4fbf2c589 --- /dev/null +++ b/latest/cases/01772/model-sbml-l3v2.xml @@ -0,0 +1,88 @@ + + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + S1_stoich + + + + + + + + + + + + + + S1 + 1.885 + + + + + + 1 + + + + + + 4 + + + + + + + + + + S1 + 1.885 + + + + + + S1_stoich + + + + + + 6 + + + + + + + diff --git a/latest/cases/01772/output.heta b/latest/cases/01772/output.heta new file mode 100644 index 000000000..2607fd3d7 --- /dev/null +++ b/latest/cases/01772/output.heta @@ -0,0 +1,70 @@ +/* +category: Test +synopsis: A local parameter shadowing a species reference in an event priority. +componentTags: Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in an event priority, and refers to the species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $0.01$ | +| J1: -> S2 | $S1_stoich$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $S1 < 1.885$ | $1$ | $k0 = 4$ | +| E1 | $S1 < 1.885$ | $S1_stoich$ | $k0 = 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $0$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 2; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J0 @Reaction { actors: 2*S1 = , }; +J0 := 0.01; +J1 @Reaction { actors: = S2, }; +J1 := S1_stoich__J1_local; + +k0 @Record { } .= 0; +k0 [E0]= 4; +k0 [E1]= 6; + +S1_stoich__J1_local @Const { } = 0.01; + +E0 @DSwitcher { trigger: S1 < 1.885, }; +E1 @DSwitcher { trigger: S1 < 1.885, }; + diff --git a/latest/cases/01772/synopsis.txt b/latest/cases/01772/synopsis.txt new file mode 100644 index 000000000..f0d06fc58 --- /dev/null +++ b/latest/cases/01772/synopsis.txt @@ -0,0 +1,45 @@ + +category: Test +synopsis: A local parameter shadowing a species reference in an event priority. +componentTags: Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in an event priority, and refers to the species reference. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (k0) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $0.01$ | +| J1: -> S2 | $S1_stoich$ |] + + +There are 2 events: + +[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* | +| E0 | $S1 < 1.885$ | $1$ | $k0 = 4$ | +| E1 | $S1 < 1.885$ | $S1_stoich$ | $k0 = 6$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter k0 | $0$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01773/l2v5/index.heta b/latest/cases/01773/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01773/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01773/l3v2/build.log b/latest/cases/01773/l3v2/build.log new file mode 100644 index 000000000..ac32d0766 --- /dev/null +++ b/latest/cases/01773/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01773/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01773/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01773/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 85 +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: J0 [ode_]= S1_stoich / 200; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01773/l3v2/index.heta b/latest/cases/01773/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01773/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01773/model-sbml-l3v2.xml b/latest/cases/01773/model-sbml-l3v2.xml new file mode 100644 index 000000000..ec1f347b9 --- /dev/null +++ b/latest/cases/01773/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + S1_stoich + 200 + + + + + + + + + + + S1_stoich + + + + + + + + + diff --git a/latest/cases/01773/synopsis.txt b/latest/cases/01773/synopsis.txt new file mode 100644 index 000000000..51c283c66 --- /dev/null +++ b/latest/cases/01773/synopsis.txt @@ -0,0 +1,36 @@ + +category: Test +synopsis: A local parameter shadowing a species reference in a kinetic law. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in a kinetic law, and refers to the species reference. + +The model contains: +* 2 species (S1, S2) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $S1_stoich / 200$ | +| J1: -> S2 | $S1_stoich$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01774/l2v5/index.heta b/latest/cases/01774/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01774/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01774/l3v2/build.log b/latest/cases/01774/l3v2/build.log new file mode 100644 index 000000000..42e952603 --- /dev/null +++ b/latest/cases/01774/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01774/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01774/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01774/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 87 +[error] Component "S1_stoich" is not found in space "nameless" as expected in expression: J2 [ode_]= S1_stoich / 20; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01774/l3v2/index.heta b/latest/cases/01774/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01774/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01774/model-sbml-l3v2.xml b/latest/cases/01774/model-sbml-l3v2.xml new file mode 100644 index 000000000..b58eb75dd --- /dev/null +++ b/latest/cases/01774/model-sbml-l3v2.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + 0.01 + + + + + + + + + + S1_stoich + + + + + + + + + + + + + + + S1_stoich + 20 + + + + + + + diff --git a/latest/cases/01774/synopsis.txt b/latest/cases/01774/synopsis.txt new file mode 100644 index 000000000..27648c111 --- /dev/null +++ b/latest/cases/01774/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: A local parameter shadowing a species reference in a kinetic law. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows a species reference. That ID is used in a kinetic law, and refers to the species reference. Similar to 1773, but the species reference and local parameter are both in different reactions from the use of the species reference in the kinetic law. + +The model contains: +* 3 species (S1, S2, S3) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: 2S1 -> | $0.01$ | +| J1: -> S2 | $S1_stoich$ | +| J2: S3 -> | $S1_stoich / 20$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial amount of species S3 | $4$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant | +| Initial volume of compartment 'C' | $2$ | constant | +| Initial value of species reference 'S1_stoich' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01775/l2v5/index.heta b/latest/cases/01775/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01775/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01775/l3v2/heta-code/output.heta b/latest/cases/01775/l3v2/heta-code/output.heta new file mode 100644 index 000000000..742ad7d1d --- /dev/null +++ b/latest/cases/01775/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01775/l3v2/index.heta b/latest/cases/01775/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01775/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01775/l3v2/json/output.json b/latest/cases/01775/l3v2/json/output.json new file mode 100644 index 000000000..d8a45b019 --- /dev/null +++ b/latest/cases/01775/l3v2/json/output.json @@ -0,0 +1,56 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01775/model-sbml-l3v2.xml b/latest/cases/01775/model-sbml-l3v2.xml new file mode 100644 index 000000000..525617604 --- /dev/null +++ b/latest/cases/01775/model-sbml-l3v2.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + avogadro + 1 24 + + + + + + + + avogadro + 1.5 24 + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01775/output.heta b/latest/cases/01775/output.heta new file mode 100644 index 000000000..05d3556cb --- /dev/null +++ b/latest/cases/01775/output.heta @@ -0,0 +1,59 @@ +/* +category: Test +synopsis: Model and species conversion factors set with avogadro. +componentTags: CSymbolAvogadro, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set via an initial assignment with the avogadro csymbol. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $avogadro / 1e24$ | constant | +| Initial value of parameter s1_cf | $avogadro / 1.5e24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; +s1_cf @Const { } = 5; + diff --git a/latest/cases/01775/synopsis.txt b/latest/cases/01775/synopsis.txt new file mode 100644 index 000000000..ad8901142 --- /dev/null +++ b/latest/cases/01775/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Model and species conversion factors set with avogadro. +componentTags: CSymbolAvogadro, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, model and species conversion factors are set via an initial assignment with the avogadro csymbol. + +The model contains: +* 2 species (S1, S2) +* 2 parameters (m_cf, s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $avogadro / 1e24$ | constant | +| Initial value of parameter s1_cf | $avogadro / 1.5e24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01776/l2v5/index.heta b/latest/cases/01776/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01776/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01776/l3v2/heta-code/output.heta b/latest/cases/01776/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4b8ce4fca --- /dev/null +++ b/latest/cases/01776/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + diff --git a/latest/cases/01776/l3v2/index.heta b/latest/cases/01776/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01776/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01776/l3v2/json/output.json b/latest/cases/01776/l3v2/json/output.json new file mode 100644 index 000000000..744238981 --- /dev/null +++ b/latest/cases/01776/l3v2/json/output.json @@ -0,0 +1,51 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "s1_cf", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01776/model-sbml-l3v2.xml b/latest/cases/01776/model-sbml-l3v2.xml new file mode 100644 index 000000000..97eca19a5 --- /dev/null +++ b/latest/cases/01776/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + avogadro + 1.5 24 + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01776/output.heta b/latest/cases/01776/output.heta new file mode 100644 index 000000000..d9558d222 --- /dev/null +++ b/latest/cases/01776/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Species conversion factor set with avogadro. +componentTags: CSymbolAvogadro, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +REVOLUTION!!!! + +In this model, a species conversion factor is set via an initial assignment with the avogadro csymbol. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $avogadro / 1.5e24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +s1_cf @Const { } = 5; + diff --git a/latest/cases/01776/synopsis.txt b/latest/cases/01776/synopsis.txt new file mode 100644 index 000000000..2067abafd --- /dev/null +++ b/latest/cases/01776/synopsis.txt @@ -0,0 +1,42 @@ + +category: Test +synopsis: Species conversion factor set with avogadro. +componentTags: CSymbolAvogadro, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +REVOLUTION!!!! + +In this model, a species conversion factor is set via an initial assignment with the avogadro csymbol. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (s1_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the species 'S1' is 's1_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter s1_cf | $avogadro / 1.5e24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01777/l2v5/index.heta b/latest/cases/01777/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01777/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01777/l3v2/heta-code/output.heta b/latest/cases/01777/l3v2/heta-code/output.heta new file mode 100644 index 000000000..785355eea --- /dev/null +++ b/latest/cases/01777/l3v2/heta-code/output.heta @@ -0,0 +1,14 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; + diff --git a/latest/cases/01777/l3v2/index.heta b/latest/cases/01777/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01777/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01777/l3v2/json/output.json b/latest/cases/01777/l3v2/json/output.json new file mode 100644 index 000000000..3a6a48e58 --- /dev/null +++ b/latest/cases/01777/l3v2/json/output.json @@ -0,0 +1,51 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3 / C" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "0.01" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "class": "Const", + "id": "m_cf", + "num": 3 + } +] \ No newline at end of file diff --git a/latest/cases/01777/model-sbml-l3v2.xml b/latest/cases/01777/model-sbml-l3v2.xml new file mode 100644 index 000000000..387dae176 --- /dev/null +++ b/latest/cases/01777/model-sbml-l3v2.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + avogadro + 1 24 + + + + + + + + + + + + + + + 0.01 + + + + + + diff --git a/latest/cases/01777/output.heta b/latest/cases/01777/output.heta new file mode 100644 index 000000000..c68c6d1c0 --- /dev/null +++ b/latest/cases/01777/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Model conversion factor set with avogadro. +componentTags: CSymbolAvogadro, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor is set via an initial assignment with the avogadro csymbol. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $avogadro / 1e24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 3 / C; + +J0 @Reaction { actors: S1 = S2, }; +J0 := 0.01; + +m_cf @Const { } = 3; + diff --git a/latest/cases/01777/synopsis.txt b/latest/cases/01777/synopsis.txt new file mode 100644 index 000000000..7da2eb9ac --- /dev/null +++ b/latest/cases/01777/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Model conversion factor set with avogadro. +componentTags: CSymbolAvogadro, Compartment, InitialAssignment, Parameter, Reaction, Species +testTags: Amount, ConversionFactors, InitialValueReassigned +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a model conversion factor is set via an initial assignment with the avogadro csymbol. + +The model contains: +* 2 species (S1, S2) +* 1 parameter (m_cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: S1 -> S2 | $0.01$ |] + +The conversion factor for the model is 'm_cf' + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter m_cf | $avogadro / 1e24$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +The species' initial quantities are given in terms of substance units to +make it easier to use the model in a discrete stochastic simulator, but +their symbols represent their values in concentration units where they +appear in expressions. + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01778/l2v5/index.heta b/latest/cases/01778/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01778/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01778/l3v2/heta-code/output.heta b/latest/cases/01778/l3v2/heta-code/output.heta new file mode 100644 index 000000000..9d5308baa --- /dev/null +++ b/latest/cases/01778/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 2; + +cf @Const { } = 10; + diff --git a/latest/cases/01778/l3v2/index.heta b/latest/cases/01778/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01778/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01778/l3v2/json/output.json b/latest/cases/01778/l3v2/json/output.json new file mode 100644 index 000000000..5866bc465 --- /dev/null +++ b/latest/cases/01778/l3v2/json/output.json @@ -0,0 +1,26 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "s1", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Const", + "id": "cf", + "num": 10 + } +] \ No newline at end of file diff --git a/latest/cases/01778/model-sbml-l3v2.xml b/latest/cases/01778/model-sbml-l3v2.xml new file mode 100644 index 000000000..484736053 --- /dev/null +++ b/latest/cases/01778/model-sbml-l3v2.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/latest/cases/01778/output.heta b/latest/cases/01778/output.heta new file mode 100644 index 000000000..6116a1215 --- /dev/null +++ b/latest/cases/01778/output.heta @@ -0,0 +1,41 @@ +/* +category: Test +synopsis: A hierarchical model with a species modified by a conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The species in the replaced submodel must be converted by the conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model. An extension of test 1477, which doesn't have the conversion factor for the species. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $10 / (s1 / cf)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species s1 | $2$ | variable | +| Initial value of parameter cf | $10$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +s1 @Species { compartment: C, } .= 2; + +cf @Const { } = 10; + diff --git a/latest/cases/01778/synopsis.txt b/latest/cases/01778/synopsis.txt new file mode 100644 index 000000000..f72e22729 --- /dev/null +++ b/latest/cases/01778/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A hierarchical model with a species modified by a conversion factor. +componentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel +testTags: Amount, comp:ConversionFactor +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Numeric +packagesPresent: comp + + The species in the replaced submodel must be converted by the conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model. An extension of test 1477, which doesn't have the conversion factor for the species. + +The 'flattened' version of this hierarchical model contains: +* 1 species (s1) +* 1 parameter (cf) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| sub2__sub1__J0: -> s1 | $10 / (s1 / cf)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species s1 | $2$ | variable | +| Initial value of parameter cf | $10$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01779/l2v5/heta-code/output.heta b/latest/cases/01779/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f6f162002 --- /dev/null +++ b/latest/cases/01779/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [E0]= 0.2; + +S1 @Species { boundary: true, compartment: C1, } .= 2; +S1 [E0]= 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01779/l2v5/index.heta b/latest/cases/01779/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01779/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01779/l2v5/json/output.json b/latest/cases/01779/l2v5/json/output.json new file mode 100644 index 000000000..3a16ca24d --- /dev/null +++ b/latest/cases/01779/l2v5/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5", + "E0": "0.2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2", + "E0": "0.2" + }, + "boundary": true, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 0.45" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01779/l3v2/heta-code/output.heta b/latest/cases/01779/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8742b6d9c --- /dev/null +++ b/latest/cases/01779/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [E0]= 0.2; + +S1 @Species { boundary: true, compartment: C1, } .= 2; +S1 [E0]= 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01779/l3v2/index.heta b/latest/cases/01779/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01779/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01779/l3v2/json/output.json b/latest/cases/01779/l3v2/json/output.json new file mode 100644 index 000000000..89261719c --- /dev/null +++ b/latest/cases/01779/l3v2/json/output.json @@ -0,0 +1,35 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5", + "E0": "0.2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2", + "E0": "0.2" + }, + "boundary": true, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 0.45" + } +] \ No newline at end of file diff --git a/latest/cases/01779/model-sbml-l2v5.xml b/latest/cases/01779/model-sbml-l2v5.xml new file mode 100644 index 000000000..6a6a20ec6 --- /dev/null +++ b/latest/cases/01779/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01779/model-sbml-l3v2.xml b/latest/cases/01779/model-sbml-l3v2.xml new file mode 100644 index 000000000..7fda24c65 --- /dev/null +++ b/latest/cases/01779/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01779/output.heta b/latest/cases/01779/output.heta new file mode 100644 index 000000000..77b0687e4 --- /dev/null +++ b/latest/cases/01779/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: A species concentration and its compartment assigned to by the same event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A species in a non-unity compartment is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is used in all situations, including the event assignment. However, another event assignment in the same event is to the volume of that species' compartment. Both assignments are made based on the current state of the model, and *not* of of the state of the model after any one of the assignments. As a result, the assignment to S1 should set the amount of S1 to 0.1. The simultaneous assignment of 0.2 to the compartment means that the concentration of S1 ends up being 0.5 (0.1/0.2). This is counter-intuitive, since the concentration of S1 was just assigned to be 0.2! But it is a consequence of S1's concentration being derived instead of atomic. + +This test is a simpler variant of 01506, when it was realized some of the subtleties of that test were complicated by the rate rules. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 0.45$ | $S1 = 0.2$ | +| | | $C1 = 0.2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [E0]= 0.2; + +S1 @Species { boundary: true, compartment: C1, } .= 2; +S1 [E0]= 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01779/synopsis.txt b/latest/cases/01779/synopsis.txt new file mode 100644 index 000000000..a3ab56079 --- /dev/null +++ b/latest/cases/01779/synopsis.txt @@ -0,0 +1,41 @@ + +category: Test +synopsis: A species concentration and its compartment assigned to by the same event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A species in a non-unity compartment is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is used in all situations, including the event assignment. However, another event assignment in the same event is to the volume of that species' compartment. Both assignments are made based on the current state of the model, and *not* of of the state of the model after any one of the assignments. As a result, the assignment to S1 should set the amount of S1 to 0.1. The simultaneous assignment of 0.2 to the compartment means that the concentration of S1 ends up being 0.5 (0.1/0.2). This is counter-intuitive, since the concentration of S1 was just assigned to be 0.2! But it is a consequence of S1's concentration being derived instead of atomic. + +This test is a simpler variant of 01506, when it was realized some of the subtleties of that test were complicated by the rate rules. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 0.45$ | $S1 = 0.2$ | +| | | $C1 = 0.2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01780/l2v5/heta-code/output.heta b/latest/cases/01780/l2v5/heta-code/output.heta new file mode 100644 index 000000000..f6f162002 --- /dev/null +++ b/latest/cases/01780/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [E0]= 0.2; + +S1 @Species { boundary: true, compartment: C1, } .= 2; +S1 [E0]= 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01780/l2v5/index.heta b/latest/cases/01780/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01780/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01780/l2v5/json/output.json b/latest/cases/01780/l2v5/json/output.json new file mode 100644 index 000000000..3a16ca24d --- /dev/null +++ b/latest/cases/01780/l2v5/json/output.json @@ -0,0 +1,60 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5", + "E0": "0.2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2", + "E0": "0.2" + }, + "boundary": true, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 0.45" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01780/l3v2/heta-code/output.heta b/latest/cases/01780/l3v2/heta-code/output.heta new file mode 100644 index 000000000..8742b6d9c --- /dev/null +++ b/latest/cases/01780/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [E0]= 0.2; + +S1 @Species { boundary: true, compartment: C1, } .= 2; +S1 [E0]= 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01780/l3v2/index.heta b/latest/cases/01780/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01780/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01780/l3v2/json/output.json b/latest/cases/01780/l3v2/json/output.json new file mode 100644 index 000000000..89261719c --- /dev/null +++ b/latest/cases/01780/l3v2/json/output.json @@ -0,0 +1,35 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C1", + "assignments": { + "start_": "0.5", + "E0": "0.2" + } + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2", + "E0": "0.2" + }, + "boundary": true, + "compartment": "C1" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "DSwitcher", + "id": "E0", + "trigger": "t >= 0.45" + } +] \ No newline at end of file diff --git a/latest/cases/01780/model-sbml-l2v5.xml b/latest/cases/01780/model-sbml-l2v5.xml new file mode 100644 index 000000000..d273e070d --- /dev/null +++ b/latest/cases/01780/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01780/model-sbml-l3v2.xml b/latest/cases/01780/model-sbml-l3v2.xml new file mode 100644 index 000000000..0dc641c26 --- /dev/null +++ b/latest/cases/01780/model-sbml-l3v2.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + S1 + + + + + + + + + + time + 0.45 + + + + + + + 0.2 + + + + + 0.2 + + + + + + + diff --git a/latest/cases/01780/output.heta b/latest/cases/01780/output.heta new file mode 100644 index 000000000..6ec4fdd0d --- /dev/null +++ b/latest/cases/01780/output.heta @@ -0,0 +1,60 @@ +/* +category: Test +synopsis: A species concentration and its compartment assigned to by the same event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model is a duplicate of 01779, with the event assignments reversed. This should make no difference in the results. + + To recap model 1779: a species in a non-unity compartment is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is used in all situations, including the event assignment. However, another event assignment in the same event is to the volume of that species' compartment. Both assignments are made based on the current state of the model, and *not* of of the state of the model after any one of the assignments. As a result, the assignment to S1 should set the amount of S1 to 0.1. The simultaneous assignment of 0.2 to the compartment means that the concentration of S1 ends up being 0.5 (0.1/0.2). This is counter-intuitive, since the concentration of S1 was just assigned to be 0.2! But it is a consequence of S1's concentration being derived instead of atomic. + + This test is a simpler variant of 01506, when it was realized some of the subtleties of that test were complicated by the rate rules. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 0.45$ | $C1 = 0.2$ | +| | | $S1 = 0.2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C1 @Compartment { } .= 0.5; +C1 [E0]= 0.2; + +S1 @Species { boundary: true, compartment: C1, } .= 2; +S1 [E0]= 0.2; + +x @Record { }; +x := S1; + +E0 @DSwitcher { trigger: t >= 0.45, }; + diff --git a/latest/cases/01780/synopsis.txt b/latest/cases/01780/synopsis.txt new file mode 100644 index 000000000..20ac07db4 --- /dev/null +++ b/latest/cases/01780/synopsis.txt @@ -0,0 +1,43 @@ + +category: Test +synopsis: A species concentration and its compartment assigned to by the same event. +componentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, Species +testTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + This model is a duplicate of 01779, with the event assignments reversed. This should make no difference in the results. + + To recap model 1779: a species in a non-unity compartment is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is used in all situations, including the event assignment. However, another event assignment in the same event is to the volume of that species' compartment. Both assignments are made based on the current state of the model, and *not* of of the state of the model after any one of the assignments. As a result, the assignment to S1 should set the amount of S1 to 0.1. The simultaneous assignment of 0.2 to the compartment means that the concentration of S1 ends up being 0.5 (0.1/0.2). This is counter-intuitive, since the concentration of S1 was just assigned to be 0.2! But it is a consequence of S1's concentration being derived instead of atomic. + + This test is a simpler variant of 01506, when it was realized some of the subtleties of that test were complicated by the rate rules. + +The model contains: +* 1 species (S1) +* 1 parameter (x) +* 1 compartment (C1) + +There is one event: + +[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* | +| E0 | $time >= 0.45$ | $C1 = 0.2$ | +| | | $S1 = 0.2$ |] + + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial volume of compartment 'C1' | $0.5$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01781/l2v5/heta-code/output.heta b/latest/cases/01781/l2v5/heta-code/output.heta new file mode 100644 index 000000000..12719a301 --- /dev/null +++ b/latest/cases/01781/l2v5/heta-code/output.heta @@ -0,0 +1,11 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x @Record { } .= ((1 < 3) ? 1 : 3); + diff --git a/latest/cases/01781/l2v5/index.heta b/latest/cases/01781/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01781/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01781/l2v5/json/output.json b/latest/cases/01781/l2v5/json/output.json new file mode 100644 index 000000000..e796dfb66 --- /dev/null +++ b/latest/cases/01781/l2v5/json/output.json @@ -0,0 +1,37 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "((1 < 3) ? 1 : 3)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01781/l3v2/build.log b/latest/cases/01781/l3v2/build.log new file mode 100644 index 000000000..b6df7f461 --- /dev/null +++ b/latest/cases/01781/l3v2/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01781/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01781/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01781/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 80 +[error] No required "num" property for "x" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01781/l3v2/index.heta b/latest/cases/01781/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01781/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01781/model-sbml-l2v5.xml b/latest/cases/01781/model-sbml-l2v5.xml new file mode 100644 index 000000000..3fed6cc7a --- /dev/null +++ b/latest/cases/01781/model-sbml-l2v5.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 1 + 3 + 2 + + + + 3 + + + + + + + diff --git a/latest/cases/01781/model-sbml-l3v2.xml b/latest/cases/01781/model-sbml-l3v2.xml new file mode 100644 index 000000000..4df6fc44c --- /dev/null +++ b/latest/cases/01781/model-sbml-l3v2.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 1 + 3 + 2 + + + + 3 + + + + + + + diff --git a/latest/cases/01781/output.heta b/latest/cases/01781/output.heta new file mode 100644 index 000000000..80e0ca8dc --- /dev/null +++ b/latest/cases/01781/output.heta @@ -0,0 +1,35 @@ +/* +category: Test +synopsis: An initial assignment with an nary relational element. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as less than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. This test is based on test 01209, except that it will fail if the interpreter mistakenly checks only the first and last arguments of the 'lt' function. + +The model contains: +* 1 parameter (x) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $piecewise(1, 1 < 3 < 2, 3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x @Record { } .= ((1 < 3) ? 1 : 3); + diff --git a/latest/cases/01781/synopsis.txt b/latest/cases/01781/synopsis.txt new file mode 100644 index 000000000..926cd2496 --- /dev/null +++ b/latest/cases/01781/synopsis.txt @@ -0,0 +1,22 @@ + +category: Test +synopsis: An initial assignment with an nary relational element. +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as less than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. This test is based on test 01209, except that it will fail if the interpreter mistakenly checks only the first and last arguments of the 'lt' function. + +The model contains: +* 1 parameter (x) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $piecewise(1, 1 < 3 < 2, 3)$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01782/l2v5/heta-code/output.heta b/latest/cases/01782/l2v5/heta-code/output.heta new file mode 100644 index 000000000..beeb90a04 --- /dev/null +++ b/latest/cases/01782/l2v5/heta-code/output.heta @@ -0,0 +1,12 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x @Record { }; +x := ((2 > 0) ? 1 : 3); + diff --git a/latest/cases/01782/l2v5/index.heta b/latest/cases/01782/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01782/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01782/l2v5/json/output.json b/latest/cases/01782/l2v5/json/output.json new file mode 100644 index 000000000..51f463a5a --- /dev/null +++ b/latest/cases/01782/l2v5/json/output.json @@ -0,0 +1,37 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "((2 > 0) ? 1 : 3)" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01782/l3v2/heta-code/output.heta b/latest/cases/01782/l3v2/heta-code/output.heta new file mode 100644 index 000000000..0dea24c7a --- /dev/null +++ b/latest/cases/01782/l3v2/heta-code/output.heta @@ -0,0 +1,7 @@ + + +t @TimeScale { }; + +x @Record { }; +x := ((2 > 0) ? 1 : 3); + diff --git a/latest/cases/01782/l3v2/index.heta b/latest/cases/01782/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01782/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01782/l3v2/json/output.json b/latest/cases/01782/l3v2/json/output.json new file mode 100644 index 000000000..b836cfd6a --- /dev/null +++ b/latest/cases/01782/l3v2/json/output.json @@ -0,0 +1,12 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "((2 > 0) ? 1 : 3)" + } + } +] \ No newline at end of file diff --git a/latest/cases/01782/model-sbml-l2v5.xml b/latest/cases/01782/model-sbml-l2v5.xml new file mode 100644 index 000000000..002d293ae --- /dev/null +++ b/latest/cases/01782/model-sbml-l2v5.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 2 + 0 + 1 + + + + 3 + + + + + + + diff --git a/latest/cases/01782/model-sbml-l3v2.xml b/latest/cases/01782/model-sbml-l3v2.xml new file mode 100644 index 000000000..7375270e0 --- /dev/null +++ b/latest/cases/01782/model-sbml-l3v2.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 2 + 0 + 1 + + + + 3 + + + + + + + diff --git a/latest/cases/01782/output.heta b/latest/cases/01782/output.heta new file mode 100644 index 000000000..6b6be6db5 --- /dev/null +++ b/latest/cases/01782/output.heta @@ -0,0 +1,37 @@ +/* +category: Test +synopsis: An assignment rule with an nary relational element. +componentTags: AssignmentRule, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. This test is based on test 01210, with the difference that it will fail if the interpreter mistakenly checks only the first and last arguments of the 'gt' function. + +The model contains: +* 1 parameter (x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $piecewise(1, 2 > 0 > 1, 3)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $piecewise(1, 2 > 0 > 1, 3)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x @Record { }; +x := ((2 > 0) ? 1 : 3); + diff --git a/latest/cases/01782/synopsis.txt b/latest/cases/01782/synopsis.txt new file mode 100644 index 000000000..c8e099627 --- /dev/null +++ b/latest/cases/01782/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: An assignment rule with an nary relational element. +componentTags: AssignmentRule, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. This test is based on test 01210, with the difference that it will fail if the interpreter mistakenly checks only the first and last arguments of the 'gt' function. + +The model contains: +* 1 parameter (x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | x | $piecewise(1, 2 > 0 > 1, 3)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $piecewise(1, 2 > 0 > 1, 3)$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01783/l2v5/heta-code/output.heta b/latest/cases/01783/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0b88caf63 --- /dev/null +++ b/latest/cases/01783/l2v5/heta-code/output.heta @@ -0,0 +1,14 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := ((2 > 0) ? 1 : 0); + +x @Record { } .= 3; + diff --git a/latest/cases/01783/l2v5/index.heta b/latest/cases/01783/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01783/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01783/l2v5/json/output.json b/latest/cases/01783/l2v5/json/output.json new file mode 100644 index 000000000..7b94f5ea8 --- /dev/null +++ b/latest/cases/01783/l2v5/json/output.json @@ -0,0 +1,50 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3" + } + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "((2 > 0) ? 1 : 0)" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01783/l3v2/heta-code/output.heta b/latest/cases/01783/l3v2/heta-code/output.heta new file mode 100644 index 000000000..cb32bcff1 --- /dev/null +++ b/latest/cases/01783/l3v2/heta-code/output.heta @@ -0,0 +1,9 @@ + + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := ((2 > 0) ? 1 : 0); + +x @Record { } .= 3; + diff --git a/latest/cases/01783/l3v2/index.heta b/latest/cases/01783/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01783/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01783/l3v2/json/output.json b/latest/cases/01783/l3v2/json/output.json new file mode 100644 index 000000000..27504a37a --- /dev/null +++ b/latest/cases/01783/l3v2/json/output.json @@ -0,0 +1,25 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "x", + "assignments": { + "start_": "3" + } + }, + { + "class": "Process", + "id": "x_proc", + "assignments": { + "ode_": "((2 > 0) ? 1 : 0)" + }, + "actors": [ + { + "target": "x", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01783/model-sbml-l2v5.xml b/latest/cases/01783/model-sbml-l2v5.xml new file mode 100644 index 000000000..8c5e163e2 --- /dev/null +++ b/latest/cases/01783/model-sbml-l2v5.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 2 + 0 + 1 + + + + 0 + + + + + + + diff --git a/latest/cases/01783/model-sbml-l3v2.xml b/latest/cases/01783/model-sbml-l3v2.xml new file mode 100644 index 000000000..b66ff9713 --- /dev/null +++ b/latest/cases/01783/model-sbml-l3v2.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + 1 + + + 2 + 0 + 1 + + + + 0 + + + + + + + diff --git a/latest/cases/01783/output.heta b/latest/cases/01783/output.heta new file mode 100644 index 000000000..d358d4fcf --- /dev/null +++ b/latest/cases/01783/output.heta @@ -0,0 +1,39 @@ +/* +category: Test +synopsis: A rate rule with an nary relational element. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the rate rule from 1 to 0. This test is based on test 01215, with the difference that it will fail if the interpreter mistakenly checks only the first and last arguments of the 'gt' function. + +The model contains: +* 1 parameter (x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $piecewise(1, 2 > 0 > 1, 0)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +x_proc @Process { actors: = x, }; +x_proc := ((2 > 0) ? 1 : 0); + +x @Record { } .= 3; + diff --git a/latest/cases/01783/synopsis.txt b/latest/cases/01783/synopsis.txt new file mode 100644 index 000000000..803eeb042 --- /dev/null +++ b/latest/cases/01783/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: A rate rule with an nary relational element. +componentTags: Parameter, RateRule +testTags: NonConstantParameter +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the rate rule from 1 to 0. This test is based on test 01215, with the difference that it will fail if the interpreter mistakenly checks only the first and last arguments of the 'gt' function. + +The model contains: +* 1 parameter (x) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | x | $piecewise(1, 2 > 0 > 1, 0)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter x | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01784/l2v5/heta-code/output.heta b/latest/cases/01784/l2v5/heta-code/output.heta new file mode 100644 index 000000000..b10ae695d --- /dev/null +++ b/latest/cases/01784/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := 1 * (1 - S1); + diff --git a/latest/cases/01784/l2v5/index.heta b/latest/cases/01784/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01784/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01784/l2v5/json/output.json b/latest/cases/01784/l2v5/json/output.json new file mode 100644 index 000000000..590f76db4 --- /dev/null +++ b/latest/cases/01784/l2v5/json/output.json @@ -0,0 +1,59 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "0" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1 * (1 - S1)" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01784/l3v2/index.heta b/latest/cases/01784/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01784/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01784/model-sbml-l2v5.xml b/latest/cases/01784/model-sbml-l2v5.xml new file mode 100644 index 000000000..ba56e943e --- /dev/null +++ b/latest/cases/01784/model-sbml-l2v5.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + 1 + S1 + + + + + + + + diff --git a/latest/cases/01784/output.heta b/latest/cases/01784/output.heta new file mode 100644 index 000000000..1d9d96695 --- /dev/null +++ b/latest/cases/01784/output.heta @@ -0,0 +1,45 @@ +/* +category: Test +synopsis: Test that L1 and L2 reactions default to fast=false. +componentTags: Compartment, Reaction, Species +testTags: Amount, DefaultValue +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric +packagesPresent: + +In this very simple model, a reaction is present that, if it was set 'fast=true', would immediately go to 1.0, but goes there asymptotically instead. This tests to ensure that in L2 and L1 model reactions with no explicit 'fast' flag, the default value of 'false' is used. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1 * (1 - S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 0; + +J0 @Reaction { actors: = S1, }; +J0 := 1 * (1 - S1); + diff --git a/latest/cases/01784/synopsis.txt b/latest/cases/01784/synopsis.txt new file mode 100644 index 000000000..81b3b949d --- /dev/null +++ b/latest/cases/01784/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Test that L1 and L2 reactions default to fast=false. +componentTags: Compartment, Reaction, Species +testTags: Amount, DefaultValue +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Numeric +packagesPresent: + +In this very simple model, a reaction is present that, if it was set 'fast=true', would immediately go to 1.0, but goes there asymptotically instead. This tests to ensure that in L2 and L1 model reactions with no explicit 'fast' flag, the default value of 'false' is used. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1 * (1 - S1)$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $0$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + diff --git a/latest/cases/01785/l2v5/build.log b/latest/cases/01785/l2v5/build.log new file mode 100644 index 000000000..eb0ccc390 --- /dev/null +++ b/latest/cases/01785/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01785/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01785/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01785/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01785/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01785/l2v5/index.heta b/latest/cases/01785/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01785/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01785/l3v2/index.heta b/latest/cases/01785/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01785/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01785/model-sbml-l2v5.xml b/latest/cases/01785/model-sbml-l2v5.xml new file mode 100644 index 000000000..54e11bb1f --- /dev/null +++ b/latest/cases/01785/model-sbml-l2v5.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + C2 + C1 + + + + + + diff --git a/latest/cases/01785/synopsis.txt b/latest/cases/01785/synopsis.txt new file mode 100644 index 000000000..5a6a74937 --- /dev/null +++ b/latest/cases/01785/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A compartment with no 'constant' attribute defaults to 'true'. +componentTags: AlgebraicRule, Compartment +testTags: InitialValueReassigned, MultiCompartment, NonUnityCompartment, DefaultValue +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a non-constant compartment, and the other is a compartment with no explicitly-set value, meaning that it defaults to constant=true. This lets C1 change to 3, and leaves C2 fixed at 3, instead of the other way 'round. + +An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. + +The model contains: +* 2 compartments (C1, C2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $C2 - C1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial volume of compartment 'C2' | $3$ | constant | +| Initial volume of compartment 'C1' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01786/l2v5/build.log b/latest/cases/01786/l2v5/build.log new file mode 100644 index 000000000..c1eaa267b --- /dev/null +++ b/latest/cases/01786/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01786/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01786/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01786/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01786/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01786/l2v5/index.heta b/latest/cases/01786/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01786/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01786/l3v2/index.heta b/latest/cases/01786/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01786/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01786/model-sbml-l2v5.xml b/latest/cases/01786/model-sbml-l2v5.xml new file mode 100644 index 000000000..53933cf48 --- /dev/null +++ b/latest/cases/01786/model-sbml-l2v5.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + C2 + C1 + + + + + + diff --git a/latest/cases/01786/synopsis.txt b/latest/cases/01786/synopsis.txt new file mode 100644 index 000000000..5b155bed0 --- /dev/null +++ b/latest/cases/01786/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A compartment with no 'constant' attribute defaults to 'true'. +componentTags: AlgebraicRule, Compartment +testTags: DefaultValue, InitialValueReassigned, MultiCompartment, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a non-constant compartment, and the other is a compartment with no explicitly-set value, meaning that it defaults to constant=true. This lets C2 change to 2, and leaves C1 fixed at 2, instead of the other way 'round.An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. This model is identical to model 17865, except which compartment is constant is reversed, to ensure that simulators don't just use 'the first compartment' or a similar rule for resolving ambiguities like this. + +The model contains: +* 2 compartments (C1, C2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $C2 - C1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial volume of compartment 'C1' | $2$ | constant | +| Initial volume of compartment 'C2' | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01787/l2v5/build.log b/latest/cases/01787/l2v5/build.log new file mode 100644 index 000000000..faf91fb53 --- /dev/null +++ b/latest/cases/01787/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01787/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01787/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01787/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01787/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01787/l2v5/index.heta b/latest/cases/01787/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01787/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01787/l3v2/index.heta b/latest/cases/01787/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01787/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01787/model-sbml-l2v5.xml b/latest/cases/01787/model-sbml-l2v5.xml new file mode 100644 index 000000000..35c6800d2 --- /dev/null +++ b/latest/cases/01787/model-sbml-l2v5.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + S2 + S1 + + + + + + diff --git a/latest/cases/01787/synopsis.txt b/latest/cases/01787/synopsis.txt new file mode 100644 index 000000000..c7ec5264b --- /dev/null +++ b/latest/cases/01787/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A species with no 'constant' attribute defaults to 'false'. +componentTags: AlgebraicRule, Compartment, Species +testTags: Amount, BoundaryCondition, DefaultValue, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a constant species, and the other is a species with no explicitly-set value, meaning that it defaults to constant=false. This lets S1 change to 3, and leaves S2 fixed at 3, instead of the other way 'round.An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $S2 - S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | variable | +| Initial concentration of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01788/l2v5/build.log b/latest/cases/01788/l2v5/build.log new file mode 100644 index 000000000..b9198f9cf --- /dev/null +++ b/latest/cases/01788/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01788/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01788/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01788/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01788/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01788/l2v5/index.heta b/latest/cases/01788/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01788/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01788/l3v2/index.heta b/latest/cases/01788/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01788/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01788/model-sbml-l2v5.xml b/latest/cases/01788/model-sbml-l2v5.xml new file mode 100644 index 000000000..985105fa8 --- /dev/null +++ b/latest/cases/01788/model-sbml-l2v5.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + S2 + S1 + + + + + + diff --git a/latest/cases/01788/synopsis.txt b/latest/cases/01788/synopsis.txt new file mode 100644 index 000000000..253c6d542 --- /dev/null +++ b/latest/cases/01788/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A species with no 'constant' attribute defaults to 'false'. +componentTags: AlgebraicRule, Compartment, Species +testTags: Amount, ConstantSpecies, DefaultValue, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a constant species, and the other is a species with no explicitly-set value, meaning that it defaults to constant=false. This lets S2 change to 2, and leaves S1 fixed at 2, instead of the other way 'round.An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. + +The model contains: +* 2 species (S1, S2) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $S2 - S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | constant | +| Initial concentration of species S2 | $3$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01789/l2v5/build.log b/latest/cases/01789/l2v5/build.log new file mode 100644 index 000000000..c34623657 --- /dev/null +++ b/latest/cases/01789/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01789/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01789/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01789/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01789/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01789/l2v5/index.heta b/latest/cases/01789/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01789/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01789/l3v2/index.heta b/latest/cases/01789/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01789/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01789/model-sbml-l2v5.xml b/latest/cases/01789/model-sbml-l2v5.xml new file mode 100644 index 000000000..124c6c398 --- /dev/null +++ b/latest/cases/01789/model-sbml-l2v5.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + P2 + P1 + + + + + + diff --git a/latest/cases/01789/synopsis.txt b/latest/cases/01789/synopsis.txt new file mode 100644 index 000000000..b2a86a5cd --- /dev/null +++ b/latest/cases/01789/synopsis.txt @@ -0,0 +1,31 @@ + +category: Test +synopsis: A parameter with no 'constant' attribute defaults to 'true'. +componentTags: AlgebraicRule, Parameter +testTags: DefaultValue, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a non-constant parameter, and the other is a parameter with no explicitly-set value, meaning that it defaults to constant=true. This lets P1 change to 3, and leaves P2 fixed at 3, instead of the other way 'round. + +An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. + +The model contains: +* 2 parameters (P1, P2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P2 - P1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P2 | $3$ | constant | +| Initial value of parameter P1 | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01790/l2v5/build.log b/latest/cases/01790/l2v5/build.log new file mode 100644 index 000000000..5e951bfa2 --- /dev/null +++ b/latest/cases/01790/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01790/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01790/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01790/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01790/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01790/l2v5/index.heta b/latest/cases/01790/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01790/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01790/l3v2/index.heta b/latest/cases/01790/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01790/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01790/model-sbml-l2v5.xml b/latest/cases/01790/model-sbml-l2v5.xml new file mode 100644 index 000000000..e7d51d20d --- /dev/null +++ b/latest/cases/01790/model-sbml-l2v5.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + P2 + P1 + + + + + + diff --git a/latest/cases/01790/synopsis.txt b/latest/cases/01790/synopsis.txt new file mode 100644 index 000000000..1596658f9 --- /dev/null +++ b/latest/cases/01790/synopsis.txt @@ -0,0 +1,29 @@ + +category: Test +synopsis: A parameter with no 'constant' attribute defaults to 'true'. +componentTags: AlgebraicRule, Parameter +testTags: DefaultValue, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a non-constant parameter, and the other is a parameter with no explicitly-set value, meaning that it defaults to constant=true. This lets P2 change to 2, and leaves P1 fixed at 2, instead of the other way 'round.An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. + +The model contains: +* 2 parameters (P1, P2) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P2 - P1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $2$ | constant | +| Initial value of parameter P2 | $3$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01791/l2v5/build.log b/latest/cases/01791/l2v5/build.log new file mode 100644 index 000000000..c41e51f0f --- /dev/null +++ b/latest/cases/01791/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01791/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01791/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01791/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01791/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01791/l2v5/index.heta b/latest/cases/01791/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01791/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01791/l3v2/index.heta b/latest/cases/01791/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01791/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01791/model-sbml-l2v5.xml b/latest/cases/01791/model-sbml-l2v5.xml new file mode 100644 index 000000000..c8ff6f654 --- /dev/null +++ b/latest/cases/01791/model-sbml-l2v5.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + P2 + C1 + + + + + + diff --git a/latest/cases/01791/synopsis.txt b/latest/cases/01791/synopsis.txt new file mode 100644 index 000000000..2c89581b6 --- /dev/null +++ b/latest/cases/01791/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A compartment or parameter with no 'constant' attribute defaults to 'true'. +componentTags: AlgebraicRule, Compartment, Parameter +testTags: DefaultValue, InitialValueReassigned, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a non-constant compartment, and the other is a parameter with no explicitly-set value, meaning that it defaults to constant=true. This lets C1 change to 3, and leaves P2 fixed at 3, instead of the other way 'round. + +An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. + +The model contains: +* 1 parameter (P2) +* 1 compartment (C1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P2 - C1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P2 | $3$ | constant | +| Initial volume of compartment 'C1' | $2$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01792/l2v5/build.log b/latest/cases/01792/l2v5/build.log new file mode 100644 index 000000000..c4daf8d52 --- /dev/null +++ b/latest/cases/01792/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01792/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01792/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01792/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01792/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01792/l2v5/index.heta b/latest/cases/01792/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01792/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01792/l3v2/index.heta b/latest/cases/01792/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01792/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01792/model-sbml-l2v5.xml b/latest/cases/01792/model-sbml-l2v5.xml new file mode 100644 index 000000000..59102dc58 --- /dev/null +++ b/latest/cases/01792/model-sbml-l2v5.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + P2 + C1 + + + + + + diff --git a/latest/cases/01792/synopsis.txt b/latest/cases/01792/synopsis.txt new file mode 100644 index 000000000..8a47b5160 --- /dev/null +++ b/latest/cases/01792/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A compartment or parameter with no 'constant' attribute defaults to 'true'. +componentTags: AlgebraicRule, Compartment, Parameter +testTags: DefaultValue, InitialValueReassigned, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a non-constant parameter, and the other is a compartment with no explicitly-set value, meaning that it defaults to constant=true. This lets P2 change to 2, and leaves C1 fixed at 2, instead of the other way 'round. + +An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. + +The model contains: +* 1 parameter (P2) +* 1 compartment (C1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P2 - C1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P2 | $3$ | variable | +| Initial volume of compartment 'C1' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01793/l2v5/build.log b/latest/cases/01793/l2v5/build.log new file mode 100644 index 000000000..5acced4db --- /dev/null +++ b/latest/cases/01793/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01793/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01793/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01793/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01793/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01793/l2v5/index.heta b/latest/cases/01793/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01793/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01793/l3v2/index.heta b/latest/cases/01793/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01793/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01793/model-sbml-l2v5.xml b/latest/cases/01793/model-sbml-l2v5.xml new file mode 100644 index 000000000..af43ae05f --- /dev/null +++ b/latest/cases/01793/model-sbml-l2v5.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + 1 + C1 + + S2 + + + + + + diff --git a/latest/cases/01793/synopsis.txt b/latest/cases/01793/synopsis.txt new file mode 100644 index 000000000..b48c690d4 --- /dev/null +++ b/latest/cases/01793/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A compartment and species with no 'constant' attributes. +componentTags: AlgebraicRule, Compartment, Species +testTags: Amount, DefaultValue, HasOnlySubstanceUnits, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a compartment with no explicitly-set 'constant', which defalts to 'true', and the other is a species with no explicitly-set 'constant' value, meaning that it defaults to constant=false. This lets S2 change to 1, and leaves C1 fixed at 1, instead of the other way 'round. + +An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. + +The model contains: +* 1 species (S2) +* 1 compartment (C1) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $1 * C1 - S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S2 | $3$ | variable | +| Initial volume of compartment 'C1' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01794/l2v5/build.log b/latest/cases/01794/l2v5/build.log new file mode 100644 index 000000000..edbc5064c --- /dev/null +++ b/latest/cases/01794/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01794/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01794/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01794/model-sbml-l2v5.xml"... +[error] "algebraicRule" from SBML module is not supported. when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01794/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01794/l2v5/index.heta b/latest/cases/01794/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01794/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01794/l3v2/index.heta b/latest/cases/01794/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01794/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01794/model-sbml-l2v5.xml b/latest/cases/01794/model-sbml-l2v5.xml new file mode 100644 index 000000000..2a9d0b1f8 --- /dev/null +++ b/latest/cases/01794/model-sbml-l2v5.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + P1 + S2 + + + + + + diff --git a/latest/cases/01794/synopsis.txt b/latest/cases/01794/synopsis.txt new file mode 100644 index 000000000..e5cd58ad9 --- /dev/null +++ b/latest/cases/01794/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A compartment and species with no 'constant' attributes. +componentTags: AlgebraicRule, Compartment, Parameter, Species +testTags: Amount, DefaultValue, HasOnlySubstanceUnits, InitialValueReassigned +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + +An algebraic rule sets the value for non-constant elements in its formula. Here, one of the two symbols used is a parameter with no explicitly-set 'constant', which defalts to 'true', and the other is a species with no explicitly-set 'constant' value, meaning that it defaults to constant=false. This lets S2 change to 2, and leaves P1 fixed at 2, instead of the other way 'round. + +An algebraic rule is the only mathematical construct that cares (outside of validation) whether an element is constant or not. + +The model contains: +* 1 species (S2) +* 1 parameter (P1) +* 1 compartment (C) + +There is one rule: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Algebraic | $0$ | $P1 - S2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S2 | $3$ | variable | +| Initial value of parameter P1 | $2$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01795/l2v5/heta-code/output.heta b/latest/cases/01795/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c15701d5d --- /dev/null +++ b/latest/cases/01795/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2; +S2 @Species { boundary: true, compartment: C, } .= 2; +S3 @Species { compartment: C, } .= 2; + +J0 @Reaction { actors: = S1, }; +J0 := 1; +J1 @Reaction { actors: = S2, }; +J1 := 1; +J2 @Reaction { actors: = S3, }; +J2 := 1; + diff --git a/latest/cases/01795/l2v5/index.heta b/latest/cases/01795/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01795/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01795/l2v5/json/output.json b/latest/cases/01795/l2v5/json/output.json new file mode 100644 index 000000000..baee48a55 --- /dev/null +++ b/latest/cases/01795/l2v5/json/output.json @@ -0,0 +1,102 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "2" + }, + "boundary": true, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "2" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "J2", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01795/l3v2/index.heta b/latest/cases/01795/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01795/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01795/model-sbml-l2v5.xml b/latest/cases/01795/model-sbml-l2v5.xml new file mode 100644 index 000000000..345a888a8 --- /dev/null +++ b/latest/cases/01795/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01795/output.heta b/latest/cases/01795/output.heta new file mode 100644 index 000000000..5a0406559 --- /dev/null +++ b/latest/cases/01795/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Default values for species boundaryCondition +componentTags: Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, DefaultValue +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In SBML L1 and L2, the value for a species 'boundaryCondition' attribute defaults to 'false'. This model tests that this value is correctly assumed, in a model where S1 has no 'boundaryCondition' attribute, S2 has it set to 'true', and S3 has it set to 'false'. S1 should follow S3, and not S2. + +The model contains: +* 3 species (S1, S2, S3) +* 1 compartment (C) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ | +| J1: -> S2 | $1$ | +| J2: -> S3 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | variable | +| Initial concentration of species S2 | $2$ | variable | +| Initial concentration of species S3 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 2; +S2 @Species { boundary: true, compartment: C, } .= 2; +S3 @Species { compartment: C, } .= 2; + +J0 @Reaction { actors: = S1, }; +J0 := 1; +J1 @Reaction { actors: = S2, }; +J1 := 1; +J2 @Reaction { actors: = S3, }; +J2 := 1; + diff --git a/latest/cases/01795/synopsis.txt b/latest/cases/01795/synopsis.txt new file mode 100644 index 000000000..48f5f8061 --- /dev/null +++ b/latest/cases/01795/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Default values for species boundaryCondition +componentTags: Compartment, Reaction, Species +testTags: Amount, BoundaryCondition, DefaultValue +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In SBML L1 and L2, the value for a species 'boundaryCondition' attribute defaults to 'false'. This model tests that this value is correctly assumed, in a model where S1 has no 'boundaryCondition' attribute, S2 has it set to 'true', and S3 has it set to 'false'. S1 should follow S3, and not S2. + +The model contains: +* 3 species (S1, S2, S3) +* 1 compartment (C) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ | +| J1: -> S2 | $1$ | +| J2: -> S3 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $2$ | variable | +| Initial concentration of species S2 | $2$ | variable | +| Initial concentration of species S3 | $2$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01796/l2v5/heta-code/output.heta b/latest/cases/01796/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8e3903558 --- /dev/null +++ b/latest/cases/01796/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 3; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 2 / C; +S3 @Species { compartment: C, isAmount: true, } .= 2; + +x @Record { }; +x := S1; +y @Record { }; +y := S2; +z @Record { }; +z := S3; + diff --git a/latest/cases/01796/l2v5/index.heta b/latest/cases/01796/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01796/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01796/l2v5/json/output.json b/latest/cases/01796/l2v5/json/output.json new file mode 100644 index 000000000..179562df4 --- /dev/null +++ b/latest/cases/01796/l2v5/json/output.json @@ -0,0 +1,84 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "3" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "2 / C" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Record", + "id": "x", + "assignments": { + "ode_": "S1" + } + }, + { + "class": "Record", + "id": "y", + "assignments": { + "ode_": "S2" + } + }, + { + "class": "Record", + "id": "z", + "assignments": { + "ode_": "S3" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01796/l3v2/index.heta b/latest/cases/01796/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01796/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01796/model-sbml-l2v5.xml b/latest/cases/01796/model-sbml-l2v5.xml new file mode 100644 index 000000000..74bac8ecf --- /dev/null +++ b/latest/cases/01796/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + S3 + + + + + S2 + + + + + S1 + + + + + diff --git a/latest/cases/01796/output.heta b/latest/cases/01796/output.heta new file mode 100644 index 000000000..8301d63b3 --- /dev/null +++ b/latest/cases/01796/output.heta @@ -0,0 +1,62 @@ +/* +category: Test +synopsis: Default values for species boundaryCondition +componentTags: AssignmentRule, Compartment, Parameter, Species +testTags: Amount, DefaultValue, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In SBML L1 and L2, the value for a species 'hasOnlySubstanceUnits' attribute defaults to 'false'. This model tests that this value is correctly assumed, in a model where S1 has no 'hasOnlySubstanceUnits' attribute, S2 has it set to 'false', and S3 has it set to 'true'. S1 should follow S2, and not S3. + +The model contains: +* 3 species (S1, S2, S3) +* 3 parameters (x, y, z) +* 1 compartment (C) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $S3$ | +| Assignment | y | $S2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $2$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial value of parameter y | $S2$ | variable | +| Initial value of parameter z | $S3$ | variable | +| Initial volume of compartment 'C' | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 3; + +S1 @Species { compartment: C, } .= 2 / C; +S2 @Species { compartment: C, } .= 2 / C; +S3 @Species { compartment: C, isAmount: true, } .= 2; + +x @Record { }; +x := S1; +y @Record { }; +y := S2; +z @Record { }; +z := S3; + diff --git a/latest/cases/01796/synopsis.txt b/latest/cases/01796/synopsis.txt new file mode 100644 index 000000000..7058f6f48 --- /dev/null +++ b/latest/cases/01796/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Default values for species boundaryCondition +componentTags: AssignmentRule, Compartment, Parameter, Species +testTags: Amount, DefaultValue, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, NonUnityCompartment +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In SBML L1 and L2, the value for a species 'hasOnlySubstanceUnits' attribute defaults to 'false'. This model tests that this value is correctly assumed, in a model where S1 has no 'hasOnlySubstanceUnits' attribute, S2 has it set to 'false', and S3 has it set to 'true'. S1 should follow S2, and not S3. + +The model contains: +* 3 species (S1, S2, S3) +* 3 parameters (x, y, z) +* 1 compartment (C) + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Assignment | z | $S3$ | +| Assignment | y | $S2$ | +| Assignment | x | $S1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $2$ | variable | +| Initial amount of species S3 | $2$ | variable | +| Initial value of parameter x | $S1$ | variable | +| Initial value of parameter y | $S2$ | variable | +| Initial value of parameter z | $S3$ | variable | +| Initial volume of compartment 'C' | $3$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01797/l2v5/heta-code/output.heta b/latest/cases/01797/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ffd0090c1 --- /dev/null +++ b/latest/cases/01797/l2v5/heta-code/output.heta @@ -0,0 +1,22 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; +S2 @Species { compartment: C, } .= 1; +S3 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := 1; +J1 @Reaction { actors: = 2*S2, }; +J1 := 1; +J2 @Reaction { actors: = S3, }; +J2 := 1; + diff --git a/latest/cases/01797/l2v5/index.heta b/latest/cases/01797/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01797/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01797/l2v5/json/output.json b/latest/cases/01797/l2v5/json/output.json new file mode 100644 index 000000000..2619bd306 --- /dev/null +++ b/latest/cases/01797/l2v5/json/output.json @@ -0,0 +1,101 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "S3", + "assignments": { + "start_": "1" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J0", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 2 + } + ] + }, + { + "class": "Reaction", + "id": "J2", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "S3", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01797/l3v2/index.heta b/latest/cases/01797/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01797/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01797/model-sbml-l2v5.xml b/latest/cases/01797/model-sbml-l2v5.xml new file mode 100644 index 000000000..39d1afbdb --- /dev/null +++ b/latest/cases/01797/model-sbml-l2v5.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + + + + + 1 + + + + + + diff --git a/latest/cases/01797/output.heta b/latest/cases/01797/output.heta new file mode 100644 index 000000000..a93b45e32 --- /dev/null +++ b/latest/cases/01797/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Default values for species boundaryCondition +componentTags: Compartment, Reaction, Species +testTags: Amount, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In SBML L2, the value for a speciesReference 'stoichiometry' attribute defaults to '1'. This model tests that this value is correctly assumed, in a model where the first speciesReference has no 'stoichiometry' attribute, the second has it set to '2', and the third has it set to '1'. The first should follow the third. + +The model contains: +* 3 species (S1, S2, S3) +* 1 compartment (C) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ | +| J1: -> 2S2 | $1$ | +| J2: -> S3 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial concentration of species S3 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, } .= 1; +S2 @Species { compartment: C, } .= 1; +S3 @Species { compartment: C, } .= 1; + +J0 @Reaction { actors: = S1, }; +J0 := 1; +J1 @Reaction { actors: = 2*S2, }; +J1 := 1; +J2 @Reaction { actors: = S3, }; +J2 := 1; + diff --git a/latest/cases/01797/synopsis.txt b/latest/cases/01797/synopsis.txt new file mode 100644 index 000000000..67e1f3a5f --- /dev/null +++ b/latest/cases/01797/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Default values for species boundaryCondition +componentTags: Compartment, Reaction, Species +testTags: Amount, DefaultValue, NonUnityStoichiometry +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In SBML L2, the value for a speciesReference 'stoichiometry' attribute defaults to '1'. This model tests that this value is correctly assumed, in a model where the first speciesReference has no 'stoichiometry' attribute, the second has it set to '2', and the third has it set to '1'. The first should follow the third. + +The model contains: +* 3 species (S1, S2, S3) +* 1 compartment (C) + +There are 3 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J0: -> S1 | $1$ | +| J1: -> 2S2 | $1$ | +| J2: -> S3 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial concentration of species S2 | $1$ | variable | +| Initial concentration of species S3 | $1$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01798/l2v5/build.log b/latest/cases/01798/l2v5/build.log new file mode 100644 index 000000000..cc09c84b2 --- /dev/null +++ b/latest/cases/01798/l2v5/build.log @@ -0,0 +1,9 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01798/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01798/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01798/model-sbml-l2v5.xml"... +[error] "delay" in event is not supported in SBML module when converting module "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01798/model-sbml-l2v5.xml" +[info] Setting references in elements, total length 84 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01798/l2v5/index.heta b/latest/cases/01798/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01798/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01798/l3v2/index.heta b/latest/cases/01798/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01798/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01798/model-sbml-l2v5.xml b/latest/cases/01798/model-sbml-l2v5.xml new file mode 100644 index 000000000..00ea7a236 --- /dev/null +++ b/latest/cases/01798/model-sbml-l2v5.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + 1 + + + + + 1 + + + + + 1 + + + + + + + + + + P1 + 1.5 + + + + + + 2 + + + + + + P1 + + + + + + + + + + P2 + 1.5 + + + + + + 2 + + + + + + P2 + + + + + + + + + + P3 + 1.5 + + + + + + 2 + + + + + + P3 + + + + + + + diff --git a/latest/cases/01798/synopsis.txt b/latest/cases/01798/synopsis.txt new file mode 100644 index 000000000..057717b36 --- /dev/null +++ b/latest/cases/01798/synopsis.txt @@ -0,0 +1,40 @@ + +category: Test +synopsis: Default values for an Event's 'useValuesFromTriggerTime' +componentTags: EventWithDelay, Parameter, RateRule +testTags: DefaultValue, EventUsesAssignmentTimeValues, EventUsesTriggerTimeValues, NonConstantParameter +testType: TimeCourse +levels: 2.4, 2.5 +generatedBy: Analytic +packagesPresent: + + In SBML L2, the value for an event's 'useValuesFromTriggerTime' attribute defaults to 'true'. This model tests that this value is correctly assumed, in a model where the first event has no 'useValuesFromTriggerTime' attribute, the second has it set to 'false', and the third has it set to 'true'. The first should follow the third. + +The model contains: +* 3 parameters (P1, P2, P3) + +There are 3 events: + +[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Use values from:* | *Delay* | *Event Assignments* | +| E1 | $P1 >= 1.5$ | Trigger time | $2$ | $P1 = P1$ | +| E2 | $P2 >= 1.5$ | Assignment time | $2$ | $P2 = P2$ | +| E3 | $P3 >= 1.5$ | Trigger time | $2$ | $P3 = P3$ |] + + +There are 3 rules: + +[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* | +| Rate | P1 | $1$ | +| Rate | P2 | $1$ | +| Rate | P3 | $1$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter P1 | $0$ | variable | +| Initial value of parameter P2 | $0$ | variable | +| Initial value of parameter P3 | $0$ | variable |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01799/l2v5/heta-code/output.heta b/latest/cases/01799/l2v5/heta-code/output.heta new file mode 100644 index 000000000..19cb9fd8c --- /dev/null +++ b/latest/cases/01799/l2v5/heta-code/output.heta @@ -0,0 +1,18 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +J1 @Reaction { actors: = S1, }; +J1 := J1__J1_local * 2; + +J1__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01799/l2v5/index.heta b/latest/cases/01799/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01799/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01799/l2v5/json/output.json b/latest/cases/01799/l2v5/json/output.json new file mode 100644 index 000000000..09faead36 --- /dev/null +++ b/latest/cases/01799/l2v5/json/output.json @@ -0,0 +1,65 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "J1__J1_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "J1__J1_local * 2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01799/l3v2/heta-code/output.heta b/latest/cases/01799/l3v2/heta-code/output.heta new file mode 100644 index 000000000..c5fa95193 --- /dev/null +++ b/latest/cases/01799/l3v2/heta-code/output.heta @@ -0,0 +1,13 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +J1 @Reaction { actors: = S1, }; +J1 := J1__J1_local * 2; + +J1__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01799/l3v2/index.heta b/latest/cases/01799/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01799/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01799/l3v2/json/output.json b/latest/cases/01799/l3v2/json/output.json new file mode 100644 index 000000000..ecbb1721d --- /dev/null +++ b/latest/cases/01799/l3v2/json/output.json @@ -0,0 +1,40 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "J1__J1_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "J1__J1_local * 2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01799/model-sbml-l2v5.xml b/latest/cases/01799/model-sbml-l2v5.xml new file mode 100644 index 000000000..ae0cb5fc8 --- /dev/null +++ b/latest/cases/01799/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + J1 + 2 + + + + + + + + + + diff --git a/latest/cases/01799/model-sbml-l3v2.xml b/latest/cases/01799/model-sbml-l3v2.xml new file mode 100644 index 000000000..bb59a861d --- /dev/null +++ b/latest/cases/01799/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + J1 + 2 + + + + + + + + + + diff --git a/latest/cases/01799/output.heta b/latest/cases/01799/output.heta new file mode 100644 index 000000000..08afe6826 --- /dev/null +++ b/latest/cases/01799/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: A local parameter shadowing its own reaction's ID. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows the ID of the reaction it is in. Its kinetic law, therefore, is actually OK and not a circular reference. + +The model contains: +* 1 species (S1) +* 1 local parameter (J1.J1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $J1 * 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of local parameter 'J1.J1' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +J1 @Reaction { actors: = S1, }; +J1 := J1__J1_local * 2; + +J1__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01799/synopsis.txt b/latest/cases/01799/synopsis.txt new file mode 100644 index 000000000..693fcc11b --- /dev/null +++ b/latest/cases/01799/synopsis.txt @@ -0,0 +1,32 @@ + +category: Test +synopsis: A local parameter shadowing its own reaction's ID. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters +testType: TimeCourse +levels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows the ID of the reaction it is in. Its kinetic law, therefore, is actually OK and not a circular reference. + +The model contains: +* 1 species (S1) +* 1 local parameter (J1.J1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $J1 * 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of local parameter 'J1.J1' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01800/l2v5/heta-code/output.heta b/latest/cases/01800/l2v5/heta-code/output.heta new file mode 100644 index 000000000..92851971a --- /dev/null +++ b/latest/cases/01800/l2v5/heta-code/output.heta @@ -0,0 +1,18 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +J1 @Reaction { actors: = S1, }; +J1 := S1_stoich__J1_local * 2; + +S1_stoich__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01800/l2v5/index.heta b/latest/cases/01800/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01800/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01800/l2v5/json/output.json b/latest/cases/01800/l2v5/json/output.json new file mode 100644 index 000000000..5d70d3422 --- /dev/null +++ b/latest/cases/01800/l2v5/json/output.json @@ -0,0 +1,65 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "S1_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "S1_stoich__J1_local * 2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01800/l3v2/heta-code/output.heta b/latest/cases/01800/l3v2/heta-code/output.heta new file mode 100644 index 000000000..5eba523ea --- /dev/null +++ b/latest/cases/01800/l3v2/heta-code/output.heta @@ -0,0 +1,13 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +J1 @Reaction { actors: = S1, }; +J1 := S1_stoich__J1_local * 2; + +S1_stoich__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01800/l3v2/index.heta b/latest/cases/01800/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01800/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01800/l3v2/json/output.json b/latest/cases/01800/l3v2/json/output.json new file mode 100644 index 000000000..8ee4be13e --- /dev/null +++ b/latest/cases/01800/l3v2/json/output.json @@ -0,0 +1,40 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "S1_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "S1_stoich__J1_local * 2" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01800/model-sbml-l2v5.xml b/latest/cases/01800/model-sbml-l2v5.xml new file mode 100644 index 000000000..daa489150 --- /dev/null +++ b/latest/cases/01800/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + S1_stoich + 2 + + + + + + + + + + diff --git a/latest/cases/01800/model-sbml-l3v2.xml b/latest/cases/01800/model-sbml-l3v2.xml new file mode 100644 index 000000000..cdf2bf2da --- /dev/null +++ b/latest/cases/01800/model-sbml-l3v2.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + S1_stoich + 2 + + + + + + + + + + diff --git a/latest/cases/01800/output.heta b/latest/cases/01800/output.heta new file mode 100644 index 000000000..e7407a3f2 --- /dev/null +++ b/latest/cases/01800/output.heta @@ -0,0 +1,49 @@ +/* +category: Test +synopsis: A local parameter shadowing a species reference from its own reaction. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows the ID of a species reference from the reaction it is in. This is valid even in SBML L2, where you cannot reference a species reference ID anywhere... because it's not being referenced. + +The model contains: +* 1 species (S1) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $S1_stoich * 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; + +J1 @Reaction { actors: = S1, }; +J1 := S1_stoich__J1_local * 2; + +S1_stoich__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01800/synopsis.txt b/latest/cases/01800/synopsis.txt new file mode 100644 index 000000000..9957aa7d4 --- /dev/null +++ b/latest/cases/01800/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: A local parameter shadowing a species reference from its own reaction. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, a local parameter shadows the ID of a species reference from the reaction it is in. This is valid even in SBML L2, where you cannot reference a species reference ID anywhere... because it's not being referenced. + +The model contains: +* 1 species (S1) +* 1 local parameter (J1.S1_stoich) +* 1 compartment (C) +* 1 species reference (S1_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: -> S1 | $S1_stoich * 2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01801/l2v5/heta-code/output.heta b/latest/cases/01801/l2v5/heta-code/output.heta new file mode 100644 index 000000000..fb19c3409 --- /dev/null +++ b/latest/cases/01801/l2v5/heta-code/output.heta @@ -0,0 +1,20 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J1 @Reaction { actors: S1 = S2, }; +J1 := S1_stoich__J1_local * S2_stoich__J1_local * 20; + +S1_stoich__J1_local @Const { } = 0.1; +S2_stoich__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01801/l2v5/index.heta b/latest/cases/01801/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01801/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01801/l2v5/json/output.json b/latest/cases/01801/l2v5/json/output.json new file mode 100644 index 000000000..4b23f0f26 --- /dev/null +++ b/latest/cases/01801/l2v5/json/output.json @@ -0,0 +1,83 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "S1_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Const", + "id": "S2_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "S1_stoich__J1_local * S2_stoich__J1_local * 20" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01801/l3v2/heta-code/output.heta b/latest/cases/01801/l3v2/heta-code/output.heta new file mode 100644 index 000000000..69cfaba58 --- /dev/null +++ b/latest/cases/01801/l3v2/heta-code/output.heta @@ -0,0 +1,15 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J1 @Reaction { actors: S1 = S2, }; +J1 := S1_stoich__J1_local * S2_stoich__J1_local * 20; + +S1_stoich__J1_local @Const { } = 0.1; +S2_stoich__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01801/l3v2/index.heta b/latest/cases/01801/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01801/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01801/l3v2/json/output.json b/latest/cases/01801/l3v2/json/output.json new file mode 100644 index 000000000..81518bc61 --- /dev/null +++ b/latest/cases/01801/l3v2/json/output.json @@ -0,0 +1,58 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "S1_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Const", + "id": "S2_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "S1_stoich__J1_local * S2_stoich__J1_local * 20" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01801/model-sbml-l2v5.xml b/latest/cases/01801/model-sbml-l2v5.xml new file mode 100644 index 000000000..b365aa2ab --- /dev/null +++ b/latest/cases/01801/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + S1_stoich + S2_stoich + 20 + + + + + + + + + + + diff --git a/latest/cases/01801/model-sbml-l3v2.xml b/latest/cases/01801/model-sbml-l3v2.xml new file mode 100644 index 000000000..948ee6a64 --- /dev/null +++ b/latest/cases/01801/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + + + + + + + S1_stoich + S2_stoich + 20 + + + + + + + + + + + diff --git a/latest/cases/01801/output.heta b/latest/cases/01801/output.heta new file mode 100644 index 000000000..f82265fbd --- /dev/null +++ b/latest/cases/01801/output.heta @@ -0,0 +1,54 @@ +/* +category: Test +synopsis: A local parameter shadowing two species references from its own reaction. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two local parameters shadow the ID of species references from the reaction they are in. + +The model contains: +* 2 species (S1, S2) +* 2 local parameters (J1.S1_stoich, J1.S2_stoich) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: S1 -> S2 | $S1_stoich * S2_stoich * 20$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.1$ | constant | +| Initial value of local parameter 'J1.S2_stoich' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | constant | +| Initial value of species reference 'S2_stoich' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J1 @Reaction { actors: S1 = S2, }; +J1 := S1_stoich__J1_local * S2_stoich__J1_local * 20; + +S1_stoich__J1_local @Const { } = 0.1; +S2_stoich__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01801/synopsis.txt b/latest/cases/01801/synopsis.txt new file mode 100644 index 000000000..8fc8d1817 --- /dev/null +++ b/latest/cases/01801/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: A local parameter shadowing two species references from its own reaction. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, two local parameters shadow the ID of species references from the reaction they are in. + +The model contains: +* 2 species (S1, S2) +* 2 local parameters (J1.S1_stoich, J1.S2_stoich) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: S1 -> S2 | $S1_stoich * S2_stoich * 20$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.1$ | constant | +| Initial value of local parameter 'J1.S2_stoich' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | constant | +| Initial value of species reference 'S2_stoich' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01802/l2v5/heta-code/output.heta b/latest/cases/01802/l2v5/heta-code/output.heta new file mode 100644 index 000000000..ec4f47503 --- /dev/null +++ b/latest/cases/01802/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J1 @Reaction { actors: S1 = S2, }; +J1 := S1_stoich__J1_local * S2_stoich__J1_local * J1__J1_local * 200; + +S1_stoich__J1_local @Const { } = 0.1; +S2_stoich__J1_local @Const { } = 0.1; +J1__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01802/l2v5/index.heta b/latest/cases/01802/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01802/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01802/l2v5/json/output.json b/latest/cases/01802/l2v5/json/output.json new file mode 100644 index 000000000..9bc4ef5cb --- /dev/null +++ b/latest/cases/01802/l2v5/json/output.json @@ -0,0 +1,88 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "S1_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Const", + "id": "S2_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Const", + "id": "J1__J1_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "S1_stoich__J1_local * S2_stoich__J1_local * J1__J1_local * 200" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01802/l3v2/heta-code/output.heta b/latest/cases/01802/l3v2/heta-code/output.heta new file mode 100644 index 000000000..a792b97af --- /dev/null +++ b/latest/cases/01802/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J1 @Reaction { actors: S1 = S2, }; +J1 := S1_stoich__J1_local * S2_stoich__J1_local * J1__J1_local * 200; + +S1_stoich__J1_local @Const { } = 0.1; +S2_stoich__J1_local @Const { } = 0.1; +J1__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01802/l3v2/index.heta b/latest/cases/01802/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01802/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01802/l3v2/json/output.json b/latest/cases/01802/l3v2/json/output.json new file mode 100644 index 000000000..7595f4f0c --- /dev/null +++ b/latest/cases/01802/l3v2/json/output.json @@ -0,0 +1,63 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "2" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Species", + "id": "S2", + "assignments": { + "start_": "3" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Const", + "id": "S1_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Const", + "id": "S2_stoich__J1_local", + "num": 0.1 + }, + { + "class": "Const", + "id": "J1__J1_local", + "num": 0.1 + }, + { + "class": "Reaction", + "id": "J1", + "assignments": { + "ode_": "S1_stoich__J1_local * S2_stoich__J1_local * J1__J1_local * 200" + }, + "actors": [ + { + "target": "S2", + "stoichiometry": 1 + }, + { + "target": "S1", + "stoichiometry": -1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01802/model-sbml-l2v5.xml b/latest/cases/01802/model-sbml-l2v5.xml new file mode 100644 index 000000000..09b48a5fb --- /dev/null +++ b/latest/cases/01802/model-sbml-l2v5.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + S1_stoich + S2_stoich + J1 + 200 + + + + + + + + + + + + diff --git a/latest/cases/01802/model-sbml-l3v2.xml b/latest/cases/01802/model-sbml-l3v2.xml new file mode 100644 index 000000000..600a3e409 --- /dev/null +++ b/latest/cases/01802/model-sbml-l3v2.xml @@ -0,0 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + + + S1_stoich + S2_stoich + J1 + 200 + + + + + + + + + + + + diff --git a/latest/cases/01802/output.heta b/latest/cases/01802/output.heta new file mode 100644 index 000000000..cbc789492 --- /dev/null +++ b/latest/cases/01802/output.heta @@ -0,0 +1,56 @@ +/* +category: Test +synopsis: Local parameters shadowing two species references and the reaction ID of their own reaction. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, local parameters shadow the ID of species references from the reaction they are in, as well as the ID of the reaction itself. + +The model contains: +* 2 species (S1, S2) +* 3 local parameters (J1.S1_stoich, J1.S2_stoich, J1.J1) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: S1 -> S2 | $S1_stoich * S2_stoich * J1 * 200$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.1$ | constant | +| Initial value of local parameter 'J1.S2_stoich' | $0.1$ | constant | +| Initial value of local parameter 'J1.J1' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | constant | +| Initial value of species reference 'S2_stoich' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +S1 @Species { compartment: C, isAmount: true, } .= 2; +S2 @Species { compartment: C, isAmount: true, } .= 3; + +J1 @Reaction { actors: S1 = S2, }; +J1 := S1_stoich__J1_local * S2_stoich__J1_local * J1__J1_local * 200; + +S1_stoich__J1_local @Const { } = 0.1; +S2_stoich__J1_local @Const { } = 0.1; +J1__J1_local @Const { } = 0.1; + diff --git a/latest/cases/01802/synopsis.txt b/latest/cases/01802/synopsis.txt new file mode 100644 index 000000000..6181c3439 --- /dev/null +++ b/latest/cases/01802/synopsis.txt @@ -0,0 +1,38 @@ + +category: Test +synopsis: Local parameters shadowing two species references and the reaction ID of their own reaction. +componentTags: Compartment, Reaction, Species +testTags: Amount, HasOnlySubstanceUnits, LocalParameters +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In this model, local parameters shadow the ID of species references from the reaction they are in, as well as the ID of the reaction itself. + +The model contains: +* 2 species (S1, S2) +* 3 local parameters (J1.S1_stoich, J1.S2_stoich, J1.J1) +* 1 compartment (C) +* 2 species references (S1_stoich, S2_stoich) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J1: S1 -> S2 | $S1_stoich * S2_stoich * J1 * 200$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial amount of species S1 | $2$ | variable | +| Initial amount of species S2 | $3$ | variable | +| Initial value of local parameter 'J1.S1_stoich' | $0.1$ | constant | +| Initial value of local parameter 'J1.S2_stoich' | $0.1$ | constant | +| Initial value of local parameter 'J1.J1' | $0.1$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial value of species reference 'S1_stoich' | $1$ | constant | +| Initial value of species reference 'S2_stoich' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01803/l2v5/heta-code/output.heta b/latest/cases/01803/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3e849f2e2 --- /dev/null +++ b/latest/cases/01803/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +param @Record { } .= 3; +Param @Record { } .= 4; +pArAm @Record { } .= 5; + diff --git a/latest/cases/01803/l2v5/index.heta b/latest/cases/01803/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01803/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01803/l2v5/json/output.json b/latest/cases/01803/l2v5/json/output.json new file mode 100644 index 000000000..322098db0 --- /dev/null +++ b/latest/cases/01803/l2v5/json/output.json @@ -0,0 +1,51 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "param", + "assignments": { + "start_": "3" + } + }, + { + "class": "Record", + "id": "Param", + "assignments": { + "start_": "4" + } + }, + { + "class": "Record", + "id": "pArAm", + "assignments": { + "start_": "5" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01803/l3v2/heta-code/output.heta b/latest/cases/01803/l3v2/heta-code/output.heta new file mode 100644 index 000000000..18ff0d61d --- /dev/null +++ b/latest/cases/01803/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +param @Const { } = 3; +Param @Const { } = 4; +pArAm @Const { } = 5; + diff --git a/latest/cases/01803/l3v2/index.heta b/latest/cases/01803/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01803/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01803/l3v2/json/output.json b/latest/cases/01803/l3v2/json/output.json new file mode 100644 index 000000000..17d81a8ab --- /dev/null +++ b/latest/cases/01803/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "param", + "num": 3 + }, + { + "class": "Const", + "id": "Param", + "num": 4 + }, + { + "class": "Const", + "id": "pArAm", + "num": 5 + } +] \ No newline at end of file diff --git a/latest/cases/01803/model-sbml-l2v5.xml b/latest/cases/01803/model-sbml-l2v5.xml new file mode 100644 index 000000000..1b0f97820 --- /dev/null +++ b/latest/cases/01803/model-sbml-l2v5.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/latest/cases/01803/model-sbml-l3v2.xml b/latest/cases/01803/model-sbml-l3v2.xml new file mode 100644 index 000000000..6cc87597d --- /dev/null +++ b/latest/cases/01803/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01803/output.heta b/latest/cases/01803/output.heta new file mode 100644 index 000000000..9b3a76540 --- /dev/null +++ b/latest/cases/01803/output.heta @@ -0,0 +1,34 @@ +/* +category: Test +synopsis: Parameters with different capitalizations. +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 parameters (param, Param, pArAm) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter param | $3$ | constant | +| Initial value of parameter Param | $4$ | constant | +| Initial value of parameter pArAm | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +param @Const { } = 3; +Param @Const { } = 4; +pArAm @Const { } = 5; + diff --git a/latest/cases/01803/synopsis.txt b/latest/cases/01803/synopsis.txt new file mode 100644 index 000000000..b076e9702 --- /dev/null +++ b/latest/cases/01803/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Parameters with different capitalizations. +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 parameters (param, Param, pArAm) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter param | $3$ | constant | +| Initial value of parameter Param | $4$ | constant | +| Initial value of parameter pArAm | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01804/l2v5/heta-code/output.heta b/latest/cases/01804/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3d86fa237 --- /dev/null +++ b/latest/cases/01804/l2v5/heta-code/output.heta @@ -0,0 +1,15 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: C, } .= 4; +sPeC @Species { compartment: C, } .= 5; + diff --git a/latest/cases/01804/l2v5/index.heta b/latest/cases/01804/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01804/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01804/l2v5/json/output.json b/latest/cases/01804/l2v5/json/output.json new file mode 100644 index 000000000..9682806e1 --- /dev/null +++ b/latest/cases/01804/l2v5/json/output.json @@ -0,0 +1,62 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "spec", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "Spec", + "assignments": { + "start_": "4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "sPeC", + "assignments": { + "start_": "5" + }, + "compartment": "C" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01804/l3v2/heta-code/output.heta b/latest/cases/01804/l3v2/heta-code/output.heta new file mode 100644 index 000000000..4bb097bb6 --- /dev/null +++ b/latest/cases/01804/l3v2/heta-code/output.heta @@ -0,0 +1,10 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: C, } .= 4; +sPeC @Species { compartment: C, } .= 5; + diff --git a/latest/cases/01804/l3v2/index.heta b/latest/cases/01804/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01804/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01804/l3v2/json/output.json b/latest/cases/01804/l3v2/json/output.json new file mode 100644 index 000000000..d84564773 --- /dev/null +++ b/latest/cases/01804/l3v2/json/output.json @@ -0,0 +1,37 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Species", + "id": "spec", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "Spec", + "assignments": { + "start_": "4" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "sPeC", + "assignments": { + "start_": "5" + }, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01804/model-sbml-l2v5.xml b/latest/cases/01804/model-sbml-l2v5.xml new file mode 100644 index 000000000..142ea17a6 --- /dev/null +++ b/latest/cases/01804/model-sbml-l2v5.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + + diff --git a/latest/cases/01804/model-sbml-l3v2.xml b/latest/cases/01804/model-sbml-l3v2.xml new file mode 100644 index 000000000..51aa265b9 --- /dev/null +++ b/latest/cases/01804/model-sbml-l3v2.xml @@ -0,0 +1,14 @@ + + + + + + + + + + + + + + diff --git a/latest/cases/01804/output.heta b/latest/cases/01804/output.heta new file mode 100644 index 000000000..6eacbe857 --- /dev/null +++ b/latest/cases/01804/output.heta @@ -0,0 +1,38 @@ +/* +category: Test +synopsis: Species with different capitalizations. +componentTags: Compartment, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 species (spec, Spec, sPeC) +* 1 compartment (C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species spec | $3$ | variable | +| Initial concentration of species Spec | $4$ | variable | +| Initial concentration of species sPeC | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: C, } .= 4; +sPeC @Species { compartment: C, } .= 5; + diff --git a/latest/cases/01804/synopsis.txt b/latest/cases/01804/synopsis.txt new file mode 100644 index 000000000..d2d16f5a4 --- /dev/null +++ b/latest/cases/01804/synopsis.txt @@ -0,0 +1,26 @@ + +category: Test +synopsis: Species with different capitalizations. +componentTags: Compartment, Species +testTags: Amount +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 species (spec, Spec, sPeC) +* 1 compartment (C) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species spec | $3$ | variable | +| Initial concentration of species Spec | $4$ | variable | +| Initial concentration of species sPeC | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01805/l2v5/heta-code/output.heta b/latest/cases/01805/l2v5/heta-code/output.heta new file mode 100644 index 000000000..398823c1d --- /dev/null +++ b/latest/cases/01805/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 3; +Comp @Compartment { boundary: true, } .= 4; +cOmP @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01805/l2v5/index.heta b/latest/cases/01805/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01805/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01805/l2v5/json/output.json b/latest/cases/01805/l2v5/json/output.json new file mode 100644 index 000000000..bd691e710 --- /dev/null +++ b/latest/cases/01805/l2v5/json/output.json @@ -0,0 +1,54 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "3" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "Comp", + "assignments": { + "start_": "4" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "cOmP", + "assignments": { + "start_": "5" + }, + "boundary": true + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01805/l3v2/heta-code/output.heta b/latest/cases/01805/l3v2/heta-code/output.heta new file mode 100644 index 000000000..6b720175d --- /dev/null +++ b/latest/cases/01805/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 3; +Comp @Compartment { boundary: true, } .= 4; +cOmP @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01805/l3v2/index.heta b/latest/cases/01805/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01805/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01805/l3v2/json/output.json b/latest/cases/01805/l3v2/json/output.json new file mode 100644 index 000000000..7ea869fcf --- /dev/null +++ b/latest/cases/01805/l3v2/json/output.json @@ -0,0 +1,29 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "comp", + "assignments": { + "start_": "3" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "Comp", + "assignments": { + "start_": "4" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "cOmP", + "assignments": { + "start_": "5" + }, + "boundary": true + } +] \ No newline at end of file diff --git a/latest/cases/01805/model-sbml-l2v5.xml b/latest/cases/01805/model-sbml-l2v5.xml new file mode 100644 index 000000000..677efa6fa --- /dev/null +++ b/latest/cases/01805/model-sbml-l2v5.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/latest/cases/01805/model-sbml-l3v2.xml b/latest/cases/01805/model-sbml-l3v2.xml new file mode 100644 index 000000000..56c1bd894 --- /dev/null +++ b/latest/cases/01805/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01805/output.heta b/latest/cases/01805/output.heta new file mode 100644 index 000000000..595b52a71 --- /dev/null +++ b/latest/cases/01805/output.heta @@ -0,0 +1,34 @@ +/* +category: Test +synopsis: Compartments with different capitalizations. +componentTags: Compartment +testTags: MultiCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 compartments (comp, Comp, cOmP) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial volume of compartment 'comp' | $3$ | constant | +| Initial volume of compartment 'Comp' | $4$ | constant | +| Initial volume of compartment 'cOmP' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +comp @Compartment { boundary: true, } .= 3; +Comp @Compartment { boundary: true, } .= 4; +cOmP @Compartment { boundary: true, } .= 5; + diff --git a/latest/cases/01805/synopsis.txt b/latest/cases/01805/synopsis.txt new file mode 100644 index 000000000..c40e6e7cb --- /dev/null +++ b/latest/cases/01805/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Compartments with different capitalizations. +componentTags: Compartment +testTags: MultiCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 compartments (comp, Comp, cOmP) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial volume of compartment 'comp' | $3$ | constant | +| Initial volume of compartment 'Comp' | $4$ | constant | +| Initial volume of compartment 'cOmP' | $5$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01806/l2v5/heta-code/output.heta b/latest/cases/01806/l2v5/heta-code/output.heta new file mode 100644 index 000000000..3390e1e66 --- /dev/null +++ b/latest/cases/01806/l2v5/heta-code/output.heta @@ -0,0 +1,16 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +c @Compartment { boundary: true, } .= 2; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: c, } .= 4; +sPeC @Species { compartment: C, } .= 5; + diff --git a/latest/cases/01806/l2v5/index.heta b/latest/cases/01806/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01806/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01806/l2v5/json/output.json b/latest/cases/01806/l2v5/json/output.json new file mode 100644 index 000000000..bccffc117 --- /dev/null +++ b/latest/cases/01806/l2v5/json/output.json @@ -0,0 +1,70 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "spec", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "Spec", + "assignments": { + "start_": "4" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "sPeC", + "assignments": { + "start_": "5" + }, + "compartment": "C" + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01806/l3v2/heta-code/output.heta b/latest/cases/01806/l3v2/heta-code/output.heta new file mode 100644 index 000000000..d0023f4fb --- /dev/null +++ b/latest/cases/01806/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +c @Compartment { boundary: true, } .= 2; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: c, } .= 4; +sPeC @Species { compartment: C, } .= 5; + diff --git a/latest/cases/01806/l3v2/index.heta b/latest/cases/01806/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01806/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01806/l3v2/json/output.json b/latest/cases/01806/l3v2/json/output.json new file mode 100644 index 000000000..98eb7740b --- /dev/null +++ b/latest/cases/01806/l3v2/json/output.json @@ -0,0 +1,45 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "spec", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "Spec", + "assignments": { + "start_": "4" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "sPeC", + "assignments": { + "start_": "5" + }, + "compartment": "C" + } +] \ No newline at end of file diff --git a/latest/cases/01806/model-sbml-l2v5.xml b/latest/cases/01806/model-sbml-l2v5.xml new file mode 100644 index 000000000..db866602b --- /dev/null +++ b/latest/cases/01806/model-sbml-l2v5.xml @@ -0,0 +1,14 @@ + + + + + + + + + + + + + + diff --git a/latest/cases/01806/model-sbml-l3v2.xml b/latest/cases/01806/model-sbml-l3v2.xml new file mode 100644 index 000000000..3a4c9ba05 --- /dev/null +++ b/latest/cases/01806/model-sbml-l3v2.xml @@ -0,0 +1,15 @@ + + + + + + + + + + + + + + + diff --git a/latest/cases/01806/output.heta b/latest/cases/01806/output.heta new file mode 100644 index 000000000..353b93563 --- /dev/null +++ b/latest/cases/01806/output.heta @@ -0,0 +1,40 @@ +/* +category: Test +synopsis: Species in compartments with different capitalizations. +componentTags: Compartment, Species +testTags: Amount, MultiCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 species (spec, Spec, sPeC) +* 2 compartments (C, c) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species spec | $3$ | variable | +| Initial concentration of species Spec | $4$ | variable | +| Initial concentration of species sPeC | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +c @Compartment { boundary: true, } .= 2; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: c, } .= 4; +sPeC @Species { compartment: C, } .= 5; + diff --git a/latest/cases/01806/synopsis.txt b/latest/cases/01806/synopsis.txt new file mode 100644 index 000000000..880985793 --- /dev/null +++ b/latest/cases/01806/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Species in compartments with different capitalizations. +componentTags: Compartment, Species +testTags: Amount, MultiCompartment, NonUnityCompartment +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 species (spec, Spec, sPeC) +* 2 compartments (C, c) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species spec | $3$ | variable | +| Initial concentration of species Spec | $4$ | variable | +| Initial concentration of species sPeC | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01807/l2v5/heta-code/output.heta b/latest/cases/01807/l2v5/heta-code/output.heta new file mode 100644 index 000000000..280b241dc --- /dev/null +++ b/latest/cases/01807/l2v5/heta-code/output.heta @@ -0,0 +1,21 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +c @Compartment { boundary: true, } .= 2; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: c, } .= 4; +sPeC @Species { compartment: C, } .= 5; + +J @Reaction { actors: = spec, }; +J := 1; +j @Reaction { actors: = Spec + 2*sPeC, }; +j := 2; + diff --git a/latest/cases/01807/l2v5/index.heta b/latest/cases/01807/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01807/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01807/l2v5/json/output.json b/latest/cases/01807/l2v5/json/output.json new file mode 100644 index 000000000..4556c59ef --- /dev/null +++ b/latest/cases/01807/l2v5/json/output.json @@ -0,0 +1,100 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "spec", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "Spec", + "assignments": { + "start_": "4" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "sPeC", + "assignments": { + "start_": "5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "spec", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "j", + "assignments": { + "ode_": "2" + }, + "actors": [ + { + "target": "Spec", + "stoichiometry": 1 + }, + { + "target": "sPeC", + "stoichiometry": 2 + } + ] + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01807/l3v2/heta-code/output.heta b/latest/cases/01807/l3v2/heta-code/output.heta new file mode 100644 index 000000000..01c93614d --- /dev/null +++ b/latest/cases/01807/l3v2/heta-code/output.heta @@ -0,0 +1,16 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +c @Compartment { boundary: true, } .= 2; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: c, } .= 4; +sPeC @Species { compartment: C, } .= 5; + +J @Reaction { actors: = spec, }; +J := 1; +j @Reaction { actors: = Spec + 2*sPeC, }; +j := 2; + diff --git a/latest/cases/01807/l3v2/index.heta b/latest/cases/01807/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01807/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01807/l3v2/json/output.json b/latest/cases/01807/l3v2/json/output.json new file mode 100644 index 000000000..8351437aa --- /dev/null +++ b/latest/cases/01807/l3v2/json/output.json @@ -0,0 +1,75 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "spec", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "Spec", + "assignments": { + "start_": "4" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "sPeC", + "assignments": { + "start_": "5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J", + "assignments": { + "ode_": "1" + }, + "actors": [ + { + "target": "spec", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "j", + "assignments": { + "ode_": "2" + }, + "actors": [ + { + "target": "Spec", + "stoichiometry": 1 + }, + { + "target": "sPeC", + "stoichiometry": 2 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01807/model-sbml-l2v5.xml b/latest/cases/01807/model-sbml-l2v5.xml new file mode 100644 index 000000000..1f257f4d0 --- /dev/null +++ b/latest/cases/01807/model-sbml-l2v5.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + 2 + + + + + + diff --git a/latest/cases/01807/model-sbml-l3v2.xml b/latest/cases/01807/model-sbml-l3v2.xml new file mode 100644 index 000000000..474500bcb --- /dev/null +++ b/latest/cases/01807/model-sbml-l3v2.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + 2 + + + + + + diff --git a/latest/cases/01807/output.heta b/latest/cases/01807/output.heta new file mode 100644 index 000000000..dbc1c8c2a --- /dev/null +++ b/latest/cases/01807/output.heta @@ -0,0 +1,52 @@ +/* +category: Test +synopsis: Species in reactions with different capitalizations. +componentTags: Compartment, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 species (spec, Spec, sPeC) +* 2 compartments (C, c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J: -> spec | $1$ | +| j: -> Spec + 2sPeC | $2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species spec | $3$ | variable | +| Initial concentration of species Spec | $4$ | variable | +| Initial concentration of species sPeC | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +c @Compartment { boundary: true, } .= 2; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: c, } .= 4; +sPeC @Species { compartment: C, } .= 5; + +J @Reaction { actors: = spec, }; +J := 1; +j @Reaction { actors: = Spec + 2*sPeC, }; +j := 2; + diff --git a/latest/cases/01807/synopsis.txt b/latest/cases/01807/synopsis.txt new file mode 100644 index 000000000..407171cdb --- /dev/null +++ b/latest/cases/01807/synopsis.txt @@ -0,0 +1,34 @@ + +category: Test +synopsis: Species in reactions with different capitalizations. +componentTags: Compartment, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 species (spec, Spec, sPeC) +* 2 compartments (C, c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J: -> spec | $1$ | +| j: -> Spec + 2sPeC | $2$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species spec | $3$ | variable | +| Initial concentration of species Spec | $4$ | variable | +| Initial concentration of species sPeC | $5$ | variable | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01808/l2v5/heta-code/output.heta b/latest/cases/01808/l2v5/heta-code/output.heta new file mode 100644 index 000000000..69d87cfdb --- /dev/null +++ b/latest/cases/01808/l2v5/heta-code/output.heta @@ -0,0 +1,24 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +c @Compartment { boundary: true, } .= 2; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: c, } .= 4; +sPeC @Species { compartment: C, } .= 5; + +J @Reaction { actors: = spec, }; +J := K; +j @Reaction { actors: = Spec + 2*sPeC, }; +j := k; + +K @Record { } .= 1; +k @Record { } .= 2; + diff --git a/latest/cases/01808/l2v5/index.heta b/latest/cases/01808/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01808/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01808/l2v5/json/output.json b/latest/cases/01808/l2v5/json/output.json new file mode 100644 index 000000000..023ea3765 --- /dev/null +++ b/latest/cases/01808/l2v5/json/output.json @@ -0,0 +1,114 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "spec", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "Spec", + "assignments": { + "start_": "4" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "sPeC", + "assignments": { + "start_": "5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J", + "assignments": { + "ode_": "K" + }, + "actors": [ + { + "target": "spec", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "j", + "assignments": { + "ode_": "k" + }, + "actors": [ + { + "target": "Spec", + "stoichiometry": 1 + }, + { + "target": "sPeC", + "stoichiometry": 2 + } + ] + }, + { + "class": "Record", + "id": "K", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "k", + "assignments": { + "start_": "2" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01808/l3v2/heta-code/output.heta b/latest/cases/01808/l3v2/heta-code/output.heta new file mode 100644 index 000000000..55b21ecea --- /dev/null +++ b/latest/cases/01808/l3v2/heta-code/output.heta @@ -0,0 +1,19 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +c @Compartment { boundary: true, } .= 2; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: c, } .= 4; +sPeC @Species { compartment: C, } .= 5; + +J @Reaction { actors: = spec, }; +J := K; +j @Reaction { actors: = Spec + 2*sPeC, }; +j := k; + +K @Const { } = 1; +k @Const { } = 2; + diff --git a/latest/cases/01808/l3v2/index.heta b/latest/cases/01808/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01808/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01808/l3v2/json/output.json b/latest/cases/01808/l3v2/json/output.json new file mode 100644 index 000000000..248a13f18 --- /dev/null +++ b/latest/cases/01808/l3v2/json/output.json @@ -0,0 +1,85 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "1" + }, + "boundary": true + }, + { + "class": "Compartment", + "id": "c", + "assignments": { + "start_": "2" + }, + "boundary": true + }, + { + "class": "Species", + "id": "spec", + "assignments": { + "start_": "3" + }, + "compartment": "C" + }, + { + "class": "Species", + "id": "Spec", + "assignments": { + "start_": "4" + }, + "compartment": "c" + }, + { + "class": "Species", + "id": "sPeC", + "assignments": { + "start_": "5" + }, + "compartment": "C" + }, + { + "class": "Reaction", + "id": "J", + "assignments": { + "ode_": "K" + }, + "actors": [ + { + "target": "spec", + "stoichiometry": 1 + } + ] + }, + { + "class": "Reaction", + "id": "j", + "assignments": { + "ode_": "k" + }, + "actors": [ + { + "target": "Spec", + "stoichiometry": 1 + }, + { + "target": "sPeC", + "stoichiometry": 2 + } + ] + }, + { + "class": "Const", + "id": "K", + "num": 1 + }, + { + "class": "Const", + "id": "k", + "num": 2 + } +] \ No newline at end of file diff --git a/latest/cases/01808/model-sbml-l2v5.xml b/latest/cases/01808/model-sbml-l2v5.xml new file mode 100644 index 000000000..e3e39b5c5 --- /dev/null +++ b/latest/cases/01808/model-sbml-l2v5.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + + + + + K + + + + + + + + + + + k + + + + + + diff --git a/latest/cases/01808/model-sbml-l3v2.xml b/latest/cases/01808/model-sbml-l3v2.xml new file mode 100644 index 000000000..0648715eb --- /dev/null +++ b/latest/cases/01808/model-sbml-l3v2.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + K + + + + + + + + + + + k + + + + + + diff --git a/latest/cases/01808/output.heta b/latest/cases/01808/output.heta new file mode 100644 index 000000000..bc6bbe194 --- /dev/null +++ b/latest/cases/01808/output.heta @@ -0,0 +1,58 @@ +/* +category: Test +synopsis: Species in reactions with different capitalizations. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 species (spec, Spec, sPeC) +* 2 parameters (K, k) +* 2 compartments (C, c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J: -> spec | $K$ | +| j: -> Spec + 2sPeC | $k$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species spec | $3$ | variable | +| Initial concentration of species Spec | $4$ | variable | +| Initial concentration of species sPeC | $5$ | variable | +| Initial value of parameter K | $1$ | constant | +| Initial value of parameter k | $2$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 1; +c @Compartment { boundary: true, } .= 2; + +spec @Species { compartment: C, } .= 3; +Spec @Species { compartment: c, } .= 4; +sPeC @Species { compartment: C, } .= 5; + +J @Reaction { actors: = spec, }; +J := K; +j @Reaction { actors: = Spec + 2*sPeC, }; +j := k; + +K @Const { } = 1; +k @Const { } = 2; + diff --git a/latest/cases/01808/synopsis.txt b/latest/cases/01808/synopsis.txt new file mode 100644 index 000000000..16c6f7682 --- /dev/null +++ b/latest/cases/01808/synopsis.txt @@ -0,0 +1,37 @@ + +category: Test +synopsis: Species in reactions with different capitalizations. +componentTags: Compartment, Parameter, Reaction, Species +testTags: Amount, MultiCompartment, NonUnityCompartment, NonUnityStoichiometry +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + A simple model to ensure that the simulator is case-sensitive. + +The model contains: +* 3 species (spec, Spec, sPeC) +* 2 parameters (K, k) +* 2 compartments (C, c) + +There are 2 reactions: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J: -> spec | $K$ | +| j: -> Spec + 2sPeC | $k$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species spec | $3$ | variable | +| Initial concentration of species Spec | $4$ | variable | +| Initial concentration of species sPeC | $5$ | variable | +| Initial value of parameter K | $1$ | constant | +| Initial value of parameter k | $2$ | constant | +| Initial volume of compartment 'C' | $1$ | constant | +| Initial volume of compartment 'c' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01809/l2v5/index.heta b/latest/cases/01809/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01809/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01809/l3v2/heta-code/output.heta b/latest/cases/01809/l3v2/heta-code/output.heta new file mode 100644 index 000000000..3184b5933 --- /dev/null +++ b/latest/cases/01809/l3v2/heta-code/output.heta @@ -0,0 +1,11 @@ + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 0; + +S1 @Species { compartment: C, isAmount: true, } .= 1 * C; + +J @Reaction { actors: = S1, }; +J := 1.5; + diff --git a/latest/cases/01809/l3v2/index.heta b/latest/cases/01809/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01809/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01809/l3v2/json/output.json b/latest/cases/01809/l3v2/json/output.json new file mode 100644 index 000000000..c293e1585 --- /dev/null +++ b/latest/cases/01809/l3v2/json/output.json @@ -0,0 +1,35 @@ +[ + { + "id": "t" + }, + { + "class": "Compartment", + "id": "C", + "assignments": { + "start_": "0" + }, + "boundary": true + }, + { + "class": "Species", + "id": "S1", + "assignments": { + "start_": "1 * C" + }, + "compartment": "C", + "isAmount": true + }, + { + "class": "Reaction", + "id": "J", + "assignments": { + "ode_": "1.5" + }, + "actors": [ + { + "target": "S1", + "stoichiometry": 1 + } + ] + } +] \ No newline at end of file diff --git a/latest/cases/01809/model-sbml-l3v2.xml b/latest/cases/01809/model-sbml-l3v2.xml new file mode 100644 index 000000000..67b6a9097 --- /dev/null +++ b/latest/cases/01809/model-sbml-l3v2.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + 1.5 + + + + + + diff --git a/latest/cases/01809/output.heta b/latest/cases/01809/output.heta new file mode 100644 index 000000000..71ecde93f --- /dev/null +++ b/latest/cases/01809/output.heta @@ -0,0 +1,43 @@ +/* +category: Test +synopsis: A reaction with a species in a 0-dimensional compartment. +componentTags: Compartment, Reaction, Species +testTags: 0D-Compartment, Amount, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In SBML L3v2, there were special rules for when a compartment had a spatialDimensions of 0. Those rules were removed for SMBL L3, so a model with a 0D compartment now behaves exactly the same as if the compartment had some other dimensionality. This model tests a non-unity compartment in a reaction, and gives the species an initial concentration, to ensure the compartment's size is being properly handled. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J: -> S1 | $1.5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +C @Compartment { boundary: true, } .= 0; + +S1 @Species { compartment: C, isAmount: true, } .= 1 * C; + +J @Reaction { actors: = S1, }; +J := 1.5; + diff --git a/latest/cases/01809/synopsis.txt b/latest/cases/01809/synopsis.txt new file mode 100644 index 000000000..533267ab3 --- /dev/null +++ b/latest/cases/01809/synopsis.txt @@ -0,0 +1,30 @@ + +category: Test +synopsis: A reaction with a species in a 0-dimensional compartment. +componentTags: Compartment, Reaction, Species +testTags: 0D-Compartment, Amount, NonUnityCompartment +testType: TimeCourse +levels: 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + + In SBML L3v2, there were special rules for when a compartment had a spatialDimensions of 0. Those rules were removed for SMBL L3, so a model with a 0D compartment now behaves exactly the same as if the compartment had some other dimensionality. This model tests a non-unity compartment in a reaction, and gives the species an initial concentration, to ensure the compartment's size is being properly handled. + +The model contains: +* 1 species (S1) +* 1 compartment (C) + +There is one reaction: + +[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | +| J: -> S1 | $1.5$ |] + +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial concentration of species S1 | $1$ | variable | +| Initial volume of compartment 'C' | $2$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01810/l2v5/heta-code/output.heta b/latest/cases/01810/l2v5/heta-code/output.heta new file mode 100644 index 000000000..8e0f5a8b4 --- /dev/null +++ b/latest/cases/01810/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +INF @Record { } .= 10; +Inf @Record { } .= 1; +inf @Record { } .= 0.1; + diff --git a/latest/cases/01810/l2v5/index.heta b/latest/cases/01810/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01810/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01810/l2v5/json/output.json b/latest/cases/01810/l2v5/json/output.json new file mode 100644 index 000000000..f8080021b --- /dev/null +++ b/latest/cases/01810/l2v5/json/output.json @@ -0,0 +1,51 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "INF", + "assignments": { + "start_": "10" + } + }, + { + "class": "Record", + "id": "Inf", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "inf", + "assignments": { + "start_": "0.1" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01810/l3v2/heta-code/output.heta b/latest/cases/01810/l3v2/heta-code/output.heta new file mode 100644 index 000000000..55fe7bd03 --- /dev/null +++ b/latest/cases/01810/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +INF @Const { } = 10; +Inf @Const { } = 1; +inf @Const { } = 0.1; + diff --git a/latest/cases/01810/l3v2/index.heta b/latest/cases/01810/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01810/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01810/l3v2/json/output.json b/latest/cases/01810/l3v2/json/output.json new file mode 100644 index 000000000..de7a5092e --- /dev/null +++ b/latest/cases/01810/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "INF", + "num": 10 + }, + { + "class": "Const", + "id": "Inf", + "num": 1 + }, + { + "class": "Const", + "id": "inf", + "num": 0.1 + } +] \ No newline at end of file diff --git a/latest/cases/01810/model-sbml-l2v5.xml b/latest/cases/01810/model-sbml-l2v5.xml new file mode 100644 index 000000000..57b1faaa3 --- /dev/null +++ b/latest/cases/01810/model-sbml-l2v5.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/latest/cases/01810/model-sbml-l3v2.xml b/latest/cases/01810/model-sbml-l3v2.xml new file mode 100644 index 000000000..902242c74 --- /dev/null +++ b/latest/cases/01810/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01810/output.heta b/latest/cases/01810/output.heta new file mode 100644 index 000000000..a56ad1962 --- /dev/null +++ b/latest/cases/01810/output.heta @@ -0,0 +1,34 @@ +/* +category: Test +synopsis: Test SBML IDs named 'inf' +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'inf' are properly handled by the simulator. + +The model contains: +* 3 parameters (INF, Inf, inf) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter INF | $10$ | constant | +| Initial value of parameter Inf | $1$ | constant | +| Initial value of parameter inf | $0.1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +INF @Const { } = 10; +Inf @Const { } = 1; +inf @Const { } = 0.1; + diff --git a/latest/cases/01810/synopsis.txt b/latest/cases/01810/synopsis.txt new file mode 100644 index 000000000..04038ecbe --- /dev/null +++ b/latest/cases/01810/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Test SBML IDs named 'inf' +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'inf' are properly handled by the simulator. + +The model contains: +* 3 parameters (INF, Inf, inf) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter INF | $10$ | constant | +| Initial value of parameter Inf | $1$ | constant | +| Initial value of parameter inf | $0.1$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01811/l2v5/heta-code/output.heta b/latest/cases/01811/l2v5/heta-code/output.heta new file mode 100644 index 000000000..0338df4ee --- /dev/null +++ b/latest/cases/01811/l2v5/heta-code/output.heta @@ -0,0 +1,17 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +INF @Record { } .= 10; +Inf @Record { } .= 1; +inf @Record { } .= 0.1; +a @Record { } .= INF; +b @Record { } .= Inf; +c @Record { } .= inf; +d @Record { } .= Infinity; + diff --git a/latest/cases/01811/l2v5/index.heta b/latest/cases/01811/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01811/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01811/l2v5/json/output.json b/latest/cases/01811/l2v5/json/output.json new file mode 100644 index 000000000..0d6e91bdb --- /dev/null +++ b/latest/cases/01811/l2v5/json/output.json @@ -0,0 +1,79 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "INF", + "assignments": { + "start_": "10" + } + }, + { + "class": "Record", + "id": "Inf", + "assignments": { + "start_": "1" + } + }, + { + "class": "Record", + "id": "inf", + "assignments": { + "start_": "0.1" + } + }, + { + "class": "Record", + "id": "a", + "assignments": { + "start_": "INF" + } + }, + { + "class": "Record", + "id": "b", + "assignments": { + "start_": "Inf" + } + }, + { + "class": "Record", + "id": "c", + "assignments": { + "start_": "inf" + } + }, + { + "class": "Record", + "id": "d", + "assignments": { + "start_": "Infinity" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01811/l3v2/build.log b/latest/cases/01811/l3v2/build.log new file mode 100644 index 000000000..7bf72296f --- /dev/null +++ b/latest/cases/01811/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01811/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01811/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01811/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 86 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01811/l3v2/index.heta b/latest/cases/01811/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01811/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01811/model-sbml-l2v5.xml b/latest/cases/01811/model-sbml-l2v5.xml new file mode 100644 index 000000000..81182450c --- /dev/null +++ b/latest/cases/01811/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + INF + + + + + Inf + + + + + inf + + + + + + + + + + diff --git a/latest/cases/01811/model-sbml-l3v2.xml b/latest/cases/01811/model-sbml-l3v2.xml new file mode 100644 index 000000000..90c1f1e3b --- /dev/null +++ b/latest/cases/01811/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + INF + + + + + Inf + + + + + inf + + + + + + + + + + diff --git a/latest/cases/01811/output.heta b/latest/cases/01811/output.heta new file mode 100644 index 000000000..54dae65d9 --- /dev/null +++ b/latest/cases/01811/output.heta @@ -0,0 +1,47 @@ +/* +category: Test +synopsis: Test SBML IDs named 'inf' +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'inf' are properly handled by the simulator when assigned as values to other parameters. + +The model contains: +* 7 parameters (INF, Inf, inf, a, b, c, d) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter INF | $10$ | constant | +| Initial value of parameter Inf | $1$ | constant | +| Initial value of parameter inf | $0.1$ | constant | +| Initial value of parameter a | $INF$ | constant | +| Initial value of parameter b | $Inf$ | constant | +| Initial value of parameter c | $inf$ | constant | +| Initial value of parameter d | $INF$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +INF @Record { } .= 10; +Inf @Record { } .= 1; +inf @Record { } .= 0.1; +a @Record { } .= INF; +b @Record { } .= Inf; +c @Record { } .= inf; +d @Record { } .= Infinity; + diff --git a/latest/cases/01811/synopsis.txt b/latest/cases/01811/synopsis.txt new file mode 100644 index 000000000..d87388019 --- /dev/null +++ b/latest/cases/01811/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Test SBML IDs named 'inf' +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'inf' are properly handled by the simulator when assigned as values to other parameters. + +The model contains: +* 7 parameters (INF, Inf, inf, a, b, c, d) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter INF | $10$ | constant | +| Initial value of parameter Inf | $1$ | constant | +| Initial value of parameter inf | $0.1$ | constant | +| Initial value of parameter a | $INF$ | constant | +| Initial value of parameter b | $Inf$ | constant | +| Initial value of parameter c | $inf$ | constant | +| Initial value of parameter d | $INF$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01812/l2v5/build.log b/latest/cases/01812/l2v5/build.log new file mode 100644 index 000000000..72e2c5a65 --- /dev/null +++ b/latest/cases/01812/l2v5/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01812/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01812/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01812/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "NaN". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01812/l2v5/index.heta b/latest/cases/01812/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01812/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01812/l3v2/build.log b/latest/cases/01812/l3v2/build.log new file mode 100644 index 000000000..47593b945 --- /dev/null +++ b/latest/cases/01812/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01812/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01812/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01812/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "NaN". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 81 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01812/l3v2/index.heta b/latest/cases/01812/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01812/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01812/model-sbml-l2v5.xml b/latest/cases/01812/model-sbml-l2v5.xml new file mode 100644 index 000000000..8645f4ef2 --- /dev/null +++ b/latest/cases/01812/model-sbml-l2v5.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/latest/cases/01812/model-sbml-l3v2.xml b/latest/cases/01812/model-sbml-l3v2.xml new file mode 100644 index 000000000..816200d1a --- /dev/null +++ b/latest/cases/01812/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01812/synopsis.txt b/latest/cases/01812/synopsis.txt new file mode 100644 index 000000000..8ca8c8a1e --- /dev/null +++ b/latest/cases/01812/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Test SBML IDs named 'nan' +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'nan' are properly handled by the simulator. + +The model contains: +* 3 parameters (NAN, NaN, nan) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter NAN | $0.1$ | constant | +| Initial value of parameter NaN | $0.01$ | constant | +| Initial value of parameter nan | $0.001$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01813/l2v5/build.log b/latest/cases/01813/l2v5/build.log new file mode 100644 index 000000000..d2da35161 --- /dev/null +++ b/latest/cases/01813/l2v5/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01813/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01813/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01813/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "NaN". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 90 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01813/l2v5/index.heta b/latest/cases/01813/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01813/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01813/l3v2/build.log b/latest/cases/01813/l3v2/build.log new file mode 100644 index 000000000..b574f9185 --- /dev/null +++ b/latest/cases/01813/l3v2/build.log @@ -0,0 +1,14 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01813/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01813/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01813/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "NaN". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 85 +[error] No required "num" property for "p" of Const. +[error] No required "num" property for "q" of Const. +[error] No required "num" property for "r" of Const. +[error] No required "num" property for "s" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01813/l3v2/index.heta b/latest/cases/01813/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01813/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01813/model-sbml-l2v5.xml b/latest/cases/01813/model-sbml-l2v5.xml new file mode 100644 index 000000000..758be49bc --- /dev/null +++ b/latest/cases/01813/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + NAN + + + + + NaN + + + + + nan + + + + + + + + + + diff --git a/latest/cases/01813/model-sbml-l3v2.xml b/latest/cases/01813/model-sbml-l3v2.xml new file mode 100644 index 000000000..2e2989655 --- /dev/null +++ b/latest/cases/01813/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + NAN + + + + + NaN + + + + + nan + + + + + + + + + + diff --git a/latest/cases/01813/synopsis.txt b/latest/cases/01813/synopsis.txt new file mode 100644 index 000000000..a87361164 --- /dev/null +++ b/latest/cases/01813/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Test SBML IDs named 'nan' +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'nan' are properly handled by the simulator when assigned as values to other parameters. + +The model contains: +* 7 parameters (NAN, NaN, nan, p, q, r, s) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter NAN | $0.1$ | constant | +| Initial value of parameter NaN | $0.01$ | constant | +| Initial value of parameter nan | $0.001$ | constant | +| Initial value of parameter p | $NAN$ | constant | +| Initial value of parameter q | $NaN$ | constant | +| Initial value of parameter r | $nan$ | constant | +| Initial value of parameter s | $NaN$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01814/l2v5/heta-code/output.heta b/latest/cases/01814/l2v5/heta-code/output.heta new file mode 100644 index 000000000..c458dd932 --- /dev/null +++ b/latest/cases/01814/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +true @Record { } .= 10; +True @Record { } .= 20; +TRUE @Record { } .= 30; + diff --git a/latest/cases/01814/l2v5/index.heta b/latest/cases/01814/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01814/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01814/l2v5/json/output.json b/latest/cases/01814/l2v5/json/output.json new file mode 100644 index 000000000..b67a6f18c --- /dev/null +++ b/latest/cases/01814/l2v5/json/output.json @@ -0,0 +1,51 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "true", + "assignments": { + "start_": "10" + } + }, + { + "class": "Record", + "id": "True", + "assignments": { + "start_": "20" + } + }, + { + "class": "Record", + "id": "TRUE", + "assignments": { + "start_": "30" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01814/l3v2/heta-code/output.heta b/latest/cases/01814/l3v2/heta-code/output.heta new file mode 100644 index 000000000..e6ef238c3 --- /dev/null +++ b/latest/cases/01814/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +true @Const { } = 10; +True @Const { } = 20; +TRUE @Const { } = 30; + diff --git a/latest/cases/01814/l3v2/index.heta b/latest/cases/01814/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01814/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01814/l3v2/json/output.json b/latest/cases/01814/l3v2/json/output.json new file mode 100644 index 000000000..9a7e482b0 --- /dev/null +++ b/latest/cases/01814/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "true", + "num": 10 + }, + { + "class": "Const", + "id": "True", + "num": 20 + }, + { + "class": "Const", + "id": "TRUE", + "num": 30 + } +] \ No newline at end of file diff --git a/latest/cases/01814/model-sbml-l2v5.xml b/latest/cases/01814/model-sbml-l2v5.xml new file mode 100644 index 000000000..92fac2854 --- /dev/null +++ b/latest/cases/01814/model-sbml-l2v5.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/latest/cases/01814/model-sbml-l3v2.xml b/latest/cases/01814/model-sbml-l3v2.xml new file mode 100644 index 000000000..a23b8c6c2 --- /dev/null +++ b/latest/cases/01814/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01814/output.heta b/latest/cases/01814/output.heta new file mode 100644 index 000000000..ed014632d --- /dev/null +++ b/latest/cases/01814/output.heta @@ -0,0 +1,34 @@ +/* +category: Test +synopsis: Test SBML IDs named 'true' +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'true' are properly handled by the simulator when assigned as values to other parameters. + +The model contains: +* 3 parameters (true, True, TRUE) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter true | $10$ | constant | +| Initial value of parameter True | $20$ | constant | +| Initial value of parameter TRUE | $30$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +true @Const { } = 10; +True @Const { } = 20; +TRUE @Const { } = 30; + diff --git a/latest/cases/01814/synopsis.txt b/latest/cases/01814/synopsis.txt new file mode 100644 index 000000000..95c5c06a9 --- /dev/null +++ b/latest/cases/01814/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Test SBML IDs named 'true' +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'true' are properly handled by the simulator when assigned as values to other parameters. + +The model contains: +* 3 parameters (true, True, TRUE) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter true | $10$ | constant | +| Initial value of parameter True | $20$ | constant | +| Initial value of parameter TRUE | $30$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01815/l2v5/build.log b/latest/cases/01815/l2v5/build.log new file mode 100644 index 000000000..52492f1e6 --- /dev/null +++ b/latest/cases/01815/l2v5/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01815/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01815/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01815/model-sbml-l2v5.xml"... +[error] Record assignments "a" should be a numeric expression. +[info] Setting references in elements, total length 90 +[error] Record "a" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01815/l2v5/index.heta b/latest/cases/01815/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01815/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01815/l3v2/build.log b/latest/cases/01815/l3v2/build.log new file mode 100644 index 000000000..074ea31e1 --- /dev/null +++ b/latest/cases/01815/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01815/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01815/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01815/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 85 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01815/l3v2/index.heta b/latest/cases/01815/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01815/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01815/model-sbml-l2v5.xml b/latest/cases/01815/model-sbml-l2v5.xml new file mode 100644 index 000000000..226932c59 --- /dev/null +++ b/latest/cases/01815/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + true + + + + + True + + + + + TRUE + + + + + diff --git a/latest/cases/01815/model-sbml-l3v2.xml b/latest/cases/01815/model-sbml-l3v2.xml new file mode 100644 index 000000000..31a698058 --- /dev/null +++ b/latest/cases/01815/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + true + + + + + True + + + + + TRUE + + + + + diff --git a/latest/cases/01815/synopsis.txt b/latest/cases/01815/synopsis.txt new file mode 100644 index 000000000..b606918fc --- /dev/null +++ b/latest/cases/01815/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Test SBML IDs named 'true' +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'true' are properly handled by the simulator when assigned as values to other parameters. + +The model contains: +* 6 parameters (true, True, TRUE, a, b, c) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter true | $10$ | constant | +| Initial value of parameter True | $20$ | constant | +| Initial value of parameter TRUE | $30$ | constant | +| Initial value of parameter a | $true$ | constant | +| Initial value of parameter b | $True$ | constant | +| Initial value of parameter c | $TRUE$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01816/l2v5/heta-code/output.heta b/latest/cases/01816/l2v5/heta-code/output.heta new file mode 100644 index 000000000..e97c1d018 --- /dev/null +++ b/latest/cases/01816/l2v5/heta-code/output.heta @@ -0,0 +1,13 @@ + +volume #defineUnit { units: litre, }; +area #defineUnit { units: metre^2, }; +length #defineUnit { units: metre, }; +substance #defineUnit { units: mole, }; +time #defineUnit { units: second, }; + +t @TimeScale { }; + +false @Record { } .= 4; +False @Record { } .= 5; +FALSE @Record { } .= 6; + diff --git a/latest/cases/01816/l2v5/index.heta b/latest/cases/01816/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01816/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01816/l2v5/json/output.json b/latest/cases/01816/l2v5/json/output.json new file mode 100644 index 000000000..c7d5fd275 --- /dev/null +++ b/latest/cases/01816/l2v5/json/output.json @@ -0,0 +1,51 @@ +[ + { + "id": "t" + }, + { + "class": "Record", + "id": "false", + "assignments": { + "start_": "4" + } + }, + { + "class": "Record", + "id": "False", + "assignments": { + "start_": "5" + } + }, + { + "class": "Record", + "id": "FALSE", + "assignments": { + "start_": "6" + } + }, + { + "id": "volume", + "units": "litre", + "action": "defineUnit" + }, + { + "id": "area", + "units": "metre^2", + "action": "defineUnit" + }, + { + "id": "length", + "units": "metre", + "action": "defineUnit" + }, + { + "id": "substance", + "units": "mole", + "action": "defineUnit" + }, + { + "id": "time", + "units": "second", + "action": "defineUnit" + } +] \ No newline at end of file diff --git a/latest/cases/01816/l3v2/heta-code/output.heta b/latest/cases/01816/l3v2/heta-code/output.heta new file mode 100644 index 000000000..2fb954288 --- /dev/null +++ b/latest/cases/01816/l3v2/heta-code/output.heta @@ -0,0 +1,8 @@ + + +t @TimeScale { }; + +false @Const { } = 4; +False @Const { } = 5; +FALSE @Const { } = 6; + diff --git a/latest/cases/01816/l3v2/index.heta b/latest/cases/01816/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01816/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01816/l3v2/json/output.json b/latest/cases/01816/l3v2/json/output.json new file mode 100644 index 000000000..2c4d9f1b3 --- /dev/null +++ b/latest/cases/01816/l3v2/json/output.json @@ -0,0 +1,20 @@ +[ + { + "id": "t" + }, + { + "class": "Const", + "id": "false", + "num": 4 + }, + { + "class": "Const", + "id": "False", + "num": 5 + }, + { + "class": "Const", + "id": "FALSE", + "num": 6 + } +] \ No newline at end of file diff --git a/latest/cases/01816/model-sbml-l2v5.xml b/latest/cases/01816/model-sbml-l2v5.xml new file mode 100644 index 000000000..6025ee480 --- /dev/null +++ b/latest/cases/01816/model-sbml-l2v5.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/latest/cases/01816/model-sbml-l3v2.xml b/latest/cases/01816/model-sbml-l3v2.xml new file mode 100644 index 000000000..3757da941 --- /dev/null +++ b/latest/cases/01816/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01816/output.heta b/latest/cases/01816/output.heta new file mode 100644 index 000000000..31d9fb073 --- /dev/null +++ b/latest/cases/01816/output.heta @@ -0,0 +1,34 @@ +/* +category: Test +synopsis: Test SBML IDs named 'false' +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'false' are properly handled by the simulator. + +The model contains: +* 3 parameters (false, False, FALSE) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter false | $4$ | constant | +| Initial value of parameter False | $5$ | constant | +| Initial value of parameter FALSE | $6$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + +*/ + + + +t @TimeScale { }; + +false @Const { } = 4; +False @Const { } = 5; +FALSE @Const { } = 6; + diff --git a/latest/cases/01816/synopsis.txt b/latest/cases/01816/synopsis.txt new file mode 100644 index 000000000..7b4613582 --- /dev/null +++ b/latest/cases/01816/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Test SBML IDs named 'false' +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'false' are properly handled by the simulator. + +The model contains: +* 3 parameters (false, False, FALSE) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter false | $4$ | constant | +| Initial value of parameter False | $5$ | constant | +| Initial value of parameter FALSE | $6$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01817/l2v5/build.log b/latest/cases/01817/l2v5/build.log new file mode 100644 index 000000000..c24588f5b --- /dev/null +++ b/latest/cases/01817/l2v5/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01817/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01817/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01817/model-sbml-l2v5.xml"... +[error] Record assignments "a" should be a numeric expression. +[info] Setting references in elements, total length 90 +[error] Record "a" is not initialized. You must set "start_" or "ode_" for the record or use abstract namespace. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01817/l2v5/index.heta b/latest/cases/01817/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01817/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01817/l3v2/build.log b/latest/cases/01817/l3v2/build.log new file mode 100644 index 000000000..16788950d --- /dev/null +++ b/latest/cases/01817/l3v2/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01817/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01817/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01817/model-sbml-l3v2.xml"... +[info] Setting references in elements, total length 85 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01817/l3v2/index.heta b/latest/cases/01817/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01817/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01817/model-sbml-l2v5.xml b/latest/cases/01817/model-sbml-l2v5.xml new file mode 100644 index 000000000..fab41a308 --- /dev/null +++ b/latest/cases/01817/model-sbml-l2v5.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + false + + + + + False + + + + + FALSE + + + + + diff --git a/latest/cases/01817/model-sbml-l3v2.xml b/latest/cases/01817/model-sbml-l3v2.xml new file mode 100644 index 000000000..e9085949f --- /dev/null +++ b/latest/cases/01817/model-sbml-l3v2.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + false + + + + + False + + + + + FALSE + + + + + diff --git a/latest/cases/01817/synopsis.txt b/latest/cases/01817/synopsis.txt new file mode 100644 index 000000000..a6616d26b --- /dev/null +++ b/latest/cases/01817/synopsis.txt @@ -0,0 +1,27 @@ + +category: Test +synopsis: Test SBML IDs named 'false' +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'false' are properly handled by the simulator and when assigned to parameters. + +The model contains: +* 6 parameters (false, False, FALSE, a, b, c) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter false | $4$ | constant | +| Initial value of parameter False | $5$ | constant | +| Initial value of parameter FALSE | $6$ | constant | +| Initial value of parameter a | $false$ | constant | +| Initial value of parameter b | $False$ | constant | +| Initial value of parameter c | $FALSE$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01818/l2v5/build.log b/latest/cases/01818/l2v5/build.log new file mode 100644 index 000000000..94ee2cac4 --- /dev/null +++ b/latest/cases/01818/l2v5/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01818/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01818/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01818/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "pi". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] id must not be a reserved word, got "PI". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 85 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01818/l2v5/index.heta b/latest/cases/01818/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01818/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01818/l3v2/build.log b/latest/cases/01818/l3v2/build.log new file mode 100644 index 000000000..344271606 --- /dev/null +++ b/latest/cases/01818/l3v2/build.log @@ -0,0 +1,12 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01818/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01818/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01818/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "pi". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] id must not be a reserved word, got "PI". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 80 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01818/l3v2/index.heta b/latest/cases/01818/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01818/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01818/model-sbml-l2v5.xml b/latest/cases/01818/model-sbml-l2v5.xml new file mode 100644 index 000000000..2931b5b3e --- /dev/null +++ b/latest/cases/01818/model-sbml-l2v5.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/latest/cases/01818/model-sbml-l3v2.xml b/latest/cases/01818/model-sbml-l3v2.xml new file mode 100644 index 000000000..db65d3deb --- /dev/null +++ b/latest/cases/01818/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01818/synopsis.txt b/latest/cases/01818/synopsis.txt new file mode 100644 index 000000000..dfd76202c --- /dev/null +++ b/latest/cases/01818/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Test SBML IDs named 'pi' +componentTags: Parameter +testTags: +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'pi' are properly handled by the simulator. + +The model contains: +* 3 parameters (pi, Pi, PI) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter pi | $7$ | constant | +| Initial value of parameter Pi | $8$ | constant | +| Initial value of parameter PI | $9$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01819/l2v5/build.log b/latest/cases/01819/l2v5/build.log new file mode 100644 index 000000000..a20a01290 --- /dev/null +++ b/latest/cases/01819/l2v5/build.log @@ -0,0 +1,13 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01819/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01819/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01819/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "pi". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] id must not be a reserved word, got "PI". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 89 +[error] Component "PI" is not found in space "nameless" as expected in expression: c [start_]= PI; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01819/l2v5/index.heta b/latest/cases/01819/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01819/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01819/l3v2/build.log b/latest/cases/01819/l3v2/build.log new file mode 100644 index 000000000..0ab97d8d2 --- /dev/null +++ b/latest/cases/01819/l3v2/build.log @@ -0,0 +1,16 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01819/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01819/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01819/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "pi". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[error] id must not be a reserved word, got "PI". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 84 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01819/l3v2/index.heta b/latest/cases/01819/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01819/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01819/model-sbml-l2v5.xml b/latest/cases/01819/model-sbml-l2v5.xml new file mode 100644 index 000000000..cc400ce9b --- /dev/null +++ b/latest/cases/01819/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + pi + + + + + Pi + + + + + PI + + + + + + + + + + diff --git a/latest/cases/01819/model-sbml-l3v2.xml b/latest/cases/01819/model-sbml-l3v2.xml new file mode 100644 index 000000000..4ea36d744 --- /dev/null +++ b/latest/cases/01819/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + pi + + + + + Pi + + + + + PI + + + + + + + + + + diff --git a/latest/cases/01819/synopsis.txt b/latest/cases/01819/synopsis.txt new file mode 100644 index 000000000..715596b03 --- /dev/null +++ b/latest/cases/01819/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Test SBML IDs named 'pi' +componentTags: InitialAssignment, Parameter +testTags: InitialValueReassigned +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'pi' are properly handled by the simulator when assigned as values to other parameters. + +The model contains: +* 7 parameters (pi, Pi, PI, a, b, c, d) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter pi | $7$ | constant | +| Initial value of parameter Pi | $8$ | constant | +| Initial value of parameter PI | $9$ | constant | +| Initial value of parameter a | $pi$ | constant | +| Initial value of parameter b | $Pi$ | constant | +| Initial value of parameter c | $PI$ | constant | +| Initial value of parameter d | $pi$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01820/l2v5/build.log b/latest/cases/01820/l2v5/build.log new file mode 100644 index 000000000..13da27379 --- /dev/null +++ b/latest/cases/01820/l2v5/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01820/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01820/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01820/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "time". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 86 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01820/l2v5/index.heta b/latest/cases/01820/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01820/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01820/l3v2/build.log b/latest/cases/01820/l3v2/build.log new file mode 100644 index 000000000..ce38227a8 --- /dev/null +++ b/latest/cases/01820/l3v2/build.log @@ -0,0 +1,10 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01820/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01820/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01820/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "time". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 81 +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01820/l3v2/index.heta b/latest/cases/01820/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01820/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01820/model-sbml-l2v5.xml b/latest/cases/01820/model-sbml-l2v5.xml new file mode 100644 index 000000000..fe3646dd8 --- /dev/null +++ b/latest/cases/01820/model-sbml-l2v5.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/latest/cases/01820/model-sbml-l3v2.xml b/latest/cases/01820/model-sbml-l3v2.xml new file mode 100644 index 000000000..250818a28 --- /dev/null +++ b/latest/cases/01820/model-sbml-l3v2.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/latest/cases/01820/synopsis.txt b/latest/cases/01820/synopsis.txt new file mode 100644 index 000000000..71a8fd30a --- /dev/null +++ b/latest/cases/01820/synopsis.txt @@ -0,0 +1,24 @@ + +category: Test +synopsis: Test SBML IDs named 'time' +componentTags: Parameter +testTags: NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'time' are properly handled by the simulator. + +The model contains: +* 3 parameters (time, Time, TIME) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter time | $10$ | constant | +| Initial value of parameter Time | $11$ | constant | +| Initial value of parameter TIME | $12$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/01821/l2v5/build.log b/latest/cases/01821/l2v5/build.log new file mode 100644 index 000000000..6ea8203a1 --- /dev/null +++ b/latest/cases/01821/l2v5/build.log @@ -0,0 +1,11 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01821/l2v5". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01821/l2v5/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01821/model-sbml-l2v5.xml"... +[error] id must not be a reserved word, got "time". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 90 +[error] Component "time" is not found in space "nameless" as expected in expression: a [start_]= time; +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01821/l2v5/index.heta b/latest/cases/01821/l2v5/index.heta new file mode 100644 index 000000000..867b345ba --- /dev/null +++ b/latest/cases/01821/l2v5/index.heta @@ -0,0 +1,10 @@ +#defineUnit volume { units: litre }; +#defineUnit area { units: metre^2 }; +#defineUnit length { units: metre }; +#defineUnit substance { units: mole }; +#defineUnit time { units: second }; + +#include { source: ../model-sbml-l2v5.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01821/l3v2/build.log b/latest/cases/01821/l3v2/build.log new file mode 100644 index 000000000..7b0baef11 --- /dev/null +++ b/latest/cases/01821/l3v2/build.log @@ -0,0 +1,14 @@ +[info] Namespace "nameless" was set as "concrete" +[info] Builder initialized in directory "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01821/l3v2". +[info] Compilation of module "index.heta" of type "heta"... +[info] Reading module of type "heta" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01821/l3v2/index.heta"... +[info] Reading module of type "sbml" from file "/home/runner/work/sbml-heta-cases/sbml-heta-cases/result/latest/cases/01821/model-sbml-l3v2.xml"... +[error] id must not be a reserved word, got "time". Reserved words list: + include, block, namespace, abstract, concrete, begin, end, NaN, Infinity, e, E, pi, PI, time, SOLVERTIME, default +[info] Setting references in elements, total length 85 +[error] No required "num" property for "a" of Const. +[error] No required "num" property for "b" of Const. +[error] No required "num" property for "c" of Const. +[error] No required "num" property for "d" of Const. +[info] Checking for circular references in Records. +[warn] Units checking and export were skipped because of errors in compilation. \ No newline at end of file diff --git a/latest/cases/01821/l3v2/index.heta b/latest/cases/01821/l3v2/index.heta new file mode 100644 index 000000000..3d9cf9e7c --- /dev/null +++ b/latest/cases/01821/l3v2/index.heta @@ -0,0 +1,4 @@ +#include { source: ../model-sbml-l3v2.xml, type: sbml }; + +#export { format: HetaCode }; +#export { format: JSON }; diff --git a/latest/cases/01821/model-sbml-l2v5.xml b/latest/cases/01821/model-sbml-l2v5.xml new file mode 100644 index 000000000..013dfb267 --- /dev/null +++ b/latest/cases/01821/model-sbml-l2v5.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + time + + + + + Time + + + + + TIME + + + + + time + + + + + diff --git a/latest/cases/01821/model-sbml-l3v2.xml b/latest/cases/01821/model-sbml-l3v2.xml new file mode 100644 index 000000000..714468d2d --- /dev/null +++ b/latest/cases/01821/model-sbml-l3v2.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + time + + + + + Time + + + + + TIME + + + + + time + + + + + diff --git a/latest/cases/01821/synopsis.txt b/latest/cases/01821/synopsis.txt new file mode 100644 index 000000000..079a7fc92 --- /dev/null +++ b/latest/cases/01821/synopsis.txt @@ -0,0 +1,28 @@ + +category: Test +synopsis: Test SBML IDs named 'time' +componentTags: CSymbolTime, InitialAssignment, Parameter +testTags: InitialValueReassigned, NonConstantParameter +testType: TimeCourse +levels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2 +generatedBy: Analytic +packagesPresent: + +This tests whether parameters named 'time' are properly handled by the simulator when assigned as values to other parameters. + +The model contains: +* 7 parameters (time, Time, TIME, a, b, c, d) +The initial conditions are as follows: + +[{width:35em,margin: 1em auto}| | *Value* | *Constant* | +| Initial value of parameter time | $10$ | constant | +| Initial value of parameter Time | $11$ | constant | +| Initial value of parameter TIME | $12$ | constant | +| Initial value of parameter a | $time$ | constant | +| Initial value of parameter b | $Time$ | constant | +| Initial value of parameter c | $TIME$ | constant | +| Initial value of parameter d | $time$ | constant |] + +Note: The test data for this model was generated from an analytical +solution of the system of equations. + diff --git a/latest/cases/index.html b/latest/cases/index.html index 6f7d93dbc..ad4fb1aa5 100644 --- a/latest/cases/index.html +++ b/latest/cases/index.html @@ -1 +1 @@ -

SBML Heta cases

\ No newline at end of file +

SBML Heta cases

\ No newline at end of file diff --git a/latest/finetune-0.jsonl b/latest/finetune-0.jsonl index bbda366f3..690e0f78b 100644 --- a/latest/finetune-0.jsonl +++ b/latest/finetune-0.jsonl @@ -24,7 +24,7 @@ {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Variant of three reactions with four species in one\r\ncompartment, with one species labeled constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, \r\ntestTags: Amount, ConstantSpecies, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and four parameters named k1, k2, k3 and\r\nk4. Species S3 is labeled a SBML boundary condition and is also labeled\r\nconstant. The model contains four reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |\r\n| S2 -> S1 | $k2 * S2 * compartment$ |\r\n| S2 -> S3 + S4 | $k3 * S2 * compartment$ |\r\n| S3 + S4 -> S2 | $k4 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$0.75$ |second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$0.4$ |second^-1^ |\r\n|Value of parameter k4 |$0.1$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 0 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, };\nreaction2 := compartment * k2 * S2;\nreaction3 @Reaction 'reaction3' { actors: S2 = S3 + S4, reversible: false, };\nreaction3 := compartment * k3 * S2;\nreaction4 @Reaction 'reaction4' { actors: S3 + S4 = S2, reversible: false, };\nreaction4 := compartment * k4 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.4;\nk4 @Const 'k4' { } = 0.1;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment and nonzero initial amounts using a function to apply \r\nthe kinetic law.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * multiply(k1,S1)$ |]\r\n\r\nThe reaction applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$1$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\n\nk1 @Const 'k1' { } = 1;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single forward reaction with two species in one compartment \r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * S1 * k1$ |]\r\n\r\nThe model contains one event that assigns value to species S1 defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.1$ | $-$ | $S1 = 1$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.1, };\n\n"} -{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the compartment size.\r\ncomponentTags: Compartment, Species, Reaction, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k * S1$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k.\r\n\r\nThe model contains one initialAssignment that assigns the initial value for\r\ncompartment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | compartment | $534 * 0.001$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this\r\ncase the value from the initialAssignment is consistent with the value\r\nattributed to the compartment by the model definition.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$ 0.0$ |mole |\r\n|Value of local parameter k |$ 100$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 0.534$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\ncompartment @Compartment 'compartment' { units: volume, boundary: true, } .= 0.534;\n\nS1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment;\nS2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k__reaction1_local * S1;\n\nk__reaction1_local @Const { } = 100;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the compartment size.\r\ncomponentTags: Compartment, Species, Reaction, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k * S1$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k.\r\n\r\nThe model contains one initialAssignment that assigns the initial value for\r\ncompartment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | compartment | $534 * 0.001$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this\r\ncase the value from the initialAssignment is consistent with the value\r\nattributed to the compartment by the model definition.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$ 0.0$ |mole |\r\n|Value of local parameter k |$ 100$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 0.534$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.534;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k__reaction1_local * S1;\n\nk__reaction1_local @Const { } = 100;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $Ceiling(S1 * p1)! / p2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 0.0$ |mole |\r\n|Value of parameter p1 |$ 4$ |litre mole^-1^ |\r\n|Value of parameter p2 |$ 25$ |second mole^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := factorial(ceil(p1 * S1)) * pow(p2, (-1));\n\np1 @Const 'p1' { } = 4;\np2 @Const 'p2' { } = 25;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic rule that assigns value to a species.\r\ncomponentTags: Compartment, Species, AssignmentRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There is one\r\nspecies named S1. The model does not contain any reactions.\r\n \r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| assignmentRule | S1 | $3 + 4$ |]\r\n\r\nThe rule assigns a value to species S1 which is consistent with the value\r\nattributed to the species by the model definition.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 7$ |mole |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 7 / compartment;\nS1 := 7;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic rule that assigns value to a species.\r\ncomponentTags: Compartment, Species, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There is one\r\nspecies named S1. The model does not contain any reactions.\r\n \r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| assignmentRule | S1 | $3 + 4$ |]\r\n\r\nIn the case there is no value attributed to the species by the model\r\ndefinition and thus the value must be calculated by the rule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ undeclared$ | mole |\r\n|Volume of compartment \"compartment\" |$ 1$ | litre |]\r\n\t\t\t\t \r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, };\nS1 := 7;\n\n"} @@ -52,8 +52,8 @@ {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments called \"compartment\" and\r\n\"compartment1\". There are three species named S1, S2 and S3 and two\r\nparameters named k1 and k2. Compartment \"compartment\" contains species S1\r\nand S2. Compartment \"compartment1\" contains species S3.\r\n\r\nThe model contains:\r\n* 3 species (S1, S2, S3)\r\n* 2 parameters (k1, k2)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |]\r\n\r\nThe first reaction occurs entirely in compartment \"compartment\", whereas\r\nthe second reaction occurs between a species in \"compartment\" and a species\r\nin \"compartment1\".\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named \"compartment\" and \"compartment1\".\r\nThere are four species named S1, S2, S3 and S4 and three parameters named\r\nk1, k2 and k3. Compartment \"compartment\" contains species S1 and S2.\r\nCompartment \"compartment1\" contains species S3 and S4.\r\n\r\nThe model contains:\r\n* 4 species (S1, S2, S3, S4)\r\n* 3 parameters (k1, k2, k3)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |\r\n| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |]\r\n\r\nThe first reaction occurs entirely within \"compartment\", the second\r\nreaction occurs between a species in \"compartment\" and a species in\r\n\"compartment1\" and the third reaction occurs entirely within\r\n\"compartment1\".\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial amount of species S4 | $0.1$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $7.5$ | constant |\r\n| Initial value of parameter k3 | $0.75$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\nreaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, };\nreaction3 := compartment * k3 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 7.5;\nk3 @Const 'k3' { } = 0.75;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named \"compartment\" and \"compartment1\".\r\nThere are two species named S1 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" contains species S1. Compartment \"compartment1\"\r\ncontains species S3.\r\n\r\nThe model contains:\r\n* 2 species (S1, S3)\r\n* 2 parameters (k1, k2)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 -> S3 | $compartment * k1 * S1$ |\r\n| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |]\r\n\r\nBoth reactions occur between species within different compartments.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, };\nreaction2 := compartment1 * k2 * (S3 + (-1) * S1);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} -{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species and parameters local to \r\n reactions.\r\ncomponentTags: Compartment, Species, Reaction \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * compartment,$ |\r\n| S2 -> S3 | $k * S2 * compartment,$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k. Reaction S2 -> S3 also\r\ndefines one (different) local parameter k. Both of these parameters have a\r\nscope local to the defining reaction.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$3.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of local parameter k |$ 1$ |second^-1^ |\r\n|Value of local parameter k |$ 2$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\ncompartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 3e-4 / compartment;\nS2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k__reaction1_local * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment * k__reaction2_local * S2;\n\nk__reaction1_local @Const { } = 1;\nk__reaction2_local @Const { } = 2;\n\n"} -{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species and parameters both global\r\n and local to reactions.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one global parameter named k. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * compartment$ |\r\n| S2 -> S3 | $k * S2 * compartment$ |]\r\n\r\nReaction S2 -> S3 defines one local parameter k.\r\n\r\nNote that the id of the local parameter k shadows the global parameter k.\r\nWithin the defining reaction, the value of the locally-defined parameter k\r\nmust be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$3.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k |$ 1$ |second^-1^ |\r\n|Value of local parameter k |$ 2$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 3e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment * k * S2;\n\nk @Const 'k' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species and parameters local to \r\n reactions.\r\ncomponentTags: Compartment, Species, Reaction \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * compartment,$ |\r\n| S2 -> S3 | $k * S2 * compartment,$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k. Reaction S2 -> S3 also\r\ndefines one (different) local parameter k. Both of these parameters have a\r\nscope local to the defining reaction.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$3.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of local parameter k |$ 1$ |second^-1^ |\r\n|Value of local parameter k |$ 2$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 3e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k__reaction1_local * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment * k__reaction2_local * S2;\n\nk__reaction1_local @Const { } = 1;\nk__reaction2_local @Const { } = 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species and parameters both global\r\n and local to reactions.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one global parameter named k. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * compartment$ |\r\n| S2 -> S3 | $k * S2 * compartment$ |]\r\n\r\nReaction S2 -> S3 defines one local parameter k.\r\n\r\nNote that the id of the local parameter k shadows the global parameter k.\r\nWithin the defining reaction, the value of the locally-defined parameter k\r\nmust be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$3.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k |$ 1$ |second^-1^ |\r\n|Value of local parameter k |$ 2$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 3e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment * k__reaction2_local * S2;\n\nk__reaction2_local @Const { } = 2;\nk @Const 'k' { } = 1;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species and parameters both global\r\n and local to reactions.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one global parameter named k. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * compartment$ |\r\n| S2 -> S3 | $S1 * S2 * compartment$ |]\r\n\r\nReaction S2 -> S3 defines one local parameter S1.\r\n\r\nNote that the id of the local parameter S1 shadows the species S1. Within\r\nthe defining reaction, the value of the locally-defined symbol S1 must be\r\nused.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$3.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k |$ 2$ |second^-1^ |\r\n|Value of local parameter S1 |$ 1$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\ncompartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 3e-4 / compartment;\nS2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, modifiers: [S1], reversible: false, };\nreaction2 := compartment * S1__reaction2_local * S2;\n\nk @Record 'k' { } .= 2;\n\nS1__reaction2_local @Const { } = 1;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a compartment \r\n where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a compartment \r\n where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1.7 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 17;\nk2 @Const 'k2' { } = 0.3;\n\n"} @@ -90,3 +90,995 @@ {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 2D compartment \r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * multiply(k1, S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 1D compartment \r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * multiply(k1, S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} {"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 0D compartment \r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $multiply(k1, S1, S2)$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |]\r\n\r\nIn this example, the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-4;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := multiply(k1, S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one 2D compartment\r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-15 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * multiply(k1, multiply(S1, S2));\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one 1D compartment\r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * multiply(k1, multiply(S1, S2));\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one 0D compartment\r\n and one function definition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThis model contains one 0-dimensional compartment called \"compartment\".\r\nThere are four species, S1, S2, S3 and S4, and two parameters, k1 and k2.\r\n\r\nThe model contains a function called \"multiply\" that takes two numerical\r\narguments and multiplies them:\r\n\r\n[{width:25em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n| multiply | x, y | $x * y$ |]\r\n\r\nThe model contains two reactions defined as:\r\n\r\n[{width:25em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $multiply(k1, multiply(S1, S2))$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:25em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example, the compartment has its spatialDimensions attribute set to\r\na value of zero; i.e., the compartment represents a point, and therefore\r\ncannot have a value for the %size% or %units% attributes. The quantities\r\nof species located in the compartment must be treated as amounts and not\r\nconcentrations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-4;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := multiply(k1, multiply(S1, S2));\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using a functionDefinition and a rateRule to vary compartment size.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and p1. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * multiply(k1,S1)$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | C | $-p1 * C$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.9$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * multiply(k1, S1);\nC_proc @Process { actors: = C, aux: {{\"metaid\":\"rule1\"}}, };\nC_proc := (-1) * C * p1;\n\nk1 @Const 'k1' { } = 0.9;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one varying compartment \r\n and one functionDefinition\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are three\r\nspecies called S1, S2 and S3 and three parameters called k1, k2 and p1. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $multiply(k1, S1, S2) * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | C | $-p1 * C$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * multiply(k1, S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nC_proc @Process { actors: = C, aux: {{\"metaid\":\"rule1\"}}, };\nC_proc := (-1) * C * p1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one varying compartment\r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | C | $-p1 * C$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 2.0$ |mole |\r\n|Initial amount of S4 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * multiply(k1, multiply(S1, S2));\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\nC_proc @Process { actors: = C, aux: {{\"metaid\":\"rule1\"}}, };\nC_proc := (-1) * C * p1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment of non-unity size using a function to apply \r\nthe kinetic law.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * multiply(k1,S1)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 2.3$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 2.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment \r\n of non-unity size using a functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\".\r\nThere are three species named S1, S2 and S3 and two parameters named k1 and k2.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 | $1.0 \\x 10^-4$ | mole |\r\n|Initial amount of S2 | $2.0 \\x 10^-4$ | mole |\r\n|Initial amount of S3 | $1.0 \\x 10^-4$ | mole |\r\n|Value of parameter k1 | $ 0.75$ | litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 | $ 0.25$ | second^-1^ |\r\n|Volume of compartment \"compartment\":| $ 2.3$ | litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units where they appear in\r\nexpressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 2.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * multiply(k1, S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one varying compartment\r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.5 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 12.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 12.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * multiply(k1, multiply(S1, S2));\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 750;\nk2 @Const 'k2' { } = 250;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments with functionDefinitions.\r\ncomponentTags: Compartment, FunctionDefinition, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are three species named S1, S2 and S3 and two parameters named k1 and\r\nk2. Compartment \"compartment\" contains species S1 and S2. Compartment\r\n\"compartment\"1 contains species S3.\r\n\r\nThe model contains:\r\n* 3 species (S1, S2, S3)\r\n* 2 parameters (k1, k2)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * S2 * multiply(k1, S1)$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |]\r\n\r\nThe first reaction occurs entirely in compartment \"compartment\", whereas\r\nthe second reaction occurs between a species in \"compartment\" and a species\r\nin \"compartment1\".\r\n\r\nThe model contains the following function definition:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * S2 * multiply(k1, S1);\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments with functionDefinitions.\r\ncomponentTags: Compartment, FunctionDefinition, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are four species named S1, S2, S3 and S4 and three parameters named\r\nk1, k2 and k3. Compartment \"compartment\" contains species S1 and S2.\r\nCompartment \"compartment1\" contains species S3 and S4.\r\n\r\nThe model contains:\r\n* 4 species (S1, S2, S3, S4)\r\n* 3 parameters (k1, k2, k3)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * multiply(S1, S2)$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |\r\n| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |]\r\n\r\nThe first reaction occurs entirely within compartment \"compartment\", the\r\nsecond reaction occurs between a species in \"compartment\" and a species in\r\n\"compartment1\", and the third reaction occurs entirely within\r\n\"compartment1\".\r\n\r\nThe model contains the following function definition:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial amount of species S4 | $0.1$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $7.5$ | constant |\r\n| Initial value of parameter k3 | $0.75$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * multiply(S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\nreaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, };\nreaction3 := compartment * k3 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 7.5;\nk3 @Const 'k3' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments with functionDefinitions.\r\ncomponentTags: Compartment, FunctionDefinition, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are two species named S1 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" contains species S1. Compartment \"compartment1\"\r\ncontains species S3.\r\n\r\nThe model contains:\r\n* 2 species (S1, S3)\r\n* 2 parameters (k1, k2)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 -> S3 | $compartment * multiply(k1, S1)$ |\r\n| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |]\r\n\r\nThe reactions occur between the species within different compartments:\r\n\r\nThe model contains the following function definition:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, };\nreaction2 := compartment1 * k2 * (S3 + (-1) * S1);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction using functionDefinitions with two \r\nspecies in a compartment where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $multiply(k1,S1)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := multiply(k1, S1);\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions using functionDefinitions with three species in a compartment \r\n where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * multiply(S1,S2)$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 1.7 $ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they\r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.02;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * multiply(S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 1.7;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functiondefinitions with four species in a compartment \r\n where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * multiply(S1,S2)$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.3 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * multiply(S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 1300000;\nk2 @Const 'k2' { } = 300000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functionDefinitions in one compartment,\r\n with one species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named k1 and k2.\r\nSpecies S1 is labeled as an SBML boundary species.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $multiply(k1,S1) * compartment$ |\r\n| S2 -> S1 | $k2 * S2 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\nreaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, };\nreaction2 := compartment * k2 * S2;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functionDefinitions in one compartment,\r\n with one species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named k1 and k2.\r\nSpecies S2 is labeled as an SBML boundary species.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $multiply(k1,S1) * compartment$ |\r\n| S2 -> S1 | $multiply(k2,S2) * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\nreaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, };\nreaction2 := compartment * multiply(k2, S2);\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functionDefinitions in one compartment,\r\n with both species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition\r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named k1 and k2.\r\nBoth species S1 and S2 are labeled as an SBML boundary species.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $multiply(k1,S1) * compartment$ |\r\n| S2 -> S1 | $k2 * S2 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\nreaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, };\nreaction2 := compartment * k2 * S2;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction using functionDefinitions\r\n with three species in a compartment where the one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition\r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k1.\r\nSpecies S3 is labeled as constant and therefore does not vary.\r\nThe model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * multiply(S1,S3) * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 2$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 2 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, };\nreaction1 := compartment * k1 * multiply(S1, S3);\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions using functionDefinitions with four species in a compartment \r\n where the one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nSpecies S4 is labeled as constant and therefore does not vary.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * multiply(S3,S4) * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.0$ |mole |\r\n|Initial amount of S4 |$ 1.5$ |mole |\r\n|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, };\nreaction2 := compartment * k2 * multiply(S3, S4);\n\nk1 @Const 'k1' { } = 1.7;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with functionDefinitions with five species \r\n in a compartment where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are five\r\nspecies named S1, S2, S3, S4 and S5 and two parameters named k1 and k2.\r\nSpecies S5 is labeled as constant and therefore does not vary.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * multiply(S1,S2) * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Initial amount of S5 |$ 1.0 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.3 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 5e-7 / compartment;\nS5 @Species 'S5' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * multiply(S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, };\nreaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1));\n\nk1 @Const 'k1' { } = 1300000;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Rate rule using a functionDefinition used to determine value of parameter\r\n which is used in a reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies called S1 and S2; two constant parameters called k2 and k3 and one\r\nvarying parameters called k1. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains one rule that determines the value of parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $add(k2, k3)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.2$ |second^-1^ |\r\n|Value of parameter k3 |$ 0.3$ |lsecond^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := add(k2, k3);\n\nk1 @Record 'k1' { } .= 1;\n\nk2 @Const 'k2' { } = 0.2;\nk3 @Const 'k3' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Rate rule using a functionDefinition used to determine value of parameter\r\n which is used in a reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies called S1, S2, S3 and S4; three constant parameters called k2, k3 and\r\np1 and one varying parameter called k1. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe model contains one rule that determines the value of parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $add(k2, k3) * p1$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k3 |$ 0.7 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 1$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 5e-7 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := p1 * add(k2, k3);\n\nk1 @Record 'k1' { } .= 1e+6;\n\nk2 @Const 'k2' { } = 300000;\nk3 @Const 'k3' { } = 700000;\np1 @Const 'p1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Rate rule using a functionDefinition used to determine value of parameter\r\n which is used in a reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies called S1, S2 and S3; four constant parameters called k2, k3, p1 and\r\np2 and one varying parameter called k1. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule that determines the value of parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $p1* add(p2 * k2, k3)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Value of parameter k3 |$ -0.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 1$ |second^-1^ |\r\n|Value of parameter p2 |$ 1$ |litre mole^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := p1 * add(k2 * p2, k3);\n\nk1 @Record 'k1' { } .= 1.7;\n\nk2 @Const 'k2' { } = 0.3;\nk3 @Const 'k3' { } = -0.1;\np1 @Const 'p1' { } = 1;\np2 @Const 'p2' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single reaction using functionDefinitions involving species\r\n with a non-unity stoichiometry.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2 S2 | $multiply(k1,S1) * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functionDefinitions involving species in one\r\ncompartment, with non-unity stoichiometries.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2 S2 | $multiply(k1,S1) * compartment$ |\r\n| 2 S2 -> S1 | $k2 * S2 * S2 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.35$ |second^-1^ |\r\n|Value of parameter k2 |$ 180$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\nreaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, };\nreaction2 := compartment * k2 * pow(S2, 2);\n\nk1 @Const 'k1' { } = 0.35;\nk2 @Const 'k2' { } = 180;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functionDefinitions with three species \r\n in one compartment, with one species having a stoichiometry of 2.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, FunctionDefinition\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| 2S1 + S2 -> S3 | $multiply(k1,S1) * S1 * S2 * compartment$ |\r\n| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1.0 \\x 10^3$ |litre^2^ mole^-2^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * S1 * S2 * multiply(k1, S1);\nreaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 1000;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functionDefinitions with four species in one compartment,\r\n with non-unity stoichiometry\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + 2S4 | $k1 * multiply(S1,S2) * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, };\nreaction1 := compartment * k1 * multiply(S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 750;\nk2 @Const 'k2' { } = 250;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functionDefinitions with three species \r\n and parameters local to reactions.\r\ncomponentTags: Compartment, Species, Reaction, FunctionDefinition \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $multiply(k,S1) * compartment,$ |\r\n| S2 -> S3 | $k * S2 * compartment,$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k. Reaction S2 -> S3 defines\r\nanother (different) local parameter k.\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$3.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of local parameter k |$ 1$ |second^-1^ |\r\n|Value of local parameter k |$ 2$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.003 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * multiply(k__reaction1_local, S1);\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment * k__reaction2_local * S2;\n\nk__reaction1_local @Const { } = 1;\nk__reaction2_local @Const { } = 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functionDefinitions with three species \r\n and parameters local to reactions.\r\ncomponentTags: Compartment, Parameter, Species, Reaction, FunctionDefinition \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * compartmen$ |\r\n| S2 -> S3 | $multiply(k,S2) * compartment,$ |]\r\n\r\nReaction S2 -> S3 defines one local parameter k. This parameter shadows the\r\nglobal parameter k and thus in reaction S2 -> S3 the value of the local\r\nparameter must be used.\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$3.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k |$ 1$ |second^-1^ |\r\n|Value of local parameter k |$ 2$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.003 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment * multiply(k__reaction2_local, S2);\n\nk__reaction2_local @Const { } = 2;\nk @Const 'k' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functionDefinitions with three species \r\n and parameters local to reactions.\r\ncomponentTags: Compartment, Species, Parameter, Reaction, FunctionDefinition \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * compartmen$ |\r\n| S2 -> S3 | $multiply(S1,S2) * compartment,$ |]\r\n\r\nReaction S2 -> S3 defines one local parameter S1. This parameter shadows\r\nthe species S1 and thus in reaction S2 -> S3 the value of the local\r\nparameter S1 must be used.\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$3.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k |$ 2$ |second^-1^ |\r\n|Value of local parameter S1 |$ 1$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { };\n\ncompartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.003 / compartment;\nS2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, modifiers: [S1], reversible: false, };\nreaction2 := compartment * multiply(S1__reaction2_local, S2);\n\nk @Record 'k' { } .= 2;\n\nS1__reaction2_local @Const { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.125 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= k1 * S2;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $k2 / 100$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this\r\ncase the value calculated by the initialAssignment is consistent with the\r\nvalue declared.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Value of parameter k1 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ $ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $1 * S2$ |]\r\n\r\nIn this case the initial value for species S3 must be calculated by the\r\nassignmentRule. Note that since this assignmentRule must always remain\r\ntrue, it should be considered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-15$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-15 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $1 * S2$ |]\r\n\r\nIn this case the initial value declared for species S3 is consistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-15$ |mole |\r\n|Initial amount of S3 |$1.125 \\x 10^-15$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ $ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-15 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125e-15 / compartment;\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to compartment \"compartment\":\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | compartment | $k1 / k1$ |]\r\n\r\nIn this case the initial value declared for compartment \"compartment\" is\r\nconsistent with the value calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 1.125$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |any |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, } .= 1;\ncompartment := 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to compartment \"compartment\":\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | compartment | $k1 / k1$ |]\r\n\r\nIn this case the initial value declared for compartment \"compartment\" is\r\niconsistent with the value calculated by the assignmentRule. The\r\ncalculated value should be used.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 1.125$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |any |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, } .= 5;\ncompartment := 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to assign value to the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to compartment \"compartment\":\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | compartment | $1$ |]\r\n\r\nIn this case the initial value declared for compartment \"compartment\" is\r\nconsistent with the value calculated by the assignmentRule.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 1.125$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ $ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, };\ncompartment := 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.125 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to assign value to the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to compartment \"compartment\":\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | compartment | $1$ |]\r\n\r\nIn this case the initial value declared for compartment \"compartment\" is\r\nconsistent with the value calculated by the assignmentRule.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, } .= 1;\ncompartment := 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to assign value to the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to compartment \"compartment\":\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | compartment | $1$ |]\r\n\r\nIn this case the initial value declared for compartment \"compartment\" is\r\ninconsistent with the value calculated by the assignmentRule. The\r\ncalculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, } .= 5;\ncompartment := 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to assign value to the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to compartment \"compartment\":\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | compartment | $1$ |]\r\n\r\nIn this case there is no initial value declared for compartment\r\n\"compartment\". Thus the value must be calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ undeclared$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, };\ncompartment := 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with three species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k2:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k2 | $5$ |]\r\n\r\nIn this case the initial value declared for parameter k2 is consistent with\r\nthe value calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.25 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ $ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0125 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk2 @Record 'k2' { } .= 5;\nk2 := 5;\n\nk1 @Const 'k1' { } = 150;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with three species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k2:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k2 | $5$ |]\r\n\r\nIn this case the initial value declared for parameter k2 is inconsistent\r\nwith the value calculated by the assignmentRule. The calculated value\r\nshould be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.25 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.005$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0125 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk2 @Record 'k2' { } .= 0.005;\nk2 := 5;\n\nk1 @Const 'k1' { } = 150;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with three species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k2:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k2 | $5$ |]\r\n\r\nIn this case there is no initial value declared for parameter k2. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.25 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0125 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk2 @Record 'k2' { };\nk2 := 5;\n\nk1 @Const 'k1' { } = 150;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case the initial value declared for parameter k1 is consistent with\r\nthe value calculated by the assignmentRule.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 0.1$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Record 'k1' { } .= 0.75;\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case the initial value declared for parameter k1 is inconsistent\r\nwith the value calculated by the assignmentRule. The calculated value\r\nshould be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 0.1$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ 750$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Record 'k1' { } .= 750;\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 0.1$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one 2-dimensional\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S4 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it must be considered during\r\nsimulation.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Area of compartment \"compartment\" |$ 1$ |rmetre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-5 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, };\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\n 2-dimensional compartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it must be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto} |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-15$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-15 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one 1-dimensional\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S4 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it must be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^3$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.0015 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, };\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 1500;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\n 1-dimensional compartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.015 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one 0-dimensional\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, 0D-Compartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nCompartment \"compartment\" is 0-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S4 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n| Initial amount of S1:| $ 1 \\x 10^-3$ | mole |\r\n| Initial amount of S2:| $ 1.5 \\x 10^-3$ | mole |\r\n| Initial amount of S3:| $ 1 \\x 10^-3$ | mole |\r\n| Initial amount of S4:| $ undeclared$ | mole |\r\n| Value of parameter k1:| $ 1.5 \\x 10^3$ | litre mole^-1^ second^-1^ |\r\n| Value of parameter k2:| $ 50$ | second^-1^ |\r\n| Value of parameter k3:| $ 1.5$ | dimensionless |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, };\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 1500;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\n 0-dimensional compartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, 0D-Compartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n| Initial amount of S1:| $ 1 \\x 10^-2$ | mole |\r\n| Initial amount of S2:| $1.5 \\x 10^-2$ | mole |\r\n| Initial amount of S3:| $ undeclared$ | mole |\r\n| Value of parameter k1:| $ 0.75$ | dimensionless |\r\n| Value of parameter k2:| $ 50$ | second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.015;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one \r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S4 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 3.25$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 1.75$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 0.01$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.01;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, };\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 3.25;\nk2 @Const 'k2' { } = 1.75;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 0.1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 0.08$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.08;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one \r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonUnityStoichiometry, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S4 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, };\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonUnityStoichiometry, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| 2S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-15$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-15 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: 2*S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and one constant\r\nparameter called k1. (Note that indeed S1 and S2 are parameters and not \r\nspecies in this model.)\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $-S1 * k1$ |\r\n | Rate | S2 | $S1 * k1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.5 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$ 0$ |same as S1 |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1;\n\nS1 @Record 'S1' { } .= 0.015;\nS2 @Record 'S2' { } .= 0;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and two constant\r\nparameters called k1 and k2. (Note that indeed S1 and S2 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $S2 * k2-S1 * k1$ |\r\n | Rate | S2 | $S1 * k1-S2 * k2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.5 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$ 0$ |same as S1 |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Value of parameter k2 |$ 0$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S2 + (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1 + (-1) * k2 * S2;\n\nS1 @Record 'S1' { } .= 0.015;\nS2 @Record 'S2' { } .= 0;\n\nk1 @Const 'k1' { } = 1;\nk2 @Const 'k2' { } = 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter \r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and two constant\r\nparameters called k1 and k2. (Note that indeed S1 and S2 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $S2 * k2-S1 * k1$ |\r\n | Rate | S2 | $S1 * k1-S2 * k2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.5 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$ 0$ |same as S1 |\r\n|Value of parameter k1 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S2 + (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1 + (-1) * k2 * S2;\n\nS1 @Record 'S1' { } .= 0.015;\nS2 @Record 'S2' { } .= 0;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter \r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and two constant\r\nparameters called k1 and k2. (Note that indeed S1 and S2 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $S2 * k2-S1 * k1$ |\r\n | Rate | S2 | $S1 * k1-S2 * k2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.5 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$1.5 \\x 10^-2$ |same as S1 |\r\n|Value of parameter k1 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S2 + (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1 + (-1) * k2 * S2;\n\nS1 @Record 'S1' { } .= 0.015;\nS2 @Record 'S2' { } .= 0.015;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and two constant\r\nparameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k2 * S3-k1 * S1 * S2$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1 * S2$ |\r\n | Rate | S3 | $k1 * S1 * S2-k2 * S3$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.5 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$ 2 \\x 10^-2$ |same as S1 |\r\n|Value of parameter S3 |$ 1 \\x 10^-2$ |same as S1 |\r\n|Value of parameter k1 |$ 0.5$ |(units of S1)^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k1 * S1 * S2 + (-1) * k2 * S3;\n\nS1 @Record 'S1' { } .= 0.015;\nS2 @Record 'S2' { } .= 0.02;\nS3 @Record 'S3' { } .= 0.01;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains four varying parameters called S1, S2, S3 and S4 and \r\ntwo constant parameters called k1 and k2. (Note\r\nthat indeed S1, S2, S3 and S4 are parameters and not species in this\r\nmodel.)\r\n\r\nThe model contains four rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k2 * S3 * S4-k1 * S1 * S2$ |\r\n | Rate | S2 | $k2 * S3 * S4-k1 * S1 * S2$ |\r\n | Rate | S3 | $k1 * S1 * S2-k2 * S3 * S4$ |\r\n | Rate | S4 | $k1 * S1 * S2-k2 * S3 * S4$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.0 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$1.0 \\x 10^-2$ |same as S1 |\r\n|Value of parameter S3 |$2.0 \\x 10^-2$ |same as S1 |\r\n|Value of parameter S4 |$1.0 \\x 10^-2$ |same as S1 |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |(units of S1)^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^2$ |(units of S1)^-1^ second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S3 * S4 + (-1) * k1 * S1 * S2;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 * S4 + (-1) * k1 * S1 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k1 * S1 * S2 + (-1) * k2 * S3 * S4;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule4\"}}, };\nS4_proc := k1 * S1 * S2 + (-1) * k2 * S3 * S4;\n\nS1 @Record 'S1' { } .= 0.01;\nS2 @Record 'S2' { } .= 0.01;\nS3 @Record 'S3' { } .= 0.02;\nS4 @Record 'S4' { } .= 0.01;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains four varying parameters called S1, S2, S3 and S4 and \r\nfour constant parameters called k1, k2, k3 and k4. (Note that indeed S1, \r\nS2, S3, and S4 are parameters and not species in this model.)\r\n\r\nThe model contains four rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k2 * S2-k1 * S1$ |\r\n | Rate | S2 | $k1 * S1-k2 * S2-k3 * S2 + k4 * S3 * S4$ |\r\n | Rate | S3 | $k3 * S2-k4 * S3 * S4$ |\r\n | Rate | S4 | $k3 * S2-k4 * S3 * S4$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.0 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$2.0 \\x 10^-2$ |same as S1 |\r\n|Value of parameter S3 |$ 0$ |same as S1 |\r\n|Value of parameter S4 |$ 0$ |same as S1 |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Value of parameter k3 |$ 0.15$ |second^-1^ |\r\n|Value of parameter k4 |$ 0.1$ |(units of S1)^-1^ second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S2 + (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1 + (-1) * k2 * S2 + (-1) * k3 * S2 + k4 * S3 * S4;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k3 * S2 + (-1) * k4 * S3 * S4;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule4\"}}, };\nS4_proc := k3 * S2 + (-1) * k4 * S3 * S4;\n\nS1 @Record 'S1' { } .= 0.01;\nS2 @Record 'S2' { } .= 0.02;\nS3 @Record 'S3' { } .= 0;\nS4 @Record 'S4' { } .= 0;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.15;\nk4 @Const 'k4' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains four varying parameters called S1, S2, S3 and S4 and \r\nthree constant parameters called k1, k2 and k3. (Note that indeed S1, \r\nS2, S3, and S4 are parameters and not species in this model.)\r\n\r\nThe model contains four rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k2 * S3-k1 * S1 * S2 + k3 * S3$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1 * S2$ |\r\n | Rate | S3 | $k1 * S1 * S2-k2 * S3-k3 * S3$ |\r\n | Rate | S4 | $k3 * S3$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$2.0 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$2.0 \\x 10^-2$ |same as S1 |\r\n|Value of parameter S3 |$ 0$ |same as S1 |\r\n|Value of parameter S4 |$ 0$ |same as S1 |\r\n|Value of parameter k1 |$ 1.0 \\x 10^2$ |(units of S1)^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.9$ |second^-1^ |\r\n|Value of parameter k3 |$ 0.7$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := (-1) * k1 * S1 * S2 + k2 * S3 + k3 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k1 * S1 * S2 + (-1) * k2 * S3 + (-1) * k3 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule4\"}}, };\nS4_proc := k3 * S3;\n\nS1 @Record 'S1' { } .= 0.02;\nS2 @Record 'S2' { } .= 0.02;\nS3 @Record 'S3' { } .= 0;\nS4 @Record 'S4' { } .= 0;\n\nk1 @Const 'k1' { } = 100;\nk2 @Const 'k2' { } = 0.9;\nk3 @Const 'k3' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains four varying parameters called S1, S2, S3 and S4 and \r\nthree constant parameters called k1, k2 and k3. (Note that indeed S1, \r\nS2, S3, and S4 are parameters and not species in this model.)\r\n\r\nThe model contains four rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $-k1 * S1$ |\r\n | Rate | S2 | $k1 * S1-k2 * S2$ |\r\n | Rate | S3 | $k2 * S2-k3 * S3$ |\r\n | Rate | S4 | $k3 * S3$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.0 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$ 0$ |same as S1 |\r\n|Value of parameter S3 |$ 0$ |same as S1 |\r\n|Value of parameter S4 |$ 0$ |same as S1 |\r\n|Value of parameter k1 |$ 0.7$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.0$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1 + (-1) * k2 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k2 * S2 + (-1) * k3 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule4\"}}, };\nS4_proc := k3 * S3;\n\nS1 @Record 'S1' { } .= 0.01;\nS2 @Record 'S2' { } .= 0;\nS3 @Record 'S3' { } .= 0;\nS4 @Record 'S4' { } .= 0;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains four varying parameters called S1, S2, S3 and S4 and \r\nfour constant parameters called k1, k2, k3 and k4. (Note that indeed S1, \r\nS2, S3, and S4 are parameters and not species in this model.)\r\n\r\nThe model contains three rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k2 * S2-k1 * S1$ |\r\n | Rate | S3 | $k3 * S2-k4 * S3 * S4$ |\r\n | Rate | S4 | $k3 * S2-k4 * S3 * S4$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.0 \\x 10^-4$ |any |\r\n|Value of parameter S2 |$2.0 \\x 10^-4$ |any |\r\n|Value of parameter S3 |$ 0$ |any |\r\n|Value of parameter S4 |$ 0$ |same as S3 |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |(units of S1) (units of S2)^-1^ second^-1^ |\r\n|Value of parameter k3 |$ 0.15$ |(units of S3) (units of S2)^-1^ second^-1^ |\r\n|Value of parameter k4 |$ 0.1$ |(units of S3)^-1^ second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S2 + (-1) * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule2\"}}, };\nS3_proc := k3 * S2 + (-1) * k4 * S3 * S4;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule3\"}}, };\nS4_proc := k3 * S2 + (-1) * k4 * S3 * S4;\n\nS1 @Record 'S1' { } .= 1e-4;\nS2 @Record 'S2' { } .= 2e-4;\nS3 @Record 'S3' { } .= 0;\nS4 @Record 'S4' { } .= 0;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.15;\nk4 @Const 'k4' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using rules and parameters with a functionDefinition.\r\ncomponentTags: Parameter, FunctionDefinition, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and one constant\r\nparameter called k1. (Note that indeed S1 and S2 are parameters and not \r\nspecies in this model.)\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $-multiply(k1, S1)$ |\r\n | Rate | S2 | $multiply(k1, S1)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.5 \\x 10^-2$ |any |\r\n|Value of parameter S2 |$1.5 \\x 10^-2$ |same as S1 |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |]\r\n\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := (-1) * multiply(k1, S1);\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := multiply(k1, S1);\n\nS1 @Record 'S1' { } .= 0.015;\nS2 @Record 'S2' { } .= 0.015;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using rules and parameters with an event.\r\ncomponentTags: Parameter, RateRule, EventNoDelay \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and one constant\r\nparameter called k1. (Note that indeed S1 and S2 are parameters and not \r\nspecies in this model.)\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $-k1 * S1$ |\r\n | Rate | S2 | $k1 * S1$ |]\r\n\r\n\r\nThe model contains one event defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | Trigger | Delay | Assignments |\r\n | Event1 | $S1 < 0.1$ | $-$ | $S1 = 1$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$ 1.0$ |any |\r\n|Value of parameter S2 |$ 0.0$ |same as S1 |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1;\n\nS1 @Record 'S1' { } .= 1;\nS1 [event1]= 1;\nS2 @Record 'S2' { } .= 0;\n\nk1 @Const 'k1' { } = 1;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using rules and parameters with a rate that causes a discontinuity\r\n in the output.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and two constant\r\nparameters called p1 and p2. (Note that indeed S1 and S2 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $-Ceiling(S1 * p1)! / p2$ |\r\n | Rate | S2 | $Ceiling(S1 * p1)! / p2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$ 1.0$ |any |\r\n|Value of parameter S2 |$ 0.0$ |same as S1 |\r\n|Value of parameter p1 |$ $ |(units of S1)^-1^ |\r\n|Value of parameter p2 |$ 2$ |second (units of S1)^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := (-1) * factorial(ceil(p1 * S1)) * pow(p2, (-1));\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := factorial(ceil(p1 * S1)) * pow(p2, (-1));\n\nS1 @Record 'S1' { } .= 1;\nS2 @Record 'S2' { } .= 0;\n\np1 @Const 'p1' { } = 4;\np2 @Const 'p2' { } = 25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using rules and parameters only.\r\ncomponentTags: Parameter, AssignmentRule \r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying parameter called S1. (Note that indeed \r\nS1 is a parameter and not species in this model.)\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S1 | $3 + 4$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$ 0.0$ |any |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1 @Record 'S1' { } .= 0;\nS1 := 7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using rules and parameters only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying parameter called S1. (Note that indeed \r\nS1 is a parameter and not species in this model.)\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $7$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$ 0.0$ |any |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := 7;\n\nS1 @Record 'S1' { } .= 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and one constant\r\nparameter called k1. (Note that indeed S1 and S2 are parameters and not \r\nspecies in this model.)\r\n \r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $-(k1 * S1)$ |\r\n | Rate | S2 | $k1 * S1$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.5 \\x 10^-1$ |any |\r\n|Value of parameter S2 |$ 0$ |same as S1 |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1;\n\nS1 @Record 'S1' { } .= 0.15;\nS2 @Record 'S2' { } .= 0;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and rules only.\r\ncomponentTags: Parameter, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and one constant\r\nparameter called k1. (Note that indeed S1 and S2 are parameters and not \r\nspecies in this model.)\r\n \r\nThe model contains three rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $0.5$ |\r\n | Rate | S1 | $-(k1 * S1)$ |\r\n | Rate | S2 | $k1 * S1$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.5 \\x 10^-1$ |any |\r\n|Value of parameter S2 |$ 0$ |same as S1 |\r\n|Value of parameter k1 |$ 1 \\x 10^-1$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := 0.5;\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule2\"}}, };\nS1_proc := (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule3\"}}, };\nS2_proc := k1 * S1;\n\nS1 @Record 'S1' { } .= 0.15;\nS2 @Record 'S2' { } .= 0;\nk1 @Record 'k1' { } .= 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and rules with a functionDefinition.\r\ncomponentTags: Parameter, FunctionDefinition, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and two constant\r\nparameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n \r\nThe model contains three rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $multiply(k1, S1, S2)$ |\r\n | Rate | S1 | $k2 * S3 - multiply(k1, S1, S2)$ |\r\n | Rate | S2 | $k2 * S3 - multiply(k1, S1, S2)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.0 \\x 10^-1$ |any |\r\n|Value of parameter S2 |$2.0 \\x 10^-1$ |same as S1 |\r\n|Value of parameter S3 |$1.0 \\x 10^-1$ |same as S1 |\r\n|Value of parameter k1 |$ 0.75$ |(units of S1)^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |]\r\n\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := multiply(k1, S1, S2) + (-1) * k2 * S3;\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule2\"}}, };\nS1_proc := k2 * S3 + (-1) * multiply(k1, S1, S2);\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule3\"}}, };\nS2_proc := k2 * S3 + (-1) * multiply(k1, S1, S2);\n\nS1 @Record 'S1' { } .= 0.1;\nS2 @Record 'S2' { } .= 0.2;\nS3 @Record 'S3' { } .= 0.1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and rules with a functionDefinition.\r\ncomponentTags: Parameter, FunctionDefinition, RateRule \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains four varying parameters called S1, S2, S3 and S4 and \r\ntwo constant parameters called k1 and k2. (Note\r\nthat indeed S1, S2, S3 and S4 are parameters and not species in this\r\nmodel.)\r\n\r\nThe model contains three rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $multiply(k1, (S1 * S2))$ |\r\n | Rate | S1 | $k2 * S3 * S4 - multiply(k1, multiply(S1, S2))$ |\r\n | Rate | S2 | $k2 * S3 * S4 - multiply(k1, multiply(S1, S2))$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$1.0 \\x 10^-1$ |any |\r\n|Value of parameter S2 |$2.0 \\x 10^-1$ |same as S1 |\r\n|Value of parameter S3 |$1.0 \\x 10^-1$ |same as S1 |\r\n|Value of parameter S4 |$1.0 \\x 10^-1$ |any |\r\n|Value of parameter k1 |$0.75 \\x 10^1$ |(units of S1)^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^1$ |(units of S4)^-1^ second^-1^ |]\r\n\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := multiply(k1, S1 * S2) + (-1) * k2 * S3 * S4;\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule2\"}}, };\nS1_proc := k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2));\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule3\"}}, };\nS2_proc := k2 * S3 * S4 + (-1) * multiply(k1, multiply(S1, S2));\n\nS1 @Record 'S1' { } .= 0.1;\nS2 @Record 'S2' { } .= 0.2;\nS3 @Record 'S3' { } .= 0.1;\nS4 @Record 'S4' { } .= 0.1;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 2.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and rules with an initialAssignment.\r\ncomponentTags: Parameter, InitialAssignment, RateRule \r\ntestTags: NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called S1 and S2 and two constant\r\nparameters called k1 and k2. (Note that indeed S1 and S2 are parameters and not \r\nspecies in this model.)\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $-k2 * S1 $ |\r\n | Rate | S2 | $k2 * S1 $ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 * S2$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this\r\ncase, the initial value of S1 has not been explicitly declared and must be\r\ncalculated using the initialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$ undeclared$ |any |\r\n|Value of parameter S2 |$2.0 \\x 10^-1$ |same as S1 |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := (-1) * k2 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S1;\n\nS1 @Record 'S1' { } .= k1 * S2;\nS2 @Record 'S2' { } .= 0.2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and both rate and assignment rules. \r\ncomponentTags: Parameter, RateRule, AssignmentRule \r\ntestTags: NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and two constant\r\nparameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $1 * S2$ |\r\n | Rate | S1 | $-k2 * S1 $ |\r\n | Rate | S2 | $k2 * S1 $ |]\r\n\r\nNote the initial value for parameter S3 is undeclared and must be\r\ncalculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$ 1$ |any |\r\n|Value of parameter S2 |$1.5 \\x 10^-15$ |same as S1 |\r\n|Value of parameter S3 |$ undeclared$ |same as S1 |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule2\"}}, };\nS1_proc := (-1) * k2 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule3\"}}, };\nS2_proc := k2 * S1;\n\nS1 @Record 'S1' { } .= 1;\nS2 @Record 'S2' { } .= 1.5e-15;\nS3 @Record 'S3' { };\nS3 := k1 * S2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and both rate and assignment rules\r\n with a functionDefinition. \r\ncomponentTags: Parameter, FunctionDefinition, RateRule, AssignmentRule \r\ntestTags: NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and two constant\r\nparameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $multiply(k1, S2)$ |\r\n | Rate | S1 | $-multiply(k2, S1)$ |\r\n | Rate | S2 | $k2 * S1 $ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nNote the initial value for parameter S3 is undeclared and must be\r\ncalculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$ 1$ |any |\r\n|Value of parameter S2 |$ 0.5$ |same as S1 |\r\n|Value of parameter S3 |$ undeclared$ |any |\r\n|Value of parameter k1 |$ 0.7$ |(units of S3) (units of S1)^-1^ |\r\n|Value of parameter k2 |$ 40$ |second^-1^ |]\r\n\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule2\"}}, };\nS1_proc := (-1) * multiply(k2, S1);\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule3\"}}, };\nS2_proc := k2 * S1;\n\nS1 @Record 'S1' { } .= 1;\nS2 @Record 'S2' { } .= 0.5;\nS3 @Record 'S3' { };\nS3 := multiply(k1, S2);\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 40;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and both rate and assignment rules\r\n including initialAssignments. \r\ncomponentTags: Parameter, InitialAssignment, RateRule, AssignmentRule \r\ntestTags: NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and two constant\r\nparameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $1 * S2$ |\r\n | Rate | S1 | $-k2 * S1 $ |\r\n | Rate | S2 | $k2 * S1 $ |]\r\n\r\nThe model contains two initialAssignments:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 0.75$ |\r\n | S2 | $k2 * 3 \\x 10^-17$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalues of parameters S1, S2 and S3 are undeclared and so must be calculated\r\nby the initialAssignments.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter S1 |$ undeclared$ |any |\r\n|Value of parameter S2 |$ undeclared$ |same as S1 |\r\n|Value of parameter S3 |$ undeclared$ |same as S1 |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule2\"}}, };\nS1_proc := (-1) * k2 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule3\"}}, };\nS2_proc := k2 * S1;\n\nS1 @Record 'S1' { } .= 1.33333333333333 * k1;\nS2 @Record 'S2' { } .= k2 * (3e-17);\nS3 @Record 'S3' { };\nS3 := k1 * S2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a one compartment,\r\n with one reaction having a rate of zero.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe value of k2 is zero, which means the \r\nreverse reaction should occur at zero rate (i.e. not at all). \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.1 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.1e-4 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a one compartment,\r\n with one reaction having a rate of zero.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe value of k1 is zero, which means the first reaction should occur at\r\nzero rate (i.e. not at all).\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.1 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 0$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.1e-4 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment,\r\n with one reaction having a rate of zero.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe value of k2 is zero, which means the reverse reaction should occur at\r\nzero rate (i.e. not at all).\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment,\r\n with one reaction having a rate of zero.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe value of k1 is zero, which means the \r\nfirst reaction should occur at zero rate (i.e. not at all). \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 0$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 0;\nk2 @Const 'k2' { } = 7500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using MathML in the rate equation.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $Piecewise({{p1, False}}, p2)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1.$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := (false ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $Piecewise({{p1, S2 >= 4}}, p2)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 10$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := ((S2 >= 4) ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $Piecewise({{p1, S2 > 7}}, p2)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 10$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := ((S2 > 7) ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $Piecewise({{p1, S1 <= 4}}, p2)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 5$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1.$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, };\nreaction2 := ((S1 <= 4) ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $Piecewise({{p1, S1 < 2.5}}, p2)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 5$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, };\nreaction2 := ((S1 < 2.5) ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using MathML in the rate equation.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * S1 * Piecewise({{p1, True}}, p2)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1.$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := S1 * compartment * (true ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $Floor(S1 * p1) / p2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 0.0$ |mole |\r\n|Value of parameter p1 |$ 10.5$ |litre |\r\n|Value of parameter p2 |$ 10$ |second |\r\n|Volume of compartment \"compartment\" |$ 1.$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := floor(p1 * S1) * pow(p2, (-1));\n\np1 @Const 'p1' { } = 10.5;\np2 @Const 'p2' { } = 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $Ceiling(S1 * p1)/p2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 0.0$ |mole |\r\n|Value of parameter p1 |$ 10.5$ |litre |\r\n|Value of parameter p2 |$ 10$ |second |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := ceil(p1 * S1) * pow(p2, (-1));\n\np1 @Const 'p1' { } = 10.5;\np2 @Const 'p2' { } = 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $Piecewise({{p1, And(S2 > 4, S1 < 5, S2 < 8)}}, p2)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 10$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1, S2], reversible: false, };\nreaction2 := ((S2 > 4 and S1 < 5 and S2 < 8) ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $Piecewise({{p1, Not(S2 < 4)}}, p2)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 10$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := ((S2 >= 4) ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $Piecewise({{p1, Or(S2 < 2, S2 > 4, S2 < 1)}}, p2)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 4$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := ((S2 < 2 or S2 > 4 or S2 < 1) ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $Piecewise({{p1, Xor(S2 < 2, S2 > 4, S2 < 1)}}, p2)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 4$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := ((S2 > 4 xor S2 < 1 xor S2 < 2) ? p1 : p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 2-dimensional\r\n non-unity compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is 2-dimensional. The model contains one reaction defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.1$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 0.6$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 0.6;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 1.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 2-dimensional\r\n non-unity compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 1.0 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 75$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 25$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 3.7$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 3.7;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in a 2-dimensional\r\n non-unity compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1.0 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 0.75 \\x 10^7$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25 \\x 10^5$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 0.01$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 0.01;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-6 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500000;\nk2 @Const 'k2' { } = 25000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 1-dimensional\r\n non-unity compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is 1-dimensional. The model contains one reaction defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.9$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 0.3$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 0.3;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-5 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 0.9;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 1-dimensional\r\n non-unity compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$ 1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 3.4$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 9.8$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 9.8;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.02 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 3.4;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in a 1-dimensional\r\n non-unity compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 2.0$ |mole |\r\n|Initial amount of S4 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 9$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 4$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 4;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 9;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 2-dimensional\r\ncompartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is two-dimensional. Species S1 and S2 are declared to have\r\nonly substance units. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-4;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a 2-dimensional\r\ncompartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Species S1, S2 and S3 are\r\ndeclared to have only substance units. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$ 75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 25$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species have been declared as having substance units only. Thus, they\r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.2;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 2-dimensional\r\ncompartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. All four species are declared\r\nto have only substance units. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 7.5 \\x 10^3$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^3$ |mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.002;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 250;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 2-dimensional\r\ncompartment, with one species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is two-dimensional. Species S1 is labeled as an SBML\r\nboundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 2-dimensional\r\ncompartment, with one species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is two-dimensional. Species S2 is labeled as an SBML\r\nboundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 2-dimensional\r\ncompartment, with both species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is two-dimensional. Both species S1 and S2 are labeled as an\r\nSBML boundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n!!!|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 2-dimensional compartment.\r\ncompartment, with one species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Species S1 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.002 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 2-dimensional compartment.\r\ncompartment, with one species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Species S3 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 2-dimensional compartment.\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Both species S1 and S2 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.02 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 2-dimensional compartment.\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Both species S1 and S3 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 2-dimensional\r\ncompartment, with one species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Species S1 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^2$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 2-dimensional\r\ncompartment, with one species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Species S4 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 2-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Both species S1 and S2 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 2-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Both species S2 and S3 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 2-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Both species S3 and S4 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 1-dimensional\r\ncompartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is one-dimensional. Species S1 and S2 are declared to have\r\nonly substance units. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species have been declared as having substance units only. Thus, they\r\nmust be treated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a 1-dimensional\r\ncompartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Species S1, S2 and S3 are\r\ndeclared to have only substance units. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Value of parameter k1 |$ 7.5$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 1-dimensional\r\ncompartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. All four species are declared\r\nto have only substance units. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 6.2 \\x 10^2$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5 \\x 10^2$ |mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.015;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.02;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 620;\nk2 @Const 'k2' { } = 500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 1-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is one-dimensional. Species S1 is labeled as an SBML\r\nboundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 1-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is one-dimensional. Species S2 is labeled as an SBML\r\nboundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 1-dimensional\r\ncompartment, with both species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is one-dimensional. Both species S1 and S2 are labeled as an\r\nSBML boundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 1-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Species S2 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 2 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 1-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Species S3 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2 / compartment;\nS3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 1-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Both species S1 and S2 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 2 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 1-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Both species S1 and S3 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Value of parameter k1 |$ 7.5$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2 / compartment;\nS3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 1-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Species S2 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 6.2 \\x 10^4$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5 \\x 10^4$ |mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 62000;\nk2 @Const 'k2' { } = 50000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 1-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Species S3 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 6.2 \\x 10^3$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5 \\x 10^3$ |mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.0015 / compartment;\nS3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.002 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 6200;\nk2 @Const 'k2' { } = 5000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 1-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Both species S1 and S2 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 6.2 \\x 10^1$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5 \\x 10^1$ |mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.1 / compartment;\nS2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.15 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.2 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 62;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 1-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Both species S3 and S4 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 6.2 \\x 10^2$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5 \\x 10^2$ |mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.015 / compartment;\nS3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.02 / compartment;\nS4 @Species 'S4' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 620;\nk2 @Const 'k2' { } = 500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 1-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Both species S2 and S4 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 6.2 \\x 10^4$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5 \\x 10^4$ |mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.5e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 62000;\nk2 @Const 'k2' { } = 50000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 0-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is 0-dimensional. Species S1 is labeled as an SBML boundary\r\nspecies. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.023$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.15;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\n\nk1 @Const 'k1' { } = 1.023;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 0-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is 0-dimensional. Species S2 is labeled as an SBML boundary\r\nspecies. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.023$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15;\nS2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\n\nk1 @Const 'k1' { } = 1.023;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 0-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Species S2 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-15$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-15$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-15$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\nS2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2e-6;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 9.8;\nk2 @Const 'k2' { } = 0.57;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 0-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Species S3 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-15$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-15$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-15$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6;\nS3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 9.8;\nk2 @Const 'k2' { } = 0.57;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with three species in a 0-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Both species S2 and S3 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-15$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-15$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-15$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\nS2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2e-6;\nS3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 9.8;\nk2 @Const 'k2' { } = 0.57;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 0-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Species S1 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 2.0$ |mole |\r\n|Initial amount of S4 |$ 0.5$ |mole |\r\n|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.6;\nk2 @Const 'k2' { } = 0.13;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 0-dimensional\r\ncompartment, with a species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Species S4 is labeled as an\r\nSBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 2.0$ |mole |\r\n|Initial amount of S4 |$ 0.5$ |mole |\r\n|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2;\nS4 @Species 'S4' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.6;\nk2 @Const 'k2' { } = 0.13;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 0-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Both species S1 and S2 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 2.0$ |mole |\r\n|Initial amount of S4 |$ 0.5$ |mole |\r\n|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1;\nS2 @Species 'S2' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1.5;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.6;\nk2 @Const 'k2' { } = 0.13;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 0-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Both species S1 and S3 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 2.0$ |mole |\r\n|Initial amount of S4 |$ 0.5$ |mole |\r\n|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\nS3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.6;\nk2 @Const 'k2' { } = 0.13;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 0-dimensional\r\ncompartment, with two species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, 0D-Compartment, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Both species S3 and S4 are\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 2.0$ |mole |\r\n|Initial amount of S4 |$ 0.5$ |mole |\r\n|Value of parameter k1 |$ 0.6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.13$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\nS3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 2;\nS4 @Species 'S4' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.6;\nk2 @Const 'k2' { } = 0.13;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in a compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k1. Species S3 is\r\nlabeled as constant and therefore cannot be changed by rules or reactions.\r\nThe model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * S3 * compartment$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0.5$ |mole |\r\n|Initial amount of S3 |$ 1.2$ |mole |\r\n|Value of parameter k1 |$ 1.78$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1.34$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1.34;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.5 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.2 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, };\nreaction1 := compartment * k1 * S1 * S3;\n\nk1 @Const 'k1' { } = 1.78;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in a compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nSpecies S4 is labeled as constant and therefore cannot be changed by rules\r\nor reactions. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$0.75 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.25 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1.68 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.27 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1.2$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1.2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 7.5e-4 / compartment;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.00125 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 1680;\nk2 @Const 'k2' { } = 270;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with five species in a compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are five\r\nspecies named S1, S2, S3, S4 and S5 and two parameters named k1 and k2.\r\nSpecies S5 is labeled as constant and therefore cannot be changed by rules\r\nor reactions. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Initial amount of S5 |$ 1.0 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.3 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 0.2$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 5e-7 / compartment;\nS5 @Species 'S5' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, };\nreaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1));\n\nk1 @Const 'k1' { } = 1300;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in a \r\n 2 dimensional compartment, where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k1. Compartment\r\n\"compartment\" is 2-dimensional. Species S3 is labeled as constant and\r\ntherefore cannot be changed by rules or reactions. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * S3 * compartment$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0.5$ |mole |\r\n|Initial amount of S3 |$ 1.2$ |mole |\r\n|Value of parameter k1 |$ 1.78$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.5 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1.2 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, };\nreaction1 := compartment * k1 * S1 * S3;\n\nk1 @Const 'k1' { } = 1.78;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in a 2 dimensional compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Species S4 is labeled as\r\nconstant and therefore cannot be changed by rules or reactions. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$0.75 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.25 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1.68 \\x 10^3$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.27 \\x 10^3$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.0015 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 7.5e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 0.00125 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 1680;\nk2 @Const 'k2' { } = 270;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with five species in a 2 dimensional compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are five\r\nspecies named S1, S2, S3, S4 and S5 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Species S5 is labeled as\r\nconstant and therefore cannot be changed by rules or reactions. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Initial amount of S5 |$ 1.0 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.3 \\x 10^6$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 1.5e-6 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 5e-7 / compartment;\nS5 @Species 'S5' { units: mole/metre^2, boundary: true, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, };\nreaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1));\n\nk1 @Const 'k1' { } = 1300000;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in a \r\n 1 dimensional compartment, where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k1. Compartment\r\n\"compartment\" is 1-dimensional. Species S3 is labeled as constant and\r\ntherefore cannot be changed by rules or reactions. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * S3 * compartment$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0.5$ |mole |\r\n|Initial amount of S3 |$ 1.2$ |mole |\r\n|Value of parameter k1 |$ 1.78$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.5 / compartment;\nS3 @Species 'S3' { units: mole/metre, boundary: true, compartment: compartment, } .= 1.2 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, };\nreaction1 := compartment * k1 * S1 * S3;\n\nk1 @Const 'k1' { } = 1.78;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in a 1 dimensional compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Species S4 is labeled as\r\nconstant and therefore cannot be changed by rules or reactions. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$0.75 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.25 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1.68 \\x 10^3$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.27 \\x 10^3$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0.0015 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 7.5e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre, boundary: true, compartment: compartment, } .= 0.00125 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 1680;\nk2 @Const 'k2' { } = 270;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with five species in a 1 dimensional compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are five\r\nspecies named S1, S2, S3, S4 and S5 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Species S5 is labeled as\r\nconstant and therefore cannot be changed by rules or reactions. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment / S5$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Initial amount of S5 |$ 1.0 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.3 \\x 10^6$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.5e-6 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-6 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 5e-7 / compartment;\nS5 @Species 'S5' { units: mole/metre, boundary: true, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, };\nreaction2 := compartment * k2 * S3 * S4 * pow(S5, (-1));\n\nk1 @Const 'k1' { } = 1300000;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in a \r\n 0 dimensional compartment, where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k1. Compartment\r\n\"compartment\" is 0-dimensional. Species S3 is labeled as constant and\r\ntherefore cannot be changed by rules or reactions. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0.5$ |mole |\r\n|Initial amount of S3 |$ 1.2$ |mole |\r\n|Value of parameter k1 |$ 1.78$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.5;\nS3 @Species 'S3' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1.2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, };\nreaction1 := k1 * S1 * S3;\n\nk1 @Const 'k1' { } = 1.78;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in a 0 dimensional compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Species S4 is labeled as\r\nconstant and therefore cannot be changed by rules or reactions. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$0.75 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.25 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1.68 \\x 10^3$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.27 \\x 10^3$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 7.5e-4;\nS4 @Species 'S4' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 0.00125;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 1680;\nk2 @Const 'k2' { } = 270;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with five species in a 0 dimensional compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ConstantSpecies, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are five\r\nspecies named S1, S2, S3, S4 and S5 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. Species S5 is labeled as\r\nconstant and therefore cannot be changed by rules or reactions. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 / S5$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Initial amount of S5 |$ 1.0 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.3 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7;\nS5 @Species 'S5' { units: mole, boundary: true, compartment: compartment, isAmount: true, } .= 1e-6;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, };\nreaction2 := k2 * S3 * S4 * pow(S5, (-1));\n\nk1 @Const 'k1' { } = 1300000;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions involving two species in one\r\n 2 dimensional compartment, with non-unity stoichiometries.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named k1 and k2. Compartment\r\n\"compartment\" is 2-dimensional. The model contains two reactions defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2 S2 | $k1 * S1 * compartment$ |\r\n| 2 S2 -> S1 | $k2 * S2 * S2 * compartment$ |]\r\n\r\nNote the stoichiometry of S2 is 2 in both reactions.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.35$ |second^-1^ |\r\n|Value of parameter k2 |$ 180$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, };\nreaction2 := compartment * k2 * pow(S2, 2);\n\nk1 @Const 'k1' { } = 0.35;\nk2 @Const 'k2' { } = 180;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions involving two species in one\r\n 1 dimensional compartment, with non-unity stoichiometries.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named k1 and k2. Compartment\r\n\"compartment\" is 1-dimensional. The model contains two reactions defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2 S2 | $k1 * S1 * compartment$ |\r\n| 2 S2 -> S1 | $k2 * S2 * S2 * compartment$ |]\r\n\r\nNote the stoichiometry of S2 is 2 in both reactions.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.35$ |second^-1^ |\r\n|Value of parameter k2 |$ 180$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.015 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, };\nreaction2 := compartment * k2 * pow(S2, 2);\n\nk1 @Const 'k1' { } = 0.35;\nk2 @Const 'k2' { } = 180;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions involving two species in one\r\n 0 dimensional compartment, with non-unity stoichiometries.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named k1 and k2. Compartment\r\n\"compartment\" is 0-dimensional. The model contains two reactions defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2 S2 | $k1 * S1$ |\r\n| 2 S2 -> S1 | $k2 * S2 * S2$ |]\r\n\r\nNote the stoichiometry of S2 is 2 in both reactions.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.35$ |second^-1^ |\r\n|Value of parameter k2 |$ 180$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-4;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: 2*S2 = S1, reversible: false, };\nreaction2 := k2 * pow(S2, 2);\n\nk1 @Const 'k1' { } = 0.35;\nk2 @Const 'k2' { } = 180;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 2D compartment,\r\n with one species having a stoichiometry of 2.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2 * compartment$ |\r\n| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$0.5 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 1.6 \\x 10^4$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.7$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 5e-5 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * pow(S1, 2) * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 16000;\nk2 @Const 'k2' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 1D compartment,\r\n with one species having a stoichiometry of 2.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2 * compartment$ |\r\n| S3 -> 2S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$0.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1.6 \\x 10^3$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.7$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 5e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * pow(S1, 2) * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 1600;\nk2 @Const 'k2' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 0D compartment,\r\n with one species having a stoichiometry of 2.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2$ |\r\n| S3 -> 2S1 + S2 | $k2 * S3t$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$0.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 1.6 \\x 10^2$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.7$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.005;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * pow(S1, 2) * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 160;\nk2 @Const 'k2' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one 2D compartment,\r\n with non-unity stoichiometry.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 0.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.9 \\x 10^6$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.15 \\x 10^6$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 5e-7 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 900000;\nk2 @Const 'k2' { } = 150000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one 1D compartment,\r\n with non-unity stoichiometry.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2 * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 0.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.9 \\x 10^6$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.15 \\x 10^6$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 5e-7 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 2e-6 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 900000;\nk2 @Const 'k2' { } = 150000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one 0D compartment,\r\n with non-unity stoichiometry.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 0.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.9 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.15 \\x 10^6$ |mole^-1^ second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 900000;\nk2 @Const 'k2' { } = 150000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $calculate(S1,p1,p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the reaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y, z | $Ceiling(x * y)! / z$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 0.0$ |mole |\r\n|Value of parameter p1 |$ 4$ |litre mole^-1^ |\r\n|Value of parameter p2 |$ 25$ |second mole^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y, z], math: factorial(ceil(x * y)) * pow(z, (-1)), };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := calculate(S1, p1, p2);\n\np1 @Const 'p1' { } = 4;\np2 @Const 'p2' { } = 25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $calculate(S2, p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the reaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y, z | $Piecewise({{y, x > 7}}, z)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 10$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y, z], math: ((x > 7) ? y : z), };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := calculate(S2, p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using MathML in the rate equation.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $calculate(p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the reaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y | $Piecewise({{x, False}}, y)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1.$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y], math: y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := calculate(p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $calculate(S2, p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the reaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y, z | $Piecewise({{y, x >= 4}}, z)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 10$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y, z], math: ((x >= 4) ? y : z), };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := calculate(S2, p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $calculate(S1, p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the reaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y, z | $Piecewise({{y, x <= 4}}, z)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 5$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1.$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y, z], math: ((x <= 4) ? y : z), };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, };\nreaction2 := calculate(S1, p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $calculate(S1, p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the reaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y, z | $Piecewise({{y, x < 2.5}}, z)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 5$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y, z], math: ((x < 2.5) ? y : z), };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1], reversible: false, };\nreaction2 := calculate(S1, p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using MathML in the rate equation.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and two parameters named p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * S1 * calculate(p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the reaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y | $Piecewise({{x, True}}, y)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1.$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y], math: x, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * S1 * calculate(p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $calculate(S1, S2, p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the reaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | w, x, y, z | $Piecewise({{y, And(x > 4, w < 5, x < 8)}}, z)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 10$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [w, x, y, z], math: ((x > 4 and w < 5 and x < 8) ? y : z), };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S1, S2], reversible: false, };\nreaction2 := calculate(S1, S2, p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $calculate(S2, p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the\r\nreaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y, z | $Piecewise({{y, Not(x < 4)}}, z)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 10$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 10$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y, z], math: ((x >= 4) ? y : z), };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 10 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := calculate(S2, p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $calculate(S2, p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the\r\nreaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y, z | $Piecewise({{y, Or(x < 2, x > 4, x < 1)}}, z)$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 4$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y, z], math: ((x < 2 or x > 4 or x < 1) ? y : z), };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := calculate(S2, p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in one\r\ncompartment using a rate that causes a discontinuity in the output.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named p1, p2 and k1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k1 * S1$ |\r\n| S3 -> S4 | $calculate(S2, p1, p2)$ |]\r\n\r\nThe model contains one functionDefinition, which is used within the\r\nreaction, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | calculate | x, y, z | $Piecewise({{y, Xor(x < 2, x > 4, x < 1)}}, z)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 4$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Value of parameter p1 |$ 1.5$ |mole second^-1^ |\r\n|Value of parameter p2 |$ 0.05$ |mole second^-1^ |\r\n|Value of parameter k1 |$ 1.0$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\ncalculate #defineFunction { arguments: [x, y, z], math: ((x > 4 xor x < 1 xor x < 2) ? y : z), };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 4 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, modifiers: [S2], reversible: false, };\nreaction2 := calculate(S2, p1, p2);\n\np1 @Const 'p1' { } = 1.5;\np2 @Const 'p2' { } = 0.05;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 2D\r\ncompartment and nonzero initial amounts using a function to apply \r\nthe kinetic law.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is 2-dimensional. The model contains one reaction defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * multiply(k1,S1)$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$0.5 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$ 1.75$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 3.5$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 3.5;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.15 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.05 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\n\nk1 @Const 'k1' { } = 1.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 1D\r\ncompartment and nonzero initial amounts using a function to apply \r\nthe kinetic law.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is 1-dimensional. The model contains one reaction defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * multiply(k1,S1)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$2.63 \\x 10^-3$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 0.07$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 0.07;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.5e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * multiply(k1, S1);\n\nk1 @Const 'k1' { } = 0.00263;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 2D compartment \r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 1.0 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 3.24$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.125$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 6.8$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 6.8;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2e-6 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * multiply(k1, S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 3.24;\nk2 @Const 'k2' { } = 0.125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 1D compartment \r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 1.0 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 3.24$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.125$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 6.8$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 6.8;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2e-6 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * multiply(k1, S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 3.24;\nk2 @Const 'k2' { } = 0.125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one 2D compartment\r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.9 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.1 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.2 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$12.75 \\x 10^1$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^1$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1.98$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1.98;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.009 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.011 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.012 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * multiply(k1, multiply(S1, S2));\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 127.5;\nk2 @Const 'k2' { } = 2.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one 1D compartment\r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.9 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.1 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.2 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1.98$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1.98;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 9e-5 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 1.1e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.2e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := compartment * multiply(k1, multiply(S1, S2));\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are four species named S1, S2, S3 and S4 and three parameters named\r\nk1, k2 and k3. Compartment \"compartment\" contains species S1 and S2.\r\nCompartment \"compartment1\" contains species S3 and S4.\r\n\r\nThe model contains:\r\n* 4 species (S1, S2, S3, S4)\r\n* 3 parameters (k1, k2, k3)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |]\r\n\r\nThe first reaction occurs entirely in compartment \"compartment\", whereas\r\nthe second reaction occurs between a species in \"compartment\" and a species\r\nin \"compartment1\".\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S4 | $k3 * S3$ |]\r\n\r\nIn this case the initial value declared for species S4 is consistent with\r\nthat calculated by the assignmentRule. Note that since this assignmentRule\r\nmust always remain true, it should be considered during simulation.\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial concentration of species S4 | $k3 * S3$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial value of parameter k3 | $0.25$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS4 := k3 * S3;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are five species named S1, S2, S3, S4 and S5 and four parameters\r\nnamed k1, k2, k3 and k4. Compartment \"compartment\" contains species S1 and\r\nS2. Compartment \"compartment1\" contains species S3, S4 and S5.\r\n\r\nThe model contains:\r\n* 5 species (S1, S2, S3, S4, S5)\r\n* 4 parameters (k1, k2, k3, k4)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |\r\n| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |]\r\n\r\nThe first reaction occurs entirely within compartment \"compartment\", the\r\nsecond reaction occurs between a species in compartment \"compartment\" and a\r\nspecies in \"compartment1\" and the third reaction occurs entirely within\r\n\"compartment1\".\r\n\r\nThe model contains one rule which assigns value to species S5:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S5 | $k4 * S2$ |]\r\n\r\nIn this case the initial value declared for species S5 is inconsistent with\r\nthat calculated by the assignmentRule; the calculated value should be used.\r\nNote that since this assignmentRule must always remain true, it should be\r\nconsidered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial amount of species S4 | $0.1$ | variable |\r\n| Initial concentration of species S5 | $k4 * S2$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $7.5$ | constant |\r\n| Initial value of parameter k3 | $0.75$ | constant |\r\n| Initial value of parameter k4 | $0.5$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1;\nS5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1;\nS5 := k4 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\nreaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, };\nreaction3 := compartment * k3 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 7.5;\nk3 @Const 'k3' { } = 0.75;\nk4 @Const 'k4' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are three species named S1, S3 and S5 and three parameters named k1,\r\nk2 and k4. Compartment \"compartment\" contains species S1. Compartment\r\n\"compartment1\" contains species S3 and S5.\r\n\r\nThe model contains:\r\n* 3 species (S1, S3, S5)\r\n* 3 parameters (k1, k2, k4)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 -> S3 | $compartment * k1 * S1$ |\r\n| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |]\r\n\r\nBoth reactions occur between species within different compartments.\r\n\r\nThe model contains one rule which assigns value to species S5:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S5 | $k4 * S3$ |]\r\n\r\nIn this case the initial value declared for species S5 is consistent with\r\nthat calculated by the assignmentRule. Note that since this assignmentRule\r\nmust always remain true, it should be considered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial concentration of species S5 | $k4 * S3$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial value of parameter k4 | $0.5$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS5 := k4 * S3;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, };\nreaction2 := compartment1 * k2 * (S3 + (-1) * S1);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk4 @Const 'k4' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are four species named S1, S2, S3 and S4 and three parameters named\r\nk1, k2 and k3. Compartment \"compartment\" contains species S1 and S2.\r\nCompartment \"compartment1\" contains species S3 and S4.\r\n\r\nThe model contains:\r\n* 4 species (S1, S2, S3, S4)\r\n* 3 parameters (k1, k2, k3)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |]\r\n\r\nThe first reaction occurs entirely in compartment, whereas the second reaction\r\noccurs between a species in compartment and a species in compartment1.\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S4 | $k3 * S3$ |]\r\n\r\nIn this case the initial value declared for species S4 is inconsistent with\r\nthat calculated by the assignmentRule; the calculated value should be used.\r\nNote that since this assignmentRule must always remain true, it should be\r\nconsidered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial concentration of species S4 | $k3 * S3$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial value of parameter k3 | $0.25$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 1 / compartment1;\nS4 := k3 * S3;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are four species named S1, S2, S3 and S4 and three parameters named\r\nk1, k2 and k3. Compartment \"compartment\" contains species S1 and S2.\r\nCompartment \"compartment1\" contains species S3 and S4.\r\n\r\nThe model contains:\r\n* 4 species (S1, S2, S3, S4)\r\n* 3 parameters (k1, k2, k3)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |]\r\n\r\nThe first reaction occurs entirely in compartment, whereas the second reaction\r\noccurs between a species in compartment and a species in compartment1.\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S4 | $k3 * S3$ |]\r\n\r\nIn this case there is no initial value declared for species S3 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial concentration of species S4 | $k3 * S3$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial value of parameter k3 | $0.25$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment1, };\nS4 := k3 * S3;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are five species named S1, S2, S3, S4 and S5 and four parameters\r\nnamed k1, k2, k3 and k4. Compartment \"compartment\" contains species S1 and\r\nS2. Compartment \"compartment1\" contains species S3, S4 and S5.\r\n\r\nThe model contains:\r\n* 5 species (S1, S2, S3, S4, S5)\r\n* 4 parameters (k1, k2, k3, k4)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |\r\n| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |]\r\n\r\nThe first reaction occurs entirely within compartment, the second reaction\r\noccurs between a species in compartment and a species in compartment1 and the\r\nthird reaction occurs entirely within compartment1.\r\n\r\nThe model contains one rule which assigns value to species S5:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S5 | $k4 * S2$ |]\r\n\r\nIn this case the initial value declared for species S5 is consistent with that calculated\r\nby the assignmentRule. Note that since this assignmentRule \r\nmust always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial amount of species S4 | $0.1$ | variable |\r\n| Initial concentration of species S5 | $k4 * S2$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $7.5$ | constant |\r\n| Initial value of parameter k3 | $0.75$ | constant |\r\n| Initial value of parameter k4 | $0.5$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1;\nS5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 0.5 / compartment1;\nS5 := k4 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\nreaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, };\nreaction3 := compartment * k3 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 7.5;\nk3 @Const 'k3' { } = 0.75;\nk4 @Const 'k4' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned, MultiCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are five species named S1, S2, S3, S4 and S5 and four parameters\r\nnamed k1, k2, k3 and k4. Compartment \"compartment\" contains species S1 and\r\nS2. Compartment \"compartment1\" contains species S3, S4 and S5.\r\n\r\nThe model contains:\r\n* 5 species (S1, S2, S3, S4, S5)\r\n* 4 parameters (k1, k2, k3, k4)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 + S2 -> 2S2 | $compartment * k1 * S1 * S2$ |\r\n| reaction2: S2 -> S3 | $compartment1 * k2 * (S2 + -1 * S3)$ |\r\n| reaction3: S3 + S4 -> 2S4 | $compartment * k3 * S3 * S4$ |]\r\n\r\nThe first reaction occurs entirely within compartment, the second reaction\r\noccurs between a species in compartment and a species in compartment1 and the\r\nthird reaction occurs entirely within compartment1.\r\n\r\nThe model contains one rule which assigns value to species S5:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S5 | $k4 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial amount of species S4 | $0.1$ | variable |\r\n| Initial concentration of species S5 | $k4 * S2$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $7.5$ | constant |\r\n| Initial value of parameter k3 | $0.75$ | constant |\r\n| Initial value of parameter k4 | $0.5$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment1, } .= 0.1 / compartment1;\nS5 @Species 'S5' { units: mole/litre, compartment: compartment1, };\nS5 := k4 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S2, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := compartment1 * k2 * (S2 + (-1) * S3);\nreaction3 @Reaction 'reaction3' { actors: S3 + S4 = 2*S4, reversible: false, };\nreaction3 := compartment * k3 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 7.5;\nk3 @Const 'k3' { } = 0.75;\nk4 @Const 'k4' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned, MultiCompartment, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are three species named S1, S3 and S5 and three parameters named k1,\r\nk2 and k4. Compartment \"compartment\" contains species S1. Compartment\r\n\"compartment1\" contains species S3 and S5.\r\n\r\nThe model contains:\r\n* 3 species (S1, S3, S5)\r\n* 3 parameters (k1, k2, k4)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 -> S3 | $compartment * k1 * S1$ |\r\n| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |]\r\n\r\nBoth reactions occur between species within different compartments.\r\n\r\nThe model contains one rule which assigns value to species S5:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S5 | $k4 * S3$ |]\r\n\r\nIn this case the initial value declared for species S5 is inconsistent with\r\nthat calculated by the assignmentRule; the calculated value should be used.\r\nNote that since this assignmentRule must always remain true, it should be\r\nconsidered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial concentration of species S5 | $k4 * S3$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial value of parameter k4 | $0.5$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS5 @Species 'S5' { units: mole/litre, compartment: compartment1, } .= 1 / compartment1;\nS5 := k4 * S3;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, };\nreaction2 := compartment1 * k2 * (S3 + (-1) * S1);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk4 @Const 'k4' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Reactions occurring between two compartments. \r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned, MultiCompartment, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThe model contains two compartments named compartment and compartment1.\r\nThere are three species named S1, S3 and S5 and three parameters named k1,\r\nk2 and k4. Compartment \"compartment\" contains species S1. Compartment\r\n\"compartment1\" contains species S3 and S5.\r\n\r\nThe model contains:\r\n* 3 species (S1, S3, S5)\r\n* 3 parameters (k1, k2, k4)\r\n* 2 compartments (compartment, compartment1)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| reaction1: S1 -> S3 | $compartment * k1 * S1$ |\r\n| reaction2: S3 -> S1 | $compartment1 * k2 * (S3 + -1 * S1)$ |]\r\n\r\nBoth reactions occur between species within different compartments.\r\n\r\nThe model contains one rule which assigns value to species S5:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S5 | $k4 * S3$ |]\r\n\r\nIn this case there is no initial value declared for species S3 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S3 | $0$ | variable |\r\n| Initial concentration of species S5 | $k4 * S3$ | variable |\r\n| Initial value of parameter k1 | $0.75$ | constant |\r\n| Initial value of parameter k2 | $0.25$ | constant |\r\n| Initial value of parameter k4 | $0.5$ | constant |\r\n| Initial volume of compartment 'compartment' | $1$ | constant |\r\n| Initial volume of compartment 'compartment1' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\ncompartment1 @Compartment 'compartment1' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment1, } .= 0 / compartment1;\nS5 @Species 'S5' { units: mole/litre, compartment: compartment1, };\nS5 := k4 * S3;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, };\nreaction2 := compartment1 * k2 * (S3 + (-1) * S1);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk4 @Const 'k4' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an AssignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k2 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3. Thus the\r\ninitial value must be calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.05$ |dimensionless |\r\n|Value of parameter k2 |$ 1.15$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.15;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k2 * S1;\n\nk1 @Const 'k1' { } = 1.05;\nk2 @Const 'k2' { } = 1.15;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$2.25 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-5;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 2.25e-5;\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an AssignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Species S3\r\nis labeled as an SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3. Thus the\r\ninitial value must be calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.05$ |dimensionless |\r\n|Value of parameter k2 |$ 1.15$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 1.05;\nk2 @Const 'k2' { } = 1.15;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an AssignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Species S1\r\nis labeled as an SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3. Thus the\r\ninitial value must be calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.05$ |dimensionless |\r\n|Value of parameter k2 |$ 1.15$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 1.05;\nk2 @Const 'k2' { } = 1.15;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nSpecies S4 is labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$2.25 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 2.25e-5 / compartment;\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nSpecies S1 is labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$2.25 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment;\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nSpecies S3 is labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n!!!|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$2.25 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment;\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nBoth species S3 and S4 are labeled as an SBML boundary species. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$2.25 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 2.25e-5 / compartment;\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an AssignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Both\r\nspecies S1 and S3 are labeled as an SBML boundary species. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3. Thus the initial value\r\nmust be calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.05$ |dimensionless |\r\n|Value of parameter k2 |$ 1.15$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 1.05;\nk2 @Const 'k2' { } = 1.15;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an AssignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, ConstantSpecies, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Species S1\r\nis labeled as both constant and an SBML boundary condition, and therefore cannot \r\nbe changed by rules or reactions. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3. Thus the\r\ninitial value must be calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.05$ |dimensionless |\r\n|Value of parameter k2 |$ 1.15$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.1 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 1.05;\nk2 @Const 'k2' { } = 1.15;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an AssignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, ConstantSpecies, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Species S2\r\nis labeled as both constant and an SBML boundary condition, and therefore \r\ncannot be changed by rules or reactions. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3. Thus the\r\ninitial value must be calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.05$ |dimensionless |\r\n|Value of parameter k2 |$ 1.15$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 1.05;\nk2 @Const 'k2' { } = 1.15;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, BoundaryCondition, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nSpecies S2 is labeled as constant and therefore cannot be changed by rules\r\nor reactions. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$2.25 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 0.5 \\x 10^-2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment;\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.005;\nk2 @Const 'k2' { } = 5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, BoundaryCondition, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nSpecies S3 is labeled as constant and therefore cannot be changed by rules\r\nor reactions. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$2.25 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 0.5 \\x 10^-2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment;\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.005;\nk2 @Const 'k2' { } = 5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nSpecies S5 is labeled as constant and therefore cannot be changed by rules\r\nor reactions. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S5 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$2.25 \\x 10^-5$ |mole |\r\n|Initial amount of S5 |$ 1 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 0.5 \\x 10^-2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1.5e-5 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 2.25e-5 / compartment;\nS4 := k3 * S2;\nS5 @Species 'S5' { units: mole/litre, boundary: true, compartment: compartment, } .= 1e-5 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S5], reversible: false, };\nreaction1 := compartment * k1 * S1 * S5;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\n\nk1 @Const 'k1' { } = 0.005;\nk2 @Const 'k2' { } = 5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an AssignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, ConstantSpecies, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Species S4\r\nis labeled as constant and therefore cannot be changed by rules or\r\nreactions. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $compartment * k2 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S4$ |]\r\n\r\nIn this case there is no initial value declared for species S3. Thus the\r\ninitial value must be calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.05$ |dimensionless |\r\n|Value of parameter k2 |$ 1.15$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, };\nS3 := k1 * S4;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.015 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k2 * S1;\n\nk1 @Const 'k1' { } = 1.05;\nk2 @Const 'k2' { } = 1.15;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a compartment\r\n whose volume is varying.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, RateRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are two\r\nspecies called S1 and S2 and three parameters called k1, p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules. The assignmentRule assigns value to C\r\nand the rateRule determines the rate at which p2 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | C | $p1 * p2$ |\r\n | Rate | p2 | $0.1 |]\r\n\r\nIn this case the initial value declared for C is consistent\r\nwith that calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.9$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |litre mole^-1^ |\r\n|Value of parameter p2 |$ 1.5$ |mole second^-1^ |\r\n|Volume of compartment C |$ 0.15$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 0.15;\nC := p1 * p2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\np2_proc @Process { actors: = p2, aux: {{\"metaid\":\"rule2\"}}, };\np2_proc := 0.1;\n\np2 @Record 'p2' { } .= 1.5;\n\nk1 @Const 'k1' { } = 0.9;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a compartment\r\n whose volume is varying.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, RateRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called \"compartment\". There are two\r\nspecies called S1 and S2 and three parameters called k1, p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains two rules. The assignmentRule assigns value to compartment\r\nand the rateRule determines the rate at which p2 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | compartment | $p1 * p2$ |\r\n | Rate | p2 | $0.1 |]\r\n\r\nIn this case, the initial value declared for compartment \"compartment\" is\r\ninconsistent with that calculated by the assignmentRule; the calculated\r\nvalue should be used. Note that since this assignmentRule must always\r\nremain true, it should be considered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.9$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |litre mole^-1^ |\r\n|Value of parameter p2 |$ 1.5$ |mole second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, } .= 1;\ncompartment := p1 * p2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\np2_proc @Process { actors: = p2, aux: {{\"metaid\":\"rule2\"}}, };\np2_proc := 0.1;\n\np2 @Record 'p2' { } .= 1.5;\n\nk1 @Const 'k1' { } = 0.9;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a compartment\r\n whose volume is varying.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, RateRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are two\r\nspecies called S1 and S2 and three parameters called k1, p1 and p2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules. The assignmentRule assigns value to C\r\nand the rateRule determines the rate at which p2 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | C | $p1 * p2$ |\r\n | Rate | p2 | $0.1 |]\r\n\r\nIn this case, the initial value is not declared for compartment\r\nC and must be calculated by the assignmentRule. Note that\r\nsince this assignmentRule must always remain true, it should be considered\r\nduring simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.9$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |litre mole^-1^ |\r\n|Value of parameter p2 |$ 1.5$ |mole second^-1^ |\r\n|Volume of compartment C |$ undeclared$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, };\nC := p1 * p2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\np2_proc @Process { actors: = p2, aux: {{\"metaid\":\"rule2\"}}, };\np2_proc := 0.1;\n\np2 @Record 'p2' { } .= 1.5;\n\nk1 @Const 'k1' { } = 0.9;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a compartment whose \r\n volume is varying.\r\ncomponentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are three\r\nspecies called S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules. The assignmentRule assigns value to C\r\nand the rateRule determines the rate at which p2 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | C | $p1 * p2$ |\r\n | Rate | p2 | $0.1 |]\r\n\r\nIn this case, the initial value declared for compartment C is\r\ninconsistent with that calculated by the assignmentRule; the calculated\r\nvalue should be used. Note that since this assignmentRule must always\r\nremain true, it should be considered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 2.5$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |litre mole^-1^ |\r\n|Value of parameter p2 |$ 1.0$ |mole second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 1;\nC := p1 * p2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\np2_proc @Process { actors: = p2, aux: {{\"metaid\":\"rule2\"}}, };\np2_proc := 0.1;\n\np2 @Record 'p2' { } .= 1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 2.5;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a compartment whose \r\n volume is varying.\r\ncomponentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are three\r\nspecies called S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules. The assignmentRule assigns value to C\r\nand the rateRule determines the rate at which p2 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | C | $p1 * p2$ |\r\n | Rate | p2 | $0.2 |]\r\n\r\nIn this case, the initial value declared for compartment C is\r\nconsistent with that calculated by the assignmentRule. Note that since\r\nthis assignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 25$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |litre mole^-1^ |\r\n|Value of parameter p2 |$ 1.0$ |mole second^-1^ |\r\n|Volume of compartment C |$ 0.1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 0.1;\nC := p1 * p2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\np2_proc @Process { actors: = p2, aux: {{\"metaid\":\"rule2\"}}, };\np2_proc := 0.2;\n\np2 @Record 'p2' { } .= 1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 25;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a compartment whose \r\n volume is varying.\r\ncomponentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are three\r\nspecies called S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules. The assignmentRule assigns value to C\r\nand the rateRule determines the rate at which p2 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | C | $p1 * p2$ |\r\n | Rate | p2 | $0.1 |]\r\n\r\nIn this case, the initial value is not declared for compartment\r\nC and must be calculated by the assignmentRule. Note that\r\nsince this assignmentRule must always remain true, it should be considered\r\nduring simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 0.1$ |mole |\r\n|Initial amount of S2 |$ 0.2$ |mole |\r\n|Initial amount of S3 |$ 0.1$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |litre mole^-1^ |\r\n|Value of parameter p2 |$ 1.0$ |mole second^-1^ |\r\n|Volume of compartment C |$ undeclared$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, };\nC := p1 * p2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\np2_proc @Process { actors: = p2, aux: {{\"metaid\":\"rule2\"}}, };\np2_proc := 0.1;\n\np2 @Record 'p2' { } .= 1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment whose \r\n volume is varying.\r\ncomponentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains two rules. The assignmentRule assigns value to C\r\nand the rateRule determines the rate at which p2 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | C | $p1 * p2$ |\r\n | Rate | p2 | $0.1$ |]\r\n\r\nIn this case, the initial value declared for compartment C is\r\ninconsistent with that calculated by the assignmentRule; the calculated\r\nvalue should be used. Note that since this assignmentRule must always\r\nremain true, it should be considered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 1.1$ |mole |\r\n|Initial amount of S4 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 0.0365$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.0025$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |litre^2^ mole^-1^ |\r\n|Value of parameter p2 |$ 1.5$ |mole second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 1;\nC := p1 * p2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.1 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\np2_proc @Process { actors: = p2, aux: {{\"metaid\":\"rule2\"}}, };\np2_proc := 0.1;\n\np2 @Record 'p2' { } .= 1.5;\n\nk1 @Const 'k1' { } = 0.0365;\nk2 @Const 'k2' { } = 0.0025;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment whose \r\n volume is varying.\r\ncomponentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains two rules. The assignmentRule assigns value to C\r\nand the rateRule determines the rate at which p2 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | C | $p1 * p2$ |\r\n | Rate | p2 | $0.1$ |]\r\n\r\nIn this case, the initial value declared for compartment C is\r\nconsistent with that calculated by the assignmentRule. Note that since\r\nthis assignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 1.1$ |mole |\r\n|Initial amount of S4 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 0.0365$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.0025$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |litre^2^ mole^-1^ |\r\n|Value of parameter p2 |$ 1.5$ |mole second^-1^ |\r\n|Volume of compartment C |$ 0.1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 0.1;\nC := p1 * p2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.1 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\np2_proc @Process { actors: = p2, aux: {{\"metaid\":\"rule2\"}}, };\np2_proc := 0.1;\n\np2 @Record 'p2' { } .= 1.5;\n\nk1 @Const 'k1' { } = 0.0365;\nk2 @Const 'k2' { } = 0.0025;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment whose \r\n volume is varying.\r\ncomponentTags: Compartment, Species, RateRule, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment, NonConstantParameter, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one varying compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains two rules. The assignmentRule assigns value to C\r\nand the rateRule determines the rate at which p2 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | C | $p1 * p2$ |\r\n | Rate | p2 | $0.1$ |]\r\n\r\nIn this case, the initial value is not declared for compartment\r\nC and must be calculated by the assignmentRule. Note that\r\nsince this assignmentRule must always remain true, it should be considered\r\nduring simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 1.5$ |mole |\r\n|Initial amount of S3 |$ 1.1$ |mole |\r\n|Initial amount of S4 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 7.5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 2.5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 0.1$ |litre^2^ mole^-1^ |\r\n|Volume of compartment C |$ undeclared$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, };\nC := p1 * p2;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.1 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\np2_proc @Process { actors: = p2, aux: {{\"metaid\":\"rule2\"}}, };\np2_proc := 0.1;\n\np2 @Record 'p2' { } .= 0.9;\n\nk1 @Const 'k1' { } = 0.0365;\nk2 @Const 'k2' { } = 0.0025;\np1 @Const 'p1' { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a 2D compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k1. Compartment\r\n\"compartment\" is 2-dimensional. The model contains one reaction defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $0.65$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.546$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.65;\n\nk1 @Const 'k1' { } = 1.546;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a 1D compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k1. Compartment\r\n\"compartment\" is 1-dimensional. The model contains one reaction defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $0.65$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.546$ |second^-1^ |\r\n|length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.65;\n\nk1 @Const 'k1' { } = 1.546;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a 0D compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k1. Compartment\r\n\"compartment\" is 0-dimensional. The model contains one reaction defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $0.65$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.546$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.65;\n\nk1 @Const 'k1' { } = 1.546;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a 2D compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$4.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.69 \\x 10^2$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.23 \\x 10^-1$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 0.015 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 0.02 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 0.04 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1 / 100);\n\nk1 @Const 'k1' { } = 69;\nk2 @Const 'k2' { } = 0.023;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a 1D compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-4$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$4.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.69 \\x 10^4$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.23 \\x 10^-2$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5e-4 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2e-4 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 4e-4 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1 / 10000);\n\nk1 @Const 'k1' { } = 6900;\nk2 @Const 'k2' { } = 0.0023;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a 0D compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$4.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.69 \\x 10^2$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.23 \\x 10^-1$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.015;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.02;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.04;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1 / 100);\n\nk1 @Const 'k1' { } = 69;\nk2 @Const 'k2' { } = 0.023;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a 2D compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/metre^2, compartment: compartment, } .= 2 / compartment;\nS3 @Species 'S3' { units: mole/metre^2, compartment: compartment, } .= 1.5 / compartment;\nS4 @Species 'S4' { units: mole/metre^2, compartment: compartment, } .= 4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a 1D compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/metre, compartment: compartment, } .= 2 / compartment;\nS3 @Species 'S3' { units: mole/metre, compartment: compartment, } .= 1.5 / compartment;\nS4 @Species 'S4' { units: mole/metre, compartment: compartment, } .= 4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a 0D compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 0-dimensional. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 0.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and one parameter named k1. The model contains\r\none reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $0.15$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1.75$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1.75;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.15;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-1$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.93;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.02 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1 / 100);\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 0.025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * k2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$ 1.75$ |second^-1^ |\r\n|Value of parameter k2 |$1.5 \\x 10^-2$ |mole |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k1 * k2;\n\nk1 @Const 'k1' { } = 1.75;\nk2 @Const 'k2' { } = 0.015;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-7$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1e-7);\n\nk1 @Const 'k1' { } = 750000;\nk2 @Const 'k2' { } = 0.00025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, HasOnlySubstanceUnits\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:25em,=}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:25em,=}| *Type* | *Variable* | *Formula* |\r\n| Rate | S3 | $k1 * 0.5 10^-3$ |\r\n| Rate | S4 | $-k2 * 0.5 10^-3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,=}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$ 4 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.693$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species have been declared as having substance units only (meaning that\r\nthe attribute %hasOnlySubstanceUnits% is set to true). Thus, they must be\r\ntreated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.004;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 5e-4 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-5e-4) * k2;\n\nk1 @Const 'k1' { } = 0.693;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Species S3\r\nis labeled as an SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * k2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 1.75$ |second^-1^ |\r\n|Value of parameter k2 |$1.5 \\x 10^-5$ |mole |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-4 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1e-4 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k1 * k2;\n\nk1 @Const 'k1' { } = 1.75;\nk2 @Const 'k2' { } = 0.000015;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Species S1\r\nis labeled as an SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * k2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1.75$ |second^-1^ |\r\n|Value of parameter k2 |$1.5 \\x 10^-4$ |mole |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.001 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k1 * k2;\n\nk1 @Const 'k1' { } = 1.75;\nk2 @Const 'k2' { } = 0.00015;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Species S2\r\nis labeled as an SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * k2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 1.75$ |second^-1^ |\r\n|Value of parameter k2 |$1.5 \\x 10^-3$ |mole |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.01 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.01 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k1 * k2;\n\nk1 @Const 'k1' { } = 1.75;\nk2 @Const 'k2' { } = 0.0015;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. Both\r\nspecies S2 and S3 are labeled as an SBML boundary species. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * k2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$ 1.75$ |second^-1^ |\r\n|Value of parameter k2 |$1.5 \\x 10^-2$ |mole |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.15 / compartment;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.1 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.1 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k1 * k2;\n\nk1 @Const 'k1' { } = 1.75;\nk2 @Const 'k2' { } = 0.015;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nSpecies S1 is labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-7$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1e-7);\n\nk1 @Const 'k1' { } = 750000;\nk2 @Const 'k2' { } = 0.00025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nSpecies S3 is labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-7$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1e-7);\n\nk1 @Const 'k1' { } = 750000;\nk2 @Const 'k2' { } = 0.00025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nSpecies S4 is labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-7$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1e-7);\n\nk1 @Const 'k1' { } = 750000;\nk2 @Const 'k2' { } = 0.00025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. Both\r\nspecies S1 and S4 are labeled as an SBML boundary species. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-7$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1e-7);\n\nk1 @Const 'k1' { } = 750000;\nk2 @Const 'k2' { } = 0.00025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. Both\r\nspecies S3 and S4 are labeled as an SBML boundary species. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-7$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 1.5e-6 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 2e-6 / compartment;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: compartment, } .= 1.5e-6 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 1e-6 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := compartment * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := compartment * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1e-7);\n\nk1 @Const 'k1' { } = 750000;\nk2 @Const 'k2' { } = 0.00025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nSpecies S1 is labeled as an SBML boundary species. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5 10^-3$ |\r\n | Rate | S4 | $-k2 * 0.5 10^-3$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$ 4 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.693$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 5e-4 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-5e-4) * k2;\n\nk1 @Const 'k1' { } = 0.693;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nSpecies S3 is labeled as an SBML boundary species. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5 10^-3$ |\r\n | Rate | S4 | $-k2 * 0.5 10^-3$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$ 4 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.693$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 5e-4 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-5e-4) * k2;\n\nk1 @Const 'k1' { } = 0.693;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nSpecies S4 is labeled as an SBML boundary species. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5 10^-3$ |\r\n | Rate | S4 | $-k2 * 0.5 10^-3$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$ 4 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.693$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 5e-4 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-5e-4) * k2;\n\nk1 @Const 'k1' { } = 0.693;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. Both\r\nspecies S1 and S4 are labeled as an SBML boundary species. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5 10^-3$ |\r\n | Rate | S4 | $-k2 * 0.5 10^-3$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$ 4 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.693$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 5e-4 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-5e-4) * k2;\n\nk1 @Const 'k1' { } = 0.693;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. Both\r\nspecies S3 and S4 are labeled as an SBML boundary species. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * compartment$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5 10^-3$ |\r\n | Rate | S4 | $-k2 * 0.5 10^-3$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$ 4 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.693$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0.002 / compartment;\nS3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0.0015 / compartment;\nS4 @Species 'S4' { units: mole/litre, compartment: compartment, } .= 0.004 / compartment;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := compartment * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 5e-4 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-5e-4) * k2;\n\nk1 @Const 'k1' { } = 0.693;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and two events that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event2]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one event that assigns value to species S1 defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS1 [event1]= (1 / 500);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0012 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 750;\nk2 @Const 'k2' { } = 250;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains two events that assign value to species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-2$ |]\r\n | Event2 | $S3 > 2.25 \\x 10^-2$ | $-$ | $S4 -> 1 \\x 10^-2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS1 [event1]= (1 / 50);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS4 [event2]= (1 / 100);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 25;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\nevent2 @DSwitcher 'event2' { trigger: S3 > (9 / 400), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and an event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-1$ |]\r\n | | | | $S4 -> 0.5 \\x 10^-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS1 [event1]= (1 / 5);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS4 [event1]= (1 / 20);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 2.5;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species using a function.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |]\r\n \r\nThe eventAssignment uses the functionDefinition defined as:\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$0.8$ |mole litre^-1^ |\r\n|Value of parameter k4 |$0.2$ |mole litre^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= add(k3, k4);\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.8;\nk4 @Const 'k4' { } = 0.2;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and two events that assigns value to a species using a function.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and four parameters called k1, k2, k3 and k4. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = add(k3, k4)$ |\r\n | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1 * divide(k3, k4)$ |]\r\n\r\nBoth eventAssignments use functionDefinitions defined as:\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |\r\n | divide | x, y | $x / y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$0.5$ |mole litre^-1^ |\r\n|Value of parameter k4 |$0.5$ |mole litre^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\ndivide #defineFunction { arguments: [x, y], math: x * pow(y, (-1)), };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event2]= divide(k3, k4);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= add(k3, k4);\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.5;\nk4 @Const 'k4' { } = 0.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 2D compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Compartment C is\r\n2-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.7$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.8$ |metre^2 mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.2$ |second^-1^ |\r\n|Area of compartment C |$1$ |metre^2 |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.8;\nk2 @Const 'k2' { } = 0.2;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.7, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 1D compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Compartment C is\r\n1-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.6$ | $-$ | $S2 = 1.5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.8$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.2$ |second^-1^ |\r\n|Length of compartment C |$1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.8;\nk2 @Const 'k2' { } = 0.2;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.6, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 0D compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Compartment C is\r\n0-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.7$ | $-$ | $S2 = 1.25$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.8$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.2$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 1;\nS2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2;\nS2 [event1]= 1.25;\nS3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 0.8;\nk2 @Const 'k2' { } = 0.2;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.7, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 2D compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Compartment C is\r\n2-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.075$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.025$ |second^-1^ |\r\n|Area of compartment C |$1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1 / C;\nS1 [event2]= 1;\nS2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.075;\nk2 @Const 'k2' { } = 0.025;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 1D compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Compartment C is\r\n1-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.075$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.025$ |second^-1^ |\r\n|Length of compartment C |$1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C;\nS1 [event2]= 1;\nS2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.075;\nk2 @Const 'k2' { } = 0.025;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.65, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 0D compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Compartment C is\r\n0-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.2$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.075$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.025$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 1;\nS1 [event2]= 0.95;\nS2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 0.075;\nk2 @Const 'k2' { } = 0.025;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.7, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 2D compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Compartment C is\r\n2-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns value to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.25$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Area of compartment C |$1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1 / C;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2 / C;\nS2 [event1]= 1.25;\nS3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 1D compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Compartment C is\r\n1-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n| Event1 | $S1 < 0.45$ | $-$ | $S2 = 1.25$ |\r\n| | | | $S1 = 0.6$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Length of compartment C |$1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C;\nS1 [event1]= 0.6;\nS2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.25;\nS3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.45, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one 0D compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Compartment C is\r\n0-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.45$ | $-$ | $S2 = 1.25$ |\r\n | | | | $S1 = 0.6$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |]\r\n\r\nIn this example the compartment has its spatialDimensions attribute set to\r\nzero; i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 1;\nS1 [event1]= 0.5;\nS2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2;\nS2 [event1]= 1.25;\nS3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$0.1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1.43$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.43;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event2]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$0.9$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.9;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.65, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.2 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$0.5 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$750$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.05$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.24$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.24;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS1 [event1]= 0.004;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0022 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 750;\nk2 @Const 'k2' { } = 0.05;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > 0.01, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains two events that assign values to species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 1.4$ |]\r\n | Event2 | $S2 < 0.03$ | $-$ | $S4 -> 1 \\x 10^-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS1 [event1]= 1.4;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS4 [event2]= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 0.0025;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\nevent2 @DSwitcher 'event2' { trigger: S2 < 0.03, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and an event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one event that assigns a value to both species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n| Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-4$ |\r\n| | | | $S4 -> 2 \\x 10^-4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$4.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$4.8 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$8.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$4.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.025 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.25$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.25;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 4e-4;\nS1 [event1]= (1 / 5000);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 4.8e-4;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 8e-4;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4e-4;\nS4 [event1]= (1 / 5000);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 250;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Species S2 is\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Species S3 is\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Both species S2\r\nand S3 are labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C;\nS2 [event1]= 1.1;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Species S2 is\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event2]= 1;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Species S3 is\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assigns values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event2]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Both species S2\r\nand S3 are labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event2]= 1.1;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C;\nS2 [event1]= 1.1;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Species S2 is\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Species S3 is\r\nlabeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. Both species S2\r\nand S3 are labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is\r\nlabeled as constant and therefore cannot be changed by rules or reactions.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C;\nS1 [event1]= (1 / 5000);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.2e-4 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4 / C;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 1e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is\r\nlabeled as constant and therefore cannot be changed by rules or reactions.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains two events that assign values to species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S2 < S4$ | $-$ | $S1 -> 2 \\x 10^-3$ |]\r\n | Event2 | $S3 > 2 \\x 10^-3$ | $-$ | $S3 -> 1 \\x 10^-3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.9 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS1 [event1]= 0.002;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0012 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.0019 / C;\nS3 [event2]= (1 / 1000);\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 750;\nk2 @Const 'k2' { } = 250;\n\nevent1 @DSwitcher 'event1' { trigger: S2 < S4, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 0.002, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and an event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. Species S4 is\r\nlabeled as constant and therefore cannot be changed by rules or reactions.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S2 < S4$ | $-$ | $S1 -> 2 \\x 10^-2$ |]\r\n | | | | $S3 -> 0.5 \\x 10^-2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS1 [event1]= (1 / 50);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS3 [event1]= (1 / 200);\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 0.01 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 25;\n\nevent1 @DSwitcher 'event1' { trigger: S2 < S4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, EventNoDelay \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k * S3 * C$ |]\r\n\r\nReaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 +\r\nS2 defines another local parameter k. Note that these parameters have a\r\nscope local to the defining reaction.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of local parameter k |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of local parameter k |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k__reaction1_local * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k__reaction2_local * S3;\n\nk__reaction1_local @Const { } = 0.75;\nk__reaction2_local @Const { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> 2S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| 2S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains two events that assign values to species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-1$ |]\r\n | Event2 | $S3 > 2.5 \\x 10^-1$ | $-$ | $S4 -> 1 \\x 10^-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS1 [event1]= (1 / 5);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS4 [event2]= (1 / 10);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: 2*S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 2.5;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\nevent2 @DSwitcher 'event2' { trigger: S3 > (1 / 4), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, EventNoDelay \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k * S3 * S4 * C$ |]\r\n\r\nReaction S1 + S2 -> S3 + S4 defines one local parameter k. Reaction S3 +\r\nS4 -> S1 + S2 defines another (different) local parameter k. Note that\r\nthese parmeters have a scope local to the defining reaction.\r\n\r\nThe model contains two events that assign values to species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-3$ |]\r\n | Event2 | $S3 > 2.25 \\x 10^-3$ | $-$ | $S4 -> 1 \\x 10^-3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of local parameter k |$0.75 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Value of local parameter k |$0.25 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS1 [event1]= (1 / 500);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0012 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS4 [event2]= (1 / 1000);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k__reaction1_local * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k__reaction2_local * S3 * S4;\n\nk__reaction1_local @Const { } = 750;\nk__reaction2_local @Const { } = 250;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\nevent2 @DSwitcher 'event2' { trigger: S3 > (9 / 4000), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.75$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.75;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, EventNoDelay \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k * S3 * C$ |]\r\n\r\nReaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 +\r\nS2 defines another (different) local parameter k. Note that these\r\nparmeters have a scope local to the defining reaction.\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of local parameter k |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of local parameter k |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k__reaction1_local * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k__reaction2_local * S3;\n\nk__reaction1_local @Const { } = 0.75;\nk__reaction2_local @Const { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only with\r\n one event that assigns value to a parameter.\r\ncomponentTags: Parameter, RateRule, EventNoDelay \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and two constant\r\nparameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ |\r\n | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ |\r\n | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |]\r\n\r\nThe model contains one event that assigns value to parameter S2 defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |any |\r\n|Initial amount of S2 |$2.0$ |same as S1 |\r\n|Initial amount of S3 |$1.0$ |same as S1 |\r\n|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k1 * S1 * S2 + (-1) * k2 * S3;\n\nS1 @Record 'S1' { } .= 1;\nS2 @Record 'S2' { } .= 2;\nS2 [event1]= 1;\nS3 @Record 'S3' { } .= 1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only with\r\n one event that assigns value to a parameter.\r\ncomponentTags: Parameter, RateRule, EventNoDelay \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and two constant\r\nparameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ |\r\n | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ |\r\n | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |]\r\n\r\nThe model contains two events, that assign value to parameters S2 and S1 respectively, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |any |\r\n|Initial amount of S2 |$2.0$ |same as S1 |\r\n|Initial amount of S3 |$1.0$ |same as S1 |\r\n|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k1 * S1 * S2 + (-1) * k2 * S3;\n\nS1 @Record 'S1' { } .= 1;\nS1 [event2]= 1;\nS2 @Record 'S2' { } .= 2;\nS2 [event1]= 1;\nS3 @Record 'S3' { } .= 1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only with\r\n one event that assigns value to two parameters.\r\ncomponentTags: Parameter, RateRule, EventNoDelay \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and two constant\r\nparameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ |\r\n | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ |\r\n | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |]\r\n\r\nThe model contains two events, that assign value to parameters S2 and S1 respectively, defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |any |\r\n|Initial amount of S2 |$2.0$ |same as S1 |\r\n|Initial amount of S3 |$1.0$ |same as S1 |\r\n|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k1 * S1 * S2 + (-1) * k2 * S3;\n\nS1 @Record 'S1' { } .= 1;\nS1 [event1]= 1;\nS2 @Record 'S2' { } .= 2;\nS2 [event1]= 1.5;\nS3 @Record 'S3' { } .= 1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = S2$ |]\r\n \r\nNote that the event assignments should happen simultaneously, not\r\nsequentially; i.e., the value of S2 assigned to S1 is the value at the\r\npoint at which the event was triggered.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= S2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic three reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and three parameters called k1, k2 and k3. The model\r\ncontains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |\r\n| S2 -> S3 | $k2 * S2 * C$ |\r\n| S3 -> S1 | $k3 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = S2$ |]\r\n \r\nNote that the event assignments should happen simultaneously, not\r\nsequentially; i.e., the value of S2 assigned to S1 is the value at the\r\npoint at which the event was triggered.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |second^-1^ |\r\n|Value of parameter k2 |$0.55$ |second^-1^ |\r\n|Value of parameter k3 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= S2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1, reversible: false, };\nreaction3 := C * k3 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.55;\nk3 @Const 'k3' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic three reactions with three species in one compartment\r\n and one event that assigns value to three species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and three parameters called k1, k2 and k3. The model\r\ncontains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |\r\n| S2 -> S3 | $k2 * S2 * C$ |\r\n| S3 -> S1 | $k3 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns values to species S1, S2 and S3:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = S3$ |\r\n | | | | $S1 = S2$ |\r\n | | | | $S3 = S1$ |]\r\n \r\nNote that the event assignments should happen simultaneously, not\r\nsequentially; i.e., the value of S2 assigned to S1 is the value at the\r\npoint at which the event was triggered.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |second^-1^ |\r\n|Value of parameter k2 |$0.55$ |second^-1^ |\r\n|Value of parameter k3 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event1]= S2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= S3;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\nS3 [event1]= S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1, reversible: false, };\nreaction3 := C * k3 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.55;\nk3 @Const 'k3' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only with\r\n and one event that assigns value to two parameters.\r\ncomponentTags: Parameter, RateRule, EventNoDelay \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and two constant\r\nparameters called k1 and k2. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k2 * S3 - k1 * S1 * S2$ |\r\n | Rate | S2 | $k2 * S3 - k1 * S1 * S2$ |\r\n | Rate | S3 | $k1 * S1 * S2 - k2 * S3$ |]\r\n\r\nThe model contains one event that assigns values to parameters S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = S2$ |]\r\n \r\nNote that the event assignments should happen simultaneously, not\r\nsequentially; i.e., the value of S2 assigned to S1 is the value at the\r\npoint at which the event was triggered.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |any |\r\n|Initial amount of S2 |$2.0$ |same as S1 |\r\n|Initial amount of S3 |$1.0$ |same as S1 |\r\n|Value of parameter k1 |$0.75$ |(unit of S1)^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k1 * S1 * S2 + (-1) * k2 * S3;\n\nS1 @Record 'S1' { } .= 1;\nS1 [event1]= S2;\nS2 @Record 'S2' { } .= 2;\nS2 [event1]= 1.5;\nS3 @Record 'S3' { } .= 1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only with\r\n and one event that assigns value to two parameters.\r\ncomponentTags: Parameter, RateRule, EventNoDelay \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and three constant\r\nparameters called k1, k2 and k3. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k3 * S3 - k1 * S1$ |\r\n | Rate | S2 | $k1 * S1 - k2 * S2$ |\r\n | Rate | S3 | $k2 * S2 - k3 * S3$ |]\r\n\r\nThe model contains one event that assigns values to both parameters S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = S2$ |]\r\n \r\nNote that the event assignments should happen simultaneously, not\r\nsequentially; i.e., the value of S2 assigned to S1 is the value at the\r\npoint at which the event was triggered.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |any |\r\n|Initial amount of S2 |$2.0$ |same as S1 |\r\n|Initial amount of S3 |$1.0$ |same as S1 |\r\n|Value of parameter k1 |$0.75$ |second^-1^ |\r\n|Value of parameter k2 |$0.55$ |second^-1^ |\r\n|Value of parameter k3 |$0.25$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k3 * S3 + (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1 + (-1) * k2 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k2 * S2 + (-1) * k3 * S3;\n\nS1 @Record 'S1' { } .= 1;\nS1 [event1]= S2;\nS2 @Record 'S2' { } .= 2;\nS2 [event1]= 1.5;\nS3 @Record 'S3' { } .= 1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.55;\nk3 @Const 'k3' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only with\r\n and one event that assigns value to three parameters.\r\ncomponentTags: Parameter, RateRule, EventNoDelay \r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called S1, S2 and S3 and three constant\r\nparameters called k1, k2 and k3. (Note that indeed S1, S2 and S3 are parameters and \r\nnot species in this model.)\r\n\r\nThe model contains three rules defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S1 | $k3 * S3 - k1 * S1$ |\r\n | Rate | S2 | $k1 * S1 - k2 * S2$ |\r\n | Rate | S3 | $k2 * S2 - k3 * S3$ |]\r\n\r\nThe model contains one event that assigns values to parameters S1, S2 and\r\nS3:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = S3$ |\r\n | | | | $S1 = S2$ |\r\n | | | | $S3 = S1$ |]\r\n \r\nNote that the event assignments should happen simultaneously, not\r\nsequentially; i.e., the value of S2 assigned to S1 is the value at the\r\npoint at which the event was triggered.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |any |\r\n|Initial amount of S2 |$2.0$ |same as S1 |\r\n|Initial amount of S3 |$1.0$ |same as S1 |\r\n|Value of parameter k1 |$0.75$ |second^-1^ |\r\n|Value of parameter k2 |$0.55$ |second^-1^ |\r\n|Value of parameter k3 |$0.25$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS1_proc @Process { actors: = S1, aux: {{\"metaid\":\"rule1\"}}, };\nS1_proc := k3 * S3 + (-1) * k1 * S1;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k1 * S1 + (-1) * k2 * S2;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule3\"}}, };\nS3_proc := k2 * S2 + (-1) * k3 * S3;\n\nS1 @Record 'S1' { } .= 1;\nS1 [event1]= S2;\nS2 @Record 'S2' { } .= 2;\nS2 [event1]= S3;\nS3 @Record 'S3' { } .= 1;\nS3 [event1]= S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.55;\nk3 @Const 'k3' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called\r\nS1 and S2 and one parameter called k1. The model contains one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model does not contain any rules.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.5 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$1$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment and nonzero initial concentrations.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called\r\nS1 and S2 and one parameter called k1. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.5 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5 \\x 10^-1$ |mole litre^-1^ |\r\n|Value of parameter k1 |$1$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.15;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment, nonzero initial concentrations, and identical reaction rates.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called\r\nS1 and S2 and two parameters called k1 and k2. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |\r\n| S2 -> S1 | $k2 * S2 * C$ |]\r\n\r\nThe rate constants are identical in both directions, leading to a system\r\nwhere the species concentrations remain the same.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.5 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5 \\x 10^-3$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$0.5$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0015;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S1, reversible: false, };\nreaction2 := C * k2 * S2;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one C.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1e-4;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three reactions with four species in one compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and three parameters called k1, k2 and k3. The model\r\ncontains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |\r\n| S3 -> S1 + S4 | $k3 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$2.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$1.0 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.9$ |second^-1^ |\r\n|Value of parameter k3 |$0.7$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, };\nreaction3 := C * k3 * S3;\n\nk1 @Const 'k1' { } = 10;\nk2 @Const 'k2' { } = 0.9;\nk3 @Const 'k3' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C.\r\nThere are four species called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |\r\n| S2 -> S3 | $k2 * S2 * C$ |\r\n| S3 -> S4 | $k3 * S3 * C$ |] \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.7$ |second^-1^ |\r\n|Value of parameter k2 |$0.5$ |second^-1^ |\r\n|Value of parameter k3 |$1$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $k2 / 100$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the parameter k1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$undeclared$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment 'C' { units: volume, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: substance/volume, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { } .= k2 / 100;\nk2 @Record 'k2' { } .= 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $k2 / 100$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for parameter k1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$100$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 100;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / 50$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$5.4$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= k2 / 50;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / 50$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= k2 / 50;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / 50$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$undeclared$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= k2 / 50;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-3$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.00125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.25 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.0000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-2$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.0125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k2 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the parameter k2 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$undeclared$ |second^-1^ |\r\n|Value of parameter p1 |$0.125$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk2 @Record 'k2' { } .= 2 * p1;\n\nk1 @Const 'k1' { } = 0.75;\np1 @Const 'p1' { } = 0.125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k2 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for parameter k2 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$1.0$ |second^-1^ |\r\n|Value of parameter p1 |$0.125$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk2 @Record 'k2' { } .= 2 * p1;\n\nk1 @Const 'k1' { } = 0.75;\np1 @Const 'p1' { } = 0.125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k2 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for parameter k2 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.125$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk2 @Record 'k2' { } .= 2 * p1;\n\nk1 @Const 'k1' { } = 0.75;\np1 @Const 'p1' { } = 0.125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |litre |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |litre |\r\n|Volume of compartment C |$3.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |litre |\r\n|Volume of compartment C |$undeclared$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a 2D compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is \r\n2-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$7.5$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$2.5$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |metre^2^ |\r\n|Area of compartment C |$1$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre^2, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1e-4 / C;\nS2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2e-4 / C;\nS3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 2.5;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a 2D compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is \r\n2-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$7.5$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$2.5$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |metre^2^ |\r\n|Area of compartment C |$3.5$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre^2, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.1 / C;\nS2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0.2 / C;\nS3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 0.1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 2.5;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a 2D compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is \r\n2-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$7.5$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$2.5$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |metre^2^ |\r\n|Area of compartment C |$undeclared$ |metre^2^ |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre^2, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.001 / C;\nS2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0.002 / C;\nS3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 2.5;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a 1D compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is \r\n1-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$3.5$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$1.5$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |metre |\r\n|Length of compartment C |$1$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre, boundary: true, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 3.5;\nk2 @Const 'k2' { } = 1.5;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a 1D compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is \r\n1-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$3.5$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$1.5$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |metre |\r\n|Length of compartment C |$3.5$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre, boundary: true, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 3.5;\nk2 @Const 'k2' { } = 1.5;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a 1D compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is \r\n1-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$3.5$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$1.5$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |metre |\r\n|Length of compartment C |$undeclared$ |metre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre, boundary: true, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/metre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/metre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 3.5;\nk2 @Const 'k2' { } = 1.5;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a 0D compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, 0D-Compartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is \r\n0-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-3$ |mole |]\r\n\r\nIn this example, the compartment has its spatialDimensions attribute set to\r\nzero, i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 2 * p1;\nS2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 0.02;\nS3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.00125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a 0D compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, 0D-Compartment\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is \r\n0-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.25 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-5$ |mole |]\r\n\r\nIn this example, the compartment has its spatialDimensions attribute set to\r\nzero, i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 2 * p1;\nS2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 2e-4;\nS3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.0000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a 0D compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, 0D-Compartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Compartment C is \r\n0-dimensional. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 $ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$0.75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-2$ |mole |]\r\n\r\nIn this example, the compartment has its spatialDimensions attribute set to\r\nzero, i.e., it represents a point and therefore cannot have size or units.\r\nThe species values must be treated as amounts and not concentrations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { boundary: true, } .= 0;\n\nS1 @Species 'S1' { units: mole, compartment: C, isAmount: true, } .= 2 * p1;\nS2 @Species 'S2' { units: mole, compartment: C, isAmount: true, } .= 0.2;\nS3 @Species 'S3' { units: mole, compartment: C, isAmount: true, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.0125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / 9$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$5.4$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= k2 / 9;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / 10$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= k2 / 10;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / 9$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$undeclared$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= k2 / 9;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.25$ |litre |\r\n|Volume of compartment C |$0.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.25$ |litre |\r\n|Volume of compartment C |$3.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.25$ |litre |\r\n|Volume of compartment C |$undeclared$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and k2. Species S1 is\r\nlabeled as an SBML boundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |dimensionless |\r\n|Value of parameter k2 |$50$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and k2. Species S1 is\r\nlabeled as an SBML boundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$30$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |dimensionless |\r\n|Value of parameter k2 |$50$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and k2. Species S1 is\r\nlabeled as an SBML boundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.125$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |dimensionless |\r\n|Value of parameter k2 |$50$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Species S1 is labeled \r\nas an SBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-4$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Species S1 is labeled \r\nas an SBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.25 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-3$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.00125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. Species S1 is labeled \r\nas an SBML boundary species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.0000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, ConstantSpecies, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled \r\nas a constant species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S4 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S4 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S4 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.25 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S4 |$undeclared$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$5 \\x 10^-2$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.025 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, };\nreaction1 := C * k1 * S1 * S4;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.05;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled \r\nas a constant species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S4 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S4 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S4 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.25 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$5 \\x 10^-4$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2.5e-4 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, };\nreaction1 := C * k1 * S1 * S4;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.0005;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, ConstantSpecies, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled \r\nas a constant species. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S4 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S4 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S4 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.25 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$5.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$5 \\x 10^-3$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0025 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2 * p1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, modifiers: [S4], reversible: false, };\nreaction1 := C * k1 * S1 * S4;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.005;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is\r\nlabeled a constant species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1 * S3$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S3 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S3 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Initial amount of S3 |$1.125$ |mole |\r\n|Value of parameter k1 |$0.75$ |dimensionless |\r\n|Value of parameter k2 |$2.7$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, };\nreaction1 := C * k2 * S1 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 2.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, ConstantSpecies, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is\r\nlabeled a constant species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1 * S3$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S3 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S3 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Initial amount of S3 |$5.7$ |mole |\r\n|Value of parameter k1 |$0.75$ |dimensionless |\r\n|Value of parameter k2 |$2.7$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, };\nreaction1 := C * k2 * S1 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 2.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, ConstantSpecies, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. Species S3 is\r\nlabeled a constant species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1 * S3$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S3 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S3 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Initial amount of S3 |$undeclared$ |mole |\r\n|Value of parameter k1 |$0.75$ |dimensionless |\r\n|Value of parameter k2 |$2.7$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, };\nreaction1 := C * k2 * S1 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 2.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityStoichiometry, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and k2. The model contains \r\none reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |dimensionless |\r\n|Value of parameter k2 |$5$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= k1 * S2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityStoichiometry, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and k2. The model contains \r\none reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$3.2$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |dimensionless |\r\n|Value of parameter k2 |$5$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= k1 * S2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and k2. The model contains \r\none reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 * S2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.125$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |dimensionless |\r\n|Value of parameter k2 |$5$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= k1 * S2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityStoichiometry, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> 2S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.0000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityStoichiometry, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> 2S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-2$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.0125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, NonUnityStoichiometry, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> 2S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-4$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = 2*S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and one parameters called p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k * S3 * C$ |]\r\n\r\nReaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1\r\n+ S2$ defines another (different) local parameter k. Note that these\r\nparameters have a scope local to the defining reaction.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter p1 |$1.25 \\x 10^-4$ |mole |\r\n|Value of parameter local k |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter local k |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k__reaction1_local * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k__reaction2_local * S3;\n\nk__reaction1_local @Const { } = 0.75;\nk__reaction2_local @Const { } = 0.25;\np1 @Const 'p1' { } = 0.000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and one parameters called p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k * S3 * C$ |]\r\n\r\nReaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1\r\n+ S2$ defines another (different) local parameter k. Note that these\r\nparameters have a scope local to the defining reaction.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.25 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter p1 |$1.25 \\x 10^-3$ |mole |\r\n|Value of parameter local k |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter local k |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k__reaction1_local * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k__reaction2_local * S3;\n\nk__reaction1_local @Const { } = 0.75;\nk__reaction2_local @Const { } = 0.25;\np1 @Const 'p1' { } = 0.00125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and one parameters called p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k * S3 * C$ |]\r\n\r\nReaction $S1 + S2 -> S3$ defines one local parameter k. Reaction $S3 -> S1\r\n+ S2$ defines another (different) local parameter k. Note that these\r\nparameters have a scope local to the defining reaction.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-4$ |mole |\r\n|Value of parameter p1 |$1.25 \\x 10^-5$ |mole |\r\n|Value of parameter local k |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter local k |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k__reaction1_local * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k__reaction2_local * S3;\n\nk__reaction1_local @Const { } = 0.75;\nk__reaction2_local @Const { } = 0.25;\np1 @Const 'p1' { } = 0.0000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and one parameter called k. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k * S1$ |]\r\n\r\nReaction $S1 -> S2$ defines one local parameter k. Note that this\r\nparameter has a scope local to the defining reaction.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k / 50$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k |$50$ |litre |\r\n|Value of local parameter k |$0.5$ |second^-1^ |\r\n|Volume of compartment C |$5.4$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= k / 50;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k__reaction1_local * S1;\n\nk__reaction1_local @Const { } = 0.5;\nk @Const 'k' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and one parameter called k. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k * S1$ |]\r\n\r\nReaction $S1 -> S2$ defines one local parameter k. Note that this\r\nparameter has a scope local to the defining reaction.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k / 50$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k |$50$ |litre |\r\n|Value of local parameter k |$0.5$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= k / 50;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k__reaction1_local * S1;\n\nk__reaction1_local @Const { } = 0.5;\nk @Const 'k' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and one parameter called k. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k * S1$ |]\r\n\r\nReaction $S1 -> S2$ defines one local parameter k. Note that this\r\nparameter has a scope local to the defining reaction.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k / 50$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k |$50$ |litre |\r\n|Value of local parameter k |$0.5$ |second^-1^ |\r\n|Volume of compartment C |$undeclared$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= k / 50;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k__reaction1_local * S1;\n\nk__reaction1_local @Const { } = 0.5;\nk @Const 'k' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $division(k2, 100)$ |]\r\n\r\nThe initialAssignment uses a functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | division | x, y | $x / y$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the parameter k1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$undeclared$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\n","completion":"\ndivision #defineFunction { arguments: [x, y], math: x / y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { } .= division(k2, 100);\n\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $multiply(k1, S2)$ |]\r\n\r\nThe initialAssignment uses a functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ $ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= multiply(k1, S2);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0015 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $division(k2, 50)$ |]\r\n\r\nThe initialAssignment uses a functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | division | x, y | $x / y$ |]\r\n\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) they must be treated as concentrations where they appear in\r\nexpressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\ndivision #defineFunction { arguments: [x, y], math: x / y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= division(k2, 50);\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment,\r\n and one species labeled as a boundary condition\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. Species S1\r\nis labeled as an SBML boundary species. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto} | |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment,\r\n and two species labeled as a boundary condition\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. Species S1\r\nand S2 are labeled as SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.01;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.02;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment,\r\n and all species labeled as a boundary condition\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. All three\r\nspecies S1, S2 and S3 are labeled as SBML boundary species. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1e-4;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 2e-4;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment,\r\n with one species having a stoichiometry of 2\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| 2S1 + S2 -> S3 | $k1 * S1 * S1 * S2 * C$ |\r\n| S3 -> 2S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Value of parameter k1 |$1.0 \\x 10^3$ |litre^2^ mole^-2^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: 2*S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * pow(S1, 2) * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = 2*S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 1000;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 2.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment,\r\n with one species acting as a boundary condition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2.\r\nSpecies S4 is labeled as an SBML boundary species. The model contains two\r\nreactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.01;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment,\r\n with non-unity stoichiometry.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + 2S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1e-4;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + 2*S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three reactions with four species in one compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |\r\n| S3 -> S1 + S4 | $k3 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$2.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$1.0 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.9$ |second^-1^ |\r\n|Value of parameter k3 |$0.7$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.002;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, };\nreaction3 := C * k3 * S3;\n\nk1 @Const 'k1' { } = 1000;\nk2 @Const 'k2' { } = 0.9;\nk3 @Const 'k3' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |\r\n| S2 -> S3 | $k2 * S2 * C$ |\r\n| S3 -> S4 | $k3 * S3 * C$ |] \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.7$ |second^-1^ |\r\n|Value of parameter k2 |$0.5$ |second^-1^ |\r\n|Value of parameter k3 |$1$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a compartment \r\n of non-unity volume. \r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment C |$ 1.5$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a compartment \r\n of non-unity volume. \r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.5 \\x 10^-4$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-2$ |second^-1^ |\r\n|Volume of compartment C |$ 0.7$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.7;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 0.0025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment \r\n of non-unity volume. \r\ncomponentTags: Compartment, Species, Reaction, Parameter\r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 1.7$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 2.0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 1.0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$ 0.3$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.7;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 2-dimensional\r\ncompartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. Compartment\r\nC is two-dimensional. The model contains one reaction defined\r\nas:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.5 \\x 10^-2$ |mole metre^-2^ |\r\n|Initial concentration of S2 |$ 0$ |mole metre^-2^ |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Area of compartment C |$1$ |metre^2^ |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.015;\nS2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a 2-dimensional compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2.\r\nCompartment C is 2-dimensional. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-4$ |mole metre^-2^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-4$ |mole metre^-2^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-4$ |mole metre^-2^ |\r\n|Value of parameter k1 |$ 0.75$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Area of compartment C |$ 1$ |metre^2^ |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 1e-4;\nS2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 2e-4;\nS3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 2-dimensional\r\ncompartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2.\r\nCompartment C is 2-dimensional. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-3$ |mole metre^-2^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-3$ |mole metre^-2^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-3$ |mole metre^-2^ |\r\n|Initial concentration of S4 |$1.0 \\x 10^-3$ |mole metre^-2^ |\r\n|Value of parameter k1 |$0.75 \\x 10^3$ |metre^2^ mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^3$ |metre^2^ mole^-1^ second^-1^ |\r\n|Area of compartment C |$ 1$ |metre^2^ |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre^2, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre^2, compartment: C, } .= 0.001;\nS2 @Species 'S2' { units: mole/metre^2, compartment: C, } .= 0.001;\nS3 @Species 'S3' { units: mole/metre^2, compartment: C, } .= 0.002;\nS4 @Species 'S4' { units: mole/metre^2, compartment: C, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 750;\nk2 @Const 'k2' { } = 250;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 1-dimensional\r\ncompartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. Compartment\r\nC is 1-dimensional. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.5 \\x 10^-1$ |mole metre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole metre^-1^ |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Length of compartment C |$ 1$ |metre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: C, } .= 0.15;\nS2 @Species 'S2' { units: mole/metre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a 1-dimensional compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2.\r\nCompartment C is 1-dimensional. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-2$ |mole metre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-2$ |mole metre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-2$ |mole metre^-1^ |\r\n|Value of parameter k1 |$ 0.75$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Length of compartment C |$ 1$ |metre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: C, } .= 0.01;\nS2 @Species 'S2' { units: mole/metre, compartment: C, } .= 0.02;\nS3 @Species 'S3' { units: mole/metre, compartment: C, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 1-dimensional\r\ncompartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2.\r\nCompartment C is 1-dimensional. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-4$ |mole metre^-1^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-4$ |mole metre^-1^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-4$ |mole metre^-1^ |\r\n|Initial concentration of S4 |$1.0 \\x 10^-4$ |mole metre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |metre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |metre mole^-1^ second^-1^ |\r\n|Length of compartment C |$ 1$ |metre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: metre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/metre, compartment: C, } .= 1e-4;\nS2 @Species 'S2' { units: mole/metre, compartment: C, } .= 1e-4;\nS3 @Species 'S3' { units: mole/metre, compartment: C, } .= 2e-4;\nS4 @Species 'S4' { units: mole/metre, compartment: C, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species and parameters local to \r\n reactions.\r\ncomponentTags: Compartment, Species, Reaction \r\ntestTags: Concentration, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * C,$ |\r\n| S2 -> S3 | $k * S2 * C,$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k. Reaction S2 -> S3 also\r\ndefines one (different) local parameter k. Both of these parameters have a\r\nscope local to the defining reaction.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$3.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 0$ |mole litre^-1^ |\r\n|Value of local parameter k |$ 1$ |second^-1^ |\r\n|Value of local parameter k |$ 2$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.003;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k__reaction1_local * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k__reaction2_local * S2;\n\nk__reaction1_local @Const { } = 1;\nk__reaction2_local @Const { } = 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species and parameters both global\r\n and local to reactions.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and one global parameter called k. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * C$ |\r\n| S2 -> S3 | $k * S2 * C$ |]\r\n\r\nReaction S2 -> S3 defines one local parameter k.\r\n\r\nNote that the id of the local parameter k shadows the global parameter k.\r\nWithin the defining reaction, the value of the locally-defined parameter k\r\nmust be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$3.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 0$ |mole litre^-1^ |\r\n|Value of parameter k |$ 1$ |second^-1^ |\r\n|Value of local parameter k |$ 2$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.3;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k__reaction2_local * S2;\n\nk__reaction2_local @Const { } = 2;\nk @Const 'k' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species and parameters both global\r\n and local to reactions.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and one global parameter called k. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * C$ |\r\n| S2 -> S3 | $S1 * S2 * C$ |]\r\n\r\nReaction S2 -> S3 defines one local parameter S1.\r\n\r\nNote that the id of the local parameter S1 shadows the species S1. Within\r\nthe defining reaction, the value of the locally-defined symbol S1 must be\r\nused.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$3.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 0$ |mole litre^-1^ |\r\n|Value of parameter k |$ 2$ |second^-1^ |\r\n|Value of local parameter S1 |$ 1$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment 'C' { units: volume, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: substance/volume, compartment: C, } .= 0.03;\nS2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0;\nS3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, modifiers: [S1], reversible: false, };\nreaction2 := C * S1__reaction2_local * S2;\n\nk @Record 'k' { } .= 2;\n\nS1__reaction2_local @Const { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in a compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and one parameter called k1. Species S3 is\r\nlabeled as constant and therefore cannot be changed by rules or reactions.\r\nThe model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 2$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1.5$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, modifiers: [S3], reversible: false, };\nreaction1 := C * k1 * S1 * S3;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions with four species in a compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2.\r\nSpecies S4 is labeled as constant and therefore cannot be changed by rules\r\nor reactions. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 2.0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 1.0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 1.5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, modifiers: [S4], reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 1.7;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with five species in a compartment \r\n where one species is constant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are five\r\nspecies called S1, S2, S3, S4 and S5 and two parameters called k1 and k2.\r\nSpecies S5 is labeled as constant and therefore cannot be changed by rules\r\nor reactions. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C / S5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.0 \\x 10^-6$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 1.5 \\x 10^-6$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 2.0 \\x 10^-6$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 0.5 \\x 10^-6$ |mole litre^-1^ |\r\n|Initial concentration of S5 |$ 1.0 \\x 10^-6$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1.3 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-6;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-6;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-6;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-7;\nS5 @Species 'S5' { units: mole/litre, boundary: true, compartment: C, } .= 1e-6;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, modifiers: [S5], reversible: false, };\nreaction2 := C * k2 * S3 * S4 * pow(S5, (-1));\n\nk1 @Const 'k1' { } = 1300000;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a compartment \r\n of non-unity volume. \r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment C |$ 1.5$ |litre |]\r\n\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a compartment \r\n of non-unity volume. \r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.5 \\x 10^-2$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-1$ |second^-1^ |\r\n|Volume of compartment C |$ 0.7$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.7;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.015;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 0.025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a compartment \r\n of non-unity volume. \r\ncomponentTags: Compartment, Species, Reaction, Parameter\r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 1.7$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 2.0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 1.0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$ 0.3$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.7;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment of non-unity size using a function to apply \r\nthe kinetic law.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * multiply(k1,S1)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.5 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5 \\x 10^-3$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Volume of compartment C |$ 2.3$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.0015;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * multiply(k1, S1);\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment \r\n of non-unity size using a functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C.\r\nThere are three species called S1, S2 and S3 and two parameters called k1 and k2.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $multiply(k1, S1, S2) * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Value of parameter k1 | $ 0.75$ | litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 | $ 2.5$ | second^-1^ |\r\n|Volume of compartment C |$ 2.3$ |litre |]\r\n\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * multiply(k1, S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 2.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one varying compartment\r\n and one functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$0.5 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$1.5 \\x 10^-3$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$ 12.5$ |litre |]\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 12.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 5e-4;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.001;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.002;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.0015;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * multiply(k1, multiply(S1, S2));\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 250;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one \r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S4 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 1.5 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 1 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ undeclared$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 0.1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3 and thus it\r\nmust be calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 0.08$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.08;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-4;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and one parameters called k. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k * S$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k which has a\r\nscope local to the defining reaction.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$1$ |mole |\r\n|Value of parameter k |$0.75$ |dimensionless |\r\n|Value of local parameter k |$5$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\nS3 := k * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k__reaction1_local * S1;\n\nk__reaction1_local @Const { } = 5;\nk @Const 'k' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S and one parameter called k.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k * S3 * C$ |]\r\n\r\nReaction S1 + S2 -> S3 defines one local parameter k. Reaction S3 -> S1 + S2 also\r\ndefines one (different) local parameter k. Both of these parameters have a\r\nscope local to the defining reaction.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k * S2$ |]\r\n\r\nNote that in this case the initial value of species S4 has not been declared and must be \r\ncalculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5 |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k |$ 1.5$ |dimensionless |\r\n|Value of local parameter k |$ 1.5 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of local parameter k |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := k * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k__reaction1_local * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k__reaction2_local * S3;\n\nk__reaction1_local @Const { } = 15000;\nk__reaction2_local @Const { } = 5;\nk @Const 'k' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is undeclared and so must be calculated\r\nby the initialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is inconsisent with the value declared by the model definition. \r\nThe value calculated by the initialAssignment should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$10$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is consisent with the value declared by the model definition. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.1$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value for species S3 must be calculated by the\r\nassignmentRule. Note that since this assignmentRule must always remain\r\ntrue, it should be considered during simulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value declared for species S3 is consistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0.375$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C;\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value declared for species S3 is inconsistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 3.75$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75 / C;\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $multiply(k3, S1)$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nThe assignmentRule applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n \r\nNote that in this case the initial value declared for species S4 is\r\ninconsistent with the value calculated by the assignmentRule. The\r\ncalculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 2.25$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C;\nS4 := multiply(k3, S1);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $multiply(k3, S1)$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nThe assignmentRule applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n \r\nNote that in this case the initial value of species S4 is not explicitly\r\ndeclared and must be calculated by the assignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := multiply(k3, S1);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $multiply(k3, S1)$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nThe assignmentRule applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n \r\nNote that in this case the initial value declared for species S4 is consistent\r\nwith the value calculated by the assignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 1.5 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS4 := multiply(k3, S1);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and three parameters called k1, p1 and p2. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $multiply(p1, p2)$ |]\r\n\r\nThe assignmentRule applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n \r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is undeclared and so must be calculated\r\nby the initialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := multiply(p1, p2);\n\np1 @Const 'p1' { } = 75;\np2 @Const 'p2' { } = 0.01;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and three parameters called k1, p1 and p2. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $multiply(p1, p2)$ |]\r\n\r\nThe assignmentRule applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n \r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is inconsisent with the value declared by the model definition. \r\nThe value calculated by the initialAssignment should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$10$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := multiply(p1, p2);\n\np1 @Const 'p1' { } = 75;\np2 @Const 'p2' { } = 0.01;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and three parameters called k1, p1 and p2. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $multiply(p1, p2)$ |]\r\n\r\nThe assignmentRule applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n \r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is consisent with the value declared by the model definition. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.1$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := multiply(p1, p2);\n\np1 @Const 'p1' { } = 75;\np2 @Const 'p2' { } = 0.01;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $multiply(k1, S2)$ |]\r\n\r\nThe assignmentRule applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n \r\nIn this case the initial value for species S3 must be calculated by the\r\nassignmentRule. Note that since this assignmentRule must always remain\r\ntrue, it should be considered during simulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := multiply(k1, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $multiply(k1, S2)$ |]\r\n\r\nThe assignmentRule applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n \r\nIn this case the initial value declared for species S3 is consistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0.375$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C;\nS3 := multiply(k1, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay, FunctionDefinition \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $multiply(k1, S2)$ |]\r\n\r\nThe assignmentRule applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n \r\nIn this case the initial value declared for species S3 is inconsistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0.5$ |mole |\r\n|Initial amount of S3 |$ 3.75$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75 / C;\nS3 := multiply(k1, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k2 * S4$ |\r\n | Rate | S4 | $-k2 * S4$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 / 0.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this case the \r\nvalue of species S1 calculated by the initialAssignment is consisent with the value \r\ndeclared by the model definition. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Value of parameter p |$ 0.75$ |mole litre^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k2 * S4;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-1) * k2 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k2 * S4$ |\r\n | Rate | S4 | $-k2 * S4$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 / 0.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this case the \r\nvalue of species S1 calculated by the initialAssignment is inconsisent with the value \r\ndeclared by the model definition. The calculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Value of parameter p |$ 0.75$ |mole litre^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k2 * S4;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-1) * k2 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k2 * S4$ |\r\n | Rate | S4 | $-k2 * S4$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 / 0.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this case the \r\nvalue of species S1 is not declared by the model definition. The calculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ undeclared$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter p |$ 0.75$ |mole litre^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k2 * S4;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-1) * k2 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.5;\np1 @Const 'p1' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and p1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is inconsistent\r\nwith the value calculated by the assignmentRule. The calculated value should be used. \r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 / 2000$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this case the \r\nvalue of species S1 calculated by the initialAssignment is consisent with the value \r\ndeclared by the model definition.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 5$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Value of parameter p1 |$ 2 \\x 10^-2$ |mole litre^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= p1 * pow(2000, (-1));\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\np1 @Const 'p1' { } = 0.02;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and p1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is inconsistent\r\nwith the value calculated by the assignmentRule. The calculated value should be used. \r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 / 2000$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this case the \r\nvalue of species S1 calculated by the initialAssignment is inconsisent with the value \r\ndeclared by the model definition. The calculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 5$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Value of parameter p1 |$ 2 \\x 10^-2$ |mole litre^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= p1 * pow(2000, (-1));\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\np1 @Const 'p1' { } = 0.02;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and four parameters called k1, k2, k3 and p1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is inconsistent\r\nwith the value calculated by the assignmentRule. The calculated value should be used. \r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 / 2000$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this case the \r\nvalue of species S1 is not declared by the model definition. The calculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ undeclared$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 5$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Value of parameter p1 |$ 2 \\x 10^-2$ |mole litre^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= p1 * pow(2000, (-1));\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\np1 @Const 'p1' { } = 0.02;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and one parameter called k1. The model contains\r\none reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $0.15$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.15;\n\nk1 @Const 'k1' { } = 1.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.5$ |mole |\r\n|Initial amount of S4 |$ 1$ |mole |\r\n|Value of parameter k1 |$0.$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.00025$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := 1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.00025;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventNoDelay \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is\r\ninconsistent with the value calculated by the assignmentRule. The\r\ncalculated value should be used.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 2.25$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS3 [event1]= (1e-5);\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventNoDelay \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value of species S4 is not explicitly\r\ndeclared and must be calculated by the assignmentRule. \r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS3 [event1]= (1e-5);\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is\r\nconsistent with the value calculated by the assignmentRule.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 > 0.000015$ | $-$ | $S3 = 0.00001$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 1.5 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS3 [event1]= (1e-5);\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 > (1.5e-5), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule with a \r\n functionDefinition to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $multiply(k1, S1)$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nNote that in this case the initial value of the species S3 is not explicitly\r\ndeclared and must be calculated by the AssignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0.5$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := multiply(k1, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 1.5;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule with a functionDefinition to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $multiply(p1, S2)$ |]\r\n\r\nThe model contains one FunctionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nNote that in this case the initial value of the species S4 is not explicitly\r\ndeclared and must be calculated by the AssignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-1$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.75$ |dimensionless |\r\n|Volume of compartment C |$ 0.86$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.86;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.015 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := multiply(p1, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 0.025;\np1 @Const 'p1' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with five species in one\r\ncompartment using an assignmentRules with functionDefinitions to vary two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are five\r\nspecies called S1, S2, S3, S4 and S5 and three parameters called k1, k2 and\r\np1. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S2 | $k2 * S5 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $func1(S3, p1)$ |\r\n | Assignment | S5 | $multiply(S4, p1)$ |]\r\n\r\nThe model contains two functionDefinitions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |\r\n | func1 | x, y | $x/(1 + y)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Initial amount of S4 |$ 0$ |mole |\r\n|Initial amount of S5 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 0.1$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.15$ |second^-1^ |\r\n|Value of parameter p1 |$ 2.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 2.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\nfunc1 #defineFunction { arguments: [x, y], math: x * pow(y + 1, (-1)), };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 := func1(S3, p1);\nS5 @Species 'S5' { units: mole/litre, compartment: C, } .= 0 / C;\nS5 := multiply(S4, p1);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S2, modifiers: [S5], reversible: false, };\nreaction2 := C * k2 * S5;\n\nk1 @Const 'k1' { } = 0.1;\nk2 @Const 'k2' { } = 0.15;\np1 @Const 'p1' { } = 2.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is\r\ninconsistent with the value calculated by the assignmentRule. The\r\ncalculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 2.25$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value of species S4 is not explicitly\r\ndeclared and must be calculated by the assignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 0.76$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.76;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is inconsistent\r\nwith the value calculated by the assignmentRule. The calculated value should be used. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 5$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1.4$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.4;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is undeclared and so must be calculated\r\nby the initialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is inconsisent with the value declared by the model definition. \r\nThe value calculated by the initialAssignment should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$10$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 0.47$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.47;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is consisent with the value declared by the model definition. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0.66$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 6.6$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 6.6;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value for species S3 must be calculated by the\r\nassignmentRule. Note that since this assignmentRule must always remain\r\ntrue, it should be considered during simulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value declared for species S3 is consistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0.375$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 0.79$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.79;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C;\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Amount, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value declared for species S3 is inconsistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 3.75$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 7.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75 / C;\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule with a \r\n functionDefinition to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $multiply(k1, S1)$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nNote that in this case the initial value of the species S3 is not explicitly\r\ndeclared and must be calculated by the AssignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0.5$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1.5$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := multiply(k1, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 1.5;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is\r\ninconsistent with the value calculated by the assignmentRule. The\r\ncalculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 1.5 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 1 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 2.25$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is undeclared and so must be calculated\r\nby the initialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$undeclared$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0.15$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value for species S3 must be calculated by the\r\nassignmentRule. Note that since this assignmentRule must always remain\r\ntrue, it should be considered during simulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ undeclared$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule with a functionDefinition to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. Species S1 \r\nis labeled as an SBML boundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $multiply(k1, S1)$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nNote that in this case the initial value of the species S3 is not explicitly\r\ndeclared and must be calculated by the AssignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0.5$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := multiply(k1, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 1.5;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule with a functionDefinition to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. Species S3 \r\nis labeled as an SBML boundary species. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $multiply(k1, S1)$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nNote that in this case the initial value of the species S3 is not explicitly\r\ndeclared and must be calculated by the AssignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0.5$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, };\nS3 := multiply(k1, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 1.5;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. \r\nSpecies S1 is labeled as an SBML boundary species.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is\r\ninconsistent with the value calculated by the assignmentRule. The\r\ncalculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 2.25$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 2.25 / C;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using both an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. \r\nSpecies S4 is labeled as an SBML boundary species.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is\r\ninconsistent with the value calculated by the assignmentRule. The\r\ncalculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ 2.25$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 2.25 / C;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. Species S1 \r\nis labeled as an SBML boundary species. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is undeclared and so must be calculated\r\nby the initialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. Species S2 \r\nis labeled as an SBML boundary species. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is undeclared and so must be calculated\r\nby the initialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. \r\nSpecies S1 is labeled as an SBML boundary species. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value for species S3 must be calculated by the\r\nassignmentRule. Note that since this assignmentRule must always remain\r\ntrue, it should be considered during simulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. \r\nSpecies S3 is labeled as an SBML boundary species. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value for species S3 must be calculated by the\r\nassignmentRule. Note that since this assignmentRule must always remain\r\ntrue, it should be considered during simulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule with a functionDefinition to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and one parameter called k.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k * S3 * C$ |]\r\n\r\nReaction S1 + S2 -> S3 defines one local parameter k which has a\r\nscope local to the defining reaction. Reaction S3 -> S1 + S2 defines another\r\n(different) local parameter k.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $multiply(k, S2)$ |]\r\n\r\nThe model contains one FunctionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nNote that in this case the initial value of the species S4 is not explicitly\r\ndeclared and must be calculated by the AssignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k |$ 0.75$ |dimensionless |\r\n|Value of local parameter k (R1) |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of local parameter k (R2) |$0.25 \\x 10^-2$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := multiply(k, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k__reaction1_local * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k__reaction2_local * S3;\n\nk__reaction1_local @Const { } = 7500;\nk__reaction2_local @Const { } = 0.0025;\nk @Const 'k' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S and three parameters called k1, k2 and k.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k * S1 * C$ |\r\n| S3 -> S1 | $k * S3 * C$ |]\r\n\r\nReaction S1 -> S3 defines one local parameter k which has a\r\nscope local to the defining reaction. Reaction S3 -> S1 defines another\r\n(different) local parameter k.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value of species S4 is not explicitly\r\ndeclared and must be calculated by the assignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k |$ 1.5$ |dimensionless |\r\n|Value of local parameter k (R1) |$ 0.015$ |second^-1^ |\r\n|Value of local parameter k (R2) |$ 0.5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := k * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k__reaction1_local * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k__reaction2_local * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk__reaction1_local @Const { } = 0.015;\nk__reaction2_local @Const { } = 0.5;\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk @Const 'k' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k * S1$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k which has a\r\nscope local to the defining reaction and is different from the global parameter k\r\nused in the initialAssignment.\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is inconsisent with the value declared by the model definition. \r\nThe value calculated by the initialAssignment should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$10$ |mole |\r\n|Initial amount of S2 |$ 0.15$ |mole |\r\n|Value of parameter k |$ undeclared$ |second^-1^ |\r\n|Value of local parameter k |$ 0.75$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k__reaction1_local * S1;\n\nk @Record 'k' { };\nk := 0.75;\n\nk__reaction1_local @Const { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and one parameter called k. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k * S1$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k which has a\r\nscope local to the defining reaction and is different from the global parameter k\r\nused in the assignmentRule.\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k * S2$ |]\r\n\r\nIn this case the initial value declared for species S3 is consistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0.375$ |mole |\r\n|Value of parameter k |$ 0.75$ |dimensionless |\r\n|Value of local parameter k |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375 / C;\nS3 := k * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k__reaction1_local * S1;\n\nk__reaction1_local @Const { } = 5;\nk @Const 'k' { } = 0.75;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 2.0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 1.5$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 4$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment C |$ 0.5$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and one parameter called k1. The model contains\r\none reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $0.15$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment C |$ 1.75$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.75;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.15;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-4$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.5 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.5 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 1 \\x 10^-4$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-2$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.93;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := 1e-4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 0.0025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Rate rule using a functionDefinition used to determine value of parameter\r\n which is used in a reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2; two constant parameters called k2 and k3 and one varying\r\nparameter called k1. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one rule that determines the value of parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $add(k2, k3)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.2$ |second^-1^ |\r\n|Value of parameter k3 |$ 0.3$ |lsecond^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.15 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := add(k2, k3);\n\nk1 @Record 'k1' { } .= 1;\n\nk2 @Const 'k2' { } = 0.2;\nk3 @Const 'k3' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Rate rule using a functionDefinition used to determine value of parameter\r\n which is used in a reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4; three constant parameters called k2, k3 and\r\np1 and one varying parameter called k1. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one rule that determines the value of parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $add(k2, k3) * p1$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k3 |$ 0.7 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 1$ |second^-1^ |\r\n|Volume of compartment C |$ 0.15$ |litre |]\r\nThe species values are given as amounts of substance to make it easier to\r\n\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.15;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-6 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-6 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-6 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-7 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := p1 * add(k2, k3);\n\nk1 @Record 'k1' { } .= 1e+6;\n\nk2 @Const 'k2' { } = 300000;\nk3 @Const 'k3' { } = 700000;\np1 @Const 'p1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Rate rule using a functionDefinition used to determine value of parameter\r\n which is used in a reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3; four constant parameters called k2, k3, p1 and\r\np2 and one varying parameter called k1. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule that determines the value of parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $p1* add(p2 * k2, k3)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Value of parameter k3 |$ -0.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 1$ |second^-1^ |\r\n|Value of parameter p2 |$ 1$ |litre mole^-1^ |\r\n|Volume of compartment C |$ 1.25$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.25;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := p1 * add(k2 * p2, k3);\n\nk1 @Record 'k1' { } .= 1.7;\n\nk2 @Const 'k2' { } = 0.3;\nk3 @Const 'k3' { } = -0.1;\np1 @Const 'p1' { } = 1;\np2 @Const 'p2' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value of species S4 is not explicitly\r\ndeclared and must be calculated by the assignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 1.5 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 1 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ undeclared$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 0.76$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.76;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value declared for species S4 is inconsistent\r\nwith the value calculated by the assignmentRule. The calculated value should be used. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 1.5 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 1 \\x 10^-5$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1.4$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.4;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5;\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, ConstantSpecies\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and one parameter called k1. Species S4 is \r\nlabeled as constant and therefore cannot be changed by rules or reactions. \r\nThe model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $0.15$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Initial amount of S4 |$ 1.0$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.15;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| 2S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^3$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-2$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.0015 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.001 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: 2*S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1 / 1000);\n\nk1 @Const 'k1' { } = 750;\nk2 @Const 'k2' { } = 0.0025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule that applies a functionDefinition\r\n with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + 2S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $multiply(k2, 4 \\x 10^-6$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-7$ |mole |\r\n|Value of parameter k1 |$ 0.75 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-6 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-6 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-6 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-7 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := multiply(k2, (1 / 2.5e+5));\n\nk1 @Const 'k1' { } = 750000;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Amount, NonUnityStoichiometry, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| 2S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value of species S4 is not explicitly\r\ndeclared and must be calculated by the assignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: 2*S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2 * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment \r\ntestTags: Amount, NonUnityStoichiometry, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k2 * S4$ |\r\n | Rate | S4 | $-k2 * S4$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 / 0.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this case the \r\nvalue of species S1 is not declared by the model definition. The calculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ undeclared$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter p |$ 0.75$ |mole litre^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k2 * S4;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-1) * k2 * S4;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.5;\np1 @Const 'p1' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k1 which has a\r\nscope local to the defining reaction and is different from the global parameter k1\r\nused in the RateRule.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Value of local parameter k1 |$0.9$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1__reaction1_local * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1__reaction1_local @Const { } = 0.9;\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule that applies a functionDefinition\r\n with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and one parameter called k. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k * S3 * C$ |]\r\n\r\nEach reaction defines one local parameter k which has a\r\nscope local to the defining reaction and is different from the global parameter k\r\nused in the RateRule.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $multiply(k2, 4 \\x 10^-6$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-7$ |mole |\r\n|Value of parameter k |$ 0.25$ |second^-1^ |\r\n|Value of local parameter k (R1) |$ 0.75 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of local parameter k (R2) |$ 0.3$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-6 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-6 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-6 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-7 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k__reaction1_local * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k__reaction2_local * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := multiply(k, (1 / 2.5e+5));\n\nk__reaction1_local @Const { } = 750000;\nk__reaction2_local @Const { } = 0.3;\nk @Const 'k' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule and a rateRule to vary species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, AssignmentRule \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S and three parameters called k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S1 | $k2 * S3 * C$ |]\r\n\r\nReaction S1 -> S3 defines one local parameter k1 and reaction S3 -> S2 defines one\r\nlocal parameter k2. These parameters have a scope local to the defining reaction \r\nand are different from the global parameters k1 and k2 used in the rules.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S1$ |\r\n | Rate | S2 | $k2 * S3-k1 * S1$ |]\r\n\r\nNote that in this case the initial value of species S4 is not explicitly\r\ndeclared and must be calculated by the assignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.015$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Value of local parameter k1 |$ 0.01$ |second^-1^ |\r\n|Value of local parameter k2 |$ 0.4$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := k3 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1__reaction1_local * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1, reversible: false, };\nreaction2 := C * k2__reaction2_local * S3;\nS2_proc @Process { actors: = S2, aux: {{\"metaid\":\"rule2\"}}, };\nS2_proc := k2 * S3 + (-1) * k1 * S1;\n\nk1__reaction1_local @Const { } = 0.01;\nk2__reaction2_local @Const { } = 0.4;\nk1 @Const 'k1' { } = 0.015;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, InitialAssignment \r\ntestTags: Amount, LocalParameters, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k1 which has a\r\nscope local to the defining reaction and is different from the global parameter k1\r\nused in the InitialAssignment.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k2 * S4$ |\r\n | Rate | S4 | $-k2 * S4$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 / 0.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this case the \r\nvalue of species S1 is not declared by the model definition. The calculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ undeclared$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |mole litre^-1^ |\r\n|Value of parameter k2 |$ 0.5$ |second^-1^ |\r\n|Value of local parameter k1 |$ 0.8$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1__reaction1_local * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k2 * S4;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-1) * k2 * S4;\n\nk1__reaction1_local @Const { } = 0.8;\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule, EventNoDelay \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> (4 * p1)S2 | $k1 * S1 * C$ |]\r\n\r\nReaction S1 -> S2 defines one local parameter k1 which has a\r\nscope local to the defining reaction and is different from the global parameter k1\r\nused in the rateRule.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Value of local parameter k1 |$ 0.8$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1__reaction1_local * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1__reaction1_local @Const { } = 0.8;\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\ncompartment using an assignmentRule with a functionDefinition to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $multiply(p1, S2)$ |]\r\n\r\nThe model contains one FunctionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nNote that in this case the initial value of the species S4 is not explicitly\r\ndeclared and must be calculated by the AssignmentRule. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.5 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ undeclared$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-1$ |second^-1^ |\r\n|Value of parameter p1 |$ 0.75$ |dimensionless |\r\n|Volume of compartment C |$ 0.86$ |litre |]\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.86;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.015;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := multiply(p1, S2);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 0.025;\np1 @Const 'p1' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with five species in one\r\ncompartment using an assignmentRules with functionDefinitions to vary two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, AssignmentRule \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are five\r\nspecies called S1, S2, S3, S4 and S5 and three parameters called k1, k2 and\r\np1. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S3 | $k1 * S1 * C$ |\r\n| S3 -> S2 | $k2 * S5 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $func1(S3, p1)$ |\r\n | Assignment | S5 | $multiply(S4, p1)$ |]\r\n\r\nThe model contains two functionDefinitions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |\r\n | func1 | x, y | $x / (1 + y)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S5 |$ 0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.1$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.15$ |second^-1^ |\r\n|Value of parameter p1 |$ 2.5$ |dimensionless |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\nfunc1 #defineFunction { arguments: [x, y], math: x * pow(y + 1, (-1)), };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0;\nS4 := func1(S3, p1);\nS5 @Species 'S5' { units: mole/litre, compartment: C, } .= 0;\nS5 := multiply(S4, p1);\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S3, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S3 = S2, modifiers: [S5], reversible: false, };\nreaction2 := C * k2 * S5;\n\nk1 @Const 'k1' { } = 0.1;\nk2 @Const 'k2' { } = 0.15;\np1 @Const 'p1' { } = 2.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Rate rule using a functionDefinition used to determine value of parameter\r\n which is used in a reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Concentration, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2; two constant parameters called k2 and k3 and one varying\r\nparameter called k1. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one rule that determines the value of parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $add(k2, k3)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.5 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.2$ |second^-1^ |\r\n|Value of parameter k3 |$ 0.3$ |lsecond^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := add(k2, k3);\n\nk1 @Record 'k1' { } .= 1;\n\nk2 @Const 'k2' { } = 0.2;\nk3 @Const 'k3' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Rate rule using a functionDefinition used to determine value of parameter\r\n which is used in a reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Concentration, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4; three constant parameters called k2, k3 and\r\np1 and one varying parameter called k1. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one rule that determines the value of parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $add(k2, k3) * p1$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.0 \\x 10^-6$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 1.5 \\x 10^-6$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 2.0 \\x 10^-6$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$ 0.5 \\x 10^-6$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k3 |$ 0.7 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 1$ |second^-1^ |\r\n|Volume of compartment C |$ 0.15$ |litre |]\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.15;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-6;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-6;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-6;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5e-7;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := p1 * add(k2, k3);\n\nk1 @Record 'k1' { } .= 1e+6;\n\nk2 @Const 'k2' { } = 300000;\nk3 @Const 'k3' { } = 700000;\np1 @Const 'p1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Rate rule using a functionDefinition used to determine value of parameter\r\n which is used in a reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, RateRule \r\ntestTags: Concentration, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3; four constant parameters called k2, k3, p1 and\r\np2 and one varying parameter called k1. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule that determines the value of parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $p1* add(p2 * k2, k3)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 2.0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 1.0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 1.7$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Value of parameter k3 |$ -0.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter p1 |$ 1$ |second^-1^ |\r\n|Value of parameter p2 |$ 1$ |litre mole^-1^ |\r\n|Volume of compartment C |$ 1.25$ |litre |]\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.25;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := p1 * add(k2 * p2, k3);\n\nk1 @Record 'k1' { } .= 1.7;\n\nk2 @Const 'k2' { } = 0.3;\nk3 @Const 'k3' { } = -0.1;\np1 @Const 'p1' { } = 1;\np2 @Const 'p2' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$0.1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |\r\n | Event2 | $S3 > 1.4$ | $-$ | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$1.43$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.43;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS1 [event2]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to both species S1 and S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.65$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S1 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Volume of compartment C |$0.9$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.9;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS1 [event1]= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.65, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.24$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.24;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1;\nS1 [event1]= 0.2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.12;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.2;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 2.5;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and two events that assign value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains two events that assign values to species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-4$ |]\r\n | Event2 | $S3 > 2.25 \\x 10^-4$ | $-$ | $S4 -> 1 \\x 10^-4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4;\nS1 [event1]= (1 / 5000);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.2e-4;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 2e-4;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4;\nS4 [event2]= (1 / 10000);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 2500;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\nevent2 @DSwitcher 'event2' { trigger: S3 > (9 / 40000), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\n and an event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and two parameters called k1 and k2. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one event that assigns a value to both species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S4 > S2$ | $-$ | $S1 -> 2 \\x 10^-2$ |\r\n | | | | $S4 -> 0.5 \\x 10^-2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$2.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.25$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.25;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01;\nS1 [event1]= (1 / 50);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.01;\nS4 [event1]= (1 / 200);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 25;\n\nevent1 @DSwitcher 'event1' { trigger: S4 > S2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value declared for species S3 is consistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.25$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 0.375$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 0.79$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.79;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.375;\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.25, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, EventNoDelay \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case the initial value declared for species S3 is inconsistent with\r\nthe value calculated by the assignmentRule. Note that since this\r\nassignmentRule must always remain true, it should be considered during\r\nsimulation.\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.1$ | $-$ | $S2 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$ 1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$ 3.75$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ 0.75$ |dimensionless |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 2.5$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 7.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5;\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 3.75;\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species using a function.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, RateRule\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species\r\ncalled S1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule that determines the rate at which species S4 \r\nis changing:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $k2 * add(S1, S3)$ |]\r\n \r\nThe model contains one event that assigns a value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |]\r\n \r\nBoth the rateRule and the eventAssignment uses the functionDefinition defined as:\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Initial amount of S4 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$0.8$ |mole litre^-1^ |\r\n|Value of parameter k4 |$0.2$ |mole litre^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 [event1]= add(k3, k4);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := k2 * add(S1, S3);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.8;\nk4 @Const 'k4' { } = 0.2;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and two events that assigns value to a species using a function.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, RateRule\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species\r\ncalled S1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule that determines the rate at which species S4 \r\nis changing:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $k2 * add(S1, S2)$ |]\r\n \r\nThe model contains two events that assign values to species S2 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = add(k3, k4)$ |\r\n | Event2 | $S3 > 1.2$ | $-$ | $S4 = 1 * divide(k3, k4)$ |]\r\n\r\nThe rateRule and both eventAssignments use functionDefinitions defined as:\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |\r\n | divide | x, y | $x / y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Initial amount of S4 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$0.5$ |mole litre^-1^ |\r\n|Value of parameter k4 |$0.5$ |mole litre^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\ndivide #defineFunction { arguments: [x, y], math: x * pow(y, (-1)), };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= add(k3, k4);\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 [event2]= divide(k3, k4);\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := k2 * add(S1, S2);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.5;\nk4 @Const 'k4' { } = 0.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species using a function.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, InitialAssignment\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and five parameters called k1, k2, k3, k4 and p1. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |]\r\n \r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $add(p1, p1)$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nBoth the eventAssignment and the initialAssignment use the functionDefinition defined as:\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$0.8$ |mole litre^-1^ |\r\n|Value of parameter k4 |$0.2$ |mole litre^-1^ |\r\n|Value of parameter p1 |$0.5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= add(p1, p1);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= add(k3, k4);\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.8;\nk4 @Const 'k4' { } = 0.2;\np1 @Const 'p1' { } = 0.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species using a function.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, InitialAssignment\r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and five parameters called k1, k2, k3, k4 and p1. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |]\r\n \r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $add(p1, p1)$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nBoth the eventAssignment and the initialAssignment use the functionDefinition defined as:\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$5.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$0.8$ |mole litre^-1^ |\r\n|Value of parameter k4 |$0.2$ |mole litre^-1^ |\r\n|Value of parameter p1 |$0.5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= add(p1, p1);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= add(k3, k4);\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.8;\nk4 @Const 'k4' { } = 0.2;\np1 @Const 'p1' { } = 0.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event that assigns value to a species using a function.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, FunctionDefinition, InitialAssignment\r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and five parameters called k1, k2, k3, k4 and p1. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = add(k3, k4)$ |]\r\n \r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $add(p1, p1)$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value has not been declared for species S1 \r\nand must be calculated using the InitialAssignment.\r\n\r\nBoth the eventAssignment and the initialAssignment use the functionDefinition defined as:\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | add | x, y | $x + y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$0.8$ |mole litre^-1^ |\r\n|Value of parameter k4 |$0.2$ |mole litre^-1^ |\r\n|Value of parameter p1 |$0.5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nadd #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= add(p1, p1);\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= add(k3, k4);\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 0.8;\nk4 @Const 'k4' { } = 0.2;\np1 @Const 'p1' { } = 0.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / 9$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$5.4$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= k2 * pow(9, (-1));\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / 10$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$5$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= k2 * pow(10, (-1));\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / 9$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$undeclared$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= k2 * pow(9, (-1));\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.25$ |litre |\r\n|Volume of compartment C |$0.5$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.25$ |litre |\r\n|Volume of compartment C |$3.5$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.25$ |litre |\r\n|Volume of compartment C |$undeclared$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= 2 * p1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is inconsisent with the value declared by the model definition. \r\nThe value calculated by the initialAssignment should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$10$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0.15$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 0.47$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.47;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in one\r\ncompartment using an assignmentRule to assign value to a parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule, InitialAssignment \r\ntestTags: Concentration, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to parameter k1:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | k1 | $0.75$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $k1 / 7.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. The initial\r\nvalue of species S1 is consisent with the value declared by the model definition. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$0.1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$ 0.15$ |mole litre^-1^ |\r\n|Value of parameter k1 |$ undeclared$ |second^-1^ |\r\n|Volume of compartment C |$ 6.6$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 6.6;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.133333333333333 * k1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.15;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { };\nk1 := 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event and one initial assignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and three parameters called k1, k2 and p1. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S2 | $p1 * S1$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S2 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$undeclared$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |dimensionless |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= S1 * pow(p1, (-1));\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event and one initial assignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and three parameters called k1, k2 and p1. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S2 | $p1 * S1$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S2 is inconsistent\r\nwith the value be calculated using the InitialAssignment; the calculated value\r\nshould be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$4.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |dimensionless |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= S1 * pow(p1, (-1));\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\n and one event and one initial assignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay, InitialAssignment \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and three parameters called k1, k2 and p1. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S2 | $p1 * S1$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S2 is consistent\r\nwith the value calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |dimensionless |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= S1 * pow(p1, (-1));\nS2 [event1]= 1;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.5;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $k2 / 100$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the parameter k1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$undeclared$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { } .= k2 * pow(100, (-1));\n\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $k2 / 100$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for parameter k1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$100$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Record 'k1' { } .= k2 * pow(100, (-1));\n\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2*(50^-1)$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$5.4$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= k2 * pow(50, (-1));\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2 / (50^-1)$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for compartment C is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= k2 * pow(50, (-1));\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one\r\ncompartment using initialAssignment to set the initial value of the compartment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called k1 and k2. The model contains one \r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k1 * S1$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | C | $k2*(50^-1)$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment C has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$1.5$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.5$ |second^-1^ |\r\n|Value of parameter k2 |$50$ |litre |\r\n|Volume of compartment C |$undeclared$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, } .= k2 * pow(50, (-1));\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 50;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-2$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-3$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.02;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.00125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$0.25 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-4$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.0000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\n The model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width 30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$undeclared$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-3$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter p1 |$1.25 \\x 10^-4$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.002;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\np1 @Const 'p1' { } = 0.000125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in a compartment using \r\ninitialAssignment to set the initial value of one parameter.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Concentration, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called k1, k2 and p1. The model contains \r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k2 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the parameter k2 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$undeclared$ |second^-1^ |\r\n|Value of parameter p1 |$0.125$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk2 @Record 'k2' { } .= 2 * p1;\n\nk1 @Const 'k1' { } = 0.75;\np1 @Const 'p1' { } = 0.125;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Zeroth order mass action kinetics.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and one parameter called k. The model contains one reaction that has\r\na kinetic law that defines zero order mass action kinetics (as referenced by \r\nSBO:0000047):\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k |$0.075$ |mole litre^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k;\n\nk @Const 'k' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: First order mass action kinetics.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and one parameter called k. The model contains one reaction that has\r\na kinetic law that defines first order mass action kinetics (as referenced by \r\nSBO:0000049):\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k |$2.5$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k * S1;\n\nk @Const 'k' { } = 2.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: First order mass action kinetics with monoexponential decay.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and one parameter called k. The model contains one reaction that has\r\na kinetic law that defines first order mass action kinetics with monoexponential\r\ndecay (as referenced by SBO:0000333):\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $(S1 * C) / k$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k |$1.5$ |second|\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * S1 * pow(k, (-1));\n\nk @Const 'k' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Second order mass action kinetics with one reactant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and one parameter called k. The model contains one reaction that has\r\na kinetic law that defines second order mass action kinetics with one reactant\r\n(as referenced by SBO:0000052):\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * S1 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k |$1.5$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k * pow(S1, 2);\n\nk @Const 'k' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Second order mass action kinetics with two reactants.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and one parameter called k. The model contains one reaction that has\r\na kinetic law that defines second order mass action kinetics with two reactants\r\n(as referenced by SBO:0000054):\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S2 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter k |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k * S1 * S2;\n\nk @Const 'k' { } = 1.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Third order mass action kinetics with one reactant.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and one parameter called k. The model contains one reaction that has\r\na kinetic law that defines third order mass action kinetics with one reactant\r\n(as referenced by SBO:0000057):\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k * S1 * S1 * S1 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k |$0.65$ |litre^2^ mole^-2^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k * pow(S1, 3);\n\nk @Const 'k' { } = 0.65;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Third order mass action kinetics with two reactants.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and one parameter called k. The model contains one reaction that has\r\na kinetic law that defines third order mass action kinetics with two reactants\r\n(as referenced by SBO:0000054):\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k * S1 * S1 * S2 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k |$1.1$ |litre^2^ mole^-2^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k * pow(S1, 2) * S2;\n\nk @Const 'k' { } = 1.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Third order mass action kinetics with three reactants.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and one parameter called k. The model contains one reaction that has\r\na kinetic law that defines third order mass action kinetics with three reactants\r\n(as referenced by SBO:0000061):\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 + S3 -> S4 | $k * S1 * S2 * S3 * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0.75$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k |$0.8$ |litre^2^ mole^-2^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.75 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 + S3 = S4, reversible: false, };\nreaction1 := C * k * S1 * S2 * S3;\n\nk @Const 'k' { } = 0.8;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2);\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, };\nreaction1 := C * (kf * S1 * S2 + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$0.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2);\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$2.3$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, };\nreaction1 := C * (kf * S1 * S2 + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.95$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.95;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0$ |mole litre^-1^ |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$0.5$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2);\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0.5$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$2.3$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, };\nreaction1 := C * (kf * S1 * S2 + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0.5$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.95$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.95;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. Species S1 is labeled as an \r\nSBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2);\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as \r\nan SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, };\nreaction1 := C * (kf * S1 * S2 + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as \r\nan SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. Species S2 is labeled as an \r\nSBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2);\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. Species S3 is labeled as \r\nan SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0.4$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0.4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, };\nreaction1 := C * (kf * S1 * S2 + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. Species S2 is labeled as \r\nan SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> 2S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2);\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + 2S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + 2*S2 = S3, };\nreaction1 := C * (kf * S1 * S2 + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + 2S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + 2*S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reversible reactions with global and local parameters.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |\r\n| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |]\r\n\r\nReaction S1 <-> S2 defines two local parameters kf and kr which have a\r\nscope local to the defining reaction and are different from the global parameters kf\r\nand kr used in the Reaction S3 <-> S4.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Value of local parameter kf |$0.8$ |second^-1^ |\r\n|Value of local parameter kr |$0.06$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, };\nreaction2 := C * (kf * S3 + (-1) * kr * S4);\n\nkf__reaction1_local @Const { } = 0.8;\nkr__reaction1_local @Const { } = 0.06;\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reversible reactions with local parameters.\r\ncomponentTags: Compartment, Species, Reaction \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |\r\n| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |]\r\n\r\nBoth reactions define two local parameters kf and kr which have a\r\nscope local to the defining reaction.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of local parameter kf (R1) |$0.8$ |second^-1^ |\r\n|Value of local parameter kr (R1) |$0.06$ |second^-1^ |\r\n|Value of local parameter kf (R1) |$0.9$ |second^-1^ |\r\n|Value of local parameter kr (R2) |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, };\nreaction2 := C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4);\n\nkf__reaction1_local @Const { } = 0.8;\nkr__reaction1_local @Const { } = 0.06;\nkf__reaction2_local @Const { } = 0.9;\nkr__reaction2_local @Const { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(multiply(kf, S1) - kr * S2) * C$ |]\r\n\r\nThe reaction applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.59$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (multiply(kf, S1) + (-1) * kr * S2);\n\nkf @Const 'kf' { } = 0.59;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(multiply(multiply(kf, S1), S2) - kr * S3) * C$ |]\r\n\r\nThe reaction applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.11$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, };\nreaction1 := C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.11;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(minus(multiply(kf, S1), kr * S2 * S3)) * C$ |]\r\n\r\nThe reaction applies two functionDefinitions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |\r\n | minus | x, y | $x - y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\nminus #defineFunction { arguments: [x, y], math: x + (-1) * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * minus(multiply(kf, S1), kr * S2 * S3);\n\nkf @Const 'kf' { } = 1.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction with an initial assignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, };\nreaction1 := C * (kf * S1 * S2 + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction with an initial assignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment. The\r\ncalculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, };\nreaction1 := C * (kf * S1 * S2 + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction with an initial assignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, };\nreaction1 := C * (kf * S1 * S2 + (-1) * kr * S3);\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which assigns value to parameter kf:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | kf | $2.5$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$undeclared$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Record 'kf' { };\nkf := 2.5;\n\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $0.5 * S1$ |]\r\n\r\nIn this case there is no initial value declared for species S4. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$undeclared$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := 0.5 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $0.5 * S1$ |]\r\n\r\nIn this case the initial value declared for species S4 is inconsistent\r\nwith the value calculated using the assignmentRule. The calculated value\r\nshould be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$5$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C;\nS4 := 0.5 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which specifies the rate at which species \r\nS4 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $-0.5 * (kf * S1 - kr * S2 * S3)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0.5$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (-0.5) * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which specifies the rate at which species \r\nS4 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $-0.5 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0.5$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (-0.5) * S1;\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which specifies the rate at which species \r\nS4 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $0.15$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0.5$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2 + S3, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2 * S3);\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := 0.15;\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reversible reactions with two species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe model contains one event that assigns values to species S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |]\r\n \r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2);\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reversible reactions with four species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species\r\ncalled S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |\r\n| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S2 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S4 = S2$ |]\r\n \r\nNote that the event assignments should happen simultaneously, not\r\nsequentially; i.e., the value of S2 assigned to S4 is the value at the\r\npoint at which the event was triggered.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Initial amount of S4 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |second^-1^ |\r\n|Value of parameter k2 |$0.15$ |second^-1^ |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 [event1]= S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, };\nreaction2 := C * (k1 * S3 + (-1) * k2 * S4);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.15;\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reversible reactions with four species in one compartment\r\n and two events that assigns value to species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species\r\ncalled S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |\r\n| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |]\r\n\r\nThe model contains two event that assigns values to species S2 and S4 respectively:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ |\r\n | Event2 | $S3 < 0.75$ | $-$ | $S4 = 0.5$ |]\r\n \r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Initial amount of S4 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |second^-1^ |\r\n|Value of parameter k2 |$0.15$ |second^-1^ |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 [event2]= 0.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, };\nreaction1 := C * (kf * S1 + (-1) * kr * S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S4, };\nreaction2 := C * (k1 * S3 + (-1) * k2 * S4);\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.15;\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\nevent2 @DSwitcher 'event2' { trigger: S3 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k1 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * time$ |\r\n| S2 -> S3 | $k2 * S2 * C * time$ |\r\n| S3 -> S4 | $k3 * S3 * C * time$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$0.7$ |second^-2^ |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of parameter k3 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three reactions with four species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C * s$ |\r\n| S3 -> S1 + S4 | $k3 * S3 * C * s$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$2.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ |\r\n|Value of parameter k2 |$0.9$ |second^-2^ |\r\n|Value of parameter k3 |$0.7$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2 * t;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 1;\nk2 @Const 'k2' { } = 0.9;\nk3 @Const 'k3' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment\r\nusing csymbol time passed to a functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, CSymbolTime\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $multiply(k1, S1, t) * C$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe reaction uses one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$0.1 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.01 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * multiply(k1, S1, t);\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time passed to a functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, CSymbolTime\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * multiply(S1, C, time)$ |\r\n| S2 -> S3 | $k2 * multiply(S2, C, time)$ |\r\n| S3 -> S4 | $k3 * multiply(S3, C, time)$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y, z | $x * y * z$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$0.7$ |second^-2^ |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of parameter k3 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y, z], math: x * y * z, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * multiply(S1, C, t);\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := k2 * multiply(S2, C, t);\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := k3 * multiply(S3, C, t);\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three reactions with four species in one compartment\r\nusing csymbol time passed to a functionDefinition.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition, CSymbolTime\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ |\r\n| S3 -> S1 + S2 | $multiply(multiply(k2, S3), multiply(C, s))$ |\r\n| S3 -> S1 + S4 | $k3 * S3 * C * s$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$2.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ |\r\n|Value of parameter k2 |$0.9$ |second^-2^ |\r\n|Value of parameter k3 |$0.7$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2 * t;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := multiply(multiply(k2, S3), multiply(C, t));\nreaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 1;\nk2 @Const 'k2' { } = 0.9;\nk3 @Const 'k3' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime\r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k1 |$1$ |second^-2^ |\r\n|Volume of compartment C |$0.57$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.57;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * time$ |\r\n| S2 -> S3 | $k2 * S2 * C * time$ |\r\n| S3 -> S4 | $k3 * S3 * C * time$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$0.7$ |second^-2^ |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of parameter k3 |$1$ |second^-2^ |\r\n|Volume of compartment C |$2.45$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.45;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three reactions with four species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C * s$ |\r\n| S3 -> S1 + S4 | $k3 * S3 * C * s$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$2.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ |\r\n|Value of parameter k2 |$0.9$ |second^-2^ |\r\n|Value of parameter k3 |$0.7$ |second^-2^ |\r\n|Volume of compartment C |$0.98$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.98;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2 * t;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 1;\nk2 @Const 'k2' { } = 0.9;\nk3 @Const 'k3' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.5 \\x 10^-3$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$1$ |second^-2^ |\r\n|Volume of compartment C |$0.9$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.9;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime\r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * time$ |\r\n| S2 -> S3 | $k2 * S2 * C * time$ |\r\n| S3 -> S4 | $k3 * S3 * C * time$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0 \\x 10^-1$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$0.7$ |second^-2^ |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of parameter k3 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1.78$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1.78;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three reactions with four species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime\r\ntestTags: Concentration, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C * s$ |\r\n| S3 -> S1 + S4 | $k3 * S3 * C * s$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$2.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$2.0$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Initial concentration of S4 |$0$ |mole litre^-1^ |\r\n|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ |\r\n|Value of parameter k2 |$0.9$ |second^-2^ |\r\n|Value of parameter k3 |$0.7$ |second^-2^ |\r\n|Volume of compartment C |$0.002$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.002;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2 * t;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 1;\nk2 @Const 'k2' { } = 0.9;\nk3 @Const 'k3' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. Species S1\r\nis labeled as an SBML boundary species. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k1 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.15 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. \r\nSpecies S1 is labeled as an SBML boundary species.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * time$ |\r\n| S2 -> S3 | $k2 * S2 * C * time$ |\r\n| S3 -> S4 | $k3 * S3 * C * time$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$0.7$ |second^-2^ |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of parameter k3 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 0.01 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three reactions with four species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. \r\nSpecies S1 is labeled as an SBML boundary species.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C * s$ |\r\n| S3 -> S1 + S4 | $k3 * S3 * C * s$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$2.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ |\r\n|Value of parameter k2 |$0.9$ |second^-2^ |\r\n|Value of parameter k3 |$0.7$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 2 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2 * t;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 1;\nk2 @Const 'k2' { } = 0.9;\nk3 @Const 'k3' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime\r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. Species S2\r\nis labeled as an SBML boundary species. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k1 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime\r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. \r\nSpecies S2 is labeled as an SBML boundary species.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * time$ |\r\n| S2 -> S3 | $k2 * S2 * C * time$ |\r\n| S3 -> S4 | $k3 * S3 * C * time$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$0.7$ |second^-2^ |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of parameter k3 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.001 / C;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three reactions with four species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. \r\nSpecies S3 is labeled as an SBML boundary species.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C * s$ |\r\n| S3 -> S1 + S4 | $k3 * S3 * C * s$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$2.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ |\r\n|Value of parameter k2 |$0.9$ |second^-2^ |\r\n|Value of parameter k3 |$0.7$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2 * t;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 1;\nk2 @Const 'k2' { } = 0.9;\nk3 @Const 'k3' { } = 0.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: BoundaryCondition, Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and three parameters called k1, k2 and k3. \r\nSpecies S3 is labeled as an SBML boundary species.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * time$ |\r\n| S2 -> S3 | $k2 * S2 * C * time$ |\r\n| S3 -> S4 | $k3 * S3 * C * time$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$0.7$ |second^-2^ |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of parameter k3 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment\r\nusing csymbol time within an initialAssignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and p1. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S2 | $p1 * S1 * time$ |]\r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nNote: SBML's InitialAssignment take effect at time t < 0 and continue to have effect \r\nup to and including time t = 0, overriding any initial values. In this model, the \r\ninitial value for the species S1 has not been explicitly declared and must be \r\ncalculated using the InitialAssignment at time = 0. \r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$undeclared$ |mole |\r\n|Value of parameter p1 |$-0.5$ |second^-1^ |\r\n|Value of parameter k1 |$1$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.0015 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= p1 * S1 * t;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\np1 @Const 'p1' { } = -0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment\r\nusing csymbol time within an initialAssignment.\r\ncomponentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and two parameters called k1 and p1. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S2 | $p1 * S1 * time$ |]\r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nNote: SBML's InitialAssignment take effect at time t < 0 and continue to have effect \r\nup to and including time t = 0, overriding any initial values. In this model, the \r\ninitial value for the species S1 is inconsistent with the value calculated using \r\nthe InitialAssignment at time = 0; the calculated value should be used. \r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-2$ |mole |\r\n|Value of parameter p1 |$-0.5$ |second^-1^ |\r\n|Value of parameter k1 |$1$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.015 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= p1 * S1 * t;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\np1 @Const 'p1' { } = -0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within an initialAssignment.\r\ncomponentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |\r\n| S2 -> S3 | $k2 * S2 * C$ |\r\n| S3 -> S4 | $k3 * S3 * C$ |] \r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $0.2 + k2* exp(t)$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nNote: SBML's InitialAssignment take effect at time t < 0 and continue to have effect \r\nup to and including time t = 0, overriding any initial values. In this model, the \r\ninitial value for the parameter k1 has not been explicitly declared and must be \r\ncalculated using the InitialAssignment at time = 0. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$undeclared$ |second^-2^ |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of parameter k3 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment 'C' { units: volume, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: substance/volume, compartment: C, } .= 1e-4 / C;\nS2 @Species 'S2' { units: substance/volume, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: substance/volume, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: substance/volume, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3;\n\nk1 @Record 'k1' { } .= k2 * exp(t) + 0.2;\nk2 @Record 'k2' { } .= 0.5;\nk3 @Record 'k3' { } .= 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule with csymbol time to vary one species.\r\ncomponentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2 * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nIn this case the initial value for species S3 must be calculated by the\r\nassignmentRule. Note that since this assignmentRule must always remain\r\ntrue, it should be considered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-15$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-15 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, };\nS3 := k1 * S2 * t;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\ncompartment using an assignmentRule with csymbol time to vary one species.\r\ncomponentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S and two parameters called k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $C * k2 * S1$ |]\r\n\r\nThe model contains one rule which assigns value to species S3:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2 * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nIn this case the initial value for species S3 is inconsistent with the\r\nvalue calculated by the assignmentRule; the calculated value should be\r\nused. Note that since this assignmentRule must always remain\r\ntrue, it should be considered during simulation.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-15$ |mole |\r\n|Initial amount of S3 |$ 1$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 2.5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 1.5e-15 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\nS3 := k1 * S2 * t;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2 * S1;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 2.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, ConstantSpecies, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nSpecies S1 is labeled as constant and a boundaryCondition and therefore \r\ncannot be changed. The model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * time$ |\r\n| S2 -> S3 | $k2 * S2 * C * time$ |\r\n| S3 -> S4 | $k3 * S3 * C * time$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$0.4$ |second^-2^ |\r\n|Value of parameter k2 |$0.3$ |second^-2^ |\r\n|Value of parameter k3 |$0.2$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 0.4;\nk2 @Const 'k2' { } = 0.3;\nk3 @Const 'k3' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\nand one event that assigns value to a species using csymbol time.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and three parameters called k1, k2 and k3. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one event that assigns a value to species S2:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = k3 * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$1$ |mole litre^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= k3 * t;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 1;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with three species in one compartment\r\nand two events that assigns value to a species using csymbol time.\r\ncomponentTags: Compartment, Species, Reaction, CSymbolTime, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and three parameters called k1, k2 and k3. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains two events that assign values to species S2 and S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = k3 * s$ |\r\n | Event2 | $S3 > 1.4$ | $-$ | $S1 = 0.25 * s$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Value of parameter k1 |$0.75$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25$ |second^-1^ |\r\n|Value of parameter k3 |$4$ |mole litre^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS1 [event2]= 0.25 * t;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= k3 * t;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\nk3 @Const 'k3' { } = 4;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\nevent2 @DSwitcher 'event2' { trigger: S3 > 1.4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in one compartment\r\nand an event that assigns value to two species using csymbol time.\r\ncomponentTags: Compartment, Species, Reaction, CSymbolTime, Parameter, EventNoDelay \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four species called\r\nS1, S2, S3 and S4 and four parameters called k1, k2, k3 and k4. The model contains\r\ntwo reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S1 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S2 > S3$ | $-$ | $S1 -> k3 * time$ |]\r\n | | | | $S4 -> k4 * S1 * time$ |]\r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$0.075 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^2$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k3 |$2 \\x 10^-2$ |mole litre^-1^ second^-1^ |\r\n|Value of parameter k4 |$2 \\x 10^-2$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS1 [event1]= k3 * t;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.012 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0.02 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS4 [event1]= k4 * S1 * t;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 25;\nk3 @Const 'k3' { } = 0.02;\nk4 @Const 'k4' { } = 0.02;\n\nevent1 @DSwitcher 'event1' { trigger: S2 > S3, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a compartment\r\nwhere rate rule uses csymbol time. \r\ncomponentTags: Compartment, Species, CSymbolTime, Reaction, Parameter, RateRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are three\r\nspecies called S1, S2 and S3 and one parameter called k1. The model contains\r\none reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $0.15 / exp(time)$ |]\r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Initial amount of S3 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 1.5 * pow(exp(t), (-1));\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a compartment\r\nwhere rate rule uses csymbol time. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime, RateRule\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |\r\n| S3 -> S1 + S2 | $k2 * S3 * C$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-5 * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-4$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^4$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-2$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2e-4 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5e-4 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1e-4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := t * pow(1e+5, (-1));\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 0.0025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a compartment\r\nwhere rate rule uses csymbol time. \r\ncomponentTags: Compartment, Species, Reaction, CSymbolTime, Parameter, RateRule \r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and two parameters called k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * 0.5 * abs(1 - s)$ |\r\n | Rate | S4 | $-k2 * 0.5$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Initial amount of S4 |$ 4$ |mole |\r\n|Value of parameter k1 |$ 0.75$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment C |$ 1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 0.5 * k1 * abs(1 + (-1) * t);\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-0.5) * k2;\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only, with csymbol time.\r\ncomponentTags: Parameter, RateRule, CSymbolTime\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called k1 and k2 and one constant\r\nparameter called k3. \r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | k1 | $-k1 * k3 * t$ |\r\n | Rate | k2 | $k1 * k3 * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter k1 |$1.5 \\x 10^-4$ |any |\r\n|Value of parameter k2 |$ 0$ |same as k1 |\r\n|Value of parameter k3 |$ 1$ |second^-2^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nk1_proc @Process { actors: = k1, aux: {{\"metaid\":\"rule1\"}}, };\nk1_proc := (-1) * k1 * k3 * t;\nk2_proc @Process { actors: = k2, aux: {{\"metaid\":\"rule2\"}}, };\nk2_proc := k1 * k3 * t;\n\nk1 @Record 'k1' { } .= 1.5e-4;\nk2 @Record 'k2' { } .= 0;\n\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model using parameters and rules only, with csymbol time.\r\ncomponentTags: Parameter, RateRule, CSymbolTime\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains two varying parameters called P1 and P2 and two constant\r\nparameters called k1 and k2.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | P1 | $P2 * k2 / exp(time)$ |\r\n | Rate | P2 | $P1 * k1 / exp(time)$ |]\r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter P1 |$1.5 \\x 10^-15$ |any |\r\n|Value of parameter P2 |$ 0$ |same as P1 |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.75$ |second^-1^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nP1_proc @Process { actors: = P1, aux: {{\"metaid\":\"rule1\"}}, };\nP1_proc := pow(e, (-1) * t) * k2 * P2;\nP2_proc @Process { actors: = P2, aux: {{\"metaid\":\"rule2\"}}, };\nP2_proc := pow(e, (-1) * t) * k1 * P1;\n\nP1 @Record 'P1' { } .= 1.5;\nP2 @Record 'P2' { } .= 0;\n\nk1 @Const 'k1' { } = 1;\nk2 @Const 'k2' { } = 0.75;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and rules only, with csymbol time.\r\ncomponentTags: Parameter, RateRule, CSymbolTime\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains three varying parameters called P1, P2 and P3 and one\r\nconstant parameter called k1.\r\n \r\nThe model contains three rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | P3 | $k1 * s$ |\r\n | Rate | P1 | $-(P3 * P1)$ |\r\n | Rate | P2 | $P3 * P1$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter P1 |$1.5 \\x 10^-3$ |any |\r\n|Value of parameter P2 |$ 0$ |same as P1 |\r\n|Value of parameter P3 |$ 1 \\x 10^-3$ |second^-1^ |\r\n|Value of parameter k1 |$ 0.5$ |second^-3^ |]\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nP3_proc @Process { actors: = P3, aux: {{\"metaid\":\"rule1\"}}, };\nP3_proc := k1 * t;\nP1_proc @Process { actors: = P1, aux: {{\"metaid\":\"rule2\"}}, };\nP1_proc := (-1) * P1 * P3;\nP2_proc @Process { actors: = P2, aux: {{\"metaid\":\"rule3\"}}, };\nP2_proc := P1 * P3;\n\nP1 @Record 'P1' { } .= 0.0015;\nP2 @Record 'P2' { } .= 0;\nP3 @Record 'P3' { } .= 0.001;\n\nk1 @Const 'k1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called C. There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> 2S2 | $k1 * S1 * C * t$ |]\r\nwhere the symbol 't' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k1 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.15 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = 2*S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C * time$ |\r\n| 2S2 -> S3 | $k2 * S2 * C * time$ |\r\n| S3 -> S4 | $k3 * S3 * C * time$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$0.7$ |second^-2^ |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of parameter k3 |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0.01 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1 * t;\nreaction2 @Reaction 'reaction2' { actors: 2*S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k3 * S3 * t;\n\nk1 @Const 'k1' { } = 0.7;\nk2 @Const 'k2' { } = 0.5;\nk3 @Const 'k3' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three reactions with four species in one compartment\r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime \r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and one parameter called k1.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2 * C * s$ |\r\n| S3 -> S1 + S2 | $k1 * S3 * C * s$ |\r\n| S3 -> S1 + S4 | $k1 * S3 * C * s$ |]\r\nwhere the symbol 's' denotes the current simulation time.\r\n\r\nBoth reactions S3 -> S1 + S2 and S3 -> S1 + S4 define a local parameters k1 which has a\r\nscope local to the defining reaction and are different from each other and the global parameter k1\r\nused in the reaction S1 + S2 -> S3.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$2.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k1 |$1.0$ |litre mole^-1^ second^-2^ |\r\n|Value of local parameter k1 (R2) |$0.9$ |second^-2^ |\r\n|Value of local parameter k1 (R3) |$0.7$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := C * k1 * S1 * S2 * t;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := C * k1__reaction2_local * S3 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S1 + S4, reversible: false, };\nreaction3 := C * k1__reaction3_local * S3 * t;\n\nk1__reaction2_local @Const { } = 0.9;\nk1__reaction3_local @Const { } = 0.7;\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Linear chain of reactions in one compartment \r\nusing csymbol time within a math expression.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, CSymbolTime\r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There are four\r\nspecies called S1, S2, S3 and S4 and one parameter called k2.\r\nThe model contains three reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k2 * S1 * C * time$ |\r\n| S2 -> S3 | $k2 * S2 * C * time$ |\r\n| S3 -> S4 | $k2 * S3 * C * time$ |] \r\nwhere the symbol 'time' denotes the current simulation time.\r\n\r\nBoth reactions S1 -> S2 and S3 -> S4 define a local parameters k2 which has a\r\nscope local to the defining reaction and are different from each other and the \r\nglobal parameter k2 used in the reaction S2 -> S3.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0$ |mole |\r\n|Value of parameter k2 |$0.5$ |second^-2^ |\r\n|Value of local parameter k2 (R1) |$0.7$ |second^-2^ |\r\n|Value of local parameter k2 (R3) |$1$ |second^-2^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1e-4 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k2__reaction1_local * S1 * t;\nreaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };\nreaction2 := C * k2 * S2 * t;\nreaction3 @Reaction 'reaction3' { actors: S3 = S4, reversible: false, };\nreaction3 := C * k2__reaction3_local * S3 * t;\n\nk2__reaction1_local @Const { } = 0.7;\nk2__reaction3_local @Const { } = 1;\nk2 @Const 'k2' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, Parameter, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying compartment called c and one constant\r\nparameter called k1. (Note that indeed c is a compartment and not \r\nspecies in this model.)\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $-c * k1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$ 5$ |litre |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: litre, } .= 5;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := (-1) * c * k1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying compartment called c. (Note that \r\nindeed c is a compartment and not species in this model.)\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $0.5 * c$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$1.5 \\x 10^-2$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: litre, } .= 0.015;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 0.5 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two varying compartments called C1 and C2.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | C1 | $C2 * 0.5 - C1 * 0.2$ |\r\n | Rate | C2 | $C1 * 0.75-C2 * 2.1$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment C1 |$1.5$ |litre |\r\n|Size of compartment C2 |$1.5$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC1 @Compartment 'C1' { units: litre, } .= 1.5;\nC2 @Compartment 'C2' { units: litre, } .= 1.5;\n\nC1_proc @Process { actors: = C1, aux: {{\"metaid\":\"rule1\"}}, };\nC1_proc := 0.5 * C2 - (0.2 * C1);\nC2_proc @Process { actors: = C2, aux: {{\"metaid\":\"rule2\"}}, };\nC2_proc := 0.75 * C1 - (2.1 * C2);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 2-dimensional compartment called c. \r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $0.25 * c$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$3.2$ |metre^2 |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre^2, } .= 3.2;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 0.25 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 1-dimensional compartment called c. \r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $0.1 * c$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$1.5 \\x 10^-4$ |metre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre, } .= 1.5e-4;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 0.1 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, Parameter, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 2-dimensional compartment called c and one constant\r\nparameter called k1. (Note that indeed c is a compartment and not \r\nspecies in this model.)\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $-c * k1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$ 0.002$ |metre^2^ |\r\n|Value of parameter k1 |$ 1.1$ |second^-1^ |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre^2, } .= 0.002;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := (-1) * c * k1;\n\nk1 @Const 'k1' { } = 1.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, Parameter, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 1-dimensional compartment called c and one constant\r\nparameter called k1. (Note that indeed c is a compartment and not \r\nspecies in this model.)\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $-c / k1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$ 22.5$ |metre |\r\n|Value of parameter k1 |$ 0.175$ |second |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre, } .= 22.5;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := (-1) * c / k1;\n\nk1 @Const 'k1' { } = 0.175;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two varying compartments called C1 and C2, where C2 \r\nis 2-dimensional.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | C1 | $C2 * 0.15 - C1 * 0.2$ |\r\n | Rate | C2 | $C1 * 0.3 - C2 * 0.1$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment C1 |$1.5$ |litre |\r\n|Size of compartment C2 |$0.75$ |metre^2^ |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC1 @Compartment 'C1' { units: litre, } .= 1.5;\nC2 @Compartment 'C2' { units: metre^2, } .= 0.75;\n\nC1_proc @Process { actors: = C1, aux: {{\"metaid\":\"rule1\"}}, };\nC1_proc := 0.15 * C2 - (0.2 * C1);\nC2_proc @Process { actors: = C2, aux: {{\"metaid\":\"rule2\"}}, };\nC2_proc := 0.3 * C1 - (0.1 * C2);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two varying compartments called C1 and C2, where C2 \r\nis 1-dimensional.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | C1 | $C2 * 0.25 + C1 * 0.4$ |\r\n | Rate | C2 | $C1 * 0.15 + C2 * 0.2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment C1 |$1.5 x 10^-2^$ |litre |\r\n|Size of compartment C2 |$1.0 x 10^-2^$ |metre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC1 @Compartment 'C1' { units: litre, } .= 0.015;\nC2 @Compartment 'C2' { units: metre, } .= 0.01;\n\nC1_proc @Process { actors: = C1, aux: {{\"metaid\":\"rule1\"}}, };\nC1_proc := 0.4 * C1 + 0.25 * C2;\nC2_proc @Process { actors: = C2, aux: {{\"metaid\":\"rule2\"}}, };\nC2_proc := 0.15 * C1 + 0.2 * C2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule \r\ntestTags: NonConstantCompartment, NonUnityCompartment, MultiCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two varying compartments called C1 and C2, where C1 \r\nis 1-dimensional and C2 is 2-dimensional.\r\n\r\nThe model contains two rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | C1 | $C2 * 0.5 + C1 * 0.3$ |\r\n | Rate | C2 | $C1 * 0.1 + C2 * 0.2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment C1 |$1.5 x 10^-2^$ |metre |\r\n|Size of compartment C2 |$1.0 x 10^-2^$ |metre^2^ |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC1 @Compartment 'C1' { units: metre, } .= 0.015;\nC2 @Compartment 'C2' { units: metre^2, } .= 0.01;\n\nC1_proc @Process { actors: = C1, aux: {{\"metaid\":\"rule1\"}}, };\nC1_proc := 0.3 * C1 + 0.5 * C2;\nC2_proc @Process { actors: = C2, aux: {{\"metaid\":\"rule2\"}}, };\nC2_proc := 0.1 * C1 + 0.2 * C2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule, FunctionDefinition \r\ntestTags: NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying compartment called c.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $multiply(0.5, c)$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$1.5$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: litre, } .= 1.5;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := multiply(c, 0.5);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule, InitialAssignment \r\ntestTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying compartment called c.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $0.25 * c$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | c | $3 / 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment c has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$undeclared$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: litre, } .= 3 / 2;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 0.25 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule, InitialAssignment \r\ntestTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying compartment called c.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $0.25 * c$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | c | $3 / 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment c is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$2$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: litre, } .= 3 / 2;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 0.25 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule, FunctionDefinition \r\ntestTags: NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 2-dimensional compartment called c.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $multiply(0.5, c)$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$0.5$ |metre^2^ |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre^2, } .= 0.5;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := multiply(c, 0.5);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule, FunctionDefinition \r\ntestTags: NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 1-dimensional compartment called c.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $multiply(0.15, c)$ |]\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$0.5$ |metre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre, } .= 0.5;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := multiply(c, 0.15);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule, InitialAssignment \r\ntestTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 2-dimensional compartment called c.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $0.5 * c$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | c | $3 / 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment c has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$undeclared$ |metre^2^ |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre^2, } .= 2 / 3;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 0.5 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule, InitialAssignment \r\ntestTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 1-dimensional compartment called c.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $0.5 * c$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | c | $3 / 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment c has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$undeclared$ |metre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre, } .= 2.2 / 3;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 0.5 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule, InitialAssignment \r\ntestTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 2-dimensional compartment called c.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $1.25 * c$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | c | $3 / 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment c is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$2$ |metre^2^ |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre^2, } .= 3.3 / 2;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 1.25 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, RateRule, InitialAssignment \r\ntestTags: NonConstantCompartment, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying 1-dimensional compartment called c.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $1.25 * c$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | c | $3 / 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the compartment c is\r\ninconsistent with the value returned by the InitialAssignment.\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Size of compartment c |$2$ |metre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: metre, } .= 2.1 / 4;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 1.25 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and initialAssignments only.\r\ncomponentTags: Parameter, InitialAssignment \r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two constant\r\nparameters called k1 and k2.\r\n\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $k2 * 2.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this\r\ncase, the initial value of k1 has not been explicitly declared and must be\r\ncalculated using the initialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter k1 |$ undeclared$ |any |\r\n|Value of parameter k2 |$0.3$ |same as k1 |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nk1 @Record 'k1' { } .= 2.5 * k2;\nk2 @Record 'k2' { } .= 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and initialAssignments only.\r\ncomponentTags: Parameter, InitialAssignment \r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two constant\r\nparameters called k1 and k2.\r\n\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $k2 * 1.5$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this\r\ncase, the initial value of k1 is inconsistent with the value \r\ncalculated using the initialAssignment. The calculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter k1 |$ 0.5$ |any |\r\n|Value of parameter k2 |$0.3$ |same as k1 |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nk1 @Const 'k1' { } = 0.5;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and initialAssignments only.\r\ncomponentTags: Parameter, InitialAssignment \r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two constant\r\nparameters called k1 and k2.\r\n\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | k1 | $k2 * 2.0$ |]\r\n\r\nNote: InitialAssignments override any declared initial values. In this\r\ncase, the initial value of k1 is consistent with the value \r\ncalculated using the initialAssignment. \r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter k1 |$ 0.6$ |any |\r\n|Value of parameter k2 |$0.3$ |same as k1 |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nk1 @Const 'k1' { } = 0.6;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and assignmentRule only.\r\ncomponentTags: Parameter, AssignmentRule \r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two constant\r\nparameters called k1 and k2.\r\n\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| assignmentRule | k1 | $k2 * 4$ |]\r\n\r\n\r\nNote: AssignmentRules override any declared initial values. In this\r\ncase, the initial value of k1 has not been explicitly declared and must be\r\ncalculated using the AssignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter k1 |$ undeclared$ |any |\r\n|Value of parameter k2 |$0.3$ |same as k1 |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nk1 @Record 'k1' { };\nk1 := 4 * k2;\n\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and assignmentRule only.\r\ncomponentTags: Parameter, AssignmentRule \r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two constant\r\nparameters called k1 and k2.\r\n\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| assignmentRule | k1 | $k2 * 3$ |]\r\n\r\n\r\nNote: AssignmentRules override any declared initial values. In this\r\ncase, the initial value of k1 is inconsistent with the value \r\ncalculated using the assignmentRule. The calculated value should be used.\r\n.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter k1 |$ 1.0$ |any |\r\n|Value of parameter k2 |$0.3$ |same as k1 |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nk1 @Record 'k1' { } .= 1;\nk1 := 3 * k2;\n\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model with parameters and assignmentRule only.\r\ncomponentTags: Parameter, AssignmentRule \r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two constant\r\nparameters called k1 and k2.\r\n\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| assignmentRule | k1 | $k2 * 3$ |]\r\n\r\n\r\nNote: AssignmentRules override any declared initial values. In this\r\ncase, the initial value of k1 is consistent with the value \r\ncalculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Value of parameter k1 |$ 0.6$ |any |\r\n|Value of parameter k2 |$0.2$ |same as k1 |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nk1 @Record 'k1' { } .= 0.6;\nk1 := 3 * k2;\n\nk2 @Const 'k2' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, Species, RateRule \r\ntestTags: Concentration, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying compartment called c and a species\r\ns. The species is not directly affected by anything but the concentration\r\nwill change as a result of the varying compartment size.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $0.5 * c$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of s |$2$ |mole litre^-1 |\r\n|Size of compartment c |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: litre, } .= 1;\n\ns @Species 's' { units: mole/litre, compartment: c, } .= 2;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 0.5 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model varying compartment using rules only.\r\ncomponentTags: Compartment, Species, RateRule \r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one varying compartment called c and a species\r\ns. The species is not directly affected by anything but the concentration\r\nwill change as a result of the varying compartment size. However the\r\namount of the species will remain constant.\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | c | $0.5 * c$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of s |$2$ |mole |\r\n|Size of compartment c |$1$ |litre |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nc @Compartment 'c' { units: litre, } .= 1;\n\ns @Species 's' { units: mole/litre, compartment: c, } .= 2 / c;\n\nc_proc @Process { actors: = c, aux: {{\"metaid\":\"rule1\"}}, };\nc_proc := 0.5 * c;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single forward reaction with two species in one compartment and an event\r\ncomponentTags: Compartment, CSymbolTime, Species, Reaction, Parameter, EventNoDelay\r\ntestTags: Amount, EventT0Firing\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"C\". There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one event that assigns value to species S1 defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $t >= 0$ | $-$ | $S1 = 1.5 \\x 10^-4$ |]\r\n \r\nThe initialValue of the Trigger is set to 'false'. Thus at t = 0 the Trigger\r\ntransitions from 'false' to 'true' and thus the event is fired.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k1 |$1$ |second^-1^ |\r\n|Volume of compartment \"C\" |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 0 / C;\nS1 [evt0]= 1.5e-4 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\nevt0 @DSwitcher { trigger: t >= 0, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single forward reaction with two species in one compartment and an event\r\ncomponentTags: Compartment, CSymbolTime, Species, Reaction, Parameter, EventNoDelay\r\ntestTags: Amount, EventT0Firing\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"C\". There are two\r\nspecies called S1 and S2 and one parameter called k1. The model contains\r\none reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1 * C$ |]\r\n\r\nThe model contains one event that assigns value to species S1 defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $t >= 0$ | $-$ | $S1 = 1$ |]\r\n \r\nThe initialValue of the Trigger is set to 'true'. Thus at t = 0 the Trigger\r\ndoes not transition from 'false' to 'true' and thus the event is not fired.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter k1 |$1$ |second^-1^ |\r\n|Volume of compartment \"C\" |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1.5e-4 / C;\nS1 [evt0]= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := C * k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\nevt0 @DSwitcher { trigger: t >= 0, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single forward reaction with two species in one compartment and an event\r\ncomponentTags: Compartment, CSymbolTime, Species, EventNoDelay, EventPriority\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"C\". There are two\r\nspecies called S1 and S2. \r\n\r\n\r\nThe model contains two events that assign value to species S1, S2 and S3 defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Priority* | *Delay* | *Assignments* |\r\n | Event1 | $t >= 0.99$ | $1$ | $-$ | $S1 = 4$ |\r\n | | | | | $S2 = 5$ |\r\n | | | | | $S3 = 6$ |\r\n | Event2 | $t >= 0.99$ | $0$ | $-$ | $S1 = 1$ |\r\n | | | | | $S2 = 2$ |\r\n | | | | | $S3 = 3$ |]\r\n \r\nThe Events will fire simultaneously and must be executed in order determined by\r\nthe Priority. Thus the assignments of Event1 will be executed followed by the \r\nassignments for Event2.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Volume of compartment \"C\" |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 0 / C;\nS1 [_E0]= 4;\nS1 [_E1]= 1;\nS2 @Species { compartment: C, } .= 0 / C;\nS2 [_E0]= 5;\nS2 [_E1]= 2;\nS3 @Species { compartment: C, } .= 0 / C;\nS3 [_E0]= 6;\nS3 [_E1]= 3;\n\n_E0 @DSwitcher { trigger: t >= 0.99, };\n_E1 @DSwitcher { trigger: t >= 0.99, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single forward reaction with two species in one compartment and an event\r\ncomponentTags: Compartment, CSymbolTime, Species, EventNoDelay, EventPriority\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one compartment called \"C\". There are two\r\nspecies called S1 and S2. \r\n\r\n\r\nThe model contains two events that assign value to species S1, S2 and S3 defined as:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Priority* | *Delay* | *Assignments* |\r\n | Event1 | $t >= 1$ | $-1$ | $-$ | $S1 = 4$ |\r\n | | | | | $S2 = 5$ |\r\n | | | | | $S3 = 6$ |\r\n | Event2 | $t >= 1$ | $0$ | $-$ | $S1 = 1$ |\r\n | | | | | $S2 = 2$ |\r\n | | | | | $S3 = 3$ |]\r\n \r\nThe Events will fire simultaneously and must be executed in order determined by\r\nthe Priority. Thus the assignments of Event2 will be executed followed by the \r\nassignments for Event1.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Volume of compartment \"C\" |$1$ |litre |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but (as\r\nper usual SBML principles) their symbols represent their values in\r\nconcentration units where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 0 / C;\nS1 [_E0]= 4;\nS1 [_E1]= 1;\nS2 @Species { compartment: C, } .= 0 / C;\nS2 [_E0]= 5;\nS2 [_E1]= 2;\nS3 @Species { compartment: C, } .= 0 / C;\nS3 [_E0]= 6;\nS3 [_E1]= 3;\n\n_E0 @DSwitcher { trigger: t >= 0.99, };\n_E1 @DSwitcher { trigger: t >= 0.99, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single forward reaction with two species in one compartment and an event\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Species\r\ntestTags: Amount, EventIsPersistent\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe Events will execute simultaneously and must be executed in order determined by\r\nthe Priority. Since the priority of all remaining events must be re-calculated\r\nafter each event is executed, the order in which the events execute changes after\r\nEvent1.\r\n\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 compartment (C)\r\n\r\nThere are 3 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| A | $time ≥ 0.99$ | $10$ | $S1 = 1$ |\r\n| | | | $S2 = 0$ |\r\n| B | $time ≥ 0.99$ | $2 * S2$ | $S1 = 2$ |\r\n| | | | $S2 = 1$ |\r\n| C1 | $time ≥ 0.99$ | $2 * S1$ | $S1 = 3$ |\r\n| | | | $S2 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $0$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 0 / C;\nS1 [A]= 1;\nS1 [B]= 2;\nS1 [C1]= 3;\nS2 @Species { compartment: C, } .= 1 / C;\nS2 [A]= 0;\nS2 [B]= 1;\nS2 [C1]= 2;\n\nA @DSwitcher { trigger: t >= 0.99, };\nB @DSwitcher { trigger: t >= 0.99, };\nC1 @DSwitcher { trigger: t >= 0.99, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single forward reaction with two species in one compartment and three events\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Species\r\ntestTags: Amount, EventIsNotPersistent, EventIsPersistent\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains three events that assign value to species S1 and S2 defined below.\r\n\r\nThe events will execute simultaneously and must be executed in order determined by\r\nthe Priority. However, since Event2 is not persistent, the execution of Event1\r\ncauses the Trigger of Event2 to return to 'false'. It must therefore be removed\r\nfrom the list of pending events.\r\n\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 compartment (C)\r\n\r\nThere are 3 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| A | $and(geq(time, 0.99), lt(S1, 0.5))$ | $10$ | true | $S1 = 1$ |\r\n| | | | | $S2 = 0$ |\r\n| B | $and(geq(time, 0.99), lt(S1, 0.5))$ | $8$ | false | $S1 = 2$ |\r\n| | | | | $S2 = 1$ |\r\n| C1 | $and(geq(time, 0.99), lt(S1, 0.5))$ | $9$ | true | $S1 = 3$ |\r\n| | | | | $S2 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $0$ | variable |\r\n| Initial amount of species S2 | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 0 / C;\nS1 [A]= 1;\nS1 [B]= 2;\nS1 [C1]= 3;\nS2 @Species { compartment: C, } .= 1 / C;\nS2 [A]= 0;\nS2 [B]= 1;\nS2 [C1]= 2;\n\nA @DSwitcher { trigger: t >= 0.99 and S1 < 0.5, };\nB @DSwitcher { trigger: t >= 0.99 and S1 < 0.5, };\nC1 @DSwitcher { trigger: t >= 0.99 and S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter.\r\ncomponentTags: Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThis model tests when an event changes a parameter involved in a kinetic law.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> S1 | $C * k1 / S1$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| event1 | $S1 > 2.1$ | $k1 = 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial value of parameter k1 | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1 / C;\n\nreaction1 @Reaction { actors: = S1, reversible: false, };\nreaction1 := (C * k1) / S1;\n\nk1 @Record { } .= 1;\nk1 [event1]= 10;\n\nevent1 @DSwitcher { trigger: S1 > 2.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic one reaction with one species in one compartment and one event that changes the size of the compartment.\r\ncomponentTags: Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThis model tests that a reaction behaves properly when a compartment size is changed by an event.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> S1 | $C * k1 / S1$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| event1 | $S1 > 2.1$ | $C = 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial value of parameter k1 | $1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | variable |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { } .= 1;\nC [event1]= 10;\n\nS1 @Species { compartment: C, } .= 1 / C;\n\nreaction1 @Reaction { actors: = S1, reversible: false, };\nreaction1 := (C * k1) / S1;\n\nk1 @Const { } = 1;\n\nevent1 @DSwitcher { trigger: S1 > 2.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter.\r\ncomponentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There is one species called S1 and two parameters, k1 and fakeC. It is identical in design and expected output to model 00945, except that instead of the event assigning to a compartment directly, it assigns to a temporary variable 'fakeC' which is then assigned to compartment C through an assignment rule.\r\n\r\nThe model contains one reaction defined as:\r\n\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 2 parameters (fakeC, k1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> S1 | $C * k1 / S1$ |]\r\n\r\n\r\nThe model contains one event that assigns a value to the temporary parameter fakeC:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| event1 | $S1 > 2.1$ | $fakeC = 10$ |]\r\n\r\n\r\nAnd the model contains one assignment rule that assigns the value of fakeC to compartment C:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | C | $fakeC$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial value of parameter k1 | $1$ | constant |\r\n| Initial value of parameter fakeC | $1$ | variable |\r\n| Initial volume of compartment 'C' | $fakeC$ | variable |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { };\nC := fakeC;\n\nS1 @Species { compartment: C, } .= 1 / C;\n\nreaction1 @Reaction { actors: = S1, reversible: false, };\nreaction1 := (C * k1) / S1;\n\nfakeC @Record { } .= 1;\nfakeC [event1]= 10;\n\nk1 @Const { } = 1;\n\nevent1 @DSwitcher { trigger: S1 > 2.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter.\r\ncomponentTags: Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Concentration, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nTest of an event changing the size of a compartment.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> S1 | $C * k1 / S1$ |]\r\n\r\n\r\nThe model contains one event that assigns a value to the compartment C:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| event1 | $S1 > 2.1$ | $C = 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial value of parameter k1 | $1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | variable |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { } .= 1;\nC [event1]= 10;\n\nS1 @Species { compartment: C, } .= 1 / C;\n\nreaction1 @Reaction { actors: = S1, reversible: false, };\nreaction1 := (C * k1) / S1;\n\nk1 @Const { } = 1;\n\nevent1 @DSwitcher { trigger: S1 > 2.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic one reaction with one species in one compartment and one event, assigning to a parameter.\r\ncomponentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Concentration, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe model contains one compartment called C. There is one species called S1 and two parameters, k1 and fakeC. It is identical in design and expected output to model 00945, except that instead of the event assigning to a compartment directly, it assigns to a temporary variable 'fakeC' which is then assigned to compartment C through an assignment rule.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 2 parameters (fakeC, k1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> S1 | $C * k1 / S1$ |]\r\n\r\n\r\nThe model contains one event that assigns a value to the temporary parameter fakeC:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| event1 | $S1 > 2.1$ | $fakeC = 10$ |]\r\n\r\n\r\nAnd the model contains one assignment rule that assigns the value of fakeC to compartment C:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | C | $fakeC$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial value of parameter k1 | $1$ | constant |\r\n| Initial value of parameter fakeC | $1$ | variable |\r\n| Initial volume of compartment 'C' | $fakeC$ | variable |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { };\nC := fakeC;\n\nS1 @Species { compartment: C, } .= 1 / C;\n\nreaction1 @Reaction { actors: = S1, reversible: false, };\nreaction1 := (C * k1) / S1;\n\nfakeC @Record { } .= 1;\nfakeC [event1]= 10;\n\nk1 @Const { } = 1;\n\nevent1 @DSwitcher { trigger: S1 > 2.1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One constant parameter.\r\ncomponentTags: Parameter\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains one parameter P. It doesn't change.\r\n\r\nThere are no rules, reactions or events.\r\n\r\nThe model contains:\r\n* 1 parameter (P)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P | $3.7$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP @Const { } = 3.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three constant parameters, with initialassignments to inf, -inf, and nan.\r\ncomponentTags: InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\n This model tests the 'INF' and 'NaN' constructs with initial assignments.\r\n\r\nThe model contains:\r\n* 3 parameters (P, Q, R)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P | $INF$ | constant |\r\n| Initial value of parameter Q | $-INF$ | constant |\r\n| Initial value of parameter R | $NaN$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP @Const { } = 0;\nQ @Const { } = 0;\nR @Const { } = 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three constant parameters, with initial values of inf, -inf, and NaN.\r\ncomponentTags: Parameter\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThis model tests the INF and NaN constructs.\r\n\r\nThe model contains:\r\n* 3 parameters (P, Q, R)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P | $INF$ | constant |\r\n| Initial value of parameter Q | $-INF$ | constant |\r\n| Initial value of parameter R | $NaN$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nP @Const { } = Infinity;\nQ @Const { } = -Infinity;\nR @Const { } = NaN;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure one event doesn't severly out-compete the other. NOTE: STOCHASTIC TEST. This test is designed to fail only one time in a million, but it still may happen.\r\ncomponentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: EventIsNotPersistent, NonConstantParameter, RandomEventExecution\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThis model contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 4, it triggers. In our simulations, this happened less often than one time in a million, so if you see it happen in your simulator more often than once, there's a good chance something is wrong.\r\n \r\nThe model contains:\r\n* 5 parameters (S, Q, R, reset, error)\r\n\r\nThere are 3 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ |\r\n| | | | | $Q = Q + 0.01$ |\r\n| Rinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ |\r\n| | | | | $R = R + 0.01$ |\r\n| error_check | $geq(abs(Q - R), 4)$ | (unset) | true | $error = 1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S | $Q + R$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter S | $Q + R$ | variable |\r\n| Initial value of parameter Q | $0$ | variable |\r\n| Initial value of parameter R | $0$ | variable |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter error | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nS @Record { } .= 0;\nS := Q + R;\nQ @Record { } .= 0;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 0;\nR [Rinc]= R + 0.01;\nreset @Record { } .= 0;\nreset [Qinc]= t;\nreset [Rinc]= t;\nerror @Record { } .= 0;\nerror [error_check]= 1;\n\nQinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nRinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nerror_check @DSwitcher { trigger: abs(Q - R) >= 4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Competing events without priorities, jointly causing a parameter to monotonically increase.\r\ncomponentTags: AssignmentRule, CSymbolTime, EventNoDelay, Parameter\r\ntestTags: NonConstantParameter, EventIsNotPersistent, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThis model contains two events with the same trigger, no priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. This model is identical to 952, except that there are no priorities, so Qinc and Rinc do not have to be chosen between at random, but can be chosen in any ratio.\r\n\r\nThe model contains:\r\n* 5 parameters (S, Q, R, reset, error)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Persistent* | *Event Assignments* |\r\n| Qinc | $geq(time - reset, 0.01)$ | false | $reset = time$ |\r\n| | | | $Q = Q + 0.01$ |\r\n| Rinc | $geq(time - reset, 0.01)$ | false | $reset = time$ |\r\n| | | | $R = R + 0.01$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S | $Q + R$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter S | $Q + R$ | variable |\r\n| Initial value of parameter Q | $0$ | variable |\r\n| Initial value of parameter R | $0$ | variable |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter error | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nS @Record { };\nS := Q + R;\nQ @Record { } .= 0;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 0;\nR [Rinc]= R + 0.01;\nreset @Record { } .= 0;\nreset [Qinc]= t;\nreset [Rinc]= t;\nerror @Record { } .= 0;\n\nQinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nRinc @DSwitcher { trigger: (t - reset) >= 0.01, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Several parameters with assignment rules, testing various L1 built-in functions acting on constants.\r\ncomponentTags: AssignmentRule, Parameter\r\ntestTags: InitialValueReassigned, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model tests the various mathematical constructs present in L1.\r\n\r\nThe model contains:\r\n* 40 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40)\r\n\r\nThere are 39 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | P2 | $abs(-1)$ |\r\n| Assignment | P3 | $abs(1)$ |\r\n| Assignment | P4 | $acos(-1)$ |\r\n| Assignment | P5 | $acos(0.5)$ |\r\n| Assignment | P6 | $asin(1)$ |\r\n| Assignment | P7 | $asin(-0.5)$ |\r\n| Assignment | P8 | $atan(2.8)$ |\r\n| Assignment | P9 | $atan(-7.09)$ |\r\n| Assignment | P10 | $ceil(0.5)$ |\r\n| Assignment | P11 | $ceil(3.55)$ |\r\n| Assignment | P12 | $ceil(-4.6)$ |\r\n| Assignment | P13 | $cos(9.1)$ |\r\n| Assignment | P14 | $cos(-0.22)$ |\r\n| Assignment | P15 | $exp(0)$ |\r\n| Assignment | P16 | $exp(1)$ |\r\n| Assignment | P17 | $exp(0.77)$ |\r\n| Assignment | P18 | $floor(-4.6)$ |\r\n| Assignment | P19 | $floor(9.1)$ |\r\n| Assignment | P20 | $log(0.2)$ |\r\n| Assignment | P21 | $log(1)$ |\r\n| Assignment | P22 | $log10(0.2)$ |\r\n| Assignment | P23 | $log10(1)$ |\r\n| Assignment | P24 | $pow(1, 2)$ |\r\n| Assignment | P25 | $pow(2, 2)$ |\r\n| Assignment | P26 | $pow(1.4, 5.1)$ |\r\n| Assignment | P27 | $pow(4, 2)$ |\r\n| Assignment | P28 | $pow(3.1, 2)$ |\r\n| Assignment | P29 | $sqrt(4)$ |\r\n| Assignment | P30 | $sqrt(7.4)$ |\r\n| Assignment | P31 | $sin(2.1)$ |\r\n| Assignment | P32 | $sin(0)$ |\r\n| Assignment | P33 | $sin(-5.9)$ |\r\n| Assignment | P34 | $tan(0)$ |\r\n| Assignment | P35 | $tan(1.11)$ |\r\n| Assignment | P36 | $tan(-6)$ |\r\n| Assignment | P37 | $1 + 2$ |\r\n| Assignment | P38 | $1 - 2$ |\r\n| Assignment | P39 | $5 / 2$ |\r\n| Assignment | P40 | $8 * 3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $3.7$ | constant |\r\n| Initial value of parameter P2 | $abs(-1)$ | variable |\r\n| Initial value of parameter P3 | $abs(1)$ | variable |\r\n| Initial value of parameter P4 | $acos(-1)$ | variable |\r\n| Initial value of parameter P5 | $acos(0.5)$ | variable |\r\n| Initial value of parameter P6 | $asin(1)$ | variable |\r\n| Initial value of parameter P7 | $asin(-0.5)$ | variable |\r\n| Initial value of parameter P8 | $atan(2.8)$ | variable |\r\n| Initial value of parameter P9 | $atan(-7.09)$ | variable |\r\n| Initial value of parameter P10 | $ceil(0.5)$ | variable |\r\n| Initial value of parameter P11 | $ceil(3.55)$ | variable |\r\n| Initial value of parameter P12 | $ceil(-4.6)$ | variable |\r\n| Initial value of parameter P13 | $cos(9.1)$ | variable |\r\n| Initial value of parameter P14 | $cos(-0.22)$ | variable |\r\n| Initial value of parameter P15 | $exp(0)$ | variable |\r\n| Initial value of parameter P16 | $exp(1)$ | variable |\r\n| Initial value of parameter P17 | $exp(0.77)$ | variable |\r\n| Initial value of parameter P18 | $floor(-4.6)$ | variable |\r\n| Initial value of parameter P19 | $floor(9.1)$ | variable |\r\n| Initial value of parameter P20 | $log(0.2)$ | variable |\r\n| Initial value of parameter P21 | $log(1)$ | variable |\r\n| Initial value of parameter P22 | $log10(0.2)$ | variable |\r\n| Initial value of parameter P23 | $log10(1)$ | variable |\r\n| Initial value of parameter P24 | $pow(1, 2)$ | variable |\r\n| Initial value of parameter P25 | $pow(2, 2)$ | variable |\r\n| Initial value of parameter P26 | $pow(1.4, 5.1)$ | variable |\r\n| Initial value of parameter P27 | $pow(4, 2)$ | variable |\r\n| Initial value of parameter P28 | $pow(3.1, 2)$ | variable |\r\n| Initial value of parameter P29 | $sqrt(4)$ | variable |\r\n| Initial value of parameter P30 | $sqrt(7.4)$ | variable |\r\n| Initial value of parameter P31 | $sin(2.1)$ | variable |\r\n| Initial value of parameter P32 | $sin(0)$ | variable |\r\n| Initial value of parameter P33 | $sin(-5.9)$ | variable |\r\n| Initial value of parameter P34 | $tan(0)$ | variable |\r\n| Initial value of parameter P35 | $tan(1.11)$ | variable |\r\n| Initial value of parameter P36 | $tan(-6)$ | variable |\r\n| Initial value of parameter P37 | $1 + 2$ | variable |\r\n| Initial value of parameter P38 | $1 - 2$ | variable |\r\n| Initial value of parameter P39 | $5 / 2$ | variable |\r\n| Initial value of parameter P40 | $8 * 3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nP2 @Record { };\nP2 := abs((-1));\nP3 @Record { };\nP3 := abs(1);\nP4 @Record { };\nP4 := acos((-1));\nP5 @Record { };\nP5 := acos(0.5);\nP6 @Record { };\nP6 := asin(1);\nP7 @Record { };\nP7 := asin((-0.5));\nP8 @Record { };\nP8 := atan(2.8);\nP9 @Record { };\nP9 := atan((-7.09));\nP10 @Record { };\nP10 := ceil(0.5);\nP11 @Record { };\nP11 := ceil(3.55);\nP12 @Record { };\nP12 := ceil((-4.6));\nP13 @Record { };\nP13 := cos(9.1);\nP14 @Record { };\nP14 := cos((-0.22));\nP15 @Record { };\nP15 := exp(0);\nP16 @Record { };\nP16 := exp(1);\nP17 @Record { };\nP17 := exp(0.77);\nP18 @Record { };\nP18 := floor((-4.6));\nP19 @Record { };\nP19 := floor(9.1);\nP20 @Record { };\nP20 := ln(0.2);\nP21 @Record { };\nP21 := ln(1);\nP22 @Record { };\nP22 := logbase(0.2, 10);\nP23 @Record { };\nP23 := logbase(1, 10);\nP24 @Record { };\nP24 := pow(1, 2);\nP25 @Record { };\nP25 := pow(2, 2);\nP26 @Record { };\nP26 := pow(1.4, 5.1);\nP27 @Record { };\nP27 := pow(4, 2);\nP28 @Record { };\nP28 := pow(3.1, 2);\nP29 @Record { };\nP29 := pow(4, 1 / 2);\nP30 @Record { };\nP30 := pow(7.4, 1 / 2);\nP31 @Record { };\nP31 := sin(2.1);\nP32 @Record { };\nP32 := sin(0);\nP33 @Record { };\nP33 := sin((-5.9));\nP34 @Record { };\nP34 := tan(0);\nP35 @Record { };\nP35 := tan(1.11);\nP36 @Record { };\nP36 := tan((-6));\nP37 @Record { };\nP37 := 1 + 2;\nP38 @Record { };\nP38 := 1 - 2;\nP39 @Record { };\nP39 := 5 / 2;\nP40 @Record { };\nP40 := 8 * 3;\n\nP1 @Const { } = 3.7;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Several parameters with assignment rules involving time, testing various L1 built-in functions.\r\ncomponentTags: AssignmentRule, CSymbolTime, Parameter\r\ntestTags: InitialValueReassigned, NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n The model tests the various mathematical constructs present in L1, as applied to the time variable. Ironically, this doesn't work in L1, since time isn't present, but hey.\r\n\r\nThe model contains:\r\n* 35 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P13, P14, P15, P16, P18, P19, P20, P22, P24, P25, P26, P29, P31, P32, P34, P35, P37, P38, P39, P40, P41, P42, P43, P44)\r\n\r\nThere are 35 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | P1 | $time$ |\r\n| Assignment | P2 | $abs(time)$ |\r\n| Assignment | P3 | $abs(-time)$ |\r\n| Assignment | P4 | $acos(time)$ |\r\n| Assignment | P5 | $acos(-time)$ |\r\n| Assignment | P6 | $asin(time)$ |\r\n| Assignment | P7 | $asin(-time)$ |\r\n| Assignment | P8 | $atan(time)$ |\r\n| Assignment | P9 | $atan(-time)$ |\r\n| Assignment | P10 | $ceil(time - 0.001)$ |\r\n| Assignment | P11 | $ceil(-time - 0.001)$ |\r\n| Assignment | P13 | $cos(time)$ |\r\n| Assignment | P14 | $cos(-time)$ |\r\n| Assignment | P15 | $exp(time)$ |\r\n| Assignment | P16 | $exp(-time)$ |\r\n| Assignment | P18 | $floor(time + 0.001)$ |\r\n| Assignment | P19 | $floor(-time + 0.001)$ |\r\n| Assignment | P20 | $ln(time + 1)$ |\r\n| Assignment | P22 | $log10(time + 1)$ |\r\n| Assignment | P24 | $time^2$ |\r\n| Assignment | P25 | $2^time$ |\r\n| Assignment | P26 | $time^time$ |\r\n| Assignment | P29 | $sqrt(time)$ |\r\n| Assignment | P31 | $sin(time)$ |\r\n| Assignment | P32 | $sin(-time)$ |\r\n| Assignment | P34 | $tan(time)$ |\r\n| Assignment | P35 | $tan(-time)$ |\r\n| Assignment | P37 | $time + 2$ |\r\n| Assignment | P38 | $time - 2$ |\r\n| Assignment | P39 | $time / 2$ |\r\n| Assignment | P40 | $time * 3$ |\r\n| Assignment | P41 | $2 + time$ |\r\n| Assignment | P42 | $2 - time$ |\r\n| Assignment | P43 | $2 / (time + 1)$ |\r\n| Assignment | P44 | $3 * time$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $time$ | variable |\r\n| Initial value of parameter P2 | $abs(time)$ | variable |\r\n| Initial value of parameter P3 | $abs(-time)$ | variable |\r\n| Initial value of parameter P4 | $acos(time)$ | variable |\r\n| Initial value of parameter P5 | $acos(-time)$ | variable |\r\n| Initial value of parameter P6 | $asin(time)$ | variable |\r\n| Initial value of parameter P7 | $asin(-time)$ | variable |\r\n| Initial value of parameter P8 | $atan(time)$ | variable |\r\n| Initial value of parameter P9 | $atan(-time)$ | variable |\r\n| Initial value of parameter P10 | $ceil(time - 0.001)$ | variable |\r\n| Initial value of parameter P11 | $ceil(-time - 0.001)$ | variable |\r\n| Initial value of parameter P13 | $cos(time)$ | variable |\r\n| Initial value of parameter P14 | $cos(-time)$ | variable |\r\n| Initial value of parameter P15 | $exp(time)$ | variable |\r\n| Initial value of parameter P16 | $exp(-time)$ | variable |\r\n| Initial value of parameter P18 | $floor(time + 0.001)$ | variable |\r\n| Initial value of parameter P19 | $floor(-time + 0.001)$ | variable |\r\n| Initial value of parameter P20 | $ln(time + 1)$ | variable |\r\n| Initial value of parameter P22 | $log10(time + 1)$ | variable |\r\n| Initial value of parameter P24 | $time^2$ | variable |\r\n| Initial value of parameter P25 | $2^time$ | variable |\r\n| Initial value of parameter P26 | $time^time$ | variable |\r\n| Initial value of parameter P29 | $sqrt(time)$ | variable |\r\n| Initial value of parameter P31 | $sin(time)$ | variable |\r\n| Initial value of parameter P32 | $sin(-time)$ | variable |\r\n| Initial value of parameter P34 | $tan(time)$ | variable |\r\n| Initial value of parameter P35 | $tan(-time)$ | variable |\r\n| Initial value of parameter P37 | $time + 2$ | variable |\r\n| Initial value of parameter P38 | $time - 2$ | variable |\r\n| Initial value of parameter P39 | $time / 2$ | variable |\r\n| Initial value of parameter P40 | $time * 3$ | variable |\r\n| Initial value of parameter P41 | $2 + time$ | variable |\r\n| Initial value of parameter P42 | $2 - time$ | variable |\r\n| Initial value of parameter P43 | $2 / (time + 1)$ | variable |\r\n| Initial value of parameter P44 | $3 * time$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP1 @Record { };\nP1 := t;\nP2 @Record { };\nP2 := abs(t);\nP3 @Record { };\nP3 := abs((-t));\nP4 @Record { };\nP4 := acos(t);\nP5 @Record { };\nP5 := acos((-t));\nP6 @Record { };\nP6 := asin(t);\nP7 @Record { };\nP7 := asin((-t));\nP8 @Record { };\nP8 := atan(t);\nP9 @Record { };\nP9 := atan((-t));\nP10 @Record { };\nP10 := ceil(t - 0.001);\nP11 @Record { };\nP11 := ceil((-t) - 0.001);\nP13 @Record { };\nP13 := cos(t);\nP14 @Record { };\nP14 := cos((-t));\nP15 @Record { };\nP15 := exp(t);\nP16 @Record { };\nP16 := exp((-t));\nP18 @Record { };\nP18 := floor(t + 0.001);\nP19 @Record { };\nP19 := floor((-t) + 0.001);\nP20 @Record { };\nP20 := ln(t + 1);\nP22 @Record { };\nP22 := logbase(t + 1, 10);\nP24 @Record { };\nP24 := pow(t, 2);\nP25 @Record { };\nP25 := pow(2, t);\nP26 @Record { };\nP26 := pow(t, t);\nP29 @Record { };\nP29 := pow(t, 1 / 2);\nP31 @Record { };\nP31 := sin(t);\nP32 @Record { };\nP32 := sin((-t));\nP34 @Record { };\nP34 := tan(t);\nP35 @Record { };\nP35 := tan((-t));\nP37 @Record { };\nP37 := t + 2;\nP38 @Record { };\nP38 := t - 2;\nP39 @Record { };\nP39 := t / 2;\nP40 @Record { };\nP40 := t * 3;\nP41 @Record { };\nP41 := 2 + t;\nP42 @Record { };\nP42 := 2 - t;\nP43 @Record { };\nP43 := 2 / (t + 1);\nP44 @Record { };\nP44 := 3 * t;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Several parameters with initial assignment rules, testing various L1 built-in functions acting on constants.\r\ncomponentTags: InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\n The model tests the various mathematical constructs present in L1, used in InitialAssignments.\r\n\r\nThe model contains:\r\n* 40 parameters (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $3.7$ | constant |\r\n| Initial value of parameter P2 | $abs(-1)$ | constant |\r\n| Initial value of parameter P3 | $abs(1)$ | constant |\r\n| Initial value of parameter P4 | $acos(-1)$ | constant |\r\n| Initial value of parameter P5 | $acos(0.5)$ | constant |\r\n| Initial value of parameter P6 | $asin(1)$ | constant |\r\n| Initial value of parameter P7 | $asin(-0.5)$ | constant |\r\n| Initial value of parameter P8 | $atan(2.8)$ | constant |\r\n| Initial value of parameter P9 | $atan(-7.09)$ | constant |\r\n| Initial value of parameter P10 | $ceil(0.5)$ | constant |\r\n| Initial value of parameter P11 | $ceil(3.55)$ | constant |\r\n| Initial value of parameter P12 | $ceil(-4.6)$ | constant |\r\n| Initial value of parameter P13 | $cos(9.1)$ | constant |\r\n| Initial value of parameter P14 | $cos(-0.22)$ | constant |\r\n| Initial value of parameter P15 | $exp(0)$ | constant |\r\n| Initial value of parameter P16 | $exp(1)$ | constant |\r\n| Initial value of parameter P17 | $exp(0.77)$ | constant |\r\n| Initial value of parameter P18 | $floor(-4.6)$ | constant |\r\n| Initial value of parameter P19 | $floor(9.1)$ | constant |\r\n| Initial value of parameter P20 | $log(0.2)$ | constant |\r\n| Initial value of parameter P21 | $log(1)$ | constant |\r\n| Initial value of parameter P22 | $log10(0.2)$ | constant |\r\n| Initial value of parameter P23 | $log10(1)$ | constant |\r\n| Initial value of parameter P24 | $pow(1, 2)$ | constant |\r\n| Initial value of parameter P25 | $pow(2, 2)$ | constant |\r\n| Initial value of parameter P26 | $pow(1.4, 5.1)$ | constant |\r\n| Initial value of parameter P27 | $pow(4, 2)$ | constant |\r\n| Initial value of parameter P28 | $pow(3.1, 2)$ | constant |\r\n| Initial value of parameter P29 | $sqrt(4)$ | constant |\r\n| Initial value of parameter P30 | $sqrt(7.4)$ | constant |\r\n| Initial value of parameter P31 | $sin(2.1)$ | constant |\r\n| Initial value of parameter P32 | $sin(0)$ | constant |\r\n| Initial value of parameter P33 | $sin(-5.9)$ | constant |\r\n| Initial value of parameter P34 | $tan(0)$ | constant |\r\n| Initial value of parameter P35 | $tan(1.11)$ | constant |\r\n| Initial value of parameter P36 | $tan(-6)$ | constant |\r\n| Initial value of parameter P37 | $1 + 2$ | constant |\r\n| Initial value of parameter P38 | $1 - 2$ | constant |\r\n| Initial value of parameter P39 | $5 / 2$ | constant |\r\n| Initial value of parameter P40 | $8 * 3$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nP1 @Record { } .= 3.7;\nP2 @Record { } .= abs((-1));\nP3 @Record { } .= abs(1);\nP4 @Record { } .= acos((-1));\nP5 @Record { } .= acos(0.5);\nP6 @Record { } .= asin(1);\nP7 @Record { } .= asin((-0.5));\nP8 @Record { } .= atan(2.8);\nP9 @Record { } .= atan((-7.09));\nP10 @Record { } .= ceil(0.5);\nP11 @Record { } .= ceil(3.55);\nP12 @Record { } .= ceil((-4.6));\nP13 @Record { } .= cos(9.1);\nP14 @Record { } .= cos((-0.22));\nP15 @Record { } .= exp(0);\nP16 @Record { } .= exp(1);\nP17 @Record { } .= exp(0.77);\nP18 @Record { } .= floor((-4.6));\nP19 @Record { } .= floor(9.1);\nP20 @Record { } .= ln(0.2);\nP21 @Record { } .= ln(1);\nP22 @Record { } .= logbase(0.2, 10);\nP23 @Record { } .= logbase(1, 10);\nP24 @Record { } .= pow(1, 2);\nP25 @Record { } .= pow(2, 2);\nP26 @Record { } .= pow(1.4, 5.1);\nP27 @Record { } .= pow(4, 2);\nP28 @Record { } .= pow(3.1, 2);\nP29 @Record { } .= pow(4, 1 / 2);\nP30 @Record { } .= pow(7.4, 1 / 2);\nP31 @Record { } .= sin(2.1);\nP32 @Record { } .= sin(0);\nP33 @Record { } .= sin((-5.9));\nP34 @Record { } .= tan(0);\nP35 @Record { } .= tan(1.11);\nP36 @Record { } .= tan((-6));\nP37 @Record { } .= 1 + 2;\nP38 @Record { } .= 1 - 2;\nP39 @Record { } .= 5 / 2;\nP40 @Record { } .= 8 * 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Four different ways of writing the avogadro number in an assignment rule.\r\ncomponentTags: AssignmentRule, CSymbolAvogadro, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model assigns avogadro's number as a csymbol to four parameters in an assignment rule. It tries to fool you by calling two of them 'time' and 'delay', and by not giving one a name at all.\r\n\r\nTo test that the value of avogadro is the same as is in the specification without requiring that you write out all 9 digits of precision, a fifth parameter is added with the value (avogadro - 6.0221e+23).\r\n\r\nThe model contains:\r\n* 5 parameters (P1, P2, P3, P4, P5)\r\n\r\nThere are 5 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | P1 | $avogadro$ |\r\n| Assignment | P2 | $time$ |\r\n| Assignment | P3 | $delay$ |\r\n| Assignment | P4 | $$ |\r\n| Assignment | P5 | $avogadro - 6.022100e+023$ |]\r\n\r\n Note: All parameters actually assigned the CSymbol 'avogadro', but the text is different for the first four cases.\r\n \r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $avogadro$ | variable |\r\n| Initial value of parameter P2 | $time$ | variable |\r\n| Initial value of parameter P3 | $delay$ | variable |\r\n| Initial value of parameter P4 | $$ | variable |\r\n| Initial value of parameter P5 | $avogadro - 6.022100e+023$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP1 @Record { };\nP1 := 6.02214076e+23;\nP2 @Record { };\nP2 := 6.02214076e+23;\nP3 @Record { };\nP3 := 6.02214076e+23;\nP4 @Record { };\nP4 := 6.02214076e+23;\nP5 @Record { };\nP5 := 6.02214076e+23 - (6.0221e+23);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases.\r\ncomponentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: EventIsNotPersistent, NonConstantParameter, RandomEventExecution\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThis model contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. \r\n\r\n Note: The 'error' parameter is a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The value of '0.2' was chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events exactly evenly.\r\n\r\nThe model contains:\r\n* 6 parameters (S, Q, R, reset, maxdiff, error)\r\n\r\nThere are 4 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ |\r\n| | | | | $Q = Q + 0.01$ |\r\n| Rinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ |\r\n| | | | | $R = R + 0.01$ |\r\n| maxcheck | $gt(abs(Q - R), maxdiff)$ | (unset) | true | $maxdiff = abs(Q - R)$ |\r\n| error_check | $and(geq(time, 99), lt(maxdiff, 0.2))$ | (unset) | true | $error = 1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S | $Q + R$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter S | $Q + R$ | variable |\r\n| Initial value of parameter Q | $0$ | variable |\r\n| Initial value of parameter R | $0$ | variable |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter maxdiff | $0$ | variable |\r\n| Initial value of parameter error | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nS @Record { } .= 0;\nS := Q + R;\nQ @Record { } .= 0;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 0;\nR [Rinc]= R + 0.01;\nreset @Record { } .= 0;\nreset [Qinc]= t;\nreset [Rinc]= t;\nmaxdiff @Record { } .= 0;\nmaxdiff [maxcheck]= abs(Q - R);\nerror @Record { } .= 0;\nerror [error_check]= 1;\n\nQinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nRinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nmaxcheck @DSwitcher { trigger: abs(Q - R) > maxdiff, };\nerror_check @DSwitcher { trigger: t >= 99 and maxdiff < 0.2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Competing events with different priorities, meaning one always fires and the other does not.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: EventIsNotPersistent, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\n This model contains two pairs of events with the same two triggers and different priorities, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, and the higher-priority event is the one that always wins. Just to make sure that simulators don't accidentally do what was designed to happen here, the two pairs of events come in the same order alphabetically and within the file, but the priorities are reversed, so if you always pick the first event instead of looking at the priority, you will fail one of the tests.\r\n\r\nThe model contains:\r\n* 6 parameters (Q, R, reset, Q2, R2, reset2)\r\n\r\nThere are 4 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ |\r\n| | | | | $Q = Q + 0.01$ |\r\n| Rinc | $geq(time - reset, 0.01)$ | $-1$ | false | $reset = time$ |\r\n| | | | | $R = R + 0.01$ |\r\n| Qinc2 | $geq(time - reset2, 0.01)$ | $-1$ | false | $reset2 = time$ |\r\n| | | | | $Q2 = Q2 + 0.01$ |\r\n| Rinc2 | $geq(time - reset2, 0.01)$ | $1$ | false | $reset2 = time$ |\r\n| | | | | $R2 = R2 + 0.01$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter Q | $0$ | variable |\r\n| Initial value of parameter R | $0$ | variable |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter Q2 | $0$ | variable |\r\n| Initial value of parameter R2 | $0$ | variable |\r\n| Initial value of parameter reset2 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nQ @Record { } .= 0;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 0;\nR [Rinc]= R + 0.01;\nreset @Record { } .= 0;\nreset [Qinc]= t;\nreset [Rinc]= t;\nQ2 @Record { } .= 0;\nQ2 [Qinc2]= Q2 + 0.01;\nR2 @Record { } .= 0;\nR2 [Rinc2]= R2 + 0.01;\nreset2 @Record { } .= 0;\nreset2 [Qinc2]= t;\nreset2 [Rinc2]= t;\n\nQinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nRinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nQinc2 @DSwitcher { trigger: (t - reset2) >= 0.01, };\nRinc2 @DSwitcher { trigger: (t - reset2) >= 0.01, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Three competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure one event doesn't severely out-compete the other two. NOTE: STOCHASTIC TEST. This test is designed to fail only one time in a million, but it still may happen.\r\ncomponentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: EventIsNotPersistent, NonConstantParameter, RandomEventExecution\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThis model contains three events with the same trigger, the same priority, and all set 'persistent=false', and all of which disable the trigger of the others. This means that every .01 seconds, one fires and the others do not, at random, and increases the parameters Q, R, and T, respectively. A fourth parameter, S, is assigned the value of Q+R+T, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure none of the three parameters are chosen more frequently than the other two--if the difference gets higher than 5, it triggers. From our simulations, this should happen less often than one time in a million, so if you see it happen in your simulator more often than once, there's a good chance something is wrong.\r\n \r\n\r\nThe model contains:\r\n* 7 parameters (S, Q, R, T, reset, tolerance, error)\r\n\r\nThere are 4 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| Qinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ |\r\n| | | | | $Q = Q + 0.01$ |\r\n| Rinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ |\r\n| | | | | $R = R + 0.01$ |\r\n| Tinc | $geq(time - reset, 0.01)$ | $1$ | false | $reset = time$ |\r\n| | | | | $T = T + 0.01$ |\r\n| error_check | $or(geq(abs(Q - R), tolerance), geq(abs(Q - T), tolerance), geq(abs(T - R), tolerance))$ | (unset) | true | $error = 1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S | $Q + R + T$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter tolerance | $5$ | constant |\r\n| Initial value of parameter S | $Q + R + T$ | variable |\r\n| Initial value of parameter Q | $0$ | variable |\r\n| Initial value of parameter R | $0$ | variable |\r\n| Initial value of parameter T | $0$ | variable |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter error | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nS @Record { } .= 0;\nS := Q + R + T;\nQ @Record { } .= 0;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 0;\nR [Rinc]= R + 0.01;\nT @Record { } .= 0;\nT [Tinc]= T + 0.01;\nreset @Record { } .= 0;\nreset [Qinc]= t;\nreset [Rinc]= t;\nreset [Tinc]= t;\nerror @Record { } .= 0;\nerror [error_check]= 1;\n\ntolerance @Const { } = 5;\n\nQinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nRinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nTinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nerror_check @DSwitcher { trigger: abs(Q - R) >= tolerance or abs(Q - T) >= tolerance or abs(T - R) >= tolerance, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure one event doesn't happen too many times in a row. NOTE: STOCHASTIC TEST. This test is designed to fail only one time in a million, but it still may happen.\r\ncomponentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: EventIsNotPersistent, EventIsPersistent, EventUsesTriggerTimeValues, NonConstantParameter, RandomEventExecution\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThis model (the same basic model as 952) contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically.\r\n\r\nIn this test, we also keep track of how many times in a row either Q or R have been chosen, through the parameters Qrun and Rrun. Another parameter, maxrun, is set by its own events to be max(maxrun, Qrun, Rrun). A final event checks to see if maxrun has exceeded 20; if so, it is set to 1. In our simulations, in 1,000,000 runs, maxrun had an average of 13.25, and never exceeded 15 at all, so exceeding 300 is an occurrence that should happen much less than one time in a million. While this doesn't mean that your simulator will never have a run where maxrun exceeds 300, it does mean that this is a very rare event, and almost certainly means that something is wrong with your simulator: it may be that the same random number is being chosen multiple times.\r\n\r\nThe model contains:\r\n* 8 parameters (S, Q, R, reset, Qrun, Rrun, maxrun, error)\r\n\r\nThere are 5 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| Qinc | $(time - reset) ≥ 0.01$ | $10$ | false | $reset = time$ |\r\n| | | | | $Rrun = 0$ |\r\n| | | | | $Qrun = Qrun + 1$ |\r\n| | | | | $Q = Q + 0.01$ |\r\n| Rinc | $(time - reset) ≥ 0.01$ | $10$ | false | $reset = time$ |\r\n| | | | | $Qrun = 0$ |\r\n| | | | | $Rrun = Rrun + 1$ |\r\n| | | | | $R = R + 0.01$ |\r\n| maxrun_check1 | $Qrun > maxrun$ | $9$ | true | $maxrun = Qrun$ |\r\n| maxrun_check2 | $Rrun > maxrun$ | $8$ | true | $maxrun = Rrun$ |\r\n| error_check | $maxrun > 300$ | $7$ | true | $error = 1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S | $Q + R$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter S | $Q + R$ | variable |\r\n| Initial value of parameter Q | $0$ | variable |\r\n| Initial value of parameter R | $0$ | variable |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter Qrun | $0$ | variable |\r\n| Initial value of parameter Rrun | $0$ | variable |\r\n| Initial value of parameter maxrun | $0$ | variable |\r\n| Initial value of parameter error | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n*)\r\n(* \r\n\r\ncategory: Test\r\ncomponentTags: Parameter, EventNoDelay, EventPriority, AssignmentRule, CSymbolTime\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe events are:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Qinc | $time - reset >= 0.01$ | $-$ | $Q = Q + 0.01, Qrun = Qrun + 1, Rrun = 0, reset = time$ |\r\n | Rinc | $time - reset >= 0.01$ | $-$ | $R = R + 0.01, Rrun = Rrun + 1, Qrun = 0, reset = time$ |\r\n | maxrun_check1 | $Qrun > maxrun$ | $-$ | $maxrun = Qrun$ |\r\n | maxrun_check2 | $Rrun > maxrun$ | $-$ | $maxrun = Rrun$ |\r\n | error_check | $maxrun > 300$ | $-$ | $error = 1$ |]\r\n\r\n\r\n The initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value*|\r\n|Value of parameter Q |$0$ |\r\n|Value of parameter R |$0$ |\r\n|Value of parameter S |$0$ |\r\n|Value of parameter reset |$0$ |\r\n|Value of parameter Qrun |$0$ |\r\n|Value of parameter Rrun |$0$ |\r\n|Value of parameter maxrun |$0$ |\r\n|Value of parameter error |$0$ |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n","completion":"\n\nt @TimeScale { };\n\nS @Record { } .= 0;\nS := Q + R;\nQ @Record { } .= 0;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 0;\nR [Rinc]= R + 0.01;\nreset @Record { } .= 0;\nreset [Qinc]= t;\nreset [Rinc]= t;\nQrun @Record { } .= 0;\nQrun [Qinc]= Qrun + 1;\nQrun [Rinc]= 0;\nRrun @Record { } .= 0;\nRrun [Qinc]= 0;\nRrun [Rinc]= Rrun + 1;\nmaxrun @Record { } .= 0;\nmaxrun [maxrun_check1]= Qrun;\nmaxrun [maxrun_check2]= Rrun;\nerror @Record { } .= 0;\nerror [error_check]= 1;\n\nQinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nRinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nmaxrun_check1 @DSwitcher { trigger: Qrun > maxrun, };\nmaxrun_check2 @DSwitcher { trigger: Rrun > maxrun, };\nerror_check @DSwitcher { trigger: maxrun > 300, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, calculating a chi-squared statistic to ensure randomness. NOTE: STOCHASTIC TEST. This test is designed to fail with a frequency of 0.00002, but it still may happen.\r\ncomponentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, FunctionDefinition, Parameter\r\ntestTags: EventIsNotPersistent, EventIsPersistent, EventUsesTriggerTimeValues, NonConstantParameter, RandomEventExecution\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThis model (the same basic model as 952) contains two events with the same trigger, the same priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically.\r\n\r\nIn this test, we also keep track of each run of 16 tests in a row, calculating the sum of Q during that run, and incrementing the appropriate frequency (chi0 -> chi16). At the end of 6,420 tests, the chi-square value is calculated from the observed and the pre-calculated expected frequencies of the 17 possible values. If this value is greater than 50, an error is triggered. The liklihood of the error being triggered is 0.00002, so it is quite unlikely (though possible) that a simulator would trigger it with a working random number generator, and almost impossible for this to happen twice in a row.\r\n\r\nThis model has a number of events, so it's probably best to look at the antimony file for more details: 00966-antimony.txt\r\n\r\n\r\nThe model contains:\r\n* 27 parameters (S, Q, R, reset, chicount, chitest, assemble, chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16, tests, finalchi, error)\r\n\r\nIt also contains 1 function definition(s):\r\n; calculateerror: $pow(x0 - 0.0952, 2) / 0.0952 + pow(x1 - 1.523, 2) / 1.523 + pow(x2 - 11.428, 2) / 11.428 + pow(x3 - 53.32, 2) / 53.32 + pow(x4 - 173.29, 2) / 173.29 + pow(x5 - 415.898, 2) / 415.898 + pow(x6 - 762.48, 2) / 762.48 + pow(x7 - 1089.26, 2) / 1089.26 + pow(x8 - 1225.415, 2) / 1225.415 + pow(x9 - 1089.26, 2) / 1089.26 + pow(x10 - 762.48, 2) / 762.48 + pow(x11 - 415.898, 2) / 415.898 + pow(x12 - 173.29, 2) / 173.29 + pow(x13 - 53.32, 2) / 53.32 + pow(x14 - 11.428, 2) / 11.428 + pow(x15 - 1.523, 2) / 1.523 + pow(x16 - 0.0952, 2) / 0.0952$\r\n\r\nThere are 23 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| Rinc | $geq(time - reset, 0.01)$ | $10$ | false | $reset = time$ |\r\n| | | | | $chicount = chicount + 1$ |\r\n| | | | | $R = R + 0.01$ |\r\n| Qinc | $geq(time - reset, 0.01)$ | $10$ | false | $reset = time$ |\r\n| | | | | $chitest = chitest + 1$ |\r\n| | | | | $chicount = chicount + 1$ |\r\n| | | | | $Q = Q + 0.01$ |\r\n| repeat | $geq(floor(chicount / 16), 1)$ | $5$ | true | $assemble = 1.5$ |\r\n| | | | | $chicount = 0$ |\r\n| _E0 | $and(geq(assemble, 1), eq(chitest, 0))$ | $3$ | true | $chi0 = chi0 + 1$ |\r\n| _E1 | $and(geq(assemble, 1), eq(chitest, 1))$ | $3$ | true | $chi1 = chi1 + 1$ |\r\n| _E2 | $and(geq(assemble, 1), eq(chitest, 2))$ | $3$ | true | $chi2 = chi2 + 1$ |\r\n| _E3 | $and(geq(assemble, 1), eq(chitest, 3))$ | $3$ | true | $chi3 = chi3 + 1$ |\r\n| _E4 | $and(geq(assemble, 1), eq(chitest, 4))$ | $3$ | true | $chi4 = chi4 + 1$ |\r\n| _E5 | $and(geq(assemble, 1), eq(chitest, 5))$ | $3$ | true | $chi5 = chi5 + 1$ |\r\n| _E6 | $and(geq(assemble, 1), eq(chitest, 6))$ | $3$ | true | $chi6 = chi6 + 1$ |\r\n| _E7 | $and(geq(assemble, 1), eq(chitest, 7))$ | $3$ | true | $chi7 = chi7 + 1$ |\r\n| _E8 | $and(geq(assemble, 1), eq(chitest, 8))$ | $3$ | true | $chi8 = chi8 + 1$ |\r\n| _E9 | $and(geq(assemble, 1), eq(chitest, 9))$ | $3$ | true | $chi9 = chi9 + 1$ |\r\n| _E10 | $and(geq(assemble, 1), eq(chitest, 10))$ | $3$ | true | $chi10 = chi10 + 1$ |\r\n| _E11 | $and(geq(assemble, 1), eq(chitest, 11))$ | $3$ | true | $chi11 = chi11 + 1$ |\r\n| _E12 | $and(geq(assemble, 1), eq(chitest, 12))$ | $3$ | true | $chi12 = chi12 + 1$ |\r\n| _E13 | $and(geq(assemble, 1), eq(chitest, 13))$ | $3$ | true | $chi13 = chi13 + 1$ |\r\n| _E14 | $and(geq(assemble, 1), eq(chitest, 14))$ | $3$ | true | $chi14 = chi14 + 1$ |\r\n| _E15 | $and(geq(assemble, 1), eq(chitest, 15))$ | $3$ | true | $chi15 = chi15 + 1$ |\r\n| _E16 | $and(geq(assemble, 1), eq(chitest, 16))$ | $3$ | true | $chi16 = chi16 + 1$ |\r\n| _E17 | $geq(assemble, 1)$ | $1$ | true | $tests = tests + 1$ |\r\n| | | | | $chitest = 0$ |\r\n| | | | | $assemble = 0$ |\r\n| _E18 | $and(geq(tests, 6240), eq(finalchi, 0))$ | $0$ | true | $finalchi = calculateerror(chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16)$ |\r\n| error_check | $gt(finalchi, 50)$ | $-1$ | true | $error = 1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S | $Q + R$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter S | $Q + R$ | variable |\r\n| Initial value of parameter Q | $0$ | variable |\r\n| Initial value of parameter R | $0$ | variable |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter chicount | $0$ | variable |\r\n| Initial value of parameter chitest | $0$ | variable |\r\n| Initial value of parameter assemble | $0$ | variable |\r\n| Initial value of parameter chi0 | $0$ | variable |\r\n| Initial value of parameter chi1 | $0$ | variable |\r\n| Initial value of parameter chi2 | $0$ | variable |\r\n| Initial value of parameter chi3 | $0$ | variable |\r\n| Initial value of parameter chi4 | $0$ | variable |\r\n| Initial value of parameter chi5 | $0$ | variable |\r\n| Initial value of parameter chi6 | $0$ | variable |\r\n| Initial value of parameter chi7 | $0$ | variable |\r\n| Initial value of parameter chi8 | $0$ | variable |\r\n| Initial value of parameter chi9 | $0$ | variable |\r\n| Initial value of parameter chi10 | $0$ | variable |\r\n| Initial value of parameter chi11 | $0$ | variable |\r\n| Initial value of parameter chi12 | $0$ | variable |\r\n| Initial value of parameter chi13 | $0$ | variable |\r\n| Initial value of parameter chi14 | $0$ | variable |\r\n| Initial value of parameter chi15 | $0$ | variable |\r\n| Initial value of parameter chi16 | $0$ | variable |\r\n| Initial value of parameter tests | $0$ | variable |\r\n| Initial value of parameter finalchi | $0$ | variable |\r\n| Initial value of parameter error | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\ncalculateerror #defineFunction { arguments: [x0, x1, x2, x3, x4, x5, x6, x7, x8, x9, x10, x11, x12, x13, x14, x15, x16], math: pow(x0 - 0.0952, 2) / 0.0952 + pow(x1 - 1.523, 2) / 1.523 + pow(x2 - 11.428, 2) / 11.428 + pow(x3 - 53.32, 2) / 53.32 + pow(x4 - 173.29, 2) / 173.29 + pow(x5 - 415.898, 2) / 415.898 + pow(x6 - 762.48, 2) / 762.48 + pow(x7 - 1089.26, 2) / 1089.26 + pow(x8 - 1225.415, 2) / 1225.415 + pow(x9 - 1089.26, 2) / 1089.26 + pow(x10 - 762.48, 2) / 762.48 + pow(x11 - 415.898, 2) / 415.898 + pow(x12 - 173.29, 2) / 173.29 + pow(x13 - 53.32, 2) / 53.32 + pow(x14 - 11.428, 2) / 11.428 + pow(x15 - 1.523, 2) / 1.523 + pow(x16 - 0.0952, 2) / 0.0952, };\n\nt @TimeScale { };\n\nS @Record { } .= 0;\nS := Q + R;\nQ @Record { } .= 0;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 0;\nR [Rinc]= R + 0.01;\nreset @Record { } .= 0;\nreset [Rinc]= t;\nreset [Qinc]= t;\nchicount @Record { } .= 0;\nchicount [Rinc]= chicount + 1;\nchicount [Qinc]= chicount + 1;\nchicount [repeat]= 0;\nchitest @Record { } .= 0;\nchitest [Qinc]= chitest + 1;\nchitest [_E17]= 0;\nassemble @Record { } .= 0;\nassemble [repeat]= 1.5;\nassemble [_E17]= 0;\nchi0 @Record { } .= 0;\nchi0 [_E0]= chi0 + 1;\nchi1 @Record { } .= 0;\nchi1 [_E1]= chi1 + 1;\nchi2 @Record { } .= 0;\nchi2 [_E2]= chi2 + 1;\nchi3 @Record { } .= 0;\nchi3 [_E3]= chi3 + 1;\nchi4 @Record { } .= 0;\nchi4 [_E4]= chi4 + 1;\nchi5 @Record { } .= 0;\nchi5 [_E5]= chi5 + 1;\nchi6 @Record { } .= 0;\nchi6 [_E6]= chi6 + 1;\nchi7 @Record { } .= 0;\nchi7 [_E7]= chi7 + 1;\nchi8 @Record { } .= 0;\nchi8 [_E8]= chi8 + 1;\nchi9 @Record { } .= 0;\nchi9 [_E9]= chi9 + 1;\nchi10 @Record { } .= 0;\nchi10 [_E10]= chi10 + 1;\nchi11 @Record { } .= 0;\nchi11 [_E11]= chi11 + 1;\nchi12 @Record { } .= 0;\nchi12 [_E12]= chi12 + 1;\nchi13 @Record { } .= 0;\nchi13 [_E13]= chi13 + 1;\nchi14 @Record { } .= 0;\nchi14 [_E14]= chi14 + 1;\nchi15 @Record { } .= 0;\nchi15 [_E15]= chi15 + 1;\nchi16 @Record { } .= 0;\nchi16 [_E16]= chi16 + 1;\ntests @Record { } .= 0;\ntests [_E17]= tests + 1;\nfinalchi @Record { } .= 0;\nfinalchi [_E18]= calculateerror(chi0, chi1, chi2, chi3, chi4, chi5, chi6, chi7, chi8, chi9, chi10, chi11, chi12, chi13, chi14, chi15, chi16);\nerror @Record { } .= 0;\nerror [error_check]= 1;\n\nRinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nQinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nrepeat @DSwitcher { trigger: floor(chicount / 16) >= 1, };\n_E0 @DSwitcher { trigger: assemble >= 1 and chitest == 0, };\n_E1 @DSwitcher { trigger: assemble >= 1 and chitest == 1, };\n_E2 @DSwitcher { trigger: assemble >= 1 and chitest == 2, };\n_E3 @DSwitcher { trigger: assemble >= 1 and chitest == 3, };\n_E4 @DSwitcher { trigger: assemble >= 1 and chitest == 4, };\n_E5 @DSwitcher { trigger: assemble >= 1 and chitest == 5, };\n_E6 @DSwitcher { trigger: assemble >= 1 and chitest == 6, };\n_E7 @DSwitcher { trigger: assemble >= 1 and chitest == 7, };\n_E8 @DSwitcher { trigger: assemble >= 1 and chitest == 8, };\n_E9 @DSwitcher { trigger: assemble >= 1 and chitest == 9, };\n_E10 @DSwitcher { trigger: assemble >= 1 and chitest == 10, };\n_E11 @DSwitcher { trigger: assemble >= 1 and chitest == 11, };\n_E12 @DSwitcher { trigger: assemble >= 1 and chitest == 12, };\n_E13 @DSwitcher { trigger: assemble >= 1 and chitest == 13, };\n_E14 @DSwitcher { trigger: assemble >= 1 and chitest == 14, };\n_E15 @DSwitcher { trigger: assemble >= 1 and chitest == 15, };\n_E16 @DSwitcher { trigger: assemble >= 1 and chitest == 16, };\n_E17 @DSwitcher { trigger: assemble >= 1, };\n_E18 @DSwitcher { trigger: tests >= 6240 and finalchi == 0, };\nerror_check @DSwitcher { trigger: finalchi > 50, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Competing events with alternating priorities, so one fires for 5 seconds, then the other fires for the next 5 seconds.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: NonConstantParameter, EventIsNotPersistent\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThis model contains two events with the same trigger, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not. One has the priority 'time' and the other the priority '5.001', meaning that for the first 5 seconds, one fires, and for the next 5 seconds, the other fires.\r\n \r\n\r\nThe model contains:\r\n* 3 parameters (reset, Q, R)\r\n\r\nThere are 2 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| Qinc | $(time - reset) ≥ 0.01$ | $time$ | false | $reset = time$ |\r\n| | | | | $Q = Q + 0.01$ |\r\n| Rinc | $(time - reset) ≥ 0.01$ | $5.001$ | false | $reset = time$ |\r\n| | | | | $R = R + 0.01$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter Q | $0$ | variable |\r\n| Initial value of parameter R | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nreset @Record { } .= 0;\nreset [Qinc]= t;\nreset [Rinc]= t;\nQ @Record { } .= 0;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 0;\nR [Rinc]= R + 0.01;\n\nQinc @DSwitcher { trigger: (t - reset) >= 0.01, };\nRinc @DSwitcher { trigger: (t - reset) >= 0.01, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A three-step reaction scheme with a model conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThis model tests conversion factors through a system of three reactions. There is a conversion factor ('modelconv') on the model of 4. This changes how S1 and S2 change in time, but not how S1 and S2 are interpreted in the reaction rates.\r\n \r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 5 parameters (k1, k2, k3, S1conv, modelconv)\r\n* 1 compartment (default_compartment)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> S1 | $k1$ |\r\n| 2S1 -> 3S2 | $k2 * S1 / S2$ |\r\n| S2 -> | $k3 * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $0$ | variable |\r\n| Initial amount of species S2 | $0.001$ | variable |\r\n| Initial value of parameter k1 | $1$ | constant |\r\n| Initial value of parameter k2 | $3$ | constant |\r\n| Initial value of parameter k3 | $1.4$ | constant |\r\n| Initial value of parameter S1conv | $3$ | constant |\r\n| Initial value of parameter modelconv | $4$ | constant |\r\n| Initial volume of compartment 'default_compartment' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ndefault_compartment @Compartment { boundary: true, aux: {{\"sboTerm\":\"SBO:0000410\"}}, } .= 1;\n\nS1 @Species { compartment: default_compartment, } .= 0 / default_compartment;\nS2 @Species { compartment: default_compartment, } .= 0.001 / default_compartment;\n\n_J0 @Reaction { actors: = S1, };\n_J0 := k1;\n_J1 @Reaction { actors: 2*S1 = 3*S2, };\n_J1 := (k2 * S1) / S2;\n_J2 @Reaction { actors: S2 = , };\n_J2 := k3 * S2;\n\nk1 @Const { } = 1;\nk2 @Const { } = 3;\nk3 @Const { } = 1.4;\nS1conv @Const { } = 3;\nmodelconv @Const { } = 4;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A three-step reaction scheme with a model conversion factor and a species conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThis model tests conversion factors through a system of three reactions. There is a conversion factor ('modelconv') on the model of 4, and a second conversion factor ('S1conv') on species S1. This means that S1 is converted according to S1conv, and S2 is converted according to modelconv. Together, this changes how S1 and S2 change in time, but not how S1 and S2 are interpreted in the reaction rates.\r\n\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 5 parameters (k1, k2, k3, S1conv, modelconv)\r\n* 1 compartment (default_compartment)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> S1 | $k1$ |\r\n| 2S1 -> 3S2 | $k2 * S1 / S2$ |\r\n| S2 -> | $k3 * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial concentration of species S2 | $0.001$ | variable |\r\n| Initial value of parameter k1 | $1$ | constant |\r\n| Initial value of parameter k2 | $3$ | constant |\r\n| Initial value of parameter k3 | $1.4$ | constant |\r\n| Initial value of parameter S1conv | $3$ | constant |\r\n| Initial value of parameter modelconv | $4$ | constant |\r\n| Initial volume of compartment 'default_compartment' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ndefault_compartment @Compartment { boundary: true, aux: {{\"sboTerm\":\"SBO:0000410\"}}, } .= 1;\n\nS1 @Species { compartment: default_compartment, } .= 0;\nS2 @Species { compartment: default_compartment, } .= 0.001;\n\n_J0 @Reaction { actors: = S1, };\n_J0 := k1;\n_J1 @Reaction { actors: 2*S1 = 3*S2, };\n_J1 := (k2 * S1) / S2;\n_J2 @Reaction { actors: S2 = , };\n_J2 := k3 * S2;\n\nk1 @Const { } = 1;\nk2 @Const { } = 3;\nk3 @Const { } = 1.4;\nS1conv @Const { } = 3;\nmodelconv @Const { } = 4;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A three-step reaction scheme with a species conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThis model tests conversion factors through a system of three reactions. There is a conversion factor ('S1conv') on species S1. This means that S1 is converted according to S1conv, and S2 is not converted. This changes how S1 change in time, but not how S1 is interpreted in the reaction rates.\r\n\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 5 parameters (k1, k2, k3, S1conv, modelconv)\r\n* 1 compartment (default_compartment)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> S1 | $k1$ |\r\n| 2S1 -> 3S2 | $k2 * S1 / S2$ |\r\n| S2 -> | $k3 * S2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial concentration of species S2 | $0.001$ | variable |\r\n| Initial value of parameter k1 | $1$ | constant |\r\n| Initial value of parameter k2 | $3$ | constant |\r\n| Initial value of parameter k3 | $1.4$ | constant |\r\n| Initial value of parameter S1conv | $3$ | constant |\r\n| Initial value of parameter modelconv | $4$ | constant |\r\n| Initial volume of compartment 'default_compartment' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ndefault_compartment @Compartment { boundary: true, aux: {{\"sboTerm\":\"SBO:0000410\"}}, } .= 1;\n\nS1 @Species { compartment: default_compartment, } .= 0;\nS2 @Species { compartment: default_compartment, } .= 0.001;\n\n_J0 @Reaction { actors: = S1, };\n_J0 := k1;\n_J1 @Reaction { actors: 2*S1 = 3*S2, };\n_J1 := (k2 * S1) / S2;\n_J2 @Reaction { actors: S2 = , };\n_J2 := k3 * S2;\n\nk1 @Const { } = 1;\nk2 @Const { } = 3;\nk3 @Const { } = 1.4;\nS1conv @Const { } = 3;\nmodelconv @Const { } = 4;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Several events conspire within the same time step to trigger three events multiple times, with different outcomes.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: EventIsNotPersistent, EventIsPersistent, EventUsesAssignmentTimeValues, EventUsesTriggerTimeValues, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThis model contains two events that trigger when the parameter multitrig increases to \r\nabove 1. The first is set 'persistent=true' and 'useValuesFromTriggerTime=false', and sets x=x+1, meaning that every time\r\nit triggers, it ends up increasing x by one. \r\n\r\nThe second is set 'persistent=true' but 'useValuesFromTriggerTime=true', meaning that it executes\r\nmultiple times, but each time uses the value of y from the time it first triggered, meaning\r\nthat y gets reset to one four times.\r\n\r\nThe third is set 'persistent=false' and 'useValuesFromTriggerTime=false',\r\nand sets z=z+3, meaning that every time it triggers, it has the potential to increase z\r\nby three, but if multitrig drops below 1 again, it will not actually do so. In the end,\r\nit only executes a single time.\r\n\r\nThe model also contains nine events with the same trigger and with decreasing priorities \r\nthat alternate setting the value of the parameter 'multitrig' from zero to 2, then to \r\nzero, then back again, etc. The priorities of all these events are higher than the first \r\ntwo, meaning that at a single time point, the first two events are triggered five times,\r\nand 'de-triggered' four times. Since the first event was persistent, x should increase\r\nfrom zero to five, and since the second event was not persistent, y should increase from\r\nzero to one.\r\n\r\nFor a different view of this model, see 00978-antimony.txt\r\n\r\nThe model contains:\r\n* 4 parameters (multitrig, x, y, z)\r\n\r\nThere are 12 events:\r\n\r\n[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Use values from:* | *Event Assignments* |\r\n| _E0 | $time ≥ 0.99$ | $10$ | true | Trigger time | $multitrig = 2$ |\r\n| _E1 | $time ≥ 0.99$ | $9$ | true | Trigger time | $multitrig = 0$ |\r\n| _E2 | $time ≥ 0.99$ | $8$ | true | Trigger time | $multitrig = 2$ |\r\n| _E3 | $time ≥ 0.99$ | $7$ | true | Trigger time | $multitrig = 0$ |\r\n| _E4 | $time ≥ 0.99$ | $6$ | true | Trigger time | $multitrig = 2$ |\r\n| _E5 | $time ≥ 0.99$ | $5$ | true | Trigger time | $multitrig = 0$ |\r\n| _E6 | $time ≥ 0.99$ | $4$ | true | Trigger time | $multitrig = 2$ |\r\n| _E7 | $time ≥ 0.99$ | $3$ | true | Trigger time | $multitrig = 0$ |\r\n| _E8 | $time ≥ 0.99$ | $2$ | true | Trigger time | $multitrig = 2$ |\r\n| _E9 | $multitrig > 1$ | $1$ | true | Assignment time | $x = x + 1$ |\r\n| _E10 | $multitrig > 1$ | $1$ | true | Trigger time | $y = y + 1$ |\r\n| _E11 | $multitrig > 1$ | $1$ | false | Assignment time | $z = z + 3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter multitrig | $0$ | variable |\r\n| Initial value of parameter x | $0$ | variable |\r\n| Initial value of parameter y | $0$ | variable |\r\n| Initial value of parameter z | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nmultitrig @Record { } .= 0;\nmultitrig [_E0]= 2;\nmultitrig [_E1]= 0;\nmultitrig [_E2]= 2;\nmultitrig [_E3]= 0;\nmultitrig [_E4]= 2;\nmultitrig [_E5]= 0;\nmultitrig [_E6]= 2;\nmultitrig [_E7]= 0;\nmultitrig [_E8]= 2;\nx @Record { } .= 0;\nx [_E9]= x + 1;\ny @Record { } .= 0;\ny [_E10]= y + 1;\nz @Record { } .= 0;\nz [_E11]= z + 3;\n\n_E0 @DSwitcher { trigger: t >= 0.99, };\n_E1 @DSwitcher { trigger: t >= 0.99, };\n_E2 @DSwitcher { trigger: t >= 0.99, };\n_E3 @DSwitcher { trigger: t >= 0.99, };\n_E4 @DSwitcher { trigger: t >= 0.99, };\n_E5 @DSwitcher { trigger: t >= 0.99, };\n_E6 @DSwitcher { trigger: t >= 0.99, };\n_E7 @DSwitcher { trigger: t >= 0.99, };\n_E8 @DSwitcher { trigger: t >= 0.99, };\n_E9 @DSwitcher { trigger: multitrig > 1, };\n_E10 @DSwitcher { trigger: multitrig > 1, };\n_E11 @DSwitcher { trigger: multitrig > 1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two event where the two event assignments should not interfere with each other. \r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\n This model contains two events that trigger when time > 0.98 and 0.99. In each, there is on event assignment that changes the value of a parameter, and a second event assignment that uses that parameter to change the value of a second parameter. However, the second event assignment should not use the changed value from the first parameter, but rather the value it had at the beginning of event assignment. (This is true regardless of the value of 'useValuesFromTriggerTime', but the value of that flag here happens to be true.)\r\n\r\nThe model contains:\r\n* 4 parameters (x, y, p, q)\r\n\r\nThere are 2 events:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time ≥ 0.98$ | $y = y + x$ |\r\n| | | $x = 2$ |\r\n| _E1 | $time ≥ 0.99$ | $p = 3$ |\r\n| | | $q = p + 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $0$ | variable |\r\n| Initial value of parameter y | $0$ | variable |\r\n| Initial value of parameter p | $0$ | variable |\r\n| Initial value of parameter q | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 0;\nx [_E0]= 2;\ny @Record { } .= 0;\ny [_E0]= y + x;\np @Record { } .= 0;\np [_E1]= 3;\nq @Record { } .= 0;\nq [_E1]= p + 1;\n\n_E0 @DSwitcher { trigger: t >= 0.98, };\n_E1 @DSwitcher { trigger: t >= 0.99, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two events with different 'initialValue's, causing one to fire and one to not fire.\r\ncomponentTags: EventNoDelay, Parameter\r\ntestTags: EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two events, one that assigns '1' to parameter p2, and one that assigns '1' to parameter p3. Both have the same trigger, p1>0, which is true the entire time, but the first trigger is set 'initialValue=\"false\"' and the second 'initialValue=\"true\"'. This causes the first to trigger at t0 and the second to not trigger.\r\n\r\nThe model contains:\r\n* 3 parameters (p1, p2, p3)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $p1 > 0$ | false | $p2 = 1$ |\r\n| E1 | $p1 > 0$ | true | $p3 = 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $1$ | constant |\r\n| Initial value of parameter p2 | $0$ | variable |\r\n| Initial value of parameter p3 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np2 @Record { } .= 0;\np2 [E0]= 1;\np3 @Record { } .= 0;\np3 [E1]= 1;\n\np1 @Const { } = 1;\n\nE0 @DSwitcher { trigger: p1 > 0, };\nE1 @DSwitcher { trigger: p1 > 0, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two events with different 'initialValue's, causing one to fire and one to not fire.\r\ncomponentTags: EventNoDelay, Parameter, RateRule\r\ntestTags: EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nThe model contains two events, one that assigns '1' to parameter p2, and one that assigns '1' to parameter p3. Both have the same trigger, p1>=1, which is true at t0, but is false thereafter due to a rate rule. The first trigger is set 'initialValue=\"false\"' and the second 'initialValue=\"true\"'. This causes the first to trigger at t0 and the second to not trigger.\r\n \r\nThe model contains:\r\n* 3 parameters (p1, p2, p3)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $p1 ≥ 1$ | false | $p2 = 1$ |\r\n| E1 | $p1 ≥ 1$ | true | $p3 = 1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p1 | $-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $-1$ | variable |\r\n| Initial value of parameter p2 | $0$ | variable |\r\n| Initial value of parameter p3 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1_proc @Process { actors: = p1, };\np1_proc := (-1);\n\np1 @Record { } .= 1;\np2 @Record { } .= 0;\np2 [E0]= 1;\np3 @Record { } .= 0;\np3 [E1]= 1;\n\nE0 @DSwitcher { trigger: p1 >= 1, };\nE1 @DSwitcher { trigger: p1 >= 1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two events with different 'initialValue's, causing one to fire and one to not fire.\r\ncomponentTags: EventNoDelay, EventPriority, Parameter\r\ntestTags: EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\n The model contains two events, one that assigns '1' to parameter p2, and one that assigns '1' to parameter p3. Both have the same trigger, p1>=1, which is true at t0, but is false thereafter due to a third event. The first trigger is set 'initialValue=\"false\"' and the second 'initialValue=\"true\"'. This causes the first to trigger at t0 and the second to not trigger.\r\n\r\nThe model contains:\r\n* 3 parameters (p1, p2, p3)\r\n\r\nThere are 3 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* |\r\n| E0 | $p1 ≥ 1$ | $2$ | false | $p2 = 1$ |\r\n| E1 | $p1 ≥ 1$ | $2$ | true | $p3 = 1$ |\r\n| E2 | $p1 ≥ 1$ | $1$ | false | $p1 = 0$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $1$ | variable |\r\n| Initial value of parameter p2 | $0$ | variable |\r\n| Initial value of parameter p3 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1 @Record { } .= 1;\np1 [E2]= 0;\np2 @Record { } .= 0;\np2 [E0]= 1;\np3 @Record { } .= 0;\np3 [E1]= 1;\n\nE0 @DSwitcher { trigger: p1 >= 1, };\nE1 @DSwitcher { trigger: p1 >= 1, };\nE2 @DSwitcher { trigger: p1 >= 1, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Species with an initialConcentration but hasOnlySubstanceUnits=\"true\".\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nThe single species in this model has an initial concentration of '1', but lives in a compartment of size 5, giving it an initial amount of 5. Since 'hasOnlySubstanceUnits' is 'true', this amount is what is used for the rate rule of the reaction (10/S1).\r\n\r\nFor comparison, if the initialConcentration of the species is changed to an initialAmount of '5', the same numerical results should be obtained.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (comp)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> S1 | $10 / S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $5$ | variable |\r\n| Initial volume of compartment 'comp' | $5$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ncomp @Compartment { boundary: true, } .= 5;\n\nS1 @Species { compartment: comp, isAmount: true, } .= 1 * comp;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := 10 / S1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Testing different versions of initialAmount vs. initialConcentration with hasOnlySubstanceUnits=true/false, in a constant and varying compartment.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, RateRule, Species\r\ntestTags: Amount, HasOnlySubstanceUnits, MultiCompartment, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\n This model has four species in a constant (non-unity) compartment with the four different combinations of being set by initialAmount or initialConcentration, and being set 'hasOnlySubstanceUnits' equal to true or false. It also has another four species with the same spread, in a different compartment whose volume changes over time. Each of these eight species is assigned to a parameter, to catch the 'hasOnlySubstanceUnits' differences (every other parameter has units of amount or concentration, respectively).\r\n\r\nThe model contains:\r\n* 8 species (S1, S2, S3, S4, S5, S6, S7, S8)\r\n* 8 parameters (p1, p2, p3, p4, p5, p6, p7, p8)\r\n* 2 compartments (comp1, comp2)\r\n\r\nThere are 9 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | comp2 | $1$ |\r\n| Assignment | p1 | $S1$ |\r\n| Assignment | p2 | $S2$ |\r\n| Assignment | p3 | $S3$ |\r\n| Assignment | p4 | $S4$ |\r\n| Assignment | p5 | $S5$ |\r\n| Assignment | p6 | $S6$ |\r\n| Assignment | p7 | $S7$ |\r\n| Assignment | p8 | $S8$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | variable |\r\n| Initial concentration of species S2 | $2$ | variable |\r\n| Initial amount of species S3 | $3$ | variable |\r\n| Initial amount of species S4 | $4$ | variable |\r\n| Initial concentration of species S5 | $5$ | variable |\r\n| Initial concentration of species S6 | $6$ | variable |\r\n| Initial amount of species S7 | $7$ | variable |\r\n| Initial amount of species S8 | $8$ | variable |\r\n| Initial value of parameter p1 | $S1$ | variable |\r\n| Initial value of parameter p2 | $S2$ | variable |\r\n| Initial value of parameter p3 | $S3$ | variable |\r\n| Initial value of parameter p4 | $S4$ | variable |\r\n| Initial value of parameter p5 | $S5$ | variable |\r\n| Initial value of parameter p6 | $S6$ | variable |\r\n| Initial value of parameter p7 | $S7$ | variable |\r\n| Initial value of parameter p8 | $S8$ | variable |\r\n| Initial volume of compartment 'comp1' | $10$ | constant |\r\n| Initial volume of compartment 'comp2' | $10$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ncomp1 @Compartment { boundary: true, } .= 10;\ncomp2 @Compartment { } .= 10;\n\nS1 @Species { compartment: comp1, } .= 1;\nS2 @Species { compartment: comp1, isAmount: true, } .= 2 * comp1;\nS3 @Species { compartment: comp1, } .= 3 / comp1;\nS4 @Species { compartment: comp1, isAmount: true, } .= 4;\nS5 @Species { compartment: comp2, } .= 5;\nS6 @Species { compartment: comp2, isAmount: true, } .= 6 * comp2;\nS7 @Species { compartment: comp2, } .= 7 / comp2;\nS8 @Species { compartment: comp2, isAmount: true, } .= 8;\n\ncomp2_proc @Process { actors: = comp2, };\ncomp2_proc := 1;\n\np1 @Record { };\np1 := S1;\np2 @Record { };\np2 := S2;\np3 @Record { };\np3 := S3;\np4 @Record { };\np4 := S4;\np5 @Record { };\np5 := S5;\np6 @Record { };\np6 := S6;\np7 @Record { };\np7 := S7;\np8 @Record { };\np8 := S8;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a size-10 compartment \r\n where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nNote: This test is a direct copy of test 00060, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a size-10 compartment \r\n where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00061, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 1.7 \\x 10^1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 17;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a size-10 compartment \r\n where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00062, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.3 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3 \\x 10^6$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 1300000;\nk2 @Const 'k2' { } = 300000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction using functionDefinitions with two \r\nspecies in a size-10 compartment where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nNote: This test is a direct copy of test 00113, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. The model contains one\r\nreaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $multiply(k1,S1)$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$ 0$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := multiply(k1, S1);\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reactions using functionDefinitions with three species in a size-10 compartment \r\n where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00114, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * multiply(S1,S2)$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-2$ |mole |\r\n|Value of parameter k1 |$ 1.7 $ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they\r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.02;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * multiply(S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 1.7;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions using functiondefinitions with four species in a size-10 compartment \r\n where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00115, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * multiply(S1,S2)$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\n\r\nThe model contains one functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$ 2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 0.5 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.3 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 5e-7;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * multiply(S1, S2);\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 1300000;\nk2 @Const 'k2' { } = 300000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 2-dimensional\r\nsize-10 compartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00208, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is two-dimensional. Species S1 and S2 are declared to have\r\nonly substance units. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-4$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-4$ |mole |\r\n|Value of parameter k1 |$ 1$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 10$ |metre^2^ |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-4;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-4;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\n\nk1 @Const 'k1' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reactions and two rate rules with four species in a size-10 compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nNote: This test is a direct copy of test 00333, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains one reaction defined as:\r\n\r\n[{width:25em,=}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe model contains two rules:\r\n\r\n[{width:25em,=}| *Type* | *Variable* | *Formula* |\r\n| Rate | S3 | $k1 * 0.5 10^-3$ |\r\n| Rate | S4 | $-k2 * 0.5 10^-3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,=}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$ 2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$ 1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$ 4 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 0.693$ |second^-1^ |\r\n|Value of parameter k2 |$ 0.25$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only (meaning that\r\nthe attribute %hasOnlySubstanceUnits% is set to true). Thus, they must be\r\ntreated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.002;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.004;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := 5e-4 * k1;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule2\"}}, };\nS4_proc := (-5e-4) * k2;\n\nk1 @Const 'k1' { } = 0.693;\nk2 @Const 'k2' { } = 0.25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a 2-dimensional\r\nsize-10 compartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00209, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. Species S1, S2 and S3 are\r\ndeclared to have only substance units. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$ 75$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 25$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 10$ |metre^2^ |]\r\n\r\nThe species have been declared as having substance units only. Thus, they\r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.2;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 75;\nk2 @Const 'k2' { } = 25;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 2-dimensional\r\ncompartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00210, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 2-dimensional. All four species are declared\r\nto have only substance units. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-3$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-3$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-3$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 7.5 \\x 10^3$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^3$ |mole^-1^ second^-1^ |\r\n|Area of compartment \"compartment\" |$ 10$ |metre^2^ |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre^2, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.0015;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.002;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 7500;\nk2 @Const 'k2' { } = 250;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with two species in a 1-dimensional\r\nsize-10 compartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nNote: This test is a direct copy of test 00223, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are two\r\nspecies named S1 and S2 and one parameter named k1. Compartment\r\n\"compartment\" is one-dimensional. Species S1 and S2 are declared to have\r\nonly substance units. The model contains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$ 1.5$ |second^-1^ |\r\n|Area of compartment \"compartment\" |$ 10$ |metre^2^ |]\r\n\r\nThe species have been declared as having substance units only. Thus, they\r\nmust be treated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\n\nk1 @Const 'k1' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction with two species in a 1-dimensional\r\n size-10 compartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00224, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. Species S1, S2 and S3 are\r\ndeclared to have only substance units. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1.0$ |mole |\r\n|Initial amount of S2 |$ 2.0$ |mole |\r\n|Initial amount of S3 |$ 1.5$ |mole |\r\n|Value of parameter k1 |$ 7.5$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 0.3$ |second^-1^ |\r\n|Length of compartment \"compartment\" |$ 10$ |metre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 7.5;\nk2 @Const 'k2' { } = 0.3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic two reactions with four species in a 1-dimensional\r\n size-10 compartment, where the species have only substance units.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00225, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2.\r\nCompartment \"compartment\" is 1-dimensional. All four species are declared\r\nto have only substance units. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 + S4 | $k1 * S1 * S2$ |\r\n| S3 + S4 -> S1 + S2 | $k2 * S3 * S4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-2$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-2$ |mole |\r\n|Initial amount of S3 |$2.0 \\x 10^-2$ |mole |\r\n|Initial amount of S4 |$1.0 \\x 10^-3$ |mole |\r\n|Value of parameter k1 |$ 6.2 \\x 10^2$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 5 \\x 10^2$ |mole^-1^ second^-1^ |\r\n|Length of compartment \"compartment\" |$ 10$ |metre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: metre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.01;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.015;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.02;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 0.001;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3 * S4;\n\nk1 @Const 'k1' { } = 620;\nk2 @Const 'k2' { } = 500;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic single forward reaction with three species in one\r\n size-10 compartment using an AssignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00295, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k2 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S3 | $k1 * S2$ |]\r\n\r\nIn this case there is no initial value declared for species S3. Thus the\r\ninitial value must be calculated by the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$ undeclared$ |mole |\r\n|Value of parameter k1 |$ 1.05$ |dimensionless |\r\n|Value of parameter k2 |$ 1.15$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.15;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, };\nS3 := k1 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k2 * S1;\n\nk1 @Const 'k1' { } = 1.05;\nk2 @Const 'k2' { } = 1.15;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions with four species in one\r\n size-10 compartment using an assignmentRule to vary one species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00296, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and three parameters named k1, k2 and k3.\r\nThe model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $k3 * S2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S2 |$ 1.5 \\x 10^-5$ |mole |\r\n|Initial amount of S3 |$ 1 \\x 10^-5$ |mole |\r\n|Initial amount of S4 |$2.25 \\x 10^-5$ |mole |\r\n|Value of parameter k1 |$ 1.5 \\x 10^5$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$ 50$ |second^-1^ |\r\n|Value of parameter k3 |$ 1.5$ |dimensionless |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-5;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1e-5;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 2.25e-5;\nS4 := k3 * S2;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\n\nk1 @Const 'k1' { } = 150000;\nk2 @Const 'k2' { } = 50;\nk3 @Const 'k3' { } = 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Basic reaction and rate rule with three species in a size-10 compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\nNote: This test is a direct copy of test 00331, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are three\r\nspecies named S1, S2 and S3 and two parameters named k1 and k2. The model\r\ncontains one reaction defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 -> S2 | $k1 * S1$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S3 | $k1 * k2$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-1$ |mole |\r\n|Initial amount of S2 |$1.0 \\x 10^-1$ |mole |\r\n|Initial amount of S3 |$1.0 \\x 10^-1$ |mole |\r\n|Value of parameter k1 |$ 1.75$ |second^-1^ |\r\n|Value of parameter k2 |$1.5 \\x 10^-2$ |mole |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical solution\r\nof the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 0.15;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 0.1;\n\nreaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };\nreaction1 := k1 * S1;\nS3_proc @Process { actors: = S3, aux: {{\"metaid\":\"rule1\"}}, };\nS3_proc := k1 * k2;\n\nk1 @Const 'k1' { } = 1.75;\nk2 @Const 'k2' { } = 0.015;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reactions and a rate rule with four species in a size-10 compartment. \r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule\r\ntestTags: Amount, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a direct copy of test 00332, but with a size-10 compartment, to test the 'hasOnlySubstanceUnits' attribute. The model should have exactly the same results, as concentration should have never been used to calculate anything.\r\n \r\nThe model contains one compartment called \"compartment\". There are four\r\nspecies named S1, S2, S3 and S4 and two parameters named k1 and k2. The\r\nmodel contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 -> S3 | $k1 * S1 * S2$ |\r\n| S3 -> S1 + S2 | $k2 * S3$ |]\r\n\r\nThe model contains one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $1 10^-7$ |]\r\n\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S2 |$2.0 \\x 10^-6$ |mole |\r\n|Initial amount of S3 |$1.5 \\x 10^-6$ |mole |\r\n|Initial amount of S4 |$ 1 \\x 10^-6$ |mole |\r\n|Value of parameter k1 |$0.75 \\x 10^6$ |mole^-1^ second^-1^ |\r\n|Value of parameter k2 |$0.25 \\x 10^-3$ |second^-1^ |\r\n|Volume of compartment \"compartment\" |$ 10$ |litre |]\r\n\r\nThe species have been declared as having substance units only. Thus, they \r\nmust be treated as amounts where they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\ncompartment @Compartment 'compartment' { units: litre, boundary: true, } .= 10;\n\nS1 @Species 'S1' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS2 @Species 'S2' { units: mole, compartment: compartment, isAmount: true, } .= 2e-6;\nS3 @Species 'S3' { units: mole, compartment: compartment, isAmount: true, } .= 1.5e-6;\nS4 @Species 'S4' { units: mole, compartment: compartment, isAmount: true, } .= 1e-6;\n\nreaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3, reversible: false, };\nreaction1 := k1 * S1 * S2;\nreaction2 @Reaction 'reaction2' { actors: S3 = S1 + S2, reversible: false, };\nreaction2 := k2 * S3;\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (1e-7);\n\nk1 @Const 'k1' { } = 750000;\nk2 @Const 'k2' { } = 0.00025;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 818, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. Species S1 is labeled as an \r\nSBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2)));\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 819, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as \r\nan SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, };\nreaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 820, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. Species S1 is labeled as \r\nan SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, boundary: true, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 821, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. Species S2 is labeled as an \r\nSBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2)));\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 822, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. Species S3 is labeled as \r\nan SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0.4$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, boundary: true, compartment: C, } .= 0.4 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, };\nreaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, BoundaryCondition\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 823, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. Species S2 is labeled as \r\nan SBML boundary species. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, boundary: true, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 824, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> 2S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: 2*S2 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2)));\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 825, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + 2S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + 2*S2, };\nreaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 826, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + 2S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + 2*S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reversible reactions with global and local parameters.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 830, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains two reactions\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |\r\n| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |]\r\n\r\nReaction S1 <-> S2 defines two local parameters kf and kr which have a\r\nscope local to the defining reaction and are different from the global parameters kf\r\nand kr used in the Reaction S3 <-> S4.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Value of local parameter kf |$0.8$ |second^-1^ |\r\n|Value of local parameter kr |$0.06$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)));\nreaction2 @Reaction 'reaction2' { actors: S4 = S3, };\nreaction2 := (-(C * (kf * S3 + (-1) * kr * S4)));\n\nkf__reaction1_local @Const { } = 0.8;\nkr__reaction1_local @Const { } = 0.06;\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reversible reactions with local parameters.\r\ncomponentTags: Compartment, Species, Reaction \r\ntestTags: Amount, ReversibleReaction, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 831, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2. The model contains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |\r\n| S3 <-> S4 | $(kf * S3 - kr * S4) * C$ |]\r\n\r\nBoth reactions define two local parameters kf and kr which have a\r\nscope local to the defining reaction.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of local parameter kf (R1) |$0.8$ |second^-1^ |\r\n|Value of local parameter kr (R1) |$0.06$ |second^-1^ |\r\n|Value of local parameter kf (R1) |$0.9$ |second^-1^ |\r\n|Value of local parameter kr (R2) |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf__reaction1_local * S1 + (-1) * kr__reaction1_local * S2)));\nreaction2 @Reaction 'reaction2' { actors: S4 = S3, };\nreaction2 := (-(C * (kf__reaction2_local * S3 + (-1) * kr__reaction2_local * S4)));\n\nkf__reaction1_local @Const { } = 0.8;\nkr__reaction1_local @Const { } = 0.06;\nkf__reaction2_local @Const { } = 0.9;\nkr__reaction2_local @Const { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 832, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(multiply(kf, S1) - kr * S2) * C$ |]\r\n\r\nThe reaction applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.59$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (multiply(kf, S1) + (-1) * kr * S2)));\n\nkf @Const 'kf' { } = 0.59;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 833, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(multiply(multiply(kf, S1), S2) - kr * S3) * C$ |]\r\n\r\nThe reaction applies the functionDefinition defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.11$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, };\nreaction1 := (-(C * (multiply(multiply(kf, S1), S2) + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.11;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, FunctionDefinition \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 834, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(minus(multiply(kf, S1), kr * S2 * S3)) * C$ |]\r\n\r\nThe reaction applies two functionDefinitions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | multiply | x, y | $x * y$ |\r\n | minus | x, y | $x - y$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\nmultiply #defineFunction { arguments: [x, y], math: x * y, };\nminus #defineFunction { arguments: [x, y], math: x + (-1) * y, };\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * minus(multiply(kf, S1), kr * S2 * S3)));\n\nkf @Const 'kf' { } = 1.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction with an initial assignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 835, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\nconsistent with the value returned by the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, };\nreaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction with an initial assignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, ReversibleReaction, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 836, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this case the initial value declared for species S1 is\r\ninconsistent with the value returned by the InitialAssignment. The\r\ncalculated value should be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, };\nreaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction with an initial assignment.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, InitialAssignment \r\ntestTags: Amount, ReversibleReaction, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 837, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe model contains one initialAssignment:\r\n\r\n[{width:30em,margin: 1em auto}| Variable | Formula |\r\n | S1 | $p1 * 2$ |]\r\n\r\nNote: SBML's InitialAssignment construct override any declared initial\r\nvalues. In this model, the initial value for the species S1 has not been\r\nexplicitly declared and must be calculated using the InitialAssignment.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$undeclared$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Value of parameter p1 |$0.5$ |mole |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 2 * p1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, };\nreaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\np1 @Const 'p1' { } = 0.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, ReversibleReaction, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 838, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which assigns value to parameter kf:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | kf | $2.5$ |]\r\n\r\nIn this case there is no initial value declared for parameter k1. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$undeclared$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\n\nkf @Record 'kf' { };\nkf := 2.5;\n\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, ReversibleReaction, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 839, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $0.5 * S1$ |]\r\n\r\nIn this case there is no initial value declared for species S4. Thus the\r\nvalue must be calculated using the assignmentRule.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$undeclared$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, };\nS4 := 0.5 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, AssignmentRule \r\ntestTags: Amount, ReversibleReaction, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 840, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which assigns value to species S4:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Assignment | S4 | $0.5 * S1$ |]\r\n\r\nIn this case the initial value declared for species S4 is inconsistent\r\nwith the value calculated using the assignmentRule. The calculated value\r\nshould be used.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$5$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 5 / C;\nS4 := 0.5 * S1;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 841, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which specifies the rate at which species \r\nS4 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $-0.5 * (kf * S1 - kr * S2 * S3)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0.5$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (-0.5) * (kf * S1 + (-1) * kr * S2 * S3);\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 842, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which specifies the rate at which species \r\nS4 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $-0.5 * S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0.5$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := (-0.5) * S1;\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, RateRule \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 843, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are four species called \r\nS1, S2, S3 and S4 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe model contains one rule which specifies the rate at which species \r\nS4 is varying:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n | Rate | S4 | $0.15$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Initial amount of S4 |$0.5$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 0.5 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\nS4_proc @Process { actors: = S4, aux: {{\"metaid\":\"rule1\"}}, };\nS4_proc := 0.15;\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: One reversible reactions with two species in one compartment\r\n and one event that assigns value to a species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 845, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species\r\ncalled S1, S2 and S3 and two parameters called k1 and k2. The model\r\ncontains one reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe model contains one event that assigns values to species S1:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.75$ | $-$ | $S2 = 1.5$ |]\r\n \r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2)));\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reversible reactions with four species in one compartment\r\n and one event that assigns value to two species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 846, with the products and reactants reversed, \r\nand a negative kinetic law. This gives the same results, but during the simulation, \r\nthe kinetic law actually goes negative (a requirement for reversibe reactions). \r\nThe reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are four species\r\ncalled S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |\r\n| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |]\r\n\r\nThe model contains one event that assigns values to both species S2 and S4:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ |\r\n | | | | $S4 = S2$ |]\r\n \r\nNote that the event assignments should happen simultaneously, not\r\nsequentially; i.e., the value of S2 assigned to S4 is the value at the\r\npoint at which the event was triggered.\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Initial amount of S4 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |second^-1^ |\r\n|Value of parameter k2 |$0.15$ |second^-1^ |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 [event1]= S2;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2)));\nreaction2 @Reaction 'reaction2' { actors: S4 = S3, };\nreaction2 := (-(C * (k1 * S3 + (-1) * k2 * S4)));\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.15;\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two reversible reactions with four species in one compartment\r\n and two events that assigns value to species.\r\ncomponentTags: Compartment, Species, Reaction, Parameter, EventNoDelay \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 847, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are four species\r\ncalled S1, S2, S3 and S4 and four parameters called k1, k2, kf and kr. The model\r\ncontains two reactions defined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |\r\n| S3 <-> S4 | $(k1 * S3 - k2 * S4) * C$ |]\r\n\r\nThe model contains two event that assigns values to species S2 and S4 respectively:\r\n\r\n[{width:30em,margin: 1em auto}| | *Trigger* | *Delay* | *Assignments* |\r\n | Event1 | $S1 < 0.5$ | $-$ | $S2 = 1.5$ |\r\n | Event2 | $S3 < 0.75$ | $-$ | $S4 = 0.5$ |]\r\n \r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$2.0$ |mole |\r\n|Initial amount of S3 |$1.0$ |mole |\r\n|Initial amount of S4 |$1.5$ |mole |\r\n|Value of parameter k1 |$0.75$ |second^-1^ |\r\n|Value of parameter k2 |$0.15$ |second^-1^ |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 2 / C;\nS2 [event1]= 1.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 1 / C;\nS4 @Species 'S4' { units: mole/litre, compartment: C, } .= 1.5 / C;\nS4 [event2]= 0.5;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2)));\nreaction2 @Reaction 'reaction2' { actors: S4 = S3, };\nreaction2 := (-(C * (k1 * S3 + (-1) * k2 * S4)));\n\nk1 @Const 'k1' { } = 0.75;\nk2 @Const 'k2' { } = 0.15;\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\nevent1 @DSwitcher 'event1' { trigger: S1 < 0.5, };\nevent2 @DSwitcher 'event2' { trigger: S3 < 0.75, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 809, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2)));\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 810, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, };\nreaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\nNote: This test is a copy of model 811, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$1$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 1;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\n Note: This test is a copy of model 812, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0$ |mole |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$0.5$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2)));\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\n Note: This test is a copy of model 813, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$2.3$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, };\nreaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Amount, ReversibleReaction, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\n Note: This test is a copy of model 814, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial amount of S1 |$1.0$ |mole |\r\n|Initial amount of S2 |$0.5$ |mole |\r\n|Initial amount of S3 |$0$ |mole |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.95$ |litre |]\r\n\r\nThe species values are given as amounts of substance to make it easier to\r\nuse the model in a discrete stochastic simulator, but (as per usual SBML\r\nprinciples) their symbols represent their values in concentration units\r\nwhere they appear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.95;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1 / C;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5 / C;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0 / C;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, ReversibleReaction, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\n Note: This test is a copy of model 815, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are two species called \r\nS1 and S2 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 | $(kf * S1 - kr * S2) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0$ |mole litre^-1^ |\r\n|Value of parameter kf |$0.9$ |second^-1^ |\r\n|Value of parameter kr |$0.075$ |second^-1^ |\r\n|Volume of compartment C |$0.5$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.5;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S2 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2)));\n\nkf @Const 'kf' { } = 0.9;\nkr @Const 'kr' { } = 0.075;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, ReversibleReaction, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\n Note: This test is a copy of model 816, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 + S2 <-> S3 | $(kf * S1 * S2 - kr * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0.5$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Value of parameter kf |$1.1$ |litre mole^-1^ second^-1^ |\r\n|Value of parameter kr |$0.09$ |second^-1^ |\r\n|Volume of compartment C |$2.3$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 2.3;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S3 = S1 + S2, };\nreaction1 := (-(C * (kf * S1 * S2 + (-1) * kr * S3)));\n\nkf @Const 'kf' { } = 1.1;\nkr @Const 'kr' { } = 0.09;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Single reversible reaction.\r\ncomponentTags: Compartment, Species, Reaction, Parameter \r\ntestTags: Concentration, ReversibleReaction, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\n\r\n Note: This test is a copy of model 817, with the products and reactants reversed, and a negative kinetic law. This gives the same results, but during the simulation, the kinetic law actually goes negative (a requirement for reversibe reactions). The reaction listed below is therfore equivalent to the one in the file, but reversed from it.\r\n\r\nThe model contains one compartment called C. There are three species called \r\nS1, S2 and S3 and two parameters called kf and kr. The model contains one reaction\r\ndefined as:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S1 <-> S2 + S3 | $(kf * S1 - kr * S2 * S3) * C$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:30em,margin: 1em auto}| |*Value* |*Units* |\r\n|Initial concentration of S1 |$1.0$ |mole litre^-1^ |\r\n|Initial concentration of S2 |$0.5$ |mole litre^-1^ |\r\n|Initial concentration of S3 |$0$ |mole litre^-1^ |\r\n|Value of parameter kf |$2.5$ |second^-1^ |\r\n|Value of parameter kr |$0.2$ |litre mole^-1^ second^-1^ |\r\n|Volume of compartment C |$0.95$ |litre |]\r\n\r\n","completion":"\n\nt @TimeScale { units: second, };\n\nC @Compartment 'C' { units: litre, boundary: true, } .= 0.95;\n\nS1 @Species 'S1' { units: mole/litre, compartment: C, } .= 1;\nS2 @Species 'S2' { units: mole/litre, compartment: C, } .= 0.5;\nS3 @Species 'S3' { units: mole/litre, compartment: C, } .= 0;\n\nreaction1 @Reaction 'reaction1' { actors: S2 + S3 = S1, };\nreaction1 := (-(C * (kf * S1 + (-1) * kr * S2 * S3)));\n\nkf @Const 'kf' { } = 2.5;\nkr @Const 'kr' { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Testing 'piecewise' without 'otherwise'.\r\ncomponentTags: InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\n MathML allows the construction of 'piecwise' functions without 'otherwise'. When all cases are accounted for, this shouldn't make a difference in the output of the model.\r\n\r\nThe model contains:\r\n* 2 parameters (a, b)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter a | $piecewise(1, true)$ | constant |\r\n| Initial value of parameter b | $piecewise(1, gt(a, 0), 2, leq(a, 0))$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\na @Record { } .= piecewise(1, true);\nb @Record { } .= piecewise(1, a > 0, 2, a <= 0);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Testing that the species amount does not change, even in a changing compartment.\r\ncomponentTags: Compartment, RateRule, Species\r\ntestTags: Amount, ConstantSpecies, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\n This model tests that the simulator should, by default, assume that a species set boundaryCondition=false and hasOnlySubstanceUnits=false, residing in a compartment that changes over time, should keep its *amount* constant, not its concentration.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | C | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { } .= 1;\n\nS1 @Species { boundary: true, compartment: C, } .= 1;\n\nC_proc @Process { actors: = C, };\nC_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A model that tests how not to vary a species.\r\ncomponentTags: Compartment, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, ConstantSpecies, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\n\r\n This model tests that the simulator should, by default, assume that a species set boundaryCondition=true and hasOnlySubstanceUnits=false, residing in a compartment that changes over time, should keep its *amount* constant, not its concentration.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | C | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { } .= 1;\n\nS1 @Species { boundary: true, compartment: C, } .= 1;\n\nC_proc @Process { actors: = C, };\nC_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Test of proper interpretation of a boundary species set hasOnlySubstanceUnits=false in a reaction rate.\r\ncomponentTags: Compartment, RateRule, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n This model is a further simplification of test 1000/1121 that only test the use of a boundary species, used in the model in terms of concentrations, from a compartment that varies in time, used in a reaction rate, with hasOnlySubstanceUnits = false.\r\n\r\nThe model contains:\r\n* 2 species (S1, S3)\r\n* 1 compartment (comp)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| _J0: S1 -> | $S3 / 10$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | comp | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S3 | $4$ | variable |\r\n| Initial volume of compartment 'comp' | $5$ | variable |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ncomp @Compartment { } .= 5;\n\nS1 @Species { compartment: comp, } .= 1 / comp;\nS3 @Species { boundary: true, compartment: comp, } .= 4 / comp;\n\n_J0 @Reaction { actors: S1 = , modifiers: [S3], };\n_J0 := S3 / 10;\ncomp_proc @Process { actors: = comp, };\ncomp_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Test of proper interpretation of a boundary species set hasOnlySubstanceUnits=true in a reaction rate.\r\ncomponentTags: Compartment, RateRule, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n This model is a further simplification of test 1000/1121 that only test the use of a boundary species, used in the model in terms of concentrations, from a compartment that varies in time, used in a reaction rate, with hasOnlySubstanceUnits = true.\r\n\r\nThe model contains:\r\n* 2 species (S1, S3)\r\n* 1 compartment (comp)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| _J0: S1 -> | $S3 / 10$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | comp | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S3 | $4$ | variable |\r\n| Initial volume of compartment 'comp' | $5$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ncomp @Compartment { } .= 5;\n\nS1 @Species { compartment: comp, } .= 1 / comp;\nS3 @Species { boundary: true, compartment: comp, isAmount: true, } .= 4;\n\n_J0 @Reaction { actors: S1 = , modifiers: [S3], };\n_J0 := S3 / 10;\ncomp_proc @Process { actors: = comp, };\ncomp_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Simple non-required comp model.\r\ncomponentTags: Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This hierarchical model replaces the single parameter in the submodel, and therefore behaves as if the submodel did not exist. The comp package 'required' attribute is therefore 'false', meaning that the mathematical meaning of the model is not changed by the presence of 'comp' elements.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (param1)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter param1 | $10.42$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nparam1 @Const { } = 10.42;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Simple non-required comp model\r\ncomponentTags: Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThis hierarchical model replaces the single parameter in the submodel, and therefore behaves as if the submodel did not exist. The comp package 'required' attribute is therefore 'false', meaning that the mathematical meaning of the model is not changed by the presence of 'comp' elements.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (param1)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter param1 | $10.42$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nparam1 @Const { } = 10.42;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple hierarchical model with a submodel parameter\r\ncomponentTags: Parameter, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel\r\ntestTags: comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThere are two parameters in this model, one in the parent model which replaces a paramter in the submodel, and a second parameter from the submodel that remains unreplaced.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (param1, submod1__subparam2)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter param1 | $10.42$ | constant |\r\n| Initial value of parameter submod1__subparam2 | $6$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nparam1 @Const { } = 10.42;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a submodel initial assignment and rate rule.\r\ncomponentTags: InitialAssignment, Parameter, RateRule, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The parent model contains a parameter that replaces a paramter of the submodel. That submodel has an initial assignment and a rate rule that both affect that replaced parameter, and should continue to affect the replacement parameter.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (param1, submod1__subparam2)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | param1 | $8 * submod1__subparam2 + param1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter submod1__subparam2 | $6$ | constant |\r\n| Initial value of parameter param1 | $submod1__subparam2 + 6$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nparam1 @Record { } .= 10.42;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An aggregate model with species.\r\ncomponentTags: Compartment, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, ConstantSpecies, MultiCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nA simple multi-level aggregate model with species and compartments.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 4 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1)\r\n* 4 compartments (C, sub1__C, sub2__C, sub2__sub1__C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $5$ | constant |\r\n| Initial amount of species sub1__S1 | $7$ | constant |\r\n| Initial amount of species sub2__S1 | $9$ | constant |\r\n| Initial amount of species sub2__sub1__S1 | $7$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub2__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub2__sub1__C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { boundary: true, compartment: C, } .= 5 / C;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a sub-submodel compartment replacement.\r\ncomponentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Concentration, ConstantSpecies, NonUnityCompartment, MultiCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This model tests replacing a compartment in a sub-submodel with a comparment from the parent model, changing the concentration of the species in that submodel.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 4 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1)\r\n* 3 compartments (C, sub1__C, sub2__C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $5$ | constant |\r\n| Initial amount of species sub1__S1 | $7$ | constant |\r\n| Initial amount of species sub2__S1 | $9$ | constant |\r\n| Initial amount of species sub2__sub1__S1 | $7$ | constant |\r\n| Initial volume of compartment 'C' | $10$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub2__C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 10;\n\nS1 @Species { boundary: true, compartment: C, } .= 5 / C;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A three-level-deep hierarchical model.\r\ncomponentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Concentration, ConstantSpecies, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This model contains submodels three levels deep. A compartment replacement changes the concentration of a species.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 8 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1, sub3__sub2__sub1__S1)\r\n* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $5$ | constant |\r\n| Initial amount of species sub1__S1 | $7$ | constant |\r\n| Initial amount of species sub2__S1 | $9$ | constant |\r\n| Initial amount of species sub2__sub1__S1 | $7$ | constant |\r\n| Initial amount of species sub3__S1 | $11$ | constant |\r\n| Initial amount of species sub3__sub1__S1 | $7$ | constant |\r\n| Initial amount of species sub3__sub2__S1 | $9$ | constant |\r\n| Initial amount of species sub3__sub2__sub1__S1 | $7$ | constant |\r\n| Initial volume of compartment 'C' | $10$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub2__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__sub1__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__sub2__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 10;\n\nS1 @Species { boundary: true, compartment: C, } .= 5 / C;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a three-level-deep replacement.\r\ncomponentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Concentration, ConstantSpecies, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This model contains submodels three levels deep, with the top model replacing the species at the deepest level, and the compartment at a level two down.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 7 species (S1, sub1__S1, sub2__S1, sub2__sub1__S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1)\r\n* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $5$ | constant |\r\n| Initial amount of species sub1__S1 | $7$ | constant |\r\n| Initial amount of species sub2__S1 | $9$ | constant |\r\n| Initial amount of species sub2__sub1__S1 | $7$ | constant |\r\n| Initial amount of species sub3__S1 | $11$ | constant |\r\n| Initial amount of species sub3__sub1__S1 | $7$ | constant |\r\n| Initial amount of species sub3__sub2__S1 | $9$ | constant |\r\n| Initial volume of compartment 'C' | $10$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub2__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__sub1__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__sub2__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 10;\n\nS1 @Species { boundary: true, compartment: C, } .= 5 / C;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species replacing one thing and replaced by something else.\r\ncomponentTags: Compartment, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Concentration, ConstantSpecies, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n A three-level deep hierarchical model with a replaced compartment, and a top-level species that replaces a three-deep speces, and is replaced in turn by a two-deep species.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 6 species (sub1__S1, sub2__S1, S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1)\r\n* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species sub1__S1 | $2.5$ | constant |\r\n| Initial amount of species sub2__S1 | $9$ | constant |\r\n| Initial concentration of species S1 | $2.5$ | constant |\r\n| Initial amount of species sub3__S1 | $11$ | constant |\r\n| Initial concentration of species sub3__sub1__S1 | $2.5$ | constant |\r\n| Initial amount of species sub3__sub2__S1 | $9$ | constant |\r\n| Initial volume of compartment 'C' | $10$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub2__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__sub1__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__sub2__C' | $1$ | constant |\r\n| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 10;\n\nS1 @Species { boundary: true, compartment: C, } .= 5 / C;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species replacing one thing and replaced by something else, with ports.\r\ncomponentTags: Compartment, Species, comp:ModelDefinition, comp:Port, comp:ReplacedBy, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Concentration, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This model is exactly the same as model 01133, but additionally contains ports in the parent model. They are (obviously) unused, so this is simply a test to ensure that their presence doesn't confuse the simulator.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 6 species (sub1__S1, sub2__S1, S1, sub3__S1, sub3__sub1__S1, sub3__sub2__S1)\r\n* 7 compartments (C, sub1__C, sub2__C, sub3__C, sub3__sub1__C, sub3__sub2__C, sub3__sub2__sub1__C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species sub1__S1 | $2.5$ | variable |\r\n| Initial amount of species sub2__S1 | $9$ | variable |\r\n| Initial concentration of species S1 | $2.5$ | variable |\r\n| Initial amount of species sub3__S1 | $11$ | variable |\r\n| Initial concentration of species sub3__sub1__S1 | $2.5$ | variable |\r\n| Initial amount of species sub3__sub2__S1 | $9$ | variable |\r\n| Initial volume of compartment 'C' | $10$ | variable |\r\n| Initial volume of compartment 'sub1__C' | $1$ | variable |\r\n| Initial volume of compartment 'sub2__C' | $1$ | variable |\r\n| Initial volume of compartment 'sub3__C' | $1$ | variable |\r\n| Initial volume of compartment 'sub3__sub1__C' | $1$ | variable |\r\n| Initial volume of compartment 'sub3__sub2__C' | $1$ | variable |\r\n| Initial volume of compartment 'sub3__sub2__sub1__C' | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { } .= 10;\n\nS1 @Species { compartment: C, } .= 5 / C;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Hierarchical model with chained replacedBys.\r\ncomponentTags: Parameter, comp:ModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:Submodel\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The parameter in the parent model is replaced by a parameter in the submodel, which in turn is replaced by a parameter in *its* submodel.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (p2)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p2 | $8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np2 @Record { } .= 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Chained replaced/replacedBy elements.\r\ncomponentTags: Parameter, comp:ModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:ReplacedElement, comp:Submodel\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n Despite starting off with five parameters at three levels, all aggregate parameters collapse down to a single parameter, as one set is replaced by parameters in models above them, and the other is replaced by parameters below them.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (p2)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p2 | $8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np2 @Record { } .= 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a conversion factor\r\ncomponentTags: AssignmentRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, NonConstantParameter, comp:ConversionFactor, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This model is a simple test of a replacement with a conversion factor that affects the assignment rule of another parameter.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 3 parameters (p8, conv, sub1__prel)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | sub1__prel | $p8 / conv / 8$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter conv | $0.1$ | constant |\r\n| Initial value of parameter p8 | $8$ | variable |\r\n| Initial value of parameter sub1__prel | $p8 / conv / 8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np8 @Record { } .= 8;\n\nconv @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a conversion factor.\r\ncomponentTags: Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, comp:ConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThis model is a simple test of a replacement with a conversion factor that affects the rate rule of the replaced parameter.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (p8, conv)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p8 | $(4 * (p8 / conv) + 3) * conv$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter conv | $0.1$ | constant |\r\n| Initial value of parameter p8 | $8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np8 @Record { } .= 8;\n\nconv @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a conversion factor on a species.\r\ncomponentTags: Compartment, Parameter, RateRule, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, MultiCompartment, comp:ConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThis model is a simple test of a replacement with a conversion factor that affects the rate rule of the replaced species.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s8)\r\n* 1 parameter (conv)\r\n* 2 compartments (C, sub1__C)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | s8 | $(4 * (s8 / conv) + 3) * conv$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s8 | $8$ | variable |\r\n| Initial value of parameter conv | $0.1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns8 @Species { compartment: C, isAmount: true, } .= 8;\n\nconv @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a conversion factor on a compartment.\r\ncomponentTags: Compartment, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantCompartment, NonUnityCompartment, comp:ConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This model is a simple test of a replacement with a conversion factor that affects the rate rule of the replaced compartment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (conv)\r\n* 1 compartment (C8)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | C8 | $(4 * (C8 / conv) + 3) * conv$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter conv | $0.1$ | constant |\r\n| Initial volume of compartment 'C8' | $8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC8 @Compartment { } .= 8;\n\nconv @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion factor affecting many components.\r\ncomponentTags: AlgebraicRule, AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, EventWithDelay, InitialAssignment, Parameter, RateRule, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n This model contains a submodel with various time-based constructs in it, contained in a model with a time conversion factor. For broken-down versions of this model that test only one construct at a time, see tests 01170-01177.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 6 parameters (timeconv, t1, t2, t3, t4, t5)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| sub1__J0: -> s1 | $1 / timeconv * (t3 * (time / timeconv) / (s1 * delay(t5, timeconv * 2.000000e-001)))$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* |\r\n| event_0 | $gt(time / timeconv, 3)$ | $timeconv * (1 / (time / timeconv))$ | $t5 = time / timeconv$ |]\r\n\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | t1 | $(time / timeconv / t1 + 3) / timeconv$ |\r\n| Assignment | t3 | $delay(t1, timeconv * 3)$ |\r\n| Algebraic | $0$ | $t4 - delay(t3, timeconv * (time / timeconv / 2))$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $0.001$ | variable |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter t1 | $1$ | variable |\r\n| Initial value of parameter t2 | $time / timeconv + 3$ | variable |\r\n| Initial value of parameter t3 | $delay(t1, timeconv * 3)$ | variable |\r\n| Initial value of parameter t4 | $1$ | variable |\r\n| Initial value of parameter t5 | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, isAmount: true, } .= 0.001;\n\nt1 @Record { } .= 1;\nt2 @Record { } .= 1;\nt3 @Record { } .= 1;\nt4 @Record { } .= 1;\nt5 @Record { } .= 1;\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a reaction modified by an extent conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\nThe reaction in the submodel must be converted by the extent conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__s1)\r\n* 1 parameter (extentconv)\r\n* 1 compartment (sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__s1 | $extentconv * 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__s1 | $1$ | variable |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $0$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nextentconv @Const { } = 1000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a submodel reaction modified by time and extent conversion factors.\r\ncomponentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThe kinetic law of the reaction in the submodel in this model must be modified by both the time conversion factor and the extent conversion factor of the parent model.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__s1)\r\n* 3 parameters (timeconv, extentconv, t3)\r\n* 1 compartment (sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__s1 | $extentconv / timeconv * sub1__s1 * t3 * (time / timeconv)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__s1 | $1$ | variable |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial value of parameter t3 | $0.2$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ntimeconv @Const { } = 60;\nextentconv @Const { } = 1000;\nt3 @Const { } = 0.2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with an extent conversion factor affecting a sub-submodel.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The extent conversion factor in the parent model must affect the reaction in the sub-submodel.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__sub1__s1)\r\n* 1 parameter (extentconv)\r\n* 1 compartment (sub1__sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__sub1__s1 | $extentconv * sub1__sub1__s1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__sub1__s1 | $0.01$ | variable |\r\n| Initial value of parameter extentconv | $10$ | constant |\r\n| Initial volume of compartment 'sub1__sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nextentconv @Const { } = 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion factor affecting an assignment rule in a sub-submodel.\r\ncomponentTags: AssignmentRule, CSymbolTime, Parameter, comp:ModelDefinition, comp:Submodel\r\ntestTags: InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The assignment rule in the sub-submodel has 'time' in it, which must be converted by the time conversion factor of the original submodel.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (timeconv, sub1__sub1__t1)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | sub1__sub1__t1 | $time / timeconv + 3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter sub1__sub1__t1 | $time / timeconv + 3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with two levels of time conversion factors.\r\ncomponentTags: AssignmentRule, CSymbolTime, InitialAssignment, Parameter, comp:ModelDefinition, comp:Submodel\r\ntestTags: InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The assignment rule in the sub-submodel must be converted by time conversion factors at both levels of submodel creation.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 4 parameters (timeconv, sub1__timeconv, sub1__timeconv_times_timeconv, sub1__sub1__t1)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | sub1__sub1__t1 | $time / sub1__timeconv_times_timeconv + 3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter sub1__timeconv | $60$ | constant |\r\n| Initial value of parameter sub1__timeconv_times_timeconv | $sub1__timeconv * timeconv$ | constant |\r\n| Initial value of parameter sub1__sub1__t1 | $time / sub1__timeconv_times_timeconv + 3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with three levels of time and extent conversion factors.\r\ncomponentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The reaction in the sub-submodel is affected by time and extent conversion factors three levels deep.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__sub1__sub1__s1)\r\n* 10 parameters (timeconv, extentconv, sub1__timeconv, sub1__extentconv, sub1__timeconv_times_timeconv, sub1__extentconv_times_extentconv, sub1__sub1__timeconv, sub1__sub1__extentconv, sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv, sub1__sub1__extentconv_times_sub1__extentconv_times_extentconv)\r\n* 1 compartment (sub1__sub1__sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__sub1__sub1__s1 | $sub1__sub1__extentconv_times_sub1__extentconv_times_extentconv / sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv * 1000000000 * sub1__sub1__sub1__s1 * (time / sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__sub1__sub1__s1 | $0.001$ | variable |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter extentconv | $10$ | constant |\r\n| Initial value of parameter sub1__timeconv | $60$ | constant |\r\n| Initial value of parameter sub1__extentconv | $10$ | constant |\r\n| Initial value of parameter sub1__timeconv_times_timeconv | $sub1__timeconv * timeconv$ | constant |\r\n| Initial value of parameter sub1__extentconv_times_extentconv | $sub1__extentconv * extentconv$ | constant |\r\n| Initial value of parameter sub1__sub1__timeconv | $60$ | constant |\r\n| Initial value of parameter sub1__sub1__extentconv | $10$ | constant |\r\n| Initial value of parameter sub1__sub1__timeconv_times_sub1__timeconv_times_timeconv | $sub1__sub1__timeconv * sub1__timeconv_times_timeconv$ | constant |\r\n| Initial value of parameter sub1__sub1__extentconv_times_sub1__extentconv_times_extentconv | $sub1__sub1__extentconv * sub1__extentconv_times_extentconv$ | constant |\r\n| Initial volume of compartment 'sub1__sub1__sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ntimeconv @Const { } = 60;\nextentconv @Const { } = 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a deleted rate rule.\r\ncomponentTags: Parameter, comp:Deletion, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The rate rule in the submodel is deleted, and should not affect the parameter.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (p8)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p8 | $8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np8 @Record { } .= 8;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a replaced rate rule.\r\ncomponentTags: Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This model contains a rate rule in the parent that replaces a rate rule in the submodel.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (p8)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p8 | $3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p8 | $8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np8_proc @Process { actors: = p8, aux: {{\"metaid\":\"p8_raterule\"}}, };\np8_proc := 3;\n\np8 @Record { } .= 8;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a deleted rate rule.\r\ncomponentTags: Parameter, RateRule, comp:Deletion, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n Flattened, this model is functionally identical to model 01150, but instead of having the parent rate rule replace the submodel rate rule, the submodel rate rule is simply deleted.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (p8)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p8 | $3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p8 | $8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np8_proc @Process { actors: = p8, aux: {{\"metaid\":\"p8_raterule\"}}, };\np8_proc := 3;\n\np8 @Record { } .= 8;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a conversion factor affecting an event assignment.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, comp:ConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The replaced parameter in the submodel is assigned a value by an event. The replacement contains a conversion factor, affecting the value given by the event.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (conv, p8)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| sub1__E1 | $gt(time, 0.31)$ | $p8 = (800 + p8 / conv) * conv$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter conv | $0.1$ | constant |\r\n| Initial value of parameter p8 | $8$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np8 @Record { } .= 8;\n\nconv @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a deleted rate rule and initial assignment\r\ncomponentTags: InitialAssignment, Parameter, comp:Deletion, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: InitialValueReassigned, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The parent model in this document contains deletions that remove an initial assignment and a rate rule two levels down. The parent model contains only an initial assignment for that parameter, leaving it constant.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 4 parameters (z, i, A__A__y, A__A__Q)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter i | $2$ | constant |\r\n| Initial value of parameter A__A__y | $7$ | constant |\r\n| Initial value of parameter A__A__Q | $2$ | constant |\r\n| Initial value of parameter z | $34 * i$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nz @Record { } .= 34 * i;\n\ni @Const { } = 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: This hierarchical model contains a deleted event.\r\ncomponentTags: Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel\r\ntestTags: comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The event that would change the values of the two parameters in this model is deleted, causing the parameters to remain unchanged.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (sub1__t1, sub1__t2)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter sub1__t1 | $1$ | variable |\r\n| Initial value of parameter sub1__t2 | $1$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: This hierarchical model deletes the delay of an event.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel\r\ntestTags: NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The event in the submodel contains a delay, but this delay is deleted when the submodel is imported into the parent model, causing the event to fire instantly.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (sub1__t1, sub1__t2)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| sub1__E0 | $gt(time, 3)$ | $sub1__t1 = 3.3$ |\r\n| | | | $sub1__t2 = 5.5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter sub1__t1 | $1$ | variable |\r\n| Initial value of parameter sub1__t2 | $1$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a deleted event priority.\r\ncomponentTags: CSymbolTime, EventWithDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel\r\ntestTags: NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n This model contains an event with a priority which is deleted when imported as part of a submodel. It is actually impossible to test the behavior of a model that deletes a priority, because the behavior of an event without a priority has fewer restrictions on its behavior in a simulator than that same event with a priority, and allowing the event to behave as if it had any arbitrary priority (including the one deleted) is actually perfectly legal. As a result, this test merely checks to ensure that the simulation occurred at all, despite containing that deletion construct.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (sub1__t1, sub1__t2)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* |\r\n| sub1__E0 | $gt(time, 3)$ | $1 / time$ | $sub1__t1 = 3.3$ |\r\n| | | | $sub1__t2 = 5.5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter sub1__t1 | $1$ | variable |\r\n| Initial value of parameter sub1__t2 | $1$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model that deletes an event assignment.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel\r\ntestTags: NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The original event in the submodel contains two event assignments, one of which is deleted when the event's submodel is imported into the parent model.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (sub1__t1, sub1__t2)\r\n\r\nThere is one event:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Delay* | *Event Assignments* |\r\n| sub1__E0 | $gt(time, 3)$ | $10$ | $1 / time$ | $sub1__t2 = 5.5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter sub1__t1 | $1$ | variable |\r\n| Initial value of parameter sub1__t2 | $1$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\n synopsis: A hierarchical model that deletes a priority, delay, and event assignment\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter, comp:Deletion, comp:ModelDefinition, comp:Submodel\r\ntestTags: NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n In this model, a submodel event is greatly changed through deletions: its delay, priority, and one of its event assignements are all deleted. As in model 01156, the fact that the priority has been deleted cannot be tested numerically, but the other deletions all directly affect the expected output of the model.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (sub1__t1, sub1__t2)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| sub1__E0 | $gt(time, 3)$ | $sub1__t1 = 3.3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter sub1__t1 | $1$ | variable |\r\n| Initial value of parameter sub1__t2 | $1$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: This hieararchical model deletes a local parameter\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:Deletion, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In the original submodel, there is a local parameter whose value is used in the kinetic law of a reaction. When it is imported as a submodel, the local parameter is deleted, causing the kinetic law to instead reference a global parameter with the same ID, but a different value.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__s1)\r\n* 1 parameter (sub1__p1)\r\n* 1 compartment (sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__s1 | $sub1__p1 * sub1__s1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__s1 | $0.001$ | variable |\r\n| Initial value of parameter sub1__p1 | $100$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a replacement of a local parameter.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nA local parameter in the submodel is replaced here by a global parameter.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__s1)\r\n* 1 parameter (new_p1)\r\n* 1 compartment (sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__s1 | $new_p1 * sub1__s1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__s1 | $0.001$ | variable |\r\n| Initial value of parameter new_p1 | $100$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nnew_p1 @Const { aux: {{\"metaid\":\"new_p1_metaid\"}}, } = 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model whose submodel has a local parameter.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, LocalParameters, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n A quick test to make sure a submodel local parameter is left alone and not renamed without a commensurate renaming of its reference in the kinetic law as part of any flattening routine a simulator might use, especially when there is a 'shadow' parameter of the same name.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__s1)\r\n* 1 parameter (sub1__p1)\r\n* 1 compartment (sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__s1 | $p1 * sub1__s1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__s1 | $0.001$ | variable |\r\n| Initial value of parameter sub1__p1 | $100$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a rate rule deleted via a port.\r\ncomponentTags: Parameter, comp:Deletion, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The rate rule for the parameter in the submodel is defined with a port, and the model that imports it sets the port as the target of a 'delete' construct. This should, by proxy, delete the rate rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (p8)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p8 | $8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np8 @Record { } .= 8;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a replaced rate rule and parameter.\r\ncomponentTags: Parameter, RateRule, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n The submodel contains a parameter and rate rule, both of which are replaced by the parent model. This means that it is not actually necessary to understand the 'comp' package to pass the test; a simulator should be able to note the 'required=\"false\"' line and attempt to simulate anyway.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (p8)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p8 | $3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p8 | $8$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np8_proc @Process { actors: = p8, aux: {{\"metaid\":\"p8_raterule\"}}, };\np8_proc := 3;\n\np8 @Record { } .= 8;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple aggregate hieararchical model.\r\ncomponentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, MultiCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n A submodel with a two-step reaction is imported twice into the parent model, creating parallel sets of species affected by parallel reactions.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 8 species (submod1__S, submod1__E, submod1__D, submod1__ES, submod2__S, submod2__E, submod2__D, submod2__ES)\r\n* 2 compartments (submod1__comp, submod2__comp)\r\n\r\nThere are 4 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| submod1__S + submod1__E -> submod1__ES | $(submod1__S + submod1__E) / submod1__ES$ |\r\n| submod1__ES -> submod1__E + submod1__D | $submod1__ES / (submod1__E + submod1__D)$ |\r\n| submod2__S + submod2__E -> submod2__ES | $(submod2__S + submod2__E) / submod2__ES$ |\r\n| submod2__ES -> submod2__E + submod2__D | $submod2__ES / (submod2__E + submod2__D)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species submod1__S | $1$ | variable |\r\n| Initial concentration of species submod1__E | $1$ | variable |\r\n| Initial concentration of species submod1__D | $1$ | variable |\r\n| Initial concentration of species submod1__ES | $1$ | variable |\r\n| Initial concentration of species submod2__S | $1$ | variable |\r\n| Initial concentration of species submod2__E | $1$ | variable |\r\n| Initial concentration of species submod2__D | $1$ | variable |\r\n| Initial concentration of species submod2__ES | $1$ | variable |\r\n| Initial volume of compartment 'submod1__comp' | $1$ | constant |\r\n| Initial volume of compartment 'submod2__comp' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model from the specification\r\ncomponentTags: Compartment, Reaction, Species, comp:Deletion, comp:ExternalModelDefinition, comp:ModelDefinition, comp:Port, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n An example from the 'comp' specification: two submodels, one simple, and one complex, are synchronized to match the complex version: 'S' converted to 'D' via an intermediate instead of via a single step.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 4 species (S, D, A__E, A__ES)\r\n* 1 compartment (comp)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| S + A__E -> A__ES | $(S + A__E) / A__ES$ |\r\n| A__ES -> A__E + D | $A__ES / (A__E + D)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S | $5$ | variable |\r\n| Initial concentration of species D | $10$ | variable |\r\n| Initial concentration of species A__E | $1$ | variable |\r\n| Initial concentration of species A__ES | $1$ | variable |\r\n| Initial volume of compartment 'comp' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ncomp @Compartment { boundary: true, } .= 1;\n\nS @Species { compartment: comp, } .= 5;\nD @Species { compartment: comp, } .= 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with two levels of external model definitions.\r\ncomponentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:Submodel\r\ntestTags: Amount, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The external model definition in the main model file references another external model definition in a second file, which in turn references an actual model in a third file.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 4 species (A__S, A__E, A__D, A__ES)\r\n* 1 compartment (A__comp)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| A__S + A__E -> A__ES | $(A__S + A__E) / A__ES$ |\r\n| A__ES -> A__E + A__D | $A__ES / (A__E + A__D)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A__S | $10$ | variable |\r\n| Initial concentration of species A__E | $5$ | variable |\r\n| Initial concentration of species A__D | $7$ | variable |\r\n| Initial concentration of species A__ES | $0.1$ | variable |\r\n| Initial volume of compartment 'A__comp' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: This hierarchical model references an external model definition with a submodel with an external model definition.\r\ncomponentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:Submodel\r\ntestTags: Amount, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\nThis model tests multiple layers of external model definitions, where the model referenced by an external model definition contains a submodel which is itself defined in a third file via an external model definition in the second file.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 7 species (A__S, A__A__E, A__A__D, A__A__ES, A__B__E, A__B__D, A__B__ES)\r\n* 1 compartment (A__comp)\r\n\r\nThere are 4 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| A__S + A__A__E -> A__A__ES | $(A__S + A__A__E) / A__A__ES$ |\r\n| A__A__ES -> A__A__E + A__A__D | $A__A__ES / (A__A__E + A__A__D)$ |\r\n| A__S + A__B__E -> A__B__ES | $(A__S + A__B__E) / A__B__ES$ |\r\n| A__B__ES -> A__B__E + A__B__D | $A__B__ES / (A__B__E + A__B__D)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A__S | $11$ | variable |\r\n| Initial concentration of species A__A__E | $5$ | variable |\r\n| Initial concentration of species A__A__D | $7$ | variable |\r\n| Initial concentration of species A__A__ES | $0.1$ | variable |\r\n| Initial concentration of species A__B__E | $5$ | variable |\r\n| Initial concentration of species A__B__D | $7$ | variable |\r\n| Initial concentration of species A__B__ES | $0.1$ | variable |\r\n| Initial volume of compartment 'A__comp' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion factor.\r\ncomponentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThis model contains a submodel with a reaction in it, contained in a model with a time conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 2 parameters (timeconv, t3)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> s1 | $1 / timeconv * t3 * (time / timeconv)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $0.001$ | variable |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter t3 | $10$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, isAmount: true, } .= 0.001;\n\nt3 @Record { } .= 10;\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion factor and a rate rule.\r\ncomponentTags: CSymbolTime, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThis model contains a submodel with a rate rule in it, contained in a model with a time conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (timeconv, t1)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | t1 | $(time / timeconv / t1 + 3) / timeconv$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter t1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nt1 @Record { } .= 1;\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion factor and delay.\r\ncomponentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThis model contains a submodel with the csymbol delay, contained in a model with a time conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 3 parameters (timeconv, t1, t3)\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | t1 | $time / timeconv$ |\r\n| Assignment | t3 | $delay(t1, timeconv * 3)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter t1 | $time / timeconv$ | variable |\r\n| Initial value of parameter t3 | $delay(t1, timeconv * 3)$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nt1 @Record { } .= 1;\nt3 @Record { } .= 1;\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion factor and an algebraic rule.\r\ncomponentTags: AlgebraicRule, CSymbolDelay, CSymbolTime, InitialAssignment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This model contains a submodel with an algebraic rule containing the csymbols 'time' and 'delay' , contained in a model with a time conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 3 parameters (timeconv, t3, t4)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Algebraic | $0$ | $t4 - delay(t3, timeconv * (time / timeconv / 2))$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter t3 | $time / timeconv + 3$ | constant |\r\n| Initial value of parameter t4 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nt4 @Record { } .= 1;\n\ntimeconv @Const { } = 60;\nt3 @Const { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion factor and reaction.\r\ncomponentTags: CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThis model contains a submodel with a reaction, contained in a model with a time conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 2 parameters (timeconv, t5)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> s1 | $1 / timeconv * (t5 * (time / timeconv) / (s1 * t5))$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $0.001$ | variable |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter t5 | $3.1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, isAmount: true, } .= 0.001;\n\nt5 @Record { } .= 3.1;\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion factor and a delay in a kinetic law.\r\ncomponentTags: AssignmentRule, CSymbolDelay, CSymbolTime, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nThis model contains a submodel with a reaction whose kinetic law contains a delay, contained in a model with a time conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 2 parameters (timeconv, t5)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> s1 | $1 / timeconv * delay(t5, timeconv * 0.2) * (time / timeconv)$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | t5 | $time / timeconv$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $0.001$ | variable |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter t5 | $time / timeconv$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, isAmount: true, } .= 0.001;\n\nt5 @Record { } .= 3.2;\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion factor.\r\ncomponentTags: CSymbolTime, EventWithDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: EventUsesTriggerTimeValues, NonConstantParameter, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\nThis model contains a submodel with an event with various time-based constructs in it, contained in a model with a time conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (timeconv, t5)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* |\r\n| | $gt(time / timeconv, 3)$ | $timeconv * (1 / (time / timeconv))$ | $t5 = time / timeconv$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter t5 | $1$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nt5 @Record { } .= 1;\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with extent conversion and a reference to a modified reaction.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, comp:ExtentConversionFactor, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference must be modified by the extent conversion factor just as the kinetic law itself is modified by the extent conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__s1)\r\n* 2 parameters (extentconv, sub1__p80)\r\n* 1 compartment (sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__s1 | $extentconv * 10$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | sub1__p80 | $sub1__J0 / extentconv + 6$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__s1 | $1$ | variable |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial value of parameter sub1__p80 | $sub1__J0 / extentconv + 6$ | variable |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nextentconv @Const { } = 1000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a time conversion and a replacement conversion factor both affecting a rate rule.\r\ncomponentTags: CSymbolTime, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, comp:ConversionFactor, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The rate rule in the submodel affects a parameter that has been replaced with a conversion factor, necessitating a conversion of the rate rule. In addition, the submodel as a whole has a time conversion factor, so the rate rule must additionally be affected by that. Just to go whole hog, the parameter itself is used in its own rate rule, as is the csymbol 'time'.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 3 parameters (timeconv, paramconv, t1)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | t1 | $(time / timeconv / (t1 / paramconv) + 3) * paramconv / timeconv$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter paramconv | $0.01$ | constant |\r\n| Initial value of parameter t1 | $1$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nt1 @Record { } .= 1;\n\ntimeconv @Const { } = 60;\nparamconv @Const { } = 0.01;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with time conversion and a reference to a modified reaction.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, comp:SubmodelOutput, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\nIn the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference must be modified by the time conversion factor just as the kinetic law itself is modified by the time conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__s1)\r\n* 2 parameters (timeconv, sub1__p80)\r\n* 1 compartment (sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__s1 | $1 / timeconv * 10$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | sub1__p80 | $sub1__J0 / (1 / timeconv) + 6$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__s1 | $1$ | variable |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter sub1__p80 | $sub1__J0 / (1 / timeconv) + 6$ | variable |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with extent and time conversion and a reference to a modified reaction.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference must be modified by the time and extent conversion factor just as the kinetic law itself is modified by the time and extent conversion factor.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub1__s1)\r\n* 3 parameters (extentconv, timeconv, sub1__p80)\r\n* 1 compartment (sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> sub1__s1 | $extentconv / timeconv * 10$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | sub1__p80 | $sub1__J0 / (extentconv / timeconv) + 6$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub1__s1 | $1$ | variable |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter sub1__p80 | $sub1__J0 / (extentconv / timeconv) + 6$ | variable |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nextentconv @Const { } = 1000;\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with time and extent conversion and a reference to a modified replaced reaction.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, MultiCompartment, comp:ExtentConversionFactor, comp:SubmodelOutput, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference would normally be modified by the time and extent conversion factors, however, the reaction is replaced, meaning that the only conversion factor to be applied is the conversion factor on the replacement. Since there is no such factor, the assignment rule should pass through unmolested, and point to the new reaction.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 species (s1, sub1__s1)\r\n* 3 parameters (extentconv, timeconv, sub1__p80)\r\n* 2 compartments (C, sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> s1 | $10$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | sub1__p80 | $J0 + 6$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $1$ | variable |\r\n| Initial amount of species sub1__s1 | $1$ | variable |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter sub1__p80 | $J0 + 6$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, isAmount: true, } .= 1;\n\nJ0 @Reaction { actors: = s1, };\nJ0 := 10;\n\nextentconv @Const { } = 1000;\ntimeconv @Const { } = 60;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\n synopsis: A hierarchical model with time and extent conversion and a reference to a modified replaced reaction, itself with a conversion factor.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, InitialValueReassigned, MultiCompartment, comp:ConversionFactor, comp:ExtentConversionFactor, comp:SubmodelOutput , comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In the submodel, there is a reference to a reaction's SId in an assignment rule math. This reference would normally be modified by the time and extent conversion factors, however, the reaction is replaced, meaning that the only conversion factor to be applied is the conversion factor on the replacement (which, unlike test 1182, exists in this model). \r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 species (s1, sub1__s1)\r\n* 4 parameters (extentconv, timeconv, extentpertimeconv, sub1__p80)\r\n* 2 compartments (C, sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| -> s1 | $10$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | sub1__p80 | $J0 / extentpertimeconv + 6$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $1$ | variable |\r\n| Initial amount of species sub1__s1 | $1$ | variable |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial value of parameter timeconv | $60$ | constant |\r\n| Initial value of parameter extentpertimeconv | $16.6667$ | constant |\r\n| Initial value of parameter sub1__p80 | $J0 / extentpertimeconv + 6$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial volume of compartment 'sub1__C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, isAmount: true, } .= 1;\n\nJ0 @Reaction { actors: = s1, };\nJ0 := 10;\n\nextentconv @Const { } = 1000;\ntimeconv @Const { } = 60;\nextentpertimeconv @Const { } = 16.6666666666667;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A kinetic law set by a constant with an initial assignment.\r\ncomponentTags: Compartment, InitialAssignment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In some software packages, constant kinetic laws are pre-processed to a single value. This tests to ensure that if a kinetic law is constant but depends on an initial assignment to a variable, this processing is still accurate.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 2 parameters (k1, y)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| _J0: -> S1 | $k1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial value of parameter k1 | $y$ | constant |\r\n| Initial value of parameter y | $3$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1 / C;\n\n_J0 @Reaction { actors: = S1, };\n_J0 := k1;\n\nk1 @Record { } .= y;\ny @Record { } .= 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A kinetic law set by a constant with an initial assignment.\r\ncomponentTags: Compartment, InitialAssignment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In some software packages, constant kinetic laws are pre-processed to a single value. This tests to ensure that if a kinetic law is constant but depends on an initial assignment to a variable, this processing is still accurate, even when that value is given an (overridden) 'value' attribute.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 2 parameters (k1, y)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| _J0: -> S1 | $k1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial value of parameter k1 | $y$ | constant |\r\n| Initial value of parameter y | $3$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1 / C;\n\n_J0 @Reaction { actors: = S1, };\n_J0 := k1;\n\nk1 @Const { } = -2;\ny @Const { } = 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Compartment with spatial dimensions of 7.\r\ncomponentTags: Compartment\r\ntestTags: NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis model contains only a compartment, but it has a spatial dimension of 7. The numerics are not affected at all; this simply tests that the existence of this dimensionality doesn't affect the simulation.\r\n\r\nThe model contains:\r\n* 1 compartment (c)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial volume of compartment 'c' | $4$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 4;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species and a compartment both under control of a rate rule.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0.4$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\n\nS1 @Species { compartment: C1, } .= 0;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0.4;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested piecewise in conditional.\r\ncomponentTags: AssignmentRule, Parameter, RateRule\r\ntestTags: InitialValueReassigned, NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n The assignment rule for parameter 'z' has a nested piecewise function in the conditional part of the piecewise function, that returns 'true' or 'false'. It is functionally equivalent to simply having the nested conditional there directly, and is there merely to test the presence of the nesting itself.\r\n\r\nThe model contains:\r\n* 2 parameters (x, z)\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | x | $1$ |\r\n| Assignment | z | $piecewise(1, piecewise(true, x >= 0.49, false), 0)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $0$ | variable |\r\n| Initial value of parameter z | $piecewise(1, piecewise(true, geq(x, 0.49), false), 0)$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx_proc @Process { actors: = x, };\nx_proc := 1;\n\nx @Record { } .= 0;\nz @Record { };\nz := (((x >= 0.49) ? true : false) ? 1 : 0);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested piecewise in return.\r\ncomponentTags: AssignmentRule, Parameter, RateRule\r\ntestTags: InitialValueReassigned, NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n This model has a nested 'piecewise' function, with the nested piecewise in the 'returned value' part of the function.\r\n\r\nThe model contains:\r\n* 3 parameters (z, y, x)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | z | $piecewise(piecewise(2, gt(y, 1.49), 1), leq(x, 0.49), 0)$ |\r\n| Rate | y | $-2$ |\r\n| Rate | x | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter z | $piecewise(piecewise(2, gt(y, 1.49), 1), leq(x, 0.49), 0)$ | variable |\r\n| Initial value of parameter y | $2$ | variable |\r\n| Initial value of parameter x | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ny_proc @Process { actors: = y, };\ny_proc := (-2);\nx_proc @Process { actors: = x, };\nx_proc := 1;\n\nz @Record { };\nz := ((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : 0);\ny @Record { } .= 2;\nx @Record { } .= 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested piecewise in conditional and return\r\ncomponentTags: AssignmentRule, Parameter, RateRule\r\ntestTags: InitialValueReassigned, NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A combination of cases 01199 and 01200, with piecewise functions nested inside a piecewise function as both a conditional and as a return value. Tests the combination of nesting piecewise functions.\r\n\r\nThe model contains:\r\n* 3 parameters (z, y, x)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), 0)$ |\r\n| Rate | y | $-2$ |\r\n| Rate | x | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), 0)$ | variable |\r\n| Initial value of parameter y | $2$ | variable |\r\n| Initial value of parameter x | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ny_proc @Process { actors: = y, };\ny_proc := (-2);\nx_proc @Process { actors: = x, };\nx_proc := 1;\n\nz @Record { };\nz := (((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : 0);\ny @Record { } .= 2;\nx @Record { } .= 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested piecewise in otherwise.\r\ncomponentTags: AssignmentRule, Parameter, RateRule\r\ntestTags: InitialValueReassigned, NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n The assignment rule for parameter 'z' has a nested piecewise function in the 'otherwise' part of the piecewise function.\r\n\r\nThe model contains:\r\n* 3 parameters (z, x, y)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | z | $piecewise(2, x <= 0.49, piecewise(1, y > 0.49, 0))$ |\r\n| Rate | x | $1$ |\r\n| Rate | y | $-2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter z | $piecewise(2, x <= 0.49, piecewise(1, y > 0.49, 0))$ | variable |\r\n| Initial value of parameter x | $0$ | variable |\r\n| Initial value of parameter y | $2$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx_proc @Process { actors: = x, };\nx_proc := 1;\ny_proc @Process { actors: = y, };\ny_proc := (-2);\n\nz @Record { };\nz := ((x <= 0.49) ? 2 : ((y > 0.49) ? 1 : 0));\nx @Record { } .= 0;\ny @Record { } .= 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested piecewise in return and otherwise.\r\ncomponentTags: AssignmentRule, Parameter, RateRule\r\ntestTags: InitialValueReassigned, NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n The assignment rule for parameter 'z' has two nested piecewise functions in the return and otherwise parts of the containing piecewise function. A combination of cases 01200 and 01202\r\n\r\nThe model contains:\r\n* 3 parameters (z, y, x)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | z | $piecewise(piecewise(2, y > 1.49, 1), x <= 0.49, piecewise(1, y > 0.49, 0))$ |\r\n| Rate | y | $-2$ |\r\n| Rate | x | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter z | $piecewise(piecewise(2, y > 1.49, 1), x <= 0.49, piecewise(1, y > 0.49, 0))$ | variable |\r\n| Initial value of parameter y | $2$ | variable |\r\n| Initial value of parameter x | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ny_proc @Process { actors: = y, };\ny_proc := (-2);\nx_proc @Process { actors: = x, };\nx_proc := 1;\n\nz @Record { };\nz := ((x <= 0.49) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0));\ny @Record { } .= 2;\nx @Record { } .= 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested piecewise in return, conditional, and otherwise.\r\ncomponentTags: AssignmentRule, Parameter, RateRule\r\ntestTags: InitialValueReassigned, NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n The assignment rule for parameter 'z' has three nested piecewise functions in the return, conditional, and otherwise parts of the containing piecewise function. A combination of 01199, 01200, and 01202, and functionally equivalent to 01203.\r\n\r\nThe model contains:\r\n* 3 parameters (z, y, x)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), piecewise(1, y > 0.49, 0))$ |\r\n| Rate | y | $-2$ |\r\n| Rate | x | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter z | $piecewise(piecewise(2, y > 1.49, 1), piecewise(true, x <= 0.49, false), piecewise(1, y > 0.49, 0))$ | variable |\r\n| Initial value of parameter y | $2$ | variable |\r\n| Initial value of parameter x | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ny_proc @Process { actors: = y, };\ny_proc := (-2);\nx_proc @Process { actors: = x, };\nx_proc := 1;\n\nz @Record { };\nz := (((x <= 0.49) ? true : false) ? ((y > 1.49) ? 2 : 1) : ((y > 0.49) ? 1 : 0));\ny @Record { } .= 2;\nx @Record { } .= 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species concentration under control of a rate rule.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A species is under control of a rate rule, and set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by this rate of change, but the volume of the compartment stays constant. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0.4$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { boundary: true, } .= 0.5;\n\nS1 @Species { compartment: C1, } .= 0;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0.4;\n\nx @Record { };\nx := S1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Constant-amount species in variable compartment.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, RateRule, Species\r\ntestTags: Amount, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the compartment size varies, making the species concentration change (which is assigned to 'x'), but the species amount does not.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $3$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\n\nS1 @Species { compartment: C1, } .= 3 / C1;\n\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Variable compartment with explicitly fixed species\r\ncomponentTags: AssignmentRule, Compartment, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n This model is exactly the same as model 1206, but the species is interpreted as an amount, not a concentration, and that amount is explicitly set to change by zero, instead of that change being implied as in 1206.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1 / C1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $3$ | variable |\r\n| Initial value of parameter x | $S1 / C1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\n\nS1 @Species { compartment: C1, isAmount: true, } .= 3;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1 / C1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Variable compartment with variable species concentration\r\ncomponentTags: AssignmentRule, Compartment, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n This model ends up exactly the same as model 1206 and 1207, with a variable compartment, and an explicit rate of change of the species concentration that ends up with the species amount not changing.\r\n\r\nIf A is the amount of S1, and V is the volume:\r\nd(A/V)/dt = [V dA/dt - A dV/dt]/V^2\r\n = -A/V^2 dV/dt\r\n = -A/V * .2 / V\r\n = -.2*A/V / V\r\n = -.2*S1/V\r\n \r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $(-0.2 * S1) / C1$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $3$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\n\nS1 @Species { compartment: C1, } .= 3 / C1;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := ((-0.2) * S1) / C1;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An initial assignment with an nary relational element.\r\ncomponentTags: InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In MathML, it is legal to have 3+ arguments to relational elements such as less than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $piecewise(1, lt(1, 2, 1), 3)$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nx @Record { } .= ((1 < 2) ? 1 : 3);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An assignment rule with an nary relational element.\r\ncomponentTags: AssignmentRule, Parameter\r\ntestTags: InitialValueReassigned, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | x | $piecewise(1, gt(2, 1, 2), 3)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $piecewise(1, gt(2, 1, 2), 3)$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { };\nx := ((2 > 1) ? 1 : 3);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A trigger with an nary relational element.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter\r\ntestTags: NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nIn MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the trigger such that it never fires.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time > 0.21 && leq(5, 5, 2)$ | $x = 5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [_E0]= 5;\n\n_E0 @DSwitcher { trigger: t > 0.21 and 5 <= 5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Priorities with nary relational elements.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the priorities on the competing events such that E0 should have the higher priority, firing first, and E1 has the lower priority, firing second, and assigning the value of '7' to x moving forward.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 0.01$ | $piecewise(1, leq(1, 2, 1), 10)$ | $x = 5$ |\r\n| E1 | $time > 0.01$ | $piecewise(10, leq(1, 2, 1), 1)$ | $x = 7$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [E0]= 5;\nx [E1]= 7;\n\nE0 @DSwitcher { trigger: t > 0.01, };\nE1 @DSwitcher { trigger: t > 0.01, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A delay with an nary relational element.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In MathML, it is legal to have 3+ arguments to relational elements such as equals. This model checks to make sure interpreters notice the third argument, which changes the event assignment to be 7, not 5.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time > 0.01$ | $x = piecewise(5, eq(1, 1, 2), 7)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [E0]= ((1 == 1) ? 5 : 7);\n\nE0 @DSwitcher { trigger: t > 0.01, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A rate rule with an nary relational element.\r\ncomponentTags: Parameter, RateRule\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the rate rule from 1 to 0.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | x | $piecewise(1, gt(2, 1, 2), 0)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx_proc @Process { actors: = x, };\nx_proc := ((2 > 1) ? 1 : 0);\n\nx @Record { } .= 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A boundary substance-only species in non-unit compartment under control of a rate rule.\r\ncomponentTags: Compartment, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nIn this model, a boundary species with 'hasOnlySubstanceUnits=true' is in a non-unity compartment, and changes according to a rate rule. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (c)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1.2$ | variable |\r\n| Initial volume of compartment 'c' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 2;\n\nS1 @Species { compartment: c, isAmount: true, } .= 1.2;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A boundary substance-only species in non-unit compartment under control of a rate rule.\r\ncomponentTags: Compartment, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nIn this model, a boundary species with 'hasOnlySubstanceUnits=true' is in a non-unity compartment, and changes according to a rate rule. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration. This model is exactly the same as test 1219, but the Species initial value is set by its concentration, not its amount.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (c)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0.6$ | variable |\r\n| Initial volume of compartment 'c' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 2;\n\nS1 @Species { compartment: c, isAmount: true, } .= 0.6 * c;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A boundary substance-only species in varying compartment under control of a rate rule.\r\ncomponentTags: Compartment, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a boundary species with 'hasOnlySubstanceUnits=true' is changing according to a rate rule, and is in a compartment which itself is changing due to a rate rule. However, since the species is always described in terms of amount, the fact that its compartment is changing does not affect it. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (c)\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $1$ |\r\n| Rate | c | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1.2$ | variable |\r\n| Initial volume of compartment 'c' | $2$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { } .= 2;\n\nS1 @Species { compartment: c, isAmount: true, } .= 1.2;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 1;\nc_proc @Process { actors: = c, };\nc_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A boundary substance-only species in varying compartment under control of a rate rule.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a boundary species with 'hasOnlySubstanceUnits=true' is changing according to a rate rule, and is in a compartment which itself changes due to an event. However, since the species is always described in terms of amount, the fact that its compartment changes does not affect it. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (c)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time > 5.5$ | $c = 4$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1.2$ | variable |\r\n| Initial volume of compartment 'c' | $2$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { } .= 2;\nc [_E0]= 4;\n\nS1 @Species { compartment: c, isAmount: true, } .= 1.2;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 1;\n\n_E0 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A boundary substance-only species in varying compartment under control of a rate rule.\r\ncomponentTags: AssignmentRule, CSymbolTime, Compartment, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a boundary species with 'hasOnlySubstanceUnits=true' is changing according to a rate rule, and is in a compartment which itself changes due to an assignment rule. However, since the species is always described in terms of amount, the fact that its compartment changes does not affect it. This test ensures that simulators apply the rate rule to the species amount, and not to the species concentration.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (c)\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $1$ |\r\n| Assignment | c | $1 * time + 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1.2$ | variable |\r\n| Initial volume of compartment 'c' | $1 * time + 2$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { };\nc := 1 * t + 2;\n\nS1 @Species { compartment: c, isAmount: true, } .= 1.2;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple reaction whose identifier is used in an initial assignment.\r\ncomponentTags: Compartment, InitialAssignment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to check using the identifier of a reaction (J0) in an initial assignment.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (p1)\r\n* 1 compartment (c)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter p1 | $J0$ | variable |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 0;\n\nJ0 @Reaction { actors: = S1, reversible: false, };\nJ0 := 1;\n\np1 @Record { } .= J0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple reaction whose identifier is used in an assignment rule.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to check using the identifier of a reaction (J0) in an assignment rule.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (p1)\r\n* 1 compartment (c)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | p1 | $J0$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter p1 | $J0$ | variable |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 0;\n\nJ0 @Reaction { actors: = S1, reversible: false, };\nJ0 := 1;\n\np1 @Record { };\np1 := J0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple reaction whose identifier is used in a rate rule.\r\ncomponentTags: Compartment, Parameter, RateRule, Reaction, Species\r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to check using the identifier of a reaction (J0) in a rate rule.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (p1)\r\n* 1 compartment (c)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p1 | $J0$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter p1 | $0$ | variable |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 0;\n\nJ0 @Reaction { actors: = S1, reversible: false, };\nJ0 := 1;\np1_proc @Process { actors: = p1, };\np1_proc := J0;\n\np1 @Record { } .= 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple reaction whose identifier is used in a trigger.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to check using the identifier of a reaction (J0) in a trigger.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 compartment (c)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $k1$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time > J0$ | $k1 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter k1 | $1.5$ | variable |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 0;\n\nJ0 @Reaction { actors: = S1, reversible: false, };\nJ0 := k1;\n\nk1 @Record { } .= 1.5;\nk1 [_E0]= 2;\n\n_E0 @DSwitcher { trigger: t > J0, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple reaction whose identifier is used in an event assignment.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to check using the identifier of a reaction (J0) in an event assignment.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 compartment (c)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $k1$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time > 5.5$ | $k1 = 1 + J0$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter k1 | $1$ | variable |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 0;\n\nJ0 @Reaction { actors: = S1, reversible: false, };\nJ0 := k1;\n\nk1 @Record { } .= 1;\nk1 [_E0]= 1 + J0;\n\n_E0 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple reaction whose identifier is used in an event priority.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species\r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to check using the identifier of a reaction (J0) in an event priority. E1 has a lower priority, and thus executes after E0, leaving k1 with a value of 2 instead of 10.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 compartment (c)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $k1$ |]\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 5.5$ | $J0$ | $k1 = 10$ |\r\n| E1 | $time > 5.5$ | $J0 - 1$ | $k1 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter k1 | $1$ | variable |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 0;\n\nJ0 @Reaction { actors: = S1, reversible: false, };\nJ0 := k1;\n\nk1 @Record { } .= 1;\nk1 [E0]= 10;\nk1 [E1]= 2;\n\nE0 @DSwitcher { trigger: t > 5.5, };\nE1 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple reaction whose identifier is used in another reaction's kinetic law.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to check using the identifier of a reaction (J0) in another reaction (J1).\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (k1)\r\n* 1 compartment (c)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $k1$ |\r\n| J1: -> S2 | $J0 + 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial concentration of species S2 | $0$ | variable |\r\n| Initial value of parameter k1 | $1$ | constant |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 0;\nS2 @Species { compartment: c, } .= 0;\n\nJ0 @Reaction { actors: = S1, reversible: false, };\nJ0 := k1;\nJ1 @Reaction { actors: = S2, reversible: false, };\nJ1 := J0 + 1;\n\nk1 @Const { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple reaction whose identifier is shadowed by another reaction's local parameter.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to check shadowing the identifier of a reaction (J0) with a local parameter of another reaction (J1).\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (k1)\r\n* 1 local parameter (J1.J0)\r\n* 1 compartment (c)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $k1$ |\r\n| J1: -> S2 | $J0$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial concentration of species S2 | $0$ | variable |\r\n| Initial value of parameter k1 | $1$ | variable |\r\n| Initial value of local parameter 'J1.J0' | $2$ | constant |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 0;\nS2 @Species { compartment: c, } .= 0;\n\nJ0 @Reaction { actors: = S1, reversible: false, };\nJ0 := k1;\nJ1 @Reaction { actors: = S2, reversible: false, };\nJ1 := J0__J1_local;\n\nk1 @Record { } .= 1;\n\nJ0__J1_local @Const { } = 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simple reaction whose identifier is used in an initial assignment.\r\ncomponentTags: Compartment, FunctionDefinition, InitialAssignment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to check using the identifier of a reaction (J0) in a function within an initial assignment.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (p1)\r\n* 1 compartment (c)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $1$ |]\r\n\r\nThe model contains the following function definition:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | addone | x | $x + 1$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter p1 | $addone(J0)$ | variable |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\naddone #defineFunction { arguments: [x], math: x + 1, };\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 0;\n\nJ0 @Reaction { actors: = S1, reversible: false, };\nJ0 := 1;\n\np1 @Record { } .= addone(J0);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An InitialAssignment with missing MathML.\r\ncomponentTags: InitialAssignment, Parameter\r\ntestTags: NoMathML\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to ensure that if an InitialAssignment with no Math child is encountered, it is ignored.\r\n\r\nThe model contains:\r\n* 1 parameter (p)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p | $3$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np @Const { } = 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An AssignmentRule with missing MathML.\r\ncomponentTags: AssignmentRule, Parameter\r\ntestTags: NoMathML\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to ensure that if an AssignmentRule with no Math child is encountered, it is ignored.\r\n\r\nThe model contains:\r\n* 1 parameter (p)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | p | $$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np @Record { } .= 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An EventAssignment with missing MathML.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter\r\ntestTags: NoMathML, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to ensure that if an EventAssignment with no Math child is encountered, it is ignored.\r\n\r\nThe model contains:\r\n* 1 parameter (p)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time > 5.5$ | $p = $ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np @Record { } .= 3;\n\nE0 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An Event with no EventAssignments.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n This test was written to ensure that if no EventAssignments are found in an Event, it is ignored.\r\n\r\nThe model contains:\r\n* 1 parameter (p)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time > 5.5$ | |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np @Record { } .= 3;\n\nE0 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An Event Priority with missing MathML.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: NoMathML, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to ensure that if an Event Priority with no MathML is encountered, the Priority is ignored.\r\n\r\nThe model contains:\r\n* 1 parameter (p)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| _E0 | $time > 5.5$ | (unset) | $p = 5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np @Record { } .= 3;\np [_E0]= 5;\n\n_E0 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two EventAssignments, one with missing MathML.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter\r\ntestTags: NoMathML, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to ensure that even if one EventAssignment is to be ignored due to it having missing MathML, there may be other EventAssignments that are normal.\r\n\r\nThe model contains:\r\n* 2 parameters (p, d)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time > 5.5$ | $d = $ |\r\n| | | $p = 5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p | $3$ | variable |\r\n| Initial value of parameter d | $5$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np @Record { } .= 3;\np [_E0]= 5;\nd @Record { } .= 5;\n\n_E0 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A Reaction with no reactants or products.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to ensure that a Reaction with no reactants nor produts is treated properly.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (c)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> | $2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 2 / c;\n\nJ0 @Reaction { actors: = , };\nJ0 := 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two Reactions; one with no reactants or products.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to ensure that a Reaction with no reactants nor produts is treated properly when another normal Reaction is present.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (c)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> | $2$ |\r\n| J1: -> S1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial volume of compartment 'c' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nc @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: c, } .= 2 / c;\n\nJ0 @Reaction { actors: = , reversible: false, };\nJ0 := 2;\nJ1 @Reaction { actors: = S1, reversible: false, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A Constraint with no MathML.\r\ncomponentTags: Parameter\r\ntestTags: NoMathML\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis test was written to ensure that a Constraint with no MathML is properly ignored.\r\n\r\nThe model contains:\r\n* 1 parameter (p)\r\n\r\nIt also contains 1 constraints ((unset)) The initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p | $3$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np @Const { } = 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A rateOf csymbol in an event priority.\r\ncomponentTags: CSymbolRateOf, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A rateOf csymbol is used here in an event priority that assigns to p2.\r\n\r\nThe model contains:\r\n* 2 parameters (p1, p2)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 5.5$ | $1.01$ | $p2 = 5$ |\r\n| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $1$ | variable |\r\n| Initial value of parameter p2 | $10$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1_proc @Process { actors: = p1, };\np1_proc := 1;\n\np1 @Record { } .= 1;\np2 @Record { } .= 10;\np2 [E0]= 5;\np2 [E1]= 3;\n\nE0 @DSwitcher { trigger: t > 5.5, };\nE1 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A variable rateOf csymbol in an event priority.\r\ncomponentTags: CSymbolRateOf, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A variable rateOf csymbol is used here in an event priority that assigns to p2. At the time the event triggers, the priority is greater than .021, meaning that it fires first, and E0 fires second, leaving the value of p2 at 5.\r\n\r\nThe model contains:\r\n* 2 parameters (p1, p2)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 5.5$ | $0.021$ | $p2 = 5$ |\r\n| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p1 | $0.01 * p1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $2$ | variable |\r\n| Initial value of parameter p2 | $10$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1_proc @Process { actors: = p1, };\np1_proc := 0.01 * p1;\n\np1 @Record { } .= 2;\np2 @Record { } .= 10;\np2 [E0]= 5;\np2 [E1]= 3;\n\nE0 @DSwitcher { trigger: t > 5.5, };\nE1 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Use of the 'max' MathML in assignment rules.\r\ncomponentTags: AssignmentRule, CSymbolTime, Parameter\r\ntestTags: InitialValueReassigned, L3v2MathML, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThree tests of the 'max' MathML construct in assignment rules.\r\n\r\nThe model contains:\r\n* 3 parameters (p1, p2, p3)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | p1 | $max(-5, -time)$ |\r\n| Assignment | p2 | $max(time)$ |\r\n| Assignment | p3 | $max(5, time)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $max(-5, -time)$ | variable |\r\n| Initial value of parameter p2 | $max(time)$ | variable |\r\n| Initial value of parameter p3 | $max(5, time)$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1 @Record { };\np1 := max((-5), (-t));\np2 @Record { };\np2 := max(t);\np3 @Record { };\np3 := max(5, t);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Use of the 'min' MathML in assignment rules.\r\ncomponentTags: AssignmentRule, CSymbolTime, Parameter\r\ntestTags: InitialValueReassigned, L3v2MathML, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nThree tests of the 'min' MathML construct in assignment rules.\r\n\r\nThe model contains:\r\n* 3 parameters (p1, p2, p3)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | p1 | $min(-5, -time)$ |\r\n| Assignment | p2 | $min(time)$ |\r\n| Assignment | p3 | $min(5, time, 7)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $min(-5, time)$ | variable |\r\n| Initial value of parameter p2 | $min(time)$ | variable |\r\n| Initial value of parameter p3 | $min(5, time, 7)$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1 @Record { };\np1 := min((-5), (-t));\np2 @Record { };\np2 := min(t);\np3 @Record { };\np3 := min(5, t, 7);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Use of a Boolean in an event priority.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: BoolNumericSwap, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThe two events have priorities of 'true' and 'false', causing the 'true' priority to fire first.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 5.5$ | $true$ | $p1 = 10$ |\r\n| E1 | $time > 5.5$ | $false$ | $p1 = 20$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $5$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1 @Record { } .= 5;\np1 [E0]= 10;\np1 [E1]= 20;\n\nE0 @DSwitcher { trigger: t > 5.5, };\nE1 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A rateOf csymbol in an event priority.\r\ncomponentTags: CSymbolRateOf, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species\r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A rateOf csymbol is used here in an event priority that assigns to p2. This is exactly the same model as 01262, with p1 changing as a species in a reaction, instead of in a rate rule.\r\n\r\nThe model contains:\r\n* 1 species (p1)\r\n* 1 parameter (p2)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> p1 | $1$ |]\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 5.5$ | $1.01$ | $p2 = 5$ |\r\n| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species p1 | $1$ | variable |\r\n| Initial value of parameter p2 | $10$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\np1 @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: = p1, };\nJ0 := 1;\n\np2 @Record { } .= 10;\np2 [E0]= 5;\np2 [E1]= 3;\n\nE0 @DSwitcher { trigger: t > 5.5, };\nE1 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A variable rateOf csymbol in an event priority.\r\ncomponentTags: CSymbolRateOf, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species\r\ntestTags: Amount, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A variable rateOf csymbol is used here in an event priority that assigns to p2. At the time the event triggers, the priority is greater than .021, meaning that it fires first, and E0 fires second, leaving the value of p2 at 5. This is exactly the same model as 01267, with p1 changing as a species in a reaction, instead of in a rate rule.\r\n\r\nThe model contains:\r\n* 1 species (p1)\r\n* 1 parameter (p2)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> p1 | $0.01 * p1$ |]\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 5.5$ | $0.021$ | $p2 = 5$ |\r\n| E1 | $time > 5.5$ | $rateOf(p1)$ | $p2 = 3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species p1 | $2$ | variable |\r\n| Initial value of parameter p2 | $10$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\np1 @Species { compartment: C, } .= 2;\n\nJ0 @Reaction { actors: = p1, };\nJ0 := 0.01 * p1;\n\np2 @Record { } .= 10;\np2 [E0]= 5;\np2 [E1]= 3;\n\nE0 @DSwitcher { trigger: t > 5.5, };\nE1 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An empty reaction's identifier used in an initial assignment.\r\ncomponentTags: InitialAssignment, Parameter, Reaction\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an initial assignment.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> | $3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $J0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ0 @Reaction { actors: = , };\nJ0 := 3;\n\np1 @Record { } .= J0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An empty reaction's identifier used in an assignment rule.\r\ncomponentTags: AssignmentRule, Parameter, Reaction\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an assignment rule.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> | $3$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | p1 | $J0$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $J0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ0 @Reaction { actors: = , };\nJ0 := 3;\n\np1 @Record { };\np1 := J0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An empty reaction's identifier used in a rate rule.\r\ncomponentTags: Parameter, RateRule, Reaction\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in a rate rule.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> | $3$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p1 | $J0$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ0 @Reaction { actors: = , };\nJ0 := 3;\np1_proc @Process { actors: = p1, };\np1_proc := J0;\n\np1 @Record { } .= 0;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An empty reaction's identifier used in an event assignment.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter, Reaction\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an event assignment.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> | $3$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time > 4.5$ | $p1 = J0$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ0 @Reaction { actors: = , };\nJ0 := 3;\n\np1 @Record { } .= 0;\np1 [_E0]= J0;\n\n_E0 @DSwitcher { trigger: t > 4.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An empty reaction's identifier used in an event trigger.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter, Reaction\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an event trigger.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> | $3$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time > (J0 + 1.5)$ | $p1 = 5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ0 @Reaction { actors: = , };\nJ0 := 3;\n\np1 @Record { } .= 0;\np1 [E0]= 5;\n\nE0 @DSwitcher { trigger: t > (J0 + 1.5), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An empty reaction's identifier used in an assignment rule.\r\ncomponentTags: AssignmentRule, CSymbolTime, Parameter, Reaction\r\ntestTags: InitialValueReassigned, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A reaction with no products nor reactants, but which has a kinetic law, has its identifier used in an assignment rule. Differs from test 01301 because the kinetic law is non-constant.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> | $time$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | p1 | $J0 + 1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $J0 + 1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ0 @Reaction { actors: = , };\nJ0 := t;\n\np1 @Record { };\np1 := J0 + 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species always used as amount, with requested output in concentration\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Concentration, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this simple model, a species whose level is always used in terms of amount in the model (initialAmount, hasOnlySubstanceUnits=true) has requested output in terms of concentration. This is more a test of the test suite system itself than a modeling test per se.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial volume of compartment 'C' | $3$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 3;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species always used as amount, with requested output in concentration\r\ncomponentTags: Compartment, RateRule, Species\r\ntestTags: Concentration, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this simple model, a species whose level is always used in terms of amount in the model (initialAmount, hasOnlySubstanceUnits=true) has requested output in terms of concentration. This is more a test of the test suite system itself than a modeling test per se.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial volume of compartment 'C' | $3$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 3;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species always used as amount, with requested output in concentration\r\ncomponentTags: Compartment, RateRule, Species\r\ntestTags: Concentration, BoundaryCondition, HasOnlySubstanceUnits, NonConstantCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this simple model, a species whose level is always used in terms of amount in the model (initialAmount, hasOnlySubstanceUnits=true) has requested output in terms of concentration. This is more a test of the test suite system itself than a modeling test per se. In this model, it is the compartment size that changes, not the species amount.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | C | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial volume of compartment 'C' | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { } .= 3;\n\nS1 @Species { boundary: true, compartment: C, isAmount: true, } .= 2;\n\nC_proc @Process { actors: = C, };\nC_proc := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Compartment with spatial dimensions of 2.7.\r\ncomponentTags: Compartment\r\ntestTags: NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis model contains only a compartment, but it has a spatial dimension of 2.7. The numerics are not affected at all; this simply tests that the existence of this dimensionality doesn't affect the simulation.\r\n\r\nThe model contains:\r\n* 1 compartment (C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial volume of compartment 'C' | $4$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 4;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested function definitions\r\ncomponentTags: FunctionDefinition, InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A very simple model that calls a function defintion with no arguments, nested three deep.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\nThe model contains the following function definitions:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | three | | $3$ |\r\n | getthree | | $three()$ |\r\n | getgetthree | | $getthree()$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $getgetthree()$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\nthree #defineFunction { arguments: [], math: 3, };\ngetthree #defineFunction { arguments: [], math: three(), };\ngetgetthree #defineFunction { arguments: [], math: getthree(), };\n\nt @TimeScale { };\n\np1 @Record { } .= getgetthree();\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested function definitions\r\ncomponentTags: FunctionDefinition, InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A very simple model that calls a function defintion with one argument, nested three deep.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\nThe model contains the following function definitions:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | this | x | $x$ |\r\n | getthis | x | $this(x)$ |\r\n | getgetthis | x | $getthis(x)$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $getgetthis(3)$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\nthis #defineFunction { arguments: [x], math: x, };\ngetthis #defineFunction { arguments: [x], math: this(x), };\ngetgetthis #defineFunction { arguments: [x], math: getthis(x), };\n\nt @TimeScale { };\n\np1 @Record { } .= getgetthis(3);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested function definitions\r\ncomponentTags: FunctionDefinition, InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A very simple model that calls a function defintion with one argument, nested three deep.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\nThe model contains the following function definitions:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | addone | x | $x + 1$ |\r\n | addoneagain | x | $addone(x) + 1$ |\r\n | addoneagainagain | x | $addoneagain(x) + 1$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $addoneagainagain(3)$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\naddone #defineFunction { arguments: [x], math: x + 1, };\naddoneagain #defineFunction { arguments: [x], math: addone(x) + 1, };\naddoneagainagain #defineFunction { arguments: [x], math: addoneagain(x) + 1, };\n\nt @TimeScale { };\n\np1 @Record { } .= addoneagainagain(3);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested function definitions\r\ncomponentTags: FunctionDefinition, InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A slightly complicated nested function definition, nested three deep.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\nThe model contains the following function definitions:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | addone | x | $x + 1$ |\r\n | addoneagain | x | $addone(x) + 1$ |\r\n | addoneagainandagain | x | $addoneagain(x) + addone(x) + 1$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $addoneagainandagain(3)$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\naddone #defineFunction { arguments: [x], math: x + 1, };\naddoneagain #defineFunction { arguments: [x], math: addone(x) + 1, };\naddoneagainandagain #defineFunction { arguments: [x], math: addoneagain(x) + addone(x) + 1, };\n\nt @TimeScale { };\n\np1 @Record { } .= addoneagainandagain(3);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Nested function definitions\r\ncomponentTags: FunctionDefinition, InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A slightly complicated nested function definition, nested three deep.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\nThe model contains the following function definitions:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | addone | x | $x + 1$ |\r\n | addoneagain2x | x | $addone(x) + addone(x) + 1$ |\r\n | addoneagainandagain2x | x | $addoneagain2x(x) + addoneagain2x(x) + addone(x) + addone(x) + 1$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $addoneagainandagain2x(3)$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\naddone #defineFunction { arguments: [x], math: x + 1, };\naddoneagain2x #defineFunction { arguments: [x], math: addone(x) + addone(x) + 1, };\naddoneagainandagain2x #defineFunction { arguments: [x], math: addoneagain2x(x) + addoneagain2x(x) + addone(x) + addone(x) + 1, };\n\nt @TimeScale { };\n\np1 @Record { } .= addoneagainandagain2x(3);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Use of a csymbol whose putative ID shadows another parameter.\r\ncomponentTags: AssignmentRule, CSymbolTime, Parameter\r\ntestTags: InitialValueReassigned, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model the 'time' csymbol is given the ID of another parameter. This ID should be ignored.\r\n\r\nThe model contains:\r\n* 2 parameters (p1, p2)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | p2 | $1 + time$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $5$ | constant |\r\n| Initial value of parameter p2 | $1 + time$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np2 @Record { };\np2 := 1 + t;\n\np1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simultaneous event using trigger-time values.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: EventUsesTriggerTimeValues, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, an event uses trigger-time values, which makes a difference to the results.\r\n\r\nThe model contains:\r\n* 2 parameters (x, y)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E1 | $time > 3.5$ | $10$ | $x = 7$ |\r\n| E2 | $time > 3.5$ | $5$ | $y = x$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |\r\n| Initial value of parameter y | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [E1]= 7;\ny @Record { } .= 0;\ny [E2]= x;\n\nE1 @DSwitcher { trigger: t > 3.5, };\nE2 @DSwitcher { trigger: t > 3.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A simultaneous event using assignment-time values.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: EventUsesAssignmentTimeValues, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, an event uses assignment-time values, which makes a difference to the results.\r\n\r\nThe model contains:\r\n* 2 parameters (x, y)\r\n\r\nThere are 2 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Use values from:* | *Event Assignments* |\r\n| E1 | $time > 3.5$ | $10$ | Trigger time | $x = 7$ |\r\n| E2 | $time > 3.5$ | $5$ | Assignment time | $y = x$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |\r\n| Initial value of parameter y | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [E1]= 7;\ny @Record { } .= 0;\ny [E2]= x;\n\nE1 @DSwitcher { trigger: t > 3.5, };\nE2 @DSwitcher { trigger: t > 3.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two events that fire at t0 with different priorities.\r\ncomponentTags: EventNoDelay, EventPriority, Parameter\r\ntestTags: EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, two events both fire at t0, with different priorities. Since both assign to the same variable, the one with the lower priority sets the value going forward in time.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\n\r\nThere are 2 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* |\r\n| E1 | $x > 2$ | $10$ | false | $x = 7$ |\r\n| E2 | $x > 2$ | $5$ | false | $x = 5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [E1]= 7;\nx [E2]= 5;\n\nE1 @DSwitcher { trigger: x > 2, };\nE2 @DSwitcher { trigger: x > 2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two events that fire at t0 with different priorities.\r\ncomponentTags: EventNoDelay, EventPriority, Parameter\r\ntestTags: EventT0Firing, EventUsesTriggerTimeValues, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, two events both fire at t0, with different priorities. The first assigns a new value to 'x', and the second assigns the value of 'x' to y, but uses the *trigger* time value, meaning that afterwards, both x and y end up with new values.\r\n\r\nThe model contains:\r\n* 2 parameters (x, y)\r\n\r\nThere are 2 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* |\r\n| E1 | $x > 2$ | $10$ | false | $x = 7$ |\r\n| E2 | $x > 2$ | $5$ | false | $y = x$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |\r\n| Initial value of parameter y | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [E1]= 7;\ny @Record { } .= 0;\ny [E2]= x;\n\nE1 @DSwitcher { trigger: x > 2, };\nE2 @DSwitcher { trigger: x > 2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two events that fire at t0 with different priorities.\r\ncomponentTags: EventNoDelay, EventPriority, Parameter\r\ntestTags: EventT0Firing, EventUsesAssignmentTimeValues, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, two events both fire at t0, with different priorities. The first assigns a new value to 'x', and the second assigns the value of 'x' to y, using the *assignment* time value, meaning that afterwards, both x and y end up with the same value.\r\n\r\nThe model contains:\r\n* 2 parameters (x, y)\r\n\r\nThere are 2 events:\r\n\r\n[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Use values from:* | *Event Assignments* |\r\n| E1 | $x > 2$ | $10$ | false | Trigger time | $x = 7$ |\r\n| E2 | $x > 2$ | $5$ | false | Assignment time | $y = x$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |\r\n| Initial value of parameter y | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [E1]= 7;\ny @Record { } .= 0;\ny [E2]= x;\n\nE1 @DSwitcher { trigger: x > 2, };\nE2 @DSwitcher { trigger: x > 2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two events that trigger at t0, one of which cancels the other.\r\ncomponentTags: EventNoDelay, EventPriority, Parameter\r\ntestTags: EventIsNotPersistent, EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, two events trigger at t0, but the first reverses the trigger of the second, which is set persistent=false, cancelling the event's execution.\r\n\r\nThe model contains:\r\n* 2 parameters (x, y)\r\n\r\nThere are 2 events:\r\n\r\n[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *initialValue* | *Event Assignments* |\r\n| E1 | $x > 2$ | $10$ | true | false | $x = 0$ |\r\n| E2 | $x > 2$ | $5$ | false | false | $y = 7$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |\r\n| Initial value of parameter y | $6$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [E1]= 0;\ny @Record { } .= 6;\ny [E2]= 7;\n\nE1 @DSwitcher { trigger: x > 2, };\nE2 @DSwitcher { trigger: x > 2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two events that trigger at t0, one of which fails to cancels the other.\r\ncomponentTags: EventNoDelay, EventPriority, Parameter\r\ntestTags: EventIsPersistent, EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, two events trigger at t0, and the first reverses the trigger of the second, but it's not set persistent=false, allowing it to continue.\r\n\r\nThis is the best test, because it's test 1337.\r\n\r\nThe model contains:\r\n* 2 parameters (x, y)\r\n\r\nThere are 2 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *initialValue* | *Event Assignments* |\r\n| E1 | $x > 2$ | $10$ | false | $x = 0$ |\r\n| E2 | $x > 2$ | $5$ | false | $y = 7$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |\r\n| Initial value of parameter y | $6$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { } .= 3;\nx [E1]= 0;\ny @Record { } .= 6;\ny [E2]= 7;\n\nE1 @DSwitcher { trigger: x > 2, };\nE2 @DSwitcher { trigger: x > 2, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two events that trigger at t0, one of which fails to cancels the other.\r\ncomponentTags: Compartment, Parameter, RateRule, Reaction, Species\r\ntestTags: Amount, NonConstantParameter, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a reaction that produces S1 starts off positive, but then goes negative, due to a parameter under control of a rate rule.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $k1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | k1 | $-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter k1 | $5$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 0;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := k1;\nk1_proc @Process { actors: = k1, };\nk1_proc := (-1);\n\nk1 @Record { } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A reaction whose rate becomes negative.\r\ncomponentTags: Compartment, Parameter, RateRule, Reaction, Species\r\ntestTags: Amount, NonConstantParameter, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a reaction that produces S1 starts off negative, but then goes positive, due to a parameter under control of a rate rule.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $k1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | k1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter k1 | $-5$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 0;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := k1;\nk1_proc @Process { actors: = k1, };\nk1_proc := 1;\n\nk1 @Record { } .= -5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A reaction whose rate goes negative due to an event.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, NonConstantParameter, ReversibleReaction\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a reaction that produces S1 starts off positive, but then goes negative, due to an event.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $k1$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time > 5.5$ | $k1 = -1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter k1 | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 0;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := k1;\n\nk1 @Record { } .= 1;\nk1 [_E0]= (-1);\n\n_E0 @DSwitcher { trigger: t > 5.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Just a compartment and a species.\r\ncomponentTags: Compartment, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n This model test the simple existence of a species and a compartment.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $2$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Just a non-unity compartment and a species.\r\ncomponentTags: Compartment, Species\r\ntestTags: Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n This model test the simple existence of a species and a non-unity compartment.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial volume of compartment 'C' | $2$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 2;\n\nS1 @Species { compartment: C, } .= 2 / C;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced reaction whose ID is used in an assignment rule.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, InitialValueReassigned, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel reaction ID is used in an assignment rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $5$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | A__x | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $J1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced reaction whose ID is used in an initial assignment.\r\ncomponentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, InitialValueReassigned, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced reaction ID is used in an initial assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $J1 + 2$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced reaction whose ID is used in an event trigger.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced reaction ID is used in an event trigger.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $5$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced reaction whose ID is used in am event priority.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced reaction ID is used in an event priority.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $5$ |]\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ |\r\n| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced reaction whose ID is used in an event assignment.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced reaction ID is used in an event assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $5$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > 5.5$ | $A__x = J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced reaction whose ID is used in an event delay.\r\ncomponentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced reaction ID is used in an event delay.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $5$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* |\r\n| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced reaction whose ID is used in an algebraic rule.\r\ncomponentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, InitialValueReassigned, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel reaction ID is used in an algebraic rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $5$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Algebraic | $0$ | $A__x - J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $unknown$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced reaction whose ID is used in a reaction.\r\ncomponentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel reaction ID is used in another reaction.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $5$ |\r\n| A__J2: S1 -> | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced reaction whose ID is used in a rate rule.\r\ncomponentTags: Compartment, Parameter, RateRule, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel reaction ID is used in a rate rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $5$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | A__x | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $0$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced parameter whose ID is used in an assignment rule.\r\ncomponentTags: AssignmentRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel parameter ID is used in an assignment rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (J1, A__x)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | A__x | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter J1 | $5$ | constant |\r\n| Initial value of parameter A__x | $J1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced parameter whose ID is used in an initial assignment.\r\ncomponentTags: InitialAssignment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced parameter ID is used in an initial assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (J1, A__x)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter J1 | $5$ | constant |\r\n| Initial value of parameter A__x | $J1 + 2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced parameter whose ID is used in an event trigger.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced parameter ID is used in an event trigger.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (J1, A__x)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter J1 | $5$ | constant |\r\n| Initial value of parameter A__x | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced parameter whose ID is used in an event priority.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced parameter ID is used in an event priority.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (J1, A__x)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ |\r\n| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter J1 | $5$ | constant |\r\n| Initial value of parameter A__x | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced parameter whose ID is used in an event assignment.\r\ncomponentTags: CSymbolTime, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced parameter ID is used in an event assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (J1, A__x)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > 5.5$ | $A__x = J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter J1 | $5$ | constant |\r\n| Initial value of parameter A__x | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced parameter whose ID is used in an event delay.\r\ncomponentTags: CSymbolTime, EventWithDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced parameter ID is used in an event delay.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (J1, A__x)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* |\r\n| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter J1 | $5$ | constant |\r\n| Initial value of parameter A__x | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced parameter whose ID is used in an algebraic rule.\r\ncomponentTags: AlgebraicRule, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel parameter ID is used in an algebraic rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (J1, A__x)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Algebraic | $0$ | $A__x - J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter J1 | $5$ | constant |\r\n| Initial value of parameter A__x | $unknown$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced parameter whose ID is used in a reaction.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel parameter ID is used in a reaction.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (J1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| A__J2: -> S1 | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter J1 | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced parameter whose ID is used in a rate rule.\r\ncomponentTags: Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel parameter ID is used in a rate rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 parameters (J1, A__x)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | A__x | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter J1 | $5$ | constant |\r\n| Initial value of parameter A__x | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced compartment whose ID is used in an assignment rule.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel compartment ID is used in an assignment rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (A__x)\r\n* 1 compartment (J1)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | A__x | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter A__x | $J1$ | variable |\r\n| Initial volume of compartment 'J1' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Compartment { boundary: true, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced compartment whose ID is used in an initial assignment.\r\ncomponentTags: Compartment, InitialAssignment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced compartment ID is used in an initial assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (A__x)\r\n* 1 compartment (J1)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter A__x | $J1 + 2$ | constant |\r\n| Initial volume of compartment 'J1' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Compartment { boundary: true, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced compartment whose ID is used in an event trigger.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced compartment ID is used in an event trigger.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (A__x)\r\n* 1 compartment (J1)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'J1' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Compartment { boundary: true, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced compartment whose ID is used in an event priority.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced compartment ID is used in an event priority.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (A__x)\r\n* 1 compartment (J1)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| A__E0 | $time > 5.5$ | $J1$ | $A__x = 4$ |\r\n| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'J1' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Compartment { boundary: true, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced compartment whose ID is used in an event assignment.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced compartment ID is used in an event assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (A__x)\r\n* 1 compartment (J1)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > 5.5$ | $A__x = J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'J1' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Compartment { boundary: true, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced compartment whose ID is used in an event delay.\r\ncomponentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced compartment ID is used in an event delay.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (A__x)\r\n* 1 compartment (J1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* |\r\n| A__E0 | $time > 0.5$ | $J1$ | $A__x = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'J1' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Compartment { boundary: true, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced compartment whose ID is used in an algebraic rule.\r\ncomponentTags: AlgebraicRule, Compartment, Parameter, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: InitialValueReassigned, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel compartment ID is used in an algebraic rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (A__x)\r\n* 1 compartment (J1)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Algebraic | $0$ | $A__x - J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter A__x | $unknown$ | variable |\r\n| Initial volume of compartment 'J1' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Compartment { boundary: true, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced compartment whose ID is used in a reaction.\r\ncomponentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, MultiCompartment, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel compartment ID is used in a reaction.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 2 compartments (C, J1)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| A__J2: -> S1 | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial volume of compartment 'J1' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\nJ1 @Compartment { boundary: true, } .= 5;\n\nS1 @Species { compartment: C, } .= 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced compartment whose ID is used in a rate rule.\r\ncomponentTags: Compartment, Parameter, RateRule, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: NonConstantParameter, NonUnityCompartment, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel compartment ID is used in a rate rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 parameter (A__x)\r\n* 1 compartment (J1)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | A__x | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter A__x | $0$ | variable |\r\n| Initial volume of compartment 'J1' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nJ1 @Compartment { boundary: true, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species whose ID is used in an assignment rule.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel species ID is used in an assignment rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (J1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (A_C)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | A__x | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species J1 | $5$ | variable |\r\n| Initial value of parameter A__x | $J1$ | variable |\r\n| Initial volume of compartment 'A_C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nA_C @Compartment { boundary: true, } .= 1;\n\nJ1 @Species { boundary: true, compartment: A_C, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species whose ID is used in an initial assignment.\r\ncomponentTags: Compartment, InitialAssignment, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced species ID is used in an initial assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (J1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (A_C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species J1 | $5$ | variable |\r\n| Initial value of parameter A__x | $J1 + 2$ | constant |\r\n| Initial volume of compartment 'A_C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nA_C @Compartment { boundary: true, } .= 1;\n\nJ1 @Species { boundary: true, compartment: A_C, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species whose ID is used in an event trigger.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, BoundaryCondition, NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced species ID is used in an event trigger.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (J1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (A_C)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > (J1 + 0.5)$ | $A__x = 4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species J1 | $5$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'A_C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nA_C @Compartment { boundary: true, } .= 1;\n\nJ1 @Species { boundary: true, compartment: A_C, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species whose ID is used in an event assignment.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, BoundaryCondition, NonConstantParameter, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced species ID is used in an event assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (J1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (A_C)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > 5.5$ | $A__x = J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species J1 | $5$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'A_C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nA_C @Compartment { boundary: true, } .= 1;\n\nJ1 @Species { boundary: true, compartment: A_C, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species whose ID is used in a reaction.\r\ncomponentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, BoundaryCondition, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel species ID is used in a reaction.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 2 species (S1, J1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| A__J2: -> S1 | $J1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial concentration of species J1 | $5$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\nJ1 @Species { boundary: true, compartment: C, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference whose ID is used in an assignment rule.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel species reference (itself in a replaced reaction) is used in an assignment rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | A__x | $J1_sr$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $J1_sr$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference whose ID is used in an initial assignment.\r\ncomponentTags: Compartment, InitialAssignment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced species reference (itself in a replaced reaction) is used in an initial assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $J1_sr + 2$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference whose ID is used in an event trigger.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced species reference (itself in a replaced reaction) is used in an event trigger.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > (J1_sr + 0.5)$ | $A__x = 4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference whose ID is used in am event priority.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced species reference (itself in a replaced reaction) is used in an event priority.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |]\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| A__E0 | $time > 5.5$ | $J1_sr$ | $A__x = 4$ |\r\n| A__E1 | $time > 5.5$ | $4$ | $A__x = 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference whose ID is used in an event assignment.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced species reference (itself in a replaced reaction) is used in an event assignment.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| A__E0 | $time > 5.5$ | $A__x = J1_sr$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference whose ID is used in an event delay.\r\ncomponentTags: CSymbolTime, Compartment, EventWithDelay, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced species reference (itself in a replaced reaction) is used in an event delay.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |]\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Delay* | *Event Assignments* |\r\n| A__E0 | $time > 0.5$ | $J1_sr$ | $A__x = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference whose ID is used in an algebraic rule.\r\ncomponentTags: AlgebraicRule, Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, InitialValueReassigned, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel species reference (itself in a replaced reaction) is used in an algebraic rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Algebraic | $0$ | $A__x - J1_sr$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $unknown$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference (itself in a replaced reaction) whose ID is used in a reaction.\r\ncomponentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel species reference (itself in a replaced reaction) is used in another reaction.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |\r\n| A__J2: S1 -> | $J1_sr$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference whose ID is used in a rate rule.\r\ncomponentTags: Compartment, Parameter, RateRule, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonConstantParameter, NonUnityStoichiometry, SpeciesReferenceInMath, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n In this model, a replaced submodel species reference (itself in a replaced reaction) is used in a rate rule.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 parameter (A__x)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | A__x | $J1_sr$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial value of parameter A__x | $0$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A replaced species reference in a replaced reaction.\r\ncomponentTags: Compartment, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: comp\r\n\r\n This is the base model for the previous 9 tests: a replaced species reference inside a replaced reaction. Neither the reaction ID nor the species reference ID are used anywhere; this is just to make sure simulator software can handle the situation in general.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n* 1 species reference (J1_sr)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> 5S1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 3;\n\nJ1 @Reaction { actors: = 5*S1, };\nJ1 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A larger model where the order of assignment rules is important.\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, InitialValueReassigned, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this real model of a reaction system, the order of the assignment rules makes a difference in how the simulation proceeds: it is important to carry out the assignments such that the independent assignments are performed first, with the dependent assignments carried out after the assignments to variables they each depend on. This has been seen to make an appreciable difference when using large timesteps and the Euler method.\r\n\r\nThe model contains:\r\n* 18 species (pp9_mrna, p9, pp8_mrna, p8, pp7_mrna, p7, pp6_mrna, p6, pp5_mrna, p5, pp4_mrna, p4, pp3_mrna, p3, pp2_mrna, p2, pp1_mrna, p1)\r\n* 90 parameters (pp8_mrna_degradation_rate, pp9_mrna_degradation_rate, p1_degradation_rate, p2_degradation_rate, p3_degradation_rate, p4_degradation_rate, p5_degradation_rate, p6_degradation_rate, p7_degradation_rate, p8_degradation_rate, p9_degradation_rate, v1_Kd, v1_h, v2_Kd, v2_h, v3_Kd, v3_h, v4_Kd, v4_h, v5_Kd, v5_h, v6_Kd, v6_h, v7_Kd, v7_h, v8_Kd, v8_h, v9_Kd, v9_h, pp1_mrna_degradation_rate, pp2_mrna_degradation_rate, pro1_strength, pro2_strength, pro3_strength, pro4_strength, pro5_strength, pro6_strength, pro7_strength, pro8_strength, pro9_strength, pp3_mrna_degradation_rate, v10_Kd, v10_h, v11_Kd, v11_h, v12_Kd, v12_h, v13_Kd, v13_h, pp4_mrna_degradation_rate, v14_Kd, v14_h, v15_Kd, v15_h, pp5_mrna_degradation_rate, rbs1_strength, rbs2_strength, rbs3_strength, rbs4_strength, rbs5_strength, rbs6_strength, rbs7_strength, rbs8_strength, rbs9_strength, pp6_mrna_degradation_rate, pp7_mrna_degradation_rate, as8, cod1, cod2, cod3, cod4, cod5, cod6, cod7, cod8, cod9, rs1, rs2, rs3, rs4, rs5, rs6, rs7, as1, as2, as3, as4, as5, as6, as7)\r\n* 1 compartment (DefaultCompartment)\r\n\r\nThere are 36 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| pp9_v1: -> pp9_mrna | $cod9$ |\r\n| pp9_v2: pp9_mrna -> | $pp9_mrna_degradation_rate * pp9_mrna$ |\r\n| pp9_v3: -> p9 | $rbs9_strength * pp9_mrna$ |\r\n| pp9_v4: p9 -> | $p9_degradation_rate * p9$ |\r\n| pp8_v1: -> pp8_mrna | $cod8$ |\r\n| pp8_v2: pp8_mrna -> | $pp8_mrna_degradation_rate * pp8_mrna$ |\r\n| pp8_v3: -> p8 | $rbs8_strength * pp8_mrna$ |\r\n| pp8_v4: p8 -> | $p8_degradation_rate * p8$ |\r\n| pp7_v1: -> pp7_mrna | $cod7$ |\r\n| pp7_v2: pp7_mrna -> | $pp7_mrna_degradation_rate * pp7_mrna$ |\r\n| pp7_v3: -> p7 | $rbs7_strength * pp7_mrna$ |\r\n| pp7_v4: p7 -> | $p7_degradation_rate * p7$ |\r\n| pp6_v1: -> pp6_mrna | $cod6$ |\r\n| pp6_v2: pp6_mrna -> | $pp6_mrna_degradation_rate * pp6_mrna$ |\r\n| pp6_v3: -> p6 | $rbs6_strength * pp6_mrna$ |\r\n| pp6_v4: p6 -> | $p6_degradation_rate * p6$ |\r\n| pp5_v1: -> pp5_mrna | $cod5$ |\r\n| pp5_v2: pp5_mrna -> | $pp5_mrna_degradation_rate * pp5_mrna$ |\r\n| pp5_v3: -> p5 | $rbs5_strength * pp5_mrna$ |\r\n| pp5_v4: p5 -> | $p5_degradation_rate * p5$ |\r\n| pp4_v1: -> pp4_mrna | $cod4$ |\r\n| pp4_v2: pp4_mrna -> | $pp4_mrna_degradation_rate * pp4_mrna$ |\r\n| pp4_v3: -> p4 | $rbs4_strength * pp4_mrna$ |\r\n| pp4_v4: p4 -> | $p4_degradation_rate * p4$ |\r\n| pp3_v1: -> pp3_mrna | $cod3$ |\r\n| pp3_v2: pp3_mrna -> | $pp3_mrna_degradation_rate * pp3_mrna$ |\r\n| pp3_v3: -> p3 | $rbs3_strength * pp3_mrna$ |\r\n| pp3_v4: p3 -> | $p3_degradation_rate * p3$ |\r\n| pp2_v1: -> pp2_mrna | $cod2$ |\r\n| pp2_v2: pp2_mrna -> | $pp2_mrna_degradation_rate * pp2_mrna$ |\r\n| pp2_v3: -> p2 | $rbs2_strength * pp2_mrna$ |\r\n| pp2_v4: p2 -> | $p2_degradation_rate * p2$ |\r\n| pp1_v1: -> pp1_mrna | $cod1$ |\r\n| pp1_v2: pp1_mrna -> | $pp1_mrna_degradation_rate * pp1_mrna$ |\r\n| pp1_v3: -> p1 | $rbs1_strength * pp1_mrna$ |\r\n| pp1_v4: p1 -> | $p1_degradation_rate * p1$ |]\r\n\r\n\r\nThere are 24 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | as8 | $(1 + (p5 / v9_Kd)^v9_h - 1) / (1 + (p5 / v9_Kd)^v9_h)$ |\r\n| Assignment | cod1 | $pro1_strength$ |\r\n| Assignment | cod2 | $pro2_strength * as1 * rs1$ |\r\n| Assignment | cod3 | $pro3_strength * rs2 * rs3$ |\r\n| Assignment | cod4 | $pro4_strength * rs7 * rs6$ |\r\n| Assignment | cod5 | $pro5_strength * as2$ |\r\n| Assignment | cod6 | $pro6_strength * (as3 + as4)$ |\r\n| Assignment | cod7 | $pro7_strength * (as7 + as8)$ |\r\n| Assignment | cod8 | $pro8_strength * as5 * rs4$ |\r\n| Assignment | cod9 | $pro9_strength * as6 * rs5$ |\r\n| Assignment | rs1 | $1 / (1 + (p9 / v13_Kd)^v13_h)$ |\r\n| Assignment | rs2 | $1 / (1 + (p2 / v2_Kd)^v2_h)$ |\r\n| Assignment | rs3 | $1 / (1 + (p3 / v3_Kd)^v3_h)$ |\r\n| Assignment | rs4 | $1 / (1 + (p8 / v11_Kd)^v11_h)$ |\r\n| Assignment | rs5 | $1 / (1 + (p8 / v12_Kd)^v12_h)$ |\r\n| Assignment | rs6 | $1 / (1 + (p2 / v14_Kd)^v14_h)$ |\r\n| Assignment | rs7 | $1 / (1 + (p3 / v15_Kd)^v15_h)$ |\r\n| Assignment | as1 | $(1 + (p1 / v1_Kd)^v1_h - 1) / (1 + (p1 / v1_Kd)^v1_h)$ |\r\n| Assignment | as2 | $(1 + (p4 / v4_Kd)^v4_h - 1) / (1 + (p4 / v4_Kd)^v4_h)$ |\r\n| Assignment | as3 | $(1 + (p5 / v5_Kd)^v5_h - 1) / (1 + (p5 / v5_Kd)^v5_h)$ |\r\n| Assignment | as4 | $(1 + (p6 / v6_Kd)^v6_h - 1) / (1 + (p6 / v6_Kd)^v6_h)$ |\r\n| Assignment | as5 | $(1 + (p7 / v7_Kd)^v7_h - 1) / (1 + (p7 / v7_Kd)^v7_h)$ |\r\n| Assignment | as6 | $(1 + (p7 / v10_Kd)^v10_h - 1) / (1 + (p7 / v10_Kd)^v10_h)$ |\r\n| Assignment | as7 | $(1 + (p6 / v8_Kd)^v8_h - 1) / (1 + (p6 / v8_Kd)^v8_h)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species pp9_mrna | $0$ | variable |\r\n| Initial amount of species p9 | $0$ | variable |\r\n| Initial amount of species pp8_mrna | $0$ | variable |\r\n| Initial amount of species p8 | $0$ | variable |\r\n| Initial amount of species pp7_mrna | $0$ | variable |\r\n| Initial amount of species p7 | $0$ | variable |\r\n| Initial amount of species pp6_mrna | $0$ | variable |\r\n| Initial amount of species p6 | $0$ | variable |\r\n| Initial amount of species pp5_mrna | $0$ | variable |\r\n| Initial amount of species p5 | $0$ | variable |\r\n| Initial amount of species pp4_mrna | $0$ | variable |\r\n| Initial amount of species p4 | $0$ | variable |\r\n| Initial amount of species pp3_mrna | $0$ | variable |\r\n| Initial amount of species p3 | $0$ | variable |\r\n| Initial amount of species pp2_mrna | $0$ | variable |\r\n| Initial amount of species p2 | $0$ | variable |\r\n| Initial amount of species pp1_mrna | $0$ | variable |\r\n| Initial amount of species p1 | $5$ | variable |\r\n| Initial value of parameter pp8_mrna_degradation_rate | $1$ | constant |\r\n| Initial value of parameter pp9_mrna_degradation_rate | $1$ | constant |\r\n| Initial value of parameter p1_degradation_rate | $0.5$ | constant |\r\n| Initial value of parameter p2_degradation_rate | $0.5$ | constant |\r\n| Initial value of parameter p3_degradation_rate | $0.5$ | constant |\r\n| Initial value of parameter p4_degradation_rate | $0.5$ | constant |\r\n| Initial value of parameter p5_degradation_rate | $0.5$ | constant |\r\n| Initial value of parameter p6_degradation_rate | $0.5$ | constant |\r\n| Initial value of parameter p7_degradation_rate | $0.5$ | constant |\r\n| Initial value of parameter p8_degradation_rate | $0.5$ | constant |\r\n| Initial value of parameter p9_degradation_rate | $0.5$ | constant |\r\n| Initial value of parameter v1_Kd | $11.147$ | constant |\r\n| Initial value of parameter v1_h | $1$ | constant |\r\n| Initial value of parameter v2_Kd | $1$ | constant |\r\n| Initial value of parameter v2_h | $4$ | constant |\r\n| Initial value of parameter v3_Kd | $20$ | constant |\r\n| Initial value of parameter v3_h | $1$ | constant |\r\n| Initial value of parameter v4_Kd | $0.2$ | constant |\r\n| Initial value of parameter v4_h | $4$ | constant |\r\n| Initial value of parameter v5_Kd | $0.2$ | constant |\r\n| Initial value of parameter v5_h | $4$ | constant |\r\n| Initial value of parameter v6_Kd | $0.04$ | constant |\r\n| Initial value of parameter v6_h | $4$ | constant |\r\n| Initial value of parameter v7_Kd | $0.02$ | constant |\r\n| Initial value of parameter v7_h | $4$ | constant |\r\n| Initial value of parameter v8_Kd | $0.04$ | constant |\r\n| Initial value of parameter v8_h | $4$ | constant |\r\n| Initial value of parameter v9_Kd | $0.2$ | constant |\r\n| Initial value of parameter v9_h | $4$ | constant |\r\n| Initial value of parameter pp1_mrna_degradation_rate | $1$ | constant |\r\n| Initial value of parameter pp2_mrna_degradation_rate | $1$ | constant |\r\n| Initial value of parameter pro1_strength | $2$ | constant |\r\n| Initial value of parameter pro2_strength | $4.5077$ | constant |\r\n| Initial value of parameter pro3_strength | $5$ | constant |\r\n| Initial value of parameter pro4_strength | $5$ | constant |\r\n| Initial value of parameter pro5_strength | $5$ | constant |\r\n| Initial value of parameter pro6_strength | $1.31$ | constant |\r\n| Initial value of parameter pro7_strength | $1.31$ | constant |\r\n| Initial value of parameter pro8_strength | $5$ | constant |\r\n| Initial value of parameter pro9_strength | $5$ | constant |\r\n| Initial value of parameter pp3_mrna_degradation_rate | $1$ | constant |\r\n| Initial value of parameter v10_Kd | $0.02$ | constant |\r\n| Initial value of parameter v10_h | $4$ | constant |\r\n| Initial value of parameter v11_Kd | $0.1$ | constant |\r\n| Initial value of parameter v11_h | $2$ | constant |\r\n| Initial value of parameter v12_Kd | $0.1$ | constant |\r\n| Initial value of parameter v12_h | $2$ | constant |\r\n| Initial value of parameter v13_Kd | $0.01$ | constant |\r\n| Initial value of parameter v13_h | $2$ | constant |\r\n| Initial value of parameter pp4_mrna_degradation_rate | $1$ | constant |\r\n| Initial value of parameter v14_Kd | $1$ | constant |\r\n| Initial value of parameter v14_h | $4$ | constant |\r\n| Initial value of parameter v15_Kd | $20$ | constant |\r\n| Initial value of parameter v15_h | $1$ | constant |\r\n| Initial value of parameter pp5_mrna_degradation_rate | $1$ | constant |\r\n| Initial value of parameter rbs1_strength | $0.3668$ | constant |\r\n| Initial value of parameter rbs2_strength | $1.4102$ | constant |\r\n| Initial value of parameter rbs3_strength | $0.8$ | constant |\r\n| Initial value of parameter rbs4_strength | $2.21$ | constant |\r\n| Initial value of parameter rbs5_strength | $0.5$ | constant |\r\n| Initial value of parameter rbs6_strength | $2$ | constant |\r\n| Initial value of parameter rbs7_strength | $5$ | constant |\r\n| Initial value of parameter rbs8_strength | $3.6377$ | constant |\r\n| Initial value of parameter rbs9_strength | $8$ | constant |\r\n| Initial value of parameter pp6_mrna_degradation_rate | $1$ | constant |\r\n| Initial value of parameter pp7_mrna_degradation_rate | $1$ | constant |\r\n| Initial value of parameter as8 | $(1 + (p5 / v9_Kd)^v9_h - 1) / (1 + (p5 / v9_Kd)^v9_h)$ | variable |\r\n| Initial value of parameter cod1 | $pro1_strength$ | variable |\r\n| Initial value of parameter cod2 | $pro2_strength * as1 * rs1$ | variable |\r\n| Initial value of parameter cod3 | $pro3_strength * rs2 * rs3$ | variable |\r\n| Initial value of parameter cod4 | $pro4_strength * rs7 * rs6$ | variable |\r\n| Initial value of parameter cod5 | $pro5_strength * as2$ | variable |\r\n| Initial value of parameter cod6 | $pro6_strength * (as3 + as4)$ | variable |\r\n| Initial value of parameter cod7 | $pro7_strength * (as7 + as8)$ | variable |\r\n| Initial value of parameter cod8 | $pro8_strength * as5 * rs4$ | variable |\r\n| Initial value of parameter cod9 | $pro9_strength * as6 * rs5$ | variable |\r\n| Initial value of parameter rs1 | $1 / (1 + (p9 / v13_Kd)^v13_h)$ | variable |\r\n| Initial value of parameter rs2 | $1 / (1 + (p2 / v2_Kd)^v2_h)$ | variable |\r\n| Initial value of parameter rs3 | $1 / (1 + (p3 / v3_Kd)^v3_h)$ | variable |\r\n| Initial value of parameter rs4 | $1 / (1 + (p8 / v11_Kd)^v11_h)$ | variable |\r\n| Initial value of parameter rs5 | $1 / (1 + (p8 / v12_Kd)^v12_h)$ | variable |\r\n| Initial value of parameter rs6 | $1 / (1 + (p2 / v14_Kd)^v14_h)$ | variable |\r\n| Initial value of parameter rs7 | $1 / (1 + (p3 / v15_Kd)^v15_h)$ | variable |\r\n| Initial value of parameter as1 | $(1 + (p1 / v1_Kd)^v1_h - 1) / (1 + (p1 / v1_Kd)^v1_h)$ | variable |\r\n| Initial value of parameter as2 | $(1 + (p4 / v4_Kd)^v4_h - 1) / (1 + (p4 / v4_Kd)^v4_h)$ | variable |\r\n| Initial value of parameter as3 | $(1 + (p5 / v5_Kd)^v5_h - 1) / (1 + (p5 / v5_Kd)^v5_h)$ | variable |\r\n| Initial value of parameter as4 | $(1 + (p6 / v6_Kd)^v6_h - 1) / (1 + (p6 / v6_Kd)^v6_h)$ | variable |\r\n| Initial value of parameter as5 | $(1 + (p7 / v7_Kd)^v7_h - 1) / (1 + (p7 / v7_Kd)^v7_h)$ | variable |\r\n| Initial value of parameter as6 | $(1 + (p7 / v10_Kd)^v10_h - 1) / (1 + (p7 / v10_Kd)^v10_h)$ | variable |\r\n| Initial value of parameter as7 | $(1 + (p6 / v8_Kd)^v8_h - 1) / (1 + (p6 / v8_Kd)^v8_h)$ | variable |\r\n| Initial volume of compartment 'DefaultCompartment' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nDefaultCompartment @Compartment 'DefaultCompartment' { boundary: true, } .= 1;\n\npp9_mrna @Species 'pp9_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\np9 @Species 'p9' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\npp8_mrna @Species 'pp8_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\np8 @Species 'p8' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\npp7_mrna @Species 'pp7_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\np7 @Species 'p7' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\npp6_mrna @Species 'pp6_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\np6 @Species 'p6' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\npp5_mrna @Species 'pp5_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\np5 @Species 'p5' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\npp4_mrna @Species 'pp4_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\np4 @Species 'p4' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\npp3_mrna @Species 'pp3_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\np3 @Species 'p3' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\npp2_mrna @Species 'pp2_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\np2 @Species 'p2' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\npp1_mrna @Species 'pp1_mrna' { compartment: DefaultCompartment, } .= 0 / DefaultCompartment;\np1 @Species 'p1' { compartment: DefaultCompartment, } .= 5 / DefaultCompartment;\n\npp9_v1 @Reaction 'pp9_v1' { actors: = pp9_mrna, reversible: false, };\npp9_v1 := cod9;\npp9_v2 @Reaction 'pp9_v2' { actors: pp9_mrna = , modifiers: [p9], reversible: false, };\npp9_v2 := pp9_mrna_degradation_rate * pp9_mrna;\npp9_v3 @Reaction 'pp9_v3' { actors: = p9, modifiers: [pp9_mrna], reversible: false, };\npp9_v3 := rbs9_strength * pp9_mrna;\npp9_v4 @Reaction 'pp9_v4' { actors: p9 = , reversible: false, };\npp9_v4 := p9_degradation_rate * p9;\npp8_v1 @Reaction 'pp8_v1' { actors: = pp8_mrna, reversible: false, };\npp8_v1 := cod8;\npp8_v2 @Reaction 'pp8_v2' { actors: pp8_mrna = , modifiers: [p8], reversible: false, };\npp8_v2 := pp8_mrna_degradation_rate * pp8_mrna;\npp8_v3 @Reaction 'pp8_v3' { actors: = p8, modifiers: [pp8_mrna], reversible: false, };\npp8_v3 := rbs8_strength * pp8_mrna;\npp8_v4 @Reaction 'pp8_v4' { actors: p8 = , reversible: false, };\npp8_v4 := p8_degradation_rate * p8;\npp7_v1 @Reaction 'pp7_v1' { actors: = pp7_mrna, reversible: false, };\npp7_v1 := cod7;\npp7_v2 @Reaction 'pp7_v2' { actors: pp7_mrna = , modifiers: [p7], reversible: false, };\npp7_v2 := pp7_mrna_degradation_rate * pp7_mrna;\npp7_v3 @Reaction 'pp7_v3' { actors: = p7, modifiers: [pp7_mrna], reversible: false, };\npp7_v3 := rbs7_strength * pp7_mrna;\npp7_v4 @Reaction 'pp7_v4' { actors: p7 = , reversible: false, };\npp7_v4 := p7_degradation_rate * p7;\npp6_v1 @Reaction 'pp6_v1' { actors: = pp6_mrna, reversible: false, };\npp6_v1 := cod6;\npp6_v2 @Reaction 'pp6_v2' { actors: pp6_mrna = , modifiers: [p6], reversible: false, };\npp6_v2 := pp6_mrna_degradation_rate * pp6_mrna;\npp6_v3 @Reaction 'pp6_v3' { actors: = p6, modifiers: [pp6_mrna], reversible: false, };\npp6_v3 := rbs6_strength * pp6_mrna;\npp6_v4 @Reaction 'pp6_v4' { actors: p6 = , reversible: false, };\npp6_v4 := p6_degradation_rate * p6;\npp5_v1 @Reaction 'pp5_v1' { actors: = pp5_mrna, reversible: false, };\npp5_v1 := cod5;\npp5_v2 @Reaction 'pp5_v2' { actors: pp5_mrna = , modifiers: [p5], reversible: false, };\npp5_v2 := pp5_mrna_degradation_rate * pp5_mrna;\npp5_v3 @Reaction 'pp5_v3' { actors: = p5, modifiers: [pp5_mrna], reversible: false, };\npp5_v3 := rbs5_strength * pp5_mrna;\npp5_v4 @Reaction 'pp5_v4' { actors: p5 = , reversible: false, };\npp5_v4 := p5_degradation_rate * p5;\npp4_v1 @Reaction 'pp4_v1' { actors: = pp4_mrna, reversible: false, };\npp4_v1 := cod4;\npp4_v2 @Reaction 'pp4_v2' { actors: pp4_mrna = , modifiers: [p4], reversible: false, };\npp4_v2 := pp4_mrna_degradation_rate * pp4_mrna;\npp4_v3 @Reaction 'pp4_v3' { actors: = p4, modifiers: [pp4_mrna], reversible: false, };\npp4_v3 := rbs4_strength * pp4_mrna;\npp4_v4 @Reaction 'pp4_v4' { actors: p4 = , reversible: false, };\npp4_v4 := p4_degradation_rate * p4;\npp3_v1 @Reaction 'pp3_v1' { actors: = pp3_mrna, reversible: false, };\npp3_v1 := cod3;\npp3_v2 @Reaction 'pp3_v2' { actors: pp3_mrna = , modifiers: [p3], reversible: false, };\npp3_v2 := pp3_mrna_degradation_rate * pp3_mrna;\npp3_v3 @Reaction 'pp3_v3' { actors: = p3, modifiers: [pp3_mrna], reversible: false, };\npp3_v3 := rbs3_strength * pp3_mrna;\npp3_v4 @Reaction 'pp3_v4' { actors: p3 = , reversible: false, };\npp3_v4 := p3_degradation_rate * p3;\npp2_v1 @Reaction 'pp2_v1' { actors: = pp2_mrna, reversible: false, };\npp2_v1 := cod2;\npp2_v2 @Reaction 'pp2_v2' { actors: pp2_mrna = , modifiers: [p2], reversible: false, };\npp2_v2 := pp2_mrna_degradation_rate * pp2_mrna;\npp2_v3 @Reaction 'pp2_v3' { actors: = p2, modifiers: [pp2_mrna], reversible: false, };\npp2_v3 := rbs2_strength * pp2_mrna;\npp2_v4 @Reaction 'pp2_v4' { actors: p2 = , reversible: false, };\npp2_v4 := p2_degradation_rate * p2;\npp1_v1 @Reaction 'pp1_v1' { actors: = pp1_mrna, reversible: false, };\npp1_v1 := cod1;\npp1_v2 @Reaction 'pp1_v2' { actors: pp1_mrna = , modifiers: [p1], reversible: false, };\npp1_v2 := pp1_mrna_degradation_rate * pp1_mrna;\npp1_v3 @Reaction 'pp1_v3' { actors: = p1, modifiers: [pp1_mrna], reversible: false, };\npp1_v3 := rbs1_strength * pp1_mrna;\npp1_v4 @Reaction 'pp1_v4' { actors: p1 = , reversible: false, };\npp1_v4 := p1_degradation_rate * p1;\n\nas8 @Record 'as8' { } .= 1;\nas8 := (1 + pow(p5 / v9_Kd, v9_h) - 1) / (1 + pow(p5 / v9_Kd, v9_h));\ncod1 @Record 'cod1' { } .= 1;\ncod1 := pro1_strength;\ncod2 @Record 'cod2' { } .= 1;\ncod2 := pro2_strength * as1 * rs1;\ncod3 @Record 'cod3' { } .= 1;\ncod3 := pro3_strength * rs2 * rs3;\ncod4 @Record 'cod4' { } .= 1;\ncod4 := pro4_strength * rs7 * rs6;\ncod5 @Record 'cod5' { } .= 1;\ncod5 := pro5_strength * as2;\ncod6 @Record 'cod6' { } .= 1;\ncod6 := pro6_strength * (as3 + as4);\ncod7 @Record 'cod7' { } .= 1;\ncod7 := pro7_strength * (as7 + as8);\ncod8 @Record 'cod8' { } .= 1;\ncod8 := pro8_strength * as5 * rs4;\ncod9 @Record 'cod9' { } .= 1;\ncod9 := pro9_strength * as6 * rs5;\nrs1 @Record 'rs1' { } .= 1;\nrs1 := 1 / (1 + pow(p9 / v13_Kd, v13_h));\nrs2 @Record 'rs2' { } .= 1;\nrs2 := 1 / (1 + pow(p2 / v2_Kd, v2_h));\nrs3 @Record 'rs3' { } .= 1;\nrs3 := 1 / (1 + pow(p3 / v3_Kd, v3_h));\nrs4 @Record 'rs4' { } .= 1;\nrs4 := 1 / (1 + pow(p8 / v11_Kd, v11_h));\nrs5 @Record 'rs5' { } .= 1;\nrs5 := 1 / (1 + pow(p8 / v12_Kd, v12_h));\nrs6 @Record 'rs6' { } .= 1;\nrs6 := 1 / (1 + pow(p2 / v14_Kd, v14_h));\nrs7 @Record 'rs7' { } .= 1;\nrs7 := 1 / (1 + pow(p3 / v15_Kd, v15_h));\nas1 @Record 'as1' { } .= 1;\nas1 := (1 + pow(p1 / v1_Kd, v1_h) - 1) / (1 + pow(p1 / v1_Kd, v1_h));\nas2 @Record 'as2' { } .= 1;\nas2 := (1 + pow(p4 / v4_Kd, v4_h) - 1) / (1 + pow(p4 / v4_Kd, v4_h));\nas3 @Record 'as3' { } .= 1;\nas3 := (1 + pow(p5 / v5_Kd, v5_h) - 1) / (1 + pow(p5 / v5_Kd, v5_h));\nas4 @Record 'as4' { } .= 1;\nas4 := (1 + pow(p6 / v6_Kd, v6_h) - 1) / (1 + pow(p6 / v6_Kd, v6_h));\nas5 @Record 'as5' { } .= 1;\nas5 := (1 + pow(p7 / v7_Kd, v7_h) - 1) / (1 + pow(p7 / v7_Kd, v7_h));\nas6 @Record 'as6' { } .= 1;\nas6 := (1 + pow(p7 / v10_Kd, v10_h) - 1) / (1 + pow(p7 / v10_Kd, v10_h));\nas7 @Record 'as7' { } .= 1;\nas7 := (1 + pow(p6 / v8_Kd, v8_h) - 1) / (1 + pow(p6 / v8_Kd, v8_h));\n\npp8_mrna_degradation_rate @Const 'pp8_mrna_degradation_rate' { } = 1;\npp9_mrna_degradation_rate @Const 'pp9_mrna_degradation_rate' { } = 1;\np1_degradation_rate @Const 'p1_degradation_rate' { } = 0.5;\np2_degradation_rate @Const 'p2_degradation_rate' { } = 0.5;\np3_degradation_rate @Const 'p3_degradation_rate' { } = 0.5;\np4_degradation_rate @Const 'p4_degradation_rate' { } = 0.5;\np5_degradation_rate @Const 'p5_degradation_rate' { } = 0.5;\np6_degradation_rate @Const 'p6_degradation_rate' { } = 0.5;\np7_degradation_rate @Const 'p7_degradation_rate' { } = 0.5;\np8_degradation_rate @Const 'p8_degradation_rate' { } = 0.5;\np9_degradation_rate @Const 'p9_degradation_rate' { } = 0.5;\nv1_Kd @Const 'v1_Kd' { } = 11.147;\nv1_h @Const 'v1_h' { } = 1;\nv2_Kd @Const 'v2_Kd' { } = 1;\nv2_h @Const 'v2_h' { } = 4;\nv3_Kd @Const 'v3_Kd' { } = 20;\nv3_h @Const 'v3_h' { } = 1;\nv4_Kd @Const 'v4_Kd' { } = 0.2;\nv4_h @Const 'v4_h' { } = 4;\nv5_Kd @Const 'v5_Kd' { } = 0.2;\nv5_h @Const 'v5_h' { } = 4;\nv6_Kd @Const 'v6_Kd' { } = 0.04;\nv6_h @Const 'v6_h' { } = 4;\nv7_Kd @Const 'v7_Kd' { } = 0.02;\nv7_h @Const 'v7_h' { } = 4;\nv8_Kd @Const 'v8_Kd' { } = 0.04;\nv8_h @Const 'v8_h' { } = 4;\nv9_Kd @Const 'v9_Kd' { } = 0.2;\nv9_h @Const 'v9_h' { } = 4;\npp1_mrna_degradation_rate @Const 'pp1_mrna_degradation_rate' { } = 1;\npp2_mrna_degradation_rate @Const 'pp2_mrna_degradation_rate' { } = 1;\npro1_strength @Const 'pro1_strength' { } = 2;\npro2_strength @Const 'pro2_strength' { } = 4.5077;\npro3_strength @Const 'pro3_strength' { } = 5;\npro4_strength @Const 'pro4_strength' { } = 5;\npro5_strength @Const 'pro5_strength' { } = 5;\npro6_strength @Const 'pro6_strength' { } = 1.31;\npro7_strength @Const 'pro7_strength' { } = 1.31;\npro8_strength @Const 'pro8_strength' { } = 5;\npro9_strength @Const 'pro9_strength' { } = 5;\npp3_mrna_degradation_rate @Const 'pp3_mrna_degradation_rate' { } = 1;\nv10_Kd @Const 'v10_Kd' { } = 0.02;\nv10_h @Const 'v10_h' { } = 4;\nv11_Kd @Const 'v11_Kd' { } = 0.1;\nv11_h @Const 'v11_h' { } = 2;\nv12_Kd @Const 'v12_Kd' { } = 0.1;\nv12_h @Const 'v12_h' { } = 2;\nv13_Kd @Const 'v13_Kd' { } = 0.01;\nv13_h @Const 'v13_h' { } = 2;\npp4_mrna_degradation_rate @Const 'pp4_mrna_degradation_rate' { } = 1;\nv14_Kd @Const 'v14_Kd' { } = 1;\nv14_h @Const 'v14_h' { } = 4;\nv15_Kd @Const 'v15_Kd' { } = 20;\nv15_h @Const 'v15_h' { } = 1;\npp5_mrna_degradation_rate @Const 'pp5_mrna_degradation_rate' { } = 1;\nrbs1_strength @Const 'rbs1_strength' { } = 0.3668;\nrbs2_strength @Const 'rbs2_strength' { } = 1.4102;\nrbs3_strength @Const 'rbs3_strength' { } = 0.8;\nrbs4_strength @Const 'rbs4_strength' { } = 2.21;\nrbs5_strength @Const 'rbs5_strength' { } = 0.5;\nrbs6_strength @Const 'rbs6_strength' { } = 2;\nrbs7_strength @Const 'rbs7_strength' { } = 5;\nrbs8_strength @Const 'rbs8_strength' { } = 3.6377;\nrbs9_strength @Const 'rbs9_strength' { } = 8;\npp6_mrna_degradation_rate @Const 'pp6_mrna_degradation_rate' { } = 1;\npp7_mrna_degradation_rate @Const 'pp7_mrna_degradation_rate' { } = 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A fast reaction with a local parameter.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, FastReaction, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nIn this model, a fast reaction has a local parameter that ensures that the reaction proceeds in reverse. \r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 local parameter (J0.k1)\r\n* 1 compartment (default_compartment)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* |\r\n| J0: S1 -> S2 | $k1 * S1 * S2$ | fast |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $5$ | variable |\r\n| Initial concentration of species S2 | $5$ | variable |\r\n| Initial value of local parameter 'J0.k1' | $-1$ | constant |\r\n| Initial volume of compartment 'default_compartment' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\ndefault_compartment @Compartment { boundary: true, aux: {{\"sboTerm\":\"SBO:0000410\"}}, } .= 1;\n\nS1 @Species { compartment: default_compartment, } .= 5;\nS2 @Species { compartment: default_compartment, } .= 5;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := k1__J0_local * S1 * S2;\n\nk1__J0_local @Const { } = -1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has two reactants that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled reactants.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: A + A -> | $-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: A + A = , };\nJ0 := (-1);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has two reactants that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled reactants.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: A + 2A -> | $-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: A + 2*A = , };\nJ0 := (-1);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has two reactants that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled reactants.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: A + -1A -> | $-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: A = A, };\nJ0 := (-1);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references--in this case, zero.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: A -> A | $-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: A = A, };\nJ0 := (-1);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: A -> 2A | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: A = 2*A, };\nJ0 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: 2A -> A | $-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: 2*A = A, };\nJ0 := (-1);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: 2A -> -3A | $-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: 3*A + 2*A = , };\nJ0 := (-1);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has a reactant and a product that both point to the same species. This is equivalent to a reaction with a single reactant whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -2A -> 3A | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: = 3*A + 2*A, };\nJ0 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has two products that both point to the same species. This is equivalent to a reaction with a single product whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> A + A | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: = A + A, };\nJ0 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has two products that both point to the same species. This is equivalent to a reaction with a single product whose stoichiometry is equal to the sum of the stoichiometries of the doubled species references.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> A + 2A | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: = A + 2*A, };\nJ0 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has multiple reactants and products that both point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references.\r\n\r\nThe model contains:\r\n* 2 species (A, B)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: A + A -> B + B | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $20$ | variable |\r\n| Initial concentration of species B | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 20;\nB @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: A + A = B + B, };\nJ0 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has multiple reactants and products that all point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references.\r\n\r\nThe model contains:\r\n* 2 species (A, B)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: A + B -> A + B | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial concentration of species B | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\nB @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: A + B = A + B, };\nJ0 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has multiple reactants and products that all point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references.\r\n\r\nThe model contains:\r\n* 2 species (A, B)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: 2A + -1B -> -1A + 2B | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $30$ | variable |\r\n| Initial concentration of species B | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 30;\nB @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: A + 2*A = 2*B + B, };\nJ0 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Multiple species references to the same species\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n In this test, a single reaction has multiple reactants and products that all point to the same species. This is equivalent to a reaction where all of the species references that point to the same species are collapsed into a single species reference with a stoichiometry equal to the sum of the stoichiometries of the original species references.\r\n\r\nThe model contains:\r\n* 1 species (A)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: A + 2A + -4A -> 5A + -2A + A + -1A | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species A | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nA @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: 2*A + A + A + 2*A = 5*A + A + 4*A, };\nJ0 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A test of random event execution at t0.\r\ncomponentTags: AssignmentRule, EventNoDelay, EventPriority, Parameter\r\ntestTags: EventIsNotPersistent, EventT0Firing, InitialValueReassigned, NonConstantParameter, RandomEventExecution\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, 200 events 'compete' in pairs to assing values to variables: if E0 fires, Eb0 will not, and visa versa, for all events E0-E99, Eb0-Eb99. Because all events have the same priority, the E# set should win about half the time (assigning a value to the corresponding 'A' variable), and the Eb# set should win the other half, assigning values to the corresponding 'B' variables.\r\n\r\n 'toodiverged' will only equal 1 if (Asum-Bsum)>100. Since the standard deviation of 100 coin flips is 5, which would correspond to a difference of 20, 'toodiverged' will only equal 1 if the observed distribution of choices is more than five standard deviations away from expected (0), which will happen approximately one time in 1.7 million.\r\n\r\nThe model contains:\r\n* 205 parameters (trig, A0, A1, A2, A3, A4, A5, A6, A7, A8, A9, A10, A11, A12, A13, A14, A15, A16, A17, A18, A19, A20, A21, A22, A23, A24, A25, A26, A27, A28, A29, A30, A31, A32, A33, A34, A35, A36, A37, A38, A39, A40, A41, A42, A43, A44, A45, A46, A47, A48, A49, A50, A51, A52, A53, A54, A55, A56, A57, A58, A59, A60, A61, A62, A63, A64, A65, A66, A67, A68, A69, A70, A71, A72, A73, A74, A75, A76, A77, A78, A79, A80, A81, A82, A83, A84, A85, A86, A87, A88, A89, A90, A91, A92, A93, A94, A95, A96, A97, A98, A99, B0, B1, B2, B3, B4, B5, B6, B7, B8, B9, B10, B11, B12, B13, B14, B15, B16, B17, B18, B19, B20, B21, B22, B23, B24, B25, B26, B27, B28, B29, B30, B31, B32, B33, B34, B35, B36, B37, B38, B39, B40, B41, B42, B43, B44, B45, B46, B47, B48, B49, B50, B51, B52, B53, B54, B55, B56, B57, B58, B59, B60, B61, B62, B63, B64, B65, B66, B67, B68, B69, B70, B71, B72, B73, B74, B75, B76, B77, B78, B79, B80, B81, B82, B83, B84, B85, B86, B87, B88, B89, B90, B91, B92, B93, B94, B95, B96, B97, B98, B99, Asum, Bsum, Allsum, toodiverged)\r\n\r\nThere are 201 events:\r\n\r\n[{width:45em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *initialValue* | *Event Assignments* |\r\n| E0 | $(trig > 0) && (A0 < 1)$ | $5$ | false | false | $B0 = 2$ |\r\n| E1 | $(trig > 0) && (A1 < 1)$ | $5$ | false | false | $B1 = 2$ |\r\n| E2 | $(trig > 0) && (A2 < 1)$ | $5$ | false | false | $B2 = 2$ |\r\n| E3 | $(trig > 0) && (A3 < 1)$ | $5$ | false | false | $B3 = 2$ |\r\n| E4 | $(trig > 0) && (A4 < 1)$ | $5$ | false | false | $B4 = 2$ |\r\n| E5 | $(trig > 0) && (A5 < 1)$ | $5$ | false | false | $B5 = 2$ |\r\n| E6 | $(trig > 0) && (A6 < 1)$ | $5$ | false | false | $B6 = 2$ |\r\n| E7 | $(trig > 0) && (A7 < 1)$ | $5$ | false | false | $B7 = 2$ |\r\n| E8 | $(trig > 0) && (A8 < 1)$ | $5$ | false | false | $B8 = 2$ |\r\n| E9 | $(trig > 0) && (A9 < 1)$ | $5$ | false | false | $B9 = 2$ |\r\n| E10 | $(trig > 0) && (A10 < 1)$ | $5$ | false | false | $B10 = 2$ |\r\n| E11 | $(trig > 0) && (A11 < 1)$ | $5$ | false | false | $B11 = 2$ |\r\n| E12 | $(trig > 0) && (A12 < 1)$ | $5$ | false | false | $B12 = 2$ |\r\n| E13 | $(trig > 0) && (A13 < 1)$ | $5$ | false | false | $B13 = 2$ |\r\n| E14 | $(trig > 0) && (A14 < 1)$ | $5$ | false | false | $B14 = 2$ |\r\n| E15 | $(trig > 0) && (A15 < 1)$ | $5$ | false | false | $B15 = 2$ |\r\n| E16 | $(trig > 0) && (A16 < 1)$ | $5$ | false | false | $B16 = 2$ |\r\n| E17 | $(trig > 0) && (A17 < 1)$ | $5$ | false | false | $B17 = 2$ |\r\n| E18 | $(trig > 0) && (A18 < 1)$ | $5$ | false | false | $B18 = 2$ |\r\n| E19 | $(trig > 0) && (A19 < 1)$ | $5$ | false | false | $B19 = 2$ |\r\n| E20 | $(trig > 0) && (A20 < 1)$ | $5$ | false | false | $B20 = 2$ |\r\n| E21 | $(trig > 0) && (A21 < 1)$ | $5$ | false | false | $B21 = 2$ |\r\n| E22 | $(trig > 0) && (A22 < 1)$ | $5$ | false | false | $B22 = 2$ |\r\n| E23 | $(trig > 0) && (A23 < 1)$ | $5$ | false | false | $B23 = 2$ |\r\n| E24 | $(trig > 0) && (A24 < 1)$ | $5$ | false | false | $B24 = 2$ |\r\n| E25 | $(trig > 0) && (A25 < 1)$ | $5$ | false | false | $B25 = 2$ |\r\n| E26 | $(trig > 0) && (A26 < 1)$ | $5$ | false | false | $B26 = 2$ |\r\n| E27 | $(trig > 0) && (A27 < 1)$ | $5$ | false | false | $B27 = 2$ |\r\n| E28 | $(trig > 0) && (A28 < 1)$ | $5$ | false | false | $B28 = 2$ |\r\n| E29 | $(trig > 0) && (A29 < 1)$ | $5$ | false | false | $B29 = 2$ |\r\n| E30 | $(trig > 0) && (A30 < 1)$ | $5$ | false | false | $B30 = 2$ |\r\n| E31 | $(trig > 0) && (A31 < 1)$ | $5$ | false | false | $B31 = 2$ |\r\n| E32 | $(trig > 0) && (A32 < 1)$ | $5$ | false | false | $B32 = 2$ |\r\n| E33 | $(trig > 0) && (A33 < 1)$ | $5$ | false | false | $B33 = 2$ |\r\n| E34 | $(trig > 0) && (A34 < 1)$ | $5$ | false | false | $B34 = 2$ |\r\n| E35 | $(trig > 0) && (A35 < 1)$ | $5$ | false | false | $B35 = 2$ |\r\n| E36 | $(trig > 0) && (A36 < 1)$ | $5$ | false | false | $B36 = 2$ |\r\n| E37 | $(trig > 0) && (A37 < 1)$ | $5$ | false | false | $B37 = 2$ |\r\n| E38 | $(trig > 0) && (A38 < 1)$ | $5$ | false | false | $B38 = 2$ |\r\n| E39 | $(trig > 0) && (A39 < 1)$ | $5$ | false | false | $B39 = 2$ |\r\n| E40 | $(trig > 0) && (A40 < 1)$ | $5$ | false | false | $B40 = 2$ |\r\n| E41 | $(trig > 0) && (A41 < 1)$ | $5$ | false | false | $B41 = 2$ |\r\n| E42 | $(trig > 0) && (A42 < 1)$ | $5$ | false | false | $B42 = 2$ |\r\n| E43 | $(trig > 0) && (A43 < 1)$ | $5$ | false | false | $B43 = 2$ |\r\n| E44 | $(trig > 0) && (A44 < 1)$ | $5$ | false | false | $B44 = 2$ |\r\n| E45 | $(trig > 0) && (A45 < 1)$ | $5$ | false | false | $B45 = 2$ |\r\n| E46 | $(trig > 0) && (A46 < 1)$ | $5$ | false | false | $B46 = 2$ |\r\n| E47 | $(trig > 0) && (A47 < 1)$ | $5$ | false | false | $B47 = 2$ |\r\n| E48 | $(trig > 0) && (A48 < 1)$ | $5$ | false | false | $B48 = 2$ |\r\n| E49 | $(trig > 0) && (A49 < 1)$ | $5$ | false | false | $B49 = 2$ |\r\n| E50 | $(trig > 0) && (A50 < 1)$ | $5$ | false | false | $B50 = 2$ |\r\n| E51 | $(trig > 0) && (A51 < 1)$ | $5$ | false | false | $B51 = 2$ |\r\n| E52 | $(trig > 0) && (A52 < 1)$ | $5$ | false | false | $B52 = 2$ |\r\n| E53 | $(trig > 0) && (A53 < 1)$ | $5$ | false | false | $B53 = 2$ |\r\n| E54 | $(trig > 0) && (A54 < 1)$ | $5$ | false | false | $B54 = 2$ |\r\n| E55 | $(trig > 0) && (A55 < 1)$ | $5$ | false | false | $B55 = 2$ |\r\n| E56 | $(trig > 0) && (A56 < 1)$ | $5$ | false | false | $B56 = 2$ |\r\n| E57 | $(trig > 0) && (A57 < 1)$ | $5$ | false | false | $B57 = 2$ |\r\n| E58 | $(trig > 0) && (A58 < 1)$ | $5$ | false | false | $B58 = 2$ |\r\n| E59 | $(trig > 0) && (A59 < 1)$ | $5$ | false | false | $B59 = 2$ |\r\n| E60 | $(trig > 0) && (A60 < 1)$ | $5$ | false | false | $B60 = 2$ |\r\n| E61 | $(trig > 0) && (A61 < 1)$ | $5$ | false | false | $B61 = 2$ |\r\n| E62 | $(trig > 0) && (A62 < 1)$ | $5$ | false | false | $B62 = 2$ |\r\n| E63 | $(trig > 0) && (A63 < 1)$ | $5$ | false | false | $B63 = 2$ |\r\n| E64 | $(trig > 0) && (A64 < 1)$ | $5$ | false | false | $B64 = 2$ |\r\n| E65 | $(trig > 0) && (A65 < 1)$ | $5$ | false | false | $B65 = 2$ |\r\n| E66 | $(trig > 0) && (A66 < 1)$ | $5$ | false | false | $B66 = 2$ |\r\n| E67 | $(trig > 0) && (A67 < 1)$ | $5$ | false | false | $B67 = 2$ |\r\n| E68 | $(trig > 0) && (A68 < 1)$ | $5$ | false | false | $B68 = 2$ |\r\n| E69 | $(trig > 0) && (A69 < 1)$ | $5$ | false | false | $B69 = 2$ |\r\n| E70 | $(trig > 0) && (A70 < 1)$ | $5$ | false | false | $B70 = 2$ |\r\n| E71 | $(trig > 0) && (A71 < 1)$ | $5$ | false | false | $B71 = 2$ |\r\n| E72 | $(trig > 0) && (A72 < 1)$ | $5$ | false | false | $B72 = 2$ |\r\n| E73 | $(trig > 0) && (A73 < 1)$ | $5$ | false | false | $B73 = 2$ |\r\n| E74 | $(trig > 0) && (A74 < 1)$ | $5$ | false | false | $B74 = 2$ |\r\n| E75 | $(trig > 0) && (A75 < 1)$ | $5$ | false | false | $B75 = 2$ |\r\n| E76 | $(trig > 0) && (A76 < 1)$ | $5$ | false | false | $B76 = 2$ |\r\n| E77 | $(trig > 0) && (A77 < 1)$ | $5$ | false | false | $B77 = 2$ |\r\n| E78 | $(trig > 0) && (A78 < 1)$ | $5$ | false | false | $B78 = 2$ |\r\n| E79 | $(trig > 0) && (A79 < 1)$ | $5$ | false | false | $B79 = 2$ |\r\n| E80 | $(trig > 0) && (A80 < 1)$ | $5$ | false | false | $B80 = 2$ |\r\n| E81 | $(trig > 0) && (A81 < 1)$ | $5$ | false | false | $B81 = 2$ |\r\n| E82 | $(trig > 0) && (A82 < 1)$ | $5$ | false | false | $B82 = 2$ |\r\n| E83 | $(trig > 0) && (A83 < 1)$ | $5$ | false | false | $B83 = 2$ |\r\n| E84 | $(trig > 0) && (A84 < 1)$ | $5$ | false | false | $B84 = 2$ |\r\n| E85 | $(trig > 0) && (A85 < 1)$ | $5$ | false | false | $B85 = 2$ |\r\n| E86 | $(trig > 0) && (A86 < 1)$ | $5$ | false | false | $B86 = 2$ |\r\n| E87 | $(trig > 0) && (A87 < 1)$ | $5$ | false | false | $B87 = 2$ |\r\n| E88 | $(trig > 0) && (A88 < 1)$ | $5$ | false | false | $B88 = 2$ |\r\n| E89 | $(trig > 0) && (A89 < 1)$ | $5$ | false | false | $B89 = 2$ |\r\n| E90 | $(trig > 0) && (A90 < 1)$ | $5$ | false | false | $B90 = 2$ |\r\n| E91 | $(trig > 0) && (A91 < 1)$ | $5$ | false | false | $B91 = 2$ |\r\n| E92 | $(trig > 0) && (A92 < 1)$ | $5$ | false | false | $B92 = 2$ |\r\n| E93 | $(trig > 0) && (A93 < 1)$ | $5$ | false | false | $B93 = 2$ |\r\n| E94 | $(trig > 0) && (A94 < 1)$ | $5$ | false | false | $B94 = 2$ |\r\n| E95 | $(trig > 0) && (A95 < 1)$ | $5$ | false | false | $B95 = 2$ |\r\n| E96 | $(trig > 0) && (A96 < 1)$ | $5$ | false | false | $B96 = 2$ |\r\n| E97 | $(trig > 0) && (A97 < 1)$ | $5$ | false | false | $B97 = 2$ |\r\n| E98 | $(trig > 0) && (A98 < 1)$ | $5$ | false | false | $B98 = 2$ |\r\n| E99 | $(trig > 0) && (A99 < 1)$ | $5$ | false | false | $B99 = 2$ |\r\n| Eb0 | $(trig > 0) && (B0 < 1)$ | $5$ | false | false | $A0 = 2$ |\r\n| Eb1 | $(trig > 0) && (B1 < 1)$ | $5$ | false | false | $A1 = 2$ |\r\n| Eb2 | $(trig > 0) && (B2 < 1)$ | $5$ | false | false | $A2 = 2$ |\r\n| Eb3 | $(trig > 0) && (B3 < 1)$ | $5$ | false | false | $A3 = 2$ |\r\n| Eb4 | $(trig > 0) && (B4 < 1)$ | $5$ | false | false | $A4 = 2$ |\r\n| Eb5 | $(trig > 0) && (B5 < 1)$ | $5$ | false | false | $A5 = 2$ |\r\n| Eb6 | $(trig > 0) && (B6 < 1)$ | $5$ | false | false | $A6 = 2$ |\r\n| Eb7 | $(trig > 0) && (B7 < 1)$ | $5$ | false | false | $A7 = 2$ |\r\n| Eb8 | $(trig > 0) && (B8 < 1)$ | $5$ | false | false | $A8 = 2$ |\r\n| Eb9 | $(trig > 0) && (B9 < 1)$ | $5$ | false | false | $A9 = 2$ |\r\n| Eb10 | $(trig > 0) && (B10 < 1)$ | $5$ | false | false | $A10 = 2$ |\r\n| Eb11 | $(trig > 0) && (B11 < 1)$ | $5$ | false | false | $A11 = 2$ |\r\n| Eb12 | $(trig > 0) && (B12 < 1)$ | $5$ | false | false | $A12 = 2$ |\r\n| Eb13 | $(trig > 0) && (B13 < 1)$ | $5$ | false | false | $A13 = 2$ |\r\n| Eb14 | $(trig > 0) && (B14 < 1)$ | $5$ | false | false | $A14 = 2$ |\r\n| Eb15 | $(trig > 0) && (B15 < 1)$ | $5$ | false | false | $A15 = 2$ |\r\n| Eb16 | $(trig > 0) && (B16 < 1)$ | $5$ | false | false | $A16 = 2$ |\r\n| Eb17 | $(trig > 0) && (B17 < 1)$ | $5$ | false | false | $A17 = 2$ |\r\n| Eb18 | $(trig > 0) && (B18 < 1)$ | $5$ | false | false | $A18 = 2$ |\r\n| Eb19 | $(trig > 0) && (B19 < 1)$ | $5$ | false | false | $A19 = 2$ |\r\n| Eb20 | $(trig > 0) && (B20 < 1)$ | $5$ | false | false | $A20 = 2$ |\r\n| Eb21 | $(trig > 0) && (B21 < 1)$ | $5$ | false | false | $A21 = 2$ |\r\n| Eb22 | $(trig > 0) && (B22 < 1)$ | $5$ | false | false | $A22 = 2$ |\r\n| Eb23 | $(trig > 0) && (B23 < 1)$ | $5$ | false | false | $A23 = 2$ |\r\n| Eb24 | $(trig > 0) && (B24 < 1)$ | $5$ | false | false | $A24 = 2$ |\r\n| Eb25 | $(trig > 0) && (B25 < 1)$ | $5$ | false | false | $A25 = 2$ |\r\n| Eb26 | $(trig > 0) && (B26 < 1)$ | $5$ | false | false | $A26 = 2$ |\r\n| Eb27 | $(trig > 0) && (B27 < 1)$ | $5$ | false | false | $A27 = 2$ |\r\n| Eb28 | $(trig > 0) && (B28 < 1)$ | $5$ | false | false | $A28 = 2$ |\r\n| Eb29 | $(trig > 0) && (B29 < 1)$ | $5$ | false | false | $A29 = 2$ |\r\n| Eb30 | $(trig > 0) && (B30 < 1)$ | $5$ | false | false | $A30 = 2$ |\r\n| Eb31 | $(trig > 0) && (B31 < 1)$ | $5$ | false | false | $A31 = 2$ |\r\n| Eb32 | $(trig > 0) && (B32 < 1)$ | $5$ | false | false | $A32 = 2$ |\r\n| Eb33 | $(trig > 0) && (B33 < 1)$ | $5$ | false | false | $A33 = 2$ |\r\n| Eb34 | $(trig > 0) && (B34 < 1)$ | $5$ | false | false | $A34 = 2$ |\r\n| Eb35 | $(trig > 0) && (B35 < 1)$ | $5$ | false | false | $A35 = 2$ |\r\n| Eb36 | $(trig > 0) && (B36 < 1)$ | $5$ | false | false | $A36 = 2$ |\r\n| Eb37 | $(trig > 0) && (B37 < 1)$ | $5$ | false | false | $A37 = 2$ |\r\n| Eb38 | $(trig > 0) && (B38 < 1)$ | $5$ | false | false | $A38 = 2$ |\r\n| Eb39 | $(trig > 0) && (B39 < 1)$ | $5$ | false | false | $A39 = 2$ |\r\n| Eb40 | $(trig > 0) && (B40 < 1)$ | $5$ | false | false | $A40 = 2$ |\r\n| Eb41 | $(trig > 0) && (B41 < 1)$ | $5$ | false | false | $A41 = 2$ |\r\n| Eb42 | $(trig > 0) && (B42 < 1)$ | $5$ | false | false | $A42 = 2$ |\r\n| Eb43 | $(trig > 0) && (B43 < 1)$ | $5$ | false | false | $A43 = 2$ |\r\n| Eb44 | $(trig > 0) && (B44 < 1)$ | $5$ | false | false | $A44 = 2$ |\r\n| Eb45 | $(trig > 0) && (B45 < 1)$ | $5$ | false | false | $A45 = 2$ |\r\n| Eb46 | $(trig > 0) && (B46 < 1)$ | $5$ | false | false | $A46 = 2$ |\r\n| Eb47 | $(trig > 0) && (B47 < 1)$ | $5$ | false | false | $A47 = 2$ |\r\n| Eb48 | $(trig > 0) && (B48 < 1)$ | $5$ | false | false | $A48 = 2$ |\r\n| Eb49 | $(trig > 0) && (B49 < 1)$ | $5$ | false | false | $A49 = 2$ |\r\n| Eb50 | $(trig > 0) && (B50 < 1)$ | $5$ | false | false | $A50 = 2$ |\r\n| Eb51 | $(trig > 0) && (B51 < 1)$ | $5$ | false | false | $A51 = 2$ |\r\n| Eb52 | $(trig > 0) && (B52 < 1)$ | $5$ | false | false | $A52 = 2$ |\r\n| Eb53 | $(trig > 0) && (B53 < 1)$ | $5$ | false | false | $A53 = 2$ |\r\n| Eb54 | $(trig > 0) && (B54 < 1)$ | $5$ | false | false | $A54 = 2$ |\r\n| Eb55 | $(trig > 0) && (B55 < 1)$ | $5$ | false | false | $A55 = 2$ |\r\n| Eb56 | $(trig > 0) && (B56 < 1)$ | $5$ | false | false | $A56 = 2$ |\r\n| Eb57 | $(trig > 0) && (B57 < 1)$ | $5$ | false | false | $A57 = 2$ |\r\n| Eb58 | $(trig > 0) && (B58 < 1)$ | $5$ | false | false | $A58 = 2$ |\r\n| Eb59 | $(trig > 0) && (B59 < 1)$ | $5$ | false | false | $A59 = 2$ |\r\n| Eb60 | $(trig > 0) && (B60 < 1)$ | $5$ | false | false | $A60 = 2$ |\r\n| Eb61 | $(trig > 0) && (B61 < 1)$ | $5$ | false | false | $A61 = 2$ |\r\n| Eb62 | $(trig > 0) && (B62 < 1)$ | $5$ | false | false | $A62 = 2$ |\r\n| Eb63 | $(trig > 0) && (B63 < 1)$ | $5$ | false | false | $A63 = 2$ |\r\n| Eb64 | $(trig > 0) && (B64 < 1)$ | $5$ | false | false | $A64 = 2$ |\r\n| Eb65 | $(trig > 0) && (B65 < 1)$ | $5$ | false | false | $A65 = 2$ |\r\n| Eb66 | $(trig > 0) && (B66 < 1)$ | $5$ | false | false | $A66 = 2$ |\r\n| Eb67 | $(trig > 0) && (B67 < 1)$ | $5$ | false | false | $A67 = 2$ |\r\n| Eb68 | $(trig > 0) && (B68 < 1)$ | $5$ | false | false | $A68 = 2$ |\r\n| Eb69 | $(trig > 0) && (B69 < 1)$ | $5$ | false | false | $A69 = 2$ |\r\n| Eb70 | $(trig > 0) && (B70 < 1)$ | $5$ | false | false | $A70 = 2$ |\r\n| Eb71 | $(trig > 0) && (B71 < 1)$ | $5$ | false | false | $A71 = 2$ |\r\n| Eb72 | $(trig > 0) && (B72 < 1)$ | $5$ | false | false | $A72 = 2$ |\r\n| Eb73 | $(trig > 0) && (B73 < 1)$ | $5$ | false | false | $A73 = 2$ |\r\n| Eb74 | $(trig > 0) && (B74 < 1)$ | $5$ | false | false | $A74 = 2$ |\r\n| Eb75 | $(trig > 0) && (B75 < 1)$ | $5$ | false | false | $A75 = 2$ |\r\n| Eb76 | $(trig > 0) && (B76 < 1)$ | $5$ | false | false | $A76 = 2$ |\r\n| Eb77 | $(trig > 0) && (B77 < 1)$ | $5$ | false | false | $A77 = 2$ |\r\n| Eb78 | $(trig > 0) && (B78 < 1)$ | $5$ | false | false | $A78 = 2$ |\r\n| Eb79 | $(trig > 0) && (B79 < 1)$ | $5$ | false | false | $A79 = 2$ |\r\n| Eb80 | $(trig > 0) && (B80 < 1)$ | $5$ | false | false | $A80 = 2$ |\r\n| Eb81 | $(trig > 0) && (B81 < 1)$ | $5$ | false | false | $A81 = 2$ |\r\n| Eb82 | $(trig > 0) && (B82 < 1)$ | $5$ | false | false | $A82 = 2$ |\r\n| Eb83 | $(trig > 0) && (B83 < 1)$ | $5$ | false | false | $A83 = 2$ |\r\n| Eb84 | $(trig > 0) && (B84 < 1)$ | $5$ | false | false | $A84 = 2$ |\r\n| Eb85 | $(trig > 0) && (B85 < 1)$ | $5$ | false | false | $A85 = 2$ |\r\n| Eb86 | $(trig > 0) && (B86 < 1)$ | $5$ | false | false | $A86 = 2$ |\r\n| Eb87 | $(trig > 0) && (B87 < 1)$ | $5$ | false | false | $A87 = 2$ |\r\n| Eb88 | $(trig > 0) && (B88 < 1)$ | $5$ | false | false | $A88 = 2$ |\r\n| Eb89 | $(trig > 0) && (B89 < 1)$ | $5$ | false | false | $A89 = 2$ |\r\n| Eb90 | $(trig > 0) && (B90 < 1)$ | $5$ | false | false | $A90 = 2$ |\r\n| Eb91 | $(trig > 0) && (B91 < 1)$ | $5$ | false | false | $A91 = 2$ |\r\n| Eb92 | $(trig > 0) && (B92 < 1)$ | $5$ | false | false | $A92 = 2$ |\r\n| Eb93 | $(trig > 0) && (B93 < 1)$ | $5$ | false | false | $A93 = 2$ |\r\n| Eb94 | $(trig > 0) && (B94 < 1)$ | $5$ | false | false | $A94 = 2$ |\r\n| Eb95 | $(trig > 0) && (B95 < 1)$ | $5$ | false | false | $A95 = 2$ |\r\n| Eb96 | $(trig > 0) && (B96 < 1)$ | $5$ | false | false | $A96 = 2$ |\r\n| Eb97 | $(trig > 0) && (B97 < 1)$ | $5$ | false | false | $A97 = 2$ |\r\n| Eb98 | $(trig > 0) && (B98 < 1)$ | $5$ | false | false | $A98 = 2$ |\r\n| Eb99 | $(trig > 0) && (B99 < 1)$ | $5$ | false | false | $A99 = 2$ |\r\n| _E0 | $abs(Asum - Bsum) > 100$ | (unset) | true | true | $toodiverged = 1$ |]\r\n\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | Asum | $A0 + A1 + A2 + A3 + A4 + A5 + A6 + A7 + A8 + A9 + A10 + A11 + A12 + A13 + A14 + A15 + A16 + A17 + A18 + A19 + A20 + A21 + A22 + A23 + A24 + A25 + A26 + A27 + A28 + A29 + A30 + A31 + A32 + A33 + A34 + A35 + A36 + A37 + A38 + A39 + A40 + A41 + A42 + A43 + A44 + A45 + A46 + A47 + A48 + A49 + A50 + A51 + A52 + A53 + A54 + A55 + A56 + A57 + A58 + A59 + A60 + A61 + A62 + A63 + A64 + A65 + A66 + A67 + A68 + A69 + A70 + A71 + A72 + A73 + A74 + A75 + A76 + A77 + A78 + A79 + A80 + A81 + A82 + A83 + A84 + A85 + A86 + A87 + A88 + A89 + A90 + A91 + A92 + A93 + A94 + A95 + A96 + A97 + A98 + A99$ |\r\n| Assignment | Bsum | $B0 + B1 + B2 + B3 + B4 + B5 + B6 + B7 + B8 + B9 + B10 + B11 + B12 + B13 + B14 + B15 + B16 + B17 + B18 + B19 + B20 + B21 + B22 + B23 + B24 + B25 + B26 + B27 + B28 + B29 + B30 + B31 + B32 + B33 + B34 + B35 + B36 + B37 + B38 + B39 + B40 + B41 + B42 + B43 + B44 + B45 + B46 + B47 + B48 + B49 + B50 + B51 + B52 + B53 + B54 + B55 + B56 + B57 + B58 + B59 + B60 + B61 + B62 + B63 + B64 + B65 + B66 + B67 + B68 + B69 + B70 + B71 + B72 + B73 + B74 + B75 + B76 + B77 + B78 + B79 + B80 + B81 + B82 + B83 + B84 + B85 + B86 + B87 + B88 + B89 + B90 + B91 + B92 + B93 + B94 + B95 + B96 + B97 + B98 + B99$ |\r\n| Assignment | Allsum | $Asum + Bsum$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter trig | $1$ | constant |\r\n| Initial value of parameter A0 | $0$ | variable |\r\n| Initial value of parameter A1 | $0$ | variable |\r\n| Initial value of parameter A2 | $0$ | variable |\r\n| Initial value of parameter A3 | $0$ | variable |\r\n| Initial value of parameter A4 | $0$ | variable |\r\n| Initial value of parameter A5 | $0$ | variable |\r\n| Initial value of parameter A6 | $0$ | variable |\r\n| Initial value of parameter A7 | $0$ | variable |\r\n| Initial value of parameter A8 | $0$ | variable |\r\n| Initial value of parameter A9 | $0$ | variable |\r\n| Initial value of parameter A10 | $0$ | variable |\r\n| Initial value of parameter A11 | $0$ | variable |\r\n| Initial value of parameter A12 | $0$ | variable |\r\n| Initial value of parameter A13 | $0$ | variable |\r\n| Initial value of parameter A14 | $0$ | variable |\r\n| Initial value of parameter A15 | $0$ | variable |\r\n| Initial value of parameter A16 | $0$ | variable |\r\n| Initial value of parameter A17 | $0$ | variable |\r\n| Initial value of parameter A18 | $0$ | variable |\r\n| Initial value of parameter A19 | $0$ | variable |\r\n| Initial value of parameter A20 | $0$ | variable |\r\n| Initial value of parameter A21 | $0$ | variable |\r\n| Initial value of parameter A22 | $0$ | variable |\r\n| Initial value of parameter A23 | $0$ | variable |\r\n| Initial value of parameter A24 | $0$ | variable |\r\n| Initial value of parameter A25 | $0$ | variable |\r\n| Initial value of parameter A26 | $0$ | variable |\r\n| Initial value of parameter A27 | $0$ | variable |\r\n| Initial value of parameter A28 | $0$ | variable |\r\n| Initial value of parameter A29 | $0$ | variable |\r\n| Initial value of parameter A30 | $0$ | variable |\r\n| Initial value of parameter A31 | $0$ | variable |\r\n| Initial value of parameter A32 | $0$ | variable |\r\n| Initial value of parameter A33 | $0$ | variable |\r\n| Initial value of parameter A34 | $0$ | variable |\r\n| Initial value of parameter A35 | $0$ | variable |\r\n| Initial value of parameter A36 | $0$ | variable |\r\n| Initial value of parameter A37 | $0$ | variable |\r\n| Initial value of parameter A38 | $0$ | variable |\r\n| Initial value of parameter A39 | $0$ | variable |\r\n| Initial value of parameter A40 | $0$ | variable |\r\n| Initial value of parameter A41 | $0$ | variable |\r\n| Initial value of parameter A42 | $0$ | variable |\r\n| Initial value of parameter A43 | $0$ | variable |\r\n| Initial value of parameter A44 | $0$ | variable |\r\n| Initial value of parameter A45 | $0$ | variable |\r\n| Initial value of parameter A46 | $0$ | variable |\r\n| Initial value of parameter A47 | $0$ | variable |\r\n| Initial value of parameter A48 | $0$ | variable |\r\n| Initial value of parameter A49 | $0$ | variable |\r\n| Initial value of parameter A50 | $0$ | variable |\r\n| Initial value of parameter A51 | $0$ | variable |\r\n| Initial value of parameter A52 | $0$ | variable |\r\n| Initial value of parameter A53 | $0$ | variable |\r\n| Initial value of parameter A54 | $0$ | variable |\r\n| Initial value of parameter A55 | $0$ | variable |\r\n| Initial value of parameter A56 | $0$ | variable |\r\n| Initial value of parameter A57 | $0$ | variable |\r\n| Initial value of parameter A58 | $0$ | variable |\r\n| Initial value of parameter A59 | $0$ | variable |\r\n| Initial value of parameter A60 | $0$ | variable |\r\n| Initial value of parameter A61 | $0$ | variable |\r\n| Initial value of parameter A62 | $0$ | variable |\r\n| Initial value of parameter A63 | $0$ | variable |\r\n| Initial value of parameter A64 | $0$ | variable |\r\n| Initial value of parameter A65 | $0$ | variable |\r\n| Initial value of parameter A66 | $0$ | variable |\r\n| Initial value of parameter A67 | $0$ | variable |\r\n| Initial value of parameter A68 | $0$ | variable |\r\n| Initial value of parameter A69 | $0$ | variable |\r\n| Initial value of parameter A70 | $0$ | variable |\r\n| Initial value of parameter A71 | $0$ | variable |\r\n| Initial value of parameter A72 | $0$ | variable |\r\n| Initial value of parameter A73 | $0$ | variable |\r\n| Initial value of parameter A74 | $0$ | variable |\r\n| Initial value of parameter A75 | $0$ | variable |\r\n| Initial value of parameter A76 | $0$ | variable |\r\n| Initial value of parameter A77 | $0$ | variable |\r\n| Initial value of parameter A78 | $0$ | variable |\r\n| Initial value of parameter A79 | $0$ | variable |\r\n| Initial value of parameter A80 | $0$ | variable |\r\n| Initial value of parameter A81 | $0$ | variable |\r\n| Initial value of parameter A82 | $0$ | variable |\r\n| Initial value of parameter A83 | $0$ | variable |\r\n| Initial value of parameter A84 | $0$ | variable |\r\n| Initial value of parameter A85 | $0$ | variable |\r\n| Initial value of parameter A86 | $0$ | variable |\r\n| Initial value of parameter A87 | $0$ | variable |\r\n| Initial value of parameter A88 | $0$ | variable |\r\n| Initial value of parameter A89 | $0$ | variable |\r\n| Initial value of parameter A90 | $0$ | variable |\r\n| Initial value of parameter A91 | $0$ | variable |\r\n| Initial value of parameter A92 | $0$ | variable |\r\n| Initial value of parameter A93 | $0$ | variable |\r\n| Initial value of parameter A94 | $0$ | variable |\r\n| Initial value of parameter A95 | $0$ | variable |\r\n| Initial value of parameter A96 | $0$ | variable |\r\n| Initial value of parameter A97 | $0$ | variable |\r\n| Initial value of parameter A98 | $0$ | variable |\r\n| Initial value of parameter A99 | $0$ | variable |\r\n| Initial value of parameter B0 | $0$ | variable |\r\n| Initial value of parameter B1 | $0$ | variable |\r\n| Initial value of parameter B2 | $0$ | variable |\r\n| Initial value of parameter B3 | $0$ | variable |\r\n| Initial value of parameter B4 | $0$ | variable |\r\n| Initial value of parameter B5 | $0$ | variable |\r\n| Initial value of parameter B6 | $0$ | variable |\r\n| Initial value of parameter B7 | $0$ | variable |\r\n| Initial value of parameter B8 | $0$ | variable |\r\n| Initial value of parameter B9 | $0$ | variable |\r\n| Initial value of parameter B10 | $0$ | variable |\r\n| Initial value of parameter B11 | $0$ | variable |\r\n| Initial value of parameter B12 | $0$ | variable |\r\n| Initial value of parameter B13 | $0$ | variable |\r\n| Initial value of parameter B14 | $0$ | variable |\r\n| Initial value of parameter B15 | $0$ | variable |\r\n| Initial value of parameter B16 | $0$ | variable |\r\n| Initial value of parameter B17 | $0$ | variable |\r\n| Initial value of parameter B18 | $0$ | variable |\r\n| Initial value of parameter B19 | $0$ | variable |\r\n| Initial value of parameter B20 | $0$ | variable |\r\n| Initial value of parameter B21 | $0$ | variable |\r\n| Initial value of parameter B22 | $0$ | variable |\r\n| Initial value of parameter B23 | $0$ | variable |\r\n| Initial value of parameter B24 | $0$ | variable |\r\n| Initial value of parameter B25 | $0$ | variable |\r\n| Initial value of parameter B26 | $0$ | variable |\r\n| Initial value of parameter B27 | $0$ | variable |\r\n| Initial value of parameter B28 | $0$ | variable |\r\n| Initial value of parameter B29 | $0$ | variable |\r\n| Initial value of parameter B30 | $0$ | variable |\r\n| Initial value of parameter B31 | $0$ | variable |\r\n| Initial value of parameter B32 | $0$ | variable |\r\n| Initial value of parameter B33 | $0$ | variable |\r\n| Initial value of parameter B34 | $0$ | variable |\r\n| Initial value of parameter B35 | $0$ | variable |\r\n| Initial value of parameter B36 | $0$ | variable |\r\n| Initial value of parameter B37 | $0$ | variable |\r\n| Initial value of parameter B38 | $0$ | variable |\r\n| Initial value of parameter B39 | $0$ | variable |\r\n| Initial value of parameter B40 | $0$ | variable |\r\n| Initial value of parameter B41 | $0$ | variable |\r\n| Initial value of parameter B42 | $0$ | variable |\r\n| Initial value of parameter B43 | $0$ | variable |\r\n| Initial value of parameter B44 | $0$ | variable |\r\n| Initial value of parameter B45 | $0$ | variable |\r\n| Initial value of parameter B46 | $0$ | variable |\r\n| Initial value of parameter B47 | $0$ | variable |\r\n| Initial value of parameter B48 | $0$ | variable |\r\n| Initial value of parameter B49 | $0$ | variable |\r\n| Initial value of parameter B50 | $0$ | variable |\r\n| Initial value of parameter B51 | $0$ | variable |\r\n| Initial value of parameter B52 | $0$ | variable |\r\n| Initial value of parameter B53 | $0$ | variable |\r\n| Initial value of parameter B54 | $0$ | variable |\r\n| Initial value of parameter B55 | $0$ | variable |\r\n| Initial value of parameter B56 | $0$ | variable |\r\n| Initial value of parameter B57 | $0$ | variable |\r\n| Initial value of parameter B58 | $0$ | variable |\r\n| Initial value of parameter B59 | $0$ | variable |\r\n| Initial value of parameter B60 | $0$ | variable |\r\n| Initial value of parameter B61 | $0$ | variable |\r\n| Initial value of parameter B62 | $0$ | variable |\r\n| Initial value of parameter B63 | $0$ | variable |\r\n| Initial value of parameter B64 | $0$ | variable |\r\n| Initial value of parameter B65 | $0$ | variable |\r\n| Initial value of parameter B66 | $0$ | variable |\r\n| Initial value of parameter B67 | $0$ | variable |\r\n| Initial value of parameter B68 | $0$ | variable |\r\n| Initial value of parameter B69 | $0$ | variable |\r\n| Initial value of parameter B70 | $0$ | variable |\r\n| Initial value of parameter B71 | $0$ | variable |\r\n| Initial value of parameter B72 | $0$ | variable |\r\n| Initial value of parameter B73 | $0$ | variable |\r\n| Initial value of parameter B74 | $0$ | variable |\r\n| Initial value of parameter B75 | $0$ | variable |\r\n| Initial value of parameter B76 | $0$ | variable |\r\n| Initial value of parameter B77 | $0$ | variable |\r\n| Initial value of parameter B78 | $0$ | variable |\r\n| Initial value of parameter B79 | $0$ | variable |\r\n| Initial value of parameter B80 | $0$ | variable |\r\n| Initial value of parameter B81 | $0$ | variable |\r\n| Initial value of parameter B82 | $0$ | variable |\r\n| Initial value of parameter B83 | $0$ | variable |\r\n| Initial value of parameter B84 | $0$ | variable |\r\n| Initial value of parameter B85 | $0$ | variable |\r\n| Initial value of parameter B86 | $0$ | variable |\r\n| Initial value of parameter B87 | $0$ | variable |\r\n| Initial value of parameter B88 | $0$ | variable |\r\n| Initial value of parameter B89 | $0$ | variable |\r\n| Initial value of parameter B90 | $0$ | variable |\r\n| Initial value of parameter B91 | $0$ | variable |\r\n| Initial value of parameter B92 | $0$ | variable |\r\n| Initial value of parameter B93 | $0$ | variable |\r\n| Initial value of parameter B94 | $0$ | variable |\r\n| Initial value of parameter B95 | $0$ | variable |\r\n| Initial value of parameter B96 | $0$ | variable |\r\n| Initial value of parameter B97 | $0$ | variable |\r\n| Initial value of parameter B98 | $0$ | variable |\r\n| Initial value of parameter B99 | $0$ | variable |\r\n| Initial value of parameter Asum | $A0 + A1 + A2 + A3 + A4 + A5 + A6 + A7 + A8 + A9 + A10 + A11 + A12 + A13 + A14 + A15 + A16 + A17 + A18 + A19 + A20 + A21 + A22 + A23 + A24 + A25 + A26 + A27 + A28 + A29 + A30 + A31 + A32 + A33 + A34 + A35 + A36 + A37 + A38 + A39 + A40 + A41 + A42 + A43 + A44 + A45 + A46 + A47 + A48 + A49 + A50 + A51 + A52 + A53 + A54 + A55 + A56 + A57 + A58 + A59 + A60 + A61 + A62 + A63 + A64 + A65 + A66 + A67 + A68 + A69 + A70 + A71 + A72 + A73 + A74 + A75 + A76 + A77 + A78 + A79 + A80 + A81 + A82 + A83 + A84 + A85 + A86 + A87 + A88 + A89 + A90 + A91 + A92 + A93 + A94 + A95 + A96 + A97 + A98 + A99$ | variable |\r\n| Initial value of parameter Bsum | $B0 + B1 + B2 + B3 + B4 + B5 + B6 + B7 + B8 + B9 + B10 + B11 + B12 + B13 + B14 + B15 + B16 + B17 + B18 + B19 + B20 + B21 + B22 + B23 + B24 + B25 + B26 + B27 + B28 + B29 + B30 + B31 + B32 + B33 + B34 + B35 + B36 + B37 + B38 + B39 + B40 + B41 + B42 + B43 + B44 + B45 + B46 + B47 + B48 + B49 + B50 + B51 + B52 + B53 + B54 + B55 + B56 + B57 + B58 + B59 + B60 + B61 + B62 + B63 + B64 + B65 + B66 + B67 + B68 + B69 + B70 + B71 + B72 + B73 + B74 + B75 + B76 + B77 + B78 + B79 + B80 + B81 + B82 + B83 + B84 + B85 + B86 + B87 + B88 + B89 + B90 + B91 + B92 + B93 + B94 + B95 + B96 + B97 + B98 + B99$ | variable |\r\n| Initial value of parameter Allsum | $Asum + Bsum$ | variable |\r\n| Initial value of parameter toodiverged | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nA0 @Record { } .= 0;\nA0 [Eb0]= 2;\nA1 @Record { } .= 0;\nA1 [Eb1]= 2;\nA2 @Record { } .= 0;\nA2 [Eb2]= 2;\nA3 @Record { } .= 0;\nA3 [Eb3]= 2;\nA4 @Record { } .= 0;\nA4 [Eb4]= 2;\nA5 @Record { } .= 0;\nA5 [Eb5]= 2;\nA6 @Record { } .= 0;\nA6 [Eb6]= 2;\nA7 @Record { } .= 0;\nA7 [Eb7]= 2;\nA8 @Record { } .= 0;\nA8 [Eb8]= 2;\nA9 @Record { } .= 0;\nA9 [Eb9]= 2;\nA10 @Record { } .= 0;\nA10 [Eb10]= 2;\nA11 @Record { } .= 0;\nA11 [Eb11]= 2;\nA12 @Record { } .= 0;\nA12 [Eb12]= 2;\nA13 @Record { } .= 0;\nA13 [Eb13]= 2;\nA14 @Record { } .= 0;\nA14 [Eb14]= 2;\nA15 @Record { } .= 0;\nA15 [Eb15]= 2;\nA16 @Record { } .= 0;\nA16 [Eb16]= 2;\nA17 @Record { } .= 0;\nA17 [Eb17]= 2;\nA18 @Record { } .= 0;\nA18 [Eb18]= 2;\nA19 @Record { } .= 0;\nA19 [Eb19]= 2;\nA20 @Record { } .= 0;\nA20 [Eb20]= 2;\nA21 @Record { } .= 0;\nA21 [Eb21]= 2;\nA22 @Record { } .= 0;\nA22 [Eb22]= 2;\nA23 @Record { } .= 0;\nA23 [Eb23]= 2;\nA24 @Record { } .= 0;\nA24 [Eb24]= 2;\nA25 @Record { } .= 0;\nA25 [Eb25]= 2;\nA26 @Record { } .= 0;\nA26 [Eb26]= 2;\nA27 @Record { } .= 0;\nA27 [Eb27]= 2;\nA28 @Record { } .= 0;\nA28 [Eb28]= 2;\nA29 @Record { } .= 0;\nA29 [Eb29]= 2;\nA30 @Record { } .= 0;\nA30 [Eb30]= 2;\nA31 @Record { } .= 0;\nA31 [Eb31]= 2;\nA32 @Record { } .= 0;\nA32 [Eb32]= 2;\nA33 @Record { } .= 0;\nA33 [Eb33]= 2;\nA34 @Record { } .= 0;\nA34 [Eb34]= 2;\nA35 @Record { } .= 0;\nA35 [Eb35]= 2;\nA36 @Record { } .= 0;\nA36 [Eb36]= 2;\nA37 @Record { } .= 0;\nA37 [Eb37]= 2;\nA38 @Record { } .= 0;\nA38 [Eb38]= 2;\nA39 @Record { } .= 0;\nA39 [Eb39]= 2;\nA40 @Record { } .= 0;\nA40 [Eb40]= 2;\nA41 @Record { } .= 0;\nA41 [Eb41]= 2;\nA42 @Record { } .= 0;\nA42 [Eb42]= 2;\nA43 @Record { } .= 0;\nA43 [Eb43]= 2;\nA44 @Record { } .= 0;\nA44 [Eb44]= 2;\nA45 @Record { } .= 0;\nA45 [Eb45]= 2;\nA46 @Record { } .= 0;\nA46 [Eb46]= 2;\nA47 @Record { } .= 0;\nA47 [Eb47]= 2;\nA48 @Record { } .= 0;\nA48 [Eb48]= 2;\nA49 @Record { } .= 0;\nA49 [Eb49]= 2;\nA50 @Record { } .= 0;\nA50 [Eb50]= 2;\nA51 @Record { } .= 0;\nA51 [Eb51]= 2;\nA52 @Record { } .= 0;\nA52 [Eb52]= 2;\nA53 @Record { } .= 0;\nA53 [Eb53]= 2;\nA54 @Record { } .= 0;\nA54 [Eb54]= 2;\nA55 @Record { } .= 0;\nA55 [Eb55]= 2;\nA56 @Record { } .= 0;\nA56 [Eb56]= 2;\nA57 @Record { } .= 0;\nA57 [Eb57]= 2;\nA58 @Record { } .= 0;\nA58 [Eb58]= 2;\nA59 @Record { } .= 0;\nA59 [Eb59]= 2;\nA60 @Record { } .= 0;\nA60 [Eb60]= 2;\nA61 @Record { } .= 0;\nA61 [Eb61]= 2;\nA62 @Record { } .= 0;\nA62 [Eb62]= 2;\nA63 @Record { } .= 0;\nA63 [Eb63]= 2;\nA64 @Record { } .= 0;\nA64 [Eb64]= 2;\nA65 @Record { } .= 0;\nA65 [Eb65]= 2;\nA66 @Record { } .= 0;\nA66 [Eb66]= 2;\nA67 @Record { } .= 0;\nA67 [Eb67]= 2;\nA68 @Record { } .= 0;\nA68 [Eb68]= 2;\nA69 @Record { } .= 0;\nA69 [Eb69]= 2;\nA70 @Record { } .= 0;\nA70 [Eb70]= 2;\nA71 @Record { } .= 0;\nA71 [Eb71]= 2;\nA72 @Record { } .= 0;\nA72 [Eb72]= 2;\nA73 @Record { } .= 0;\nA73 [Eb73]= 2;\nA74 @Record { } .= 0;\nA74 [Eb74]= 2;\nA75 @Record { } .= 0;\nA75 [Eb75]= 2;\nA76 @Record { } .= 0;\nA76 [Eb76]= 2;\nA77 @Record { } .= 0;\nA77 [Eb77]= 2;\nA78 @Record { } .= 0;\nA78 [Eb78]= 2;\nA79 @Record { } .= 0;\nA79 [Eb79]= 2;\nA80 @Record { } .= 0;\nA80 [Eb80]= 2;\nA81 @Record { } .= 0;\nA81 [Eb81]= 2;\nA82 @Record { } .= 0;\nA82 [Eb82]= 2;\nA83 @Record { } .= 0;\nA83 [Eb83]= 2;\nA84 @Record { } .= 0;\nA84 [Eb84]= 2;\nA85 @Record { } .= 0;\nA85 [Eb85]= 2;\nA86 @Record { } .= 0;\nA86 [Eb86]= 2;\nA87 @Record { } .= 0;\nA87 [Eb87]= 2;\nA88 @Record { } .= 0;\nA88 [Eb88]= 2;\nA89 @Record { } .= 0;\nA89 [Eb89]= 2;\nA90 @Record { } .= 0;\nA90 [Eb90]= 2;\nA91 @Record { } .= 0;\nA91 [Eb91]= 2;\nA92 @Record { } .= 0;\nA92 [Eb92]= 2;\nA93 @Record { } .= 0;\nA93 [Eb93]= 2;\nA94 @Record { } .= 0;\nA94 [Eb94]= 2;\nA95 @Record { } .= 0;\nA95 [Eb95]= 2;\nA96 @Record { } .= 0;\nA96 [Eb96]= 2;\nA97 @Record { } .= 0;\nA97 [Eb97]= 2;\nA98 @Record { } .= 0;\nA98 [Eb98]= 2;\nA99 @Record { } .= 0;\nA99 [Eb99]= 2;\nB0 @Record { } .= 0;\nB0 [E0]= 2;\nB1 @Record { } .= 0;\nB1 [E1]= 2;\nB2 @Record { } .= 0;\nB2 [E2]= 2;\nB3 @Record { } .= 0;\nB3 [E3]= 2;\nB4 @Record { } .= 0;\nB4 [E4]= 2;\nB5 @Record { } .= 0;\nB5 [E5]= 2;\nB6 @Record { } .= 0;\nB6 [E6]= 2;\nB7 @Record { } .= 0;\nB7 [E7]= 2;\nB8 @Record { } .= 0;\nB8 [E8]= 2;\nB9 @Record { } .= 0;\nB9 [E9]= 2;\nB10 @Record { } .= 0;\nB10 [E10]= 2;\nB11 @Record { } .= 0;\nB11 [E11]= 2;\nB12 @Record { } .= 0;\nB12 [E12]= 2;\nB13 @Record { } .= 0;\nB13 [E13]= 2;\nB14 @Record { } .= 0;\nB14 [E14]= 2;\nB15 @Record { } .= 0;\nB15 [E15]= 2;\nB16 @Record { } .= 0;\nB16 [E16]= 2;\nB17 @Record { } .= 0;\nB17 [E17]= 2;\nB18 @Record { } .= 0;\nB18 [E18]= 2;\nB19 @Record { } .= 0;\nB19 [E19]= 2;\nB20 @Record { } .= 0;\nB20 [E20]= 2;\nB21 @Record { } .= 0;\nB21 [E21]= 2;\nB22 @Record { } .= 0;\nB22 [E22]= 2;\nB23 @Record { } .= 0;\nB23 [E23]= 2;\nB24 @Record { } .= 0;\nB24 [E24]= 2;\nB25 @Record { } .= 0;\nB25 [E25]= 2;\nB26 @Record { } .= 0;\nB26 [E26]= 2;\nB27 @Record { } .= 0;\nB27 [E27]= 2;\nB28 @Record { } .= 0;\nB28 [E28]= 2;\nB29 @Record { } .= 0;\nB29 [E29]= 2;\nB30 @Record { } .= 0;\nB30 [E30]= 2;\nB31 @Record { } .= 0;\nB31 [E31]= 2;\nB32 @Record { } .= 0;\nB32 [E32]= 2;\nB33 @Record { } .= 0;\nB33 [E33]= 2;\nB34 @Record { } .= 0;\nB34 [E34]= 2;\nB35 @Record { } .= 0;\nB35 [E35]= 2;\nB36 @Record { } .= 0;\nB36 [E36]= 2;\nB37 @Record { } .= 0;\nB37 [E37]= 2;\nB38 @Record { } .= 0;\nB38 [E38]= 2;\nB39 @Record { } .= 0;\nB39 [E39]= 2;\nB40 @Record { } .= 0;\nB40 [E40]= 2;\nB41 @Record { } .= 0;\nB41 [E41]= 2;\nB42 @Record { } .= 0;\nB42 [E42]= 2;\nB43 @Record { } .= 0;\nB43 [E43]= 2;\nB44 @Record { } .= 0;\nB44 [E44]= 2;\nB45 @Record { } .= 0;\nB45 [E45]= 2;\nB46 @Record { } .= 0;\nB46 [E46]= 2;\nB47 @Record { } .= 0;\nB47 [E47]= 2;\nB48 @Record { } .= 0;\nB48 [E48]= 2;\nB49 @Record { } .= 0;\nB49 [E49]= 2;\nB50 @Record { } .= 0;\nB50 [E50]= 2;\nB51 @Record { } .= 0;\nB51 [E51]= 2;\nB52 @Record { } .= 0;\nB52 [E52]= 2;\nB53 @Record { } .= 0;\nB53 [E53]= 2;\nB54 @Record { } .= 0;\nB54 [E54]= 2;\nB55 @Record { } .= 0;\nB55 [E55]= 2;\nB56 @Record { } .= 0;\nB56 [E56]= 2;\nB57 @Record { } .= 0;\nB57 [E57]= 2;\nB58 @Record { } .= 0;\nB58 [E58]= 2;\nB59 @Record { } .= 0;\nB59 [E59]= 2;\nB60 @Record { } .= 0;\nB60 [E60]= 2;\nB61 @Record { } .= 0;\nB61 [E61]= 2;\nB62 @Record { } .= 0;\nB62 [E62]= 2;\nB63 @Record { } .= 0;\nB63 [E63]= 2;\nB64 @Record { } .= 0;\nB64 [E64]= 2;\nB65 @Record { } .= 0;\nB65 [E65]= 2;\nB66 @Record { } .= 0;\nB66 [E66]= 2;\nB67 @Record { } .= 0;\nB67 [E67]= 2;\nB68 @Record { } .= 0;\nB68 [E68]= 2;\nB69 @Record { } .= 0;\nB69 [E69]= 2;\nB70 @Record { } .= 0;\nB70 [E70]= 2;\nB71 @Record { } .= 0;\nB71 [E71]= 2;\nB72 @Record { } .= 0;\nB72 [E72]= 2;\nB73 @Record { } .= 0;\nB73 [E73]= 2;\nB74 @Record { } .= 0;\nB74 [E74]= 2;\nB75 @Record { } .= 0;\nB75 [E75]= 2;\nB76 @Record { } .= 0;\nB76 [E76]= 2;\nB77 @Record { } .= 0;\nB77 [E77]= 2;\nB78 @Record { } .= 0;\nB78 [E78]= 2;\nB79 @Record { } .= 0;\nB79 [E79]= 2;\nB80 @Record { } .= 0;\nB80 [E80]= 2;\nB81 @Record { } .= 0;\nB81 [E81]= 2;\nB82 @Record { } .= 0;\nB82 [E82]= 2;\nB83 @Record { } .= 0;\nB83 [E83]= 2;\nB84 @Record { } .= 0;\nB84 [E84]= 2;\nB85 @Record { } .= 0;\nB85 [E85]= 2;\nB86 @Record { } .= 0;\nB86 [E86]= 2;\nB87 @Record { } .= 0;\nB87 [E87]= 2;\nB88 @Record { } .= 0;\nB88 [E88]= 2;\nB89 @Record { } .= 0;\nB89 [E89]= 2;\nB90 @Record { } .= 0;\nB90 [E90]= 2;\nB91 @Record { } .= 0;\nB91 [E91]= 2;\nB92 @Record { } .= 0;\nB92 [E92]= 2;\nB93 @Record { } .= 0;\nB93 [E93]= 2;\nB94 @Record { } .= 0;\nB94 [E94]= 2;\nB95 @Record { } .= 0;\nB95 [E95]= 2;\nB96 @Record { } .= 0;\nB96 [E96]= 2;\nB97 @Record { } .= 0;\nB97 [E97]= 2;\nB98 @Record { } .= 0;\nB98 [E98]= 2;\nB99 @Record { } .= 0;\nB99 [E99]= 2;\nAsum @Record { };\nAsum := A0 + A1 + A2 + A3 + A4 + A5 + A6 + A7 + A8 + A9 + A10 + A11 + A12 + A13 + A14 + A15 + A16 + A17 + A18 + A19 + A20 + A21 + A22 + A23 + A24 + A25 + A26 + A27 + A28 + A29 + A30 + A31 + A32 + A33 + A34 + A35 + A36 + A37 + A38 + A39 + A40 + A41 + A42 + A43 + A44 + A45 + A46 + A47 + A48 + A49 + A50 + A51 + A52 + A53 + A54 + A55 + A56 + A57 + A58 + A59 + A60 + A61 + A62 + A63 + A64 + A65 + A66 + A67 + A68 + A69 + A70 + A71 + A72 + A73 + A74 + A75 + A76 + A77 + A78 + A79 + A80 + A81 + A82 + A83 + A84 + A85 + A86 + A87 + A88 + A89 + A90 + A91 + A92 + A93 + A94 + A95 + A96 + A97 + A98 + A99;\nBsum @Record { };\nBsum := B0 + B1 + B2 + B3 + B4 + B5 + B6 + B7 + B8 + B9 + B10 + B11 + B12 + B13 + B14 + B15 + B16 + B17 + B18 + B19 + B20 + B21 + B22 + B23 + B24 + B25 + B26 + B27 + B28 + B29 + B30 + B31 + B32 + B33 + B34 + B35 + B36 + B37 + B38 + B39 + B40 + B41 + B42 + B43 + B44 + B45 + B46 + B47 + B48 + B49 + B50 + B51 + B52 + B53 + B54 + B55 + B56 + B57 + B58 + B59 + B60 + B61 + B62 + B63 + B64 + B65 + B66 + B67 + B68 + B69 + B70 + B71 + B72 + B73 + B74 + B75 + B76 + B77 + B78 + B79 + B80 + B81 + B82 + B83 + B84 + B85 + B86 + B87 + B88 + B89 + B90 + B91 + B92 + B93 + B94 + B95 + B96 + B97 + B98 + B99;\nAllsum @Record { };\nAllsum := Asum + Bsum;\ntoodiverged @Record { } .= 0;\ntoodiverged [_E0]= 1;\n\ntrig @Const { } = 1;\n\nE0 @DSwitcher { trigger: trig > 0 and A0 < 1, };\nE1 @DSwitcher { trigger: trig > 0 and A1 < 1, };\nE2 @DSwitcher { trigger: trig > 0 and A2 < 1, };\nE3 @DSwitcher { trigger: trig > 0 and A3 < 1, };\nE4 @DSwitcher { trigger: trig > 0 and A4 < 1, };\nE5 @DSwitcher { trigger: trig > 0 and A5 < 1, };\nE6 @DSwitcher { trigger: trig > 0 and A6 < 1, };\nE7 @DSwitcher { trigger: trig > 0 and A7 < 1, };\nE8 @DSwitcher { trigger: trig > 0 and A8 < 1, };\nE9 @DSwitcher { trigger: trig > 0 and A9 < 1, };\nE10 @DSwitcher { trigger: trig > 0 and A10 < 1, };\nE11 @DSwitcher { trigger: trig > 0 and A11 < 1, };\nE12 @DSwitcher { trigger: trig > 0 and A12 < 1, };\nE13 @DSwitcher { trigger: trig > 0 and A13 < 1, };\nE14 @DSwitcher { trigger: trig > 0 and A14 < 1, };\nE15 @DSwitcher { trigger: trig > 0 and A15 < 1, };\nE16 @DSwitcher { trigger: trig > 0 and A16 < 1, };\nE17 @DSwitcher { trigger: trig > 0 and A17 < 1, };\nE18 @DSwitcher { trigger: trig > 0 and A18 < 1, };\nE19 @DSwitcher { trigger: trig > 0 and A19 < 1, };\nE20 @DSwitcher { trigger: trig > 0 and A20 < 1, };\nE21 @DSwitcher { trigger: trig > 0 and A21 < 1, };\nE22 @DSwitcher { trigger: trig > 0 and A22 < 1, };\nE23 @DSwitcher { trigger: trig > 0 and A23 < 1, };\nE24 @DSwitcher { trigger: trig > 0 and A24 < 1, };\nE25 @DSwitcher { trigger: trig > 0 and A25 < 1, };\nE26 @DSwitcher { trigger: trig > 0 and A26 < 1, };\nE27 @DSwitcher { trigger: trig > 0 and A27 < 1, };\nE28 @DSwitcher { trigger: trig > 0 and A28 < 1, };\nE29 @DSwitcher { trigger: trig > 0 and A29 < 1, };\nE30 @DSwitcher { trigger: trig > 0 and A30 < 1, };\nE31 @DSwitcher { trigger: trig > 0 and A31 < 1, };\nE32 @DSwitcher { trigger: trig > 0 and A32 < 1, };\nE33 @DSwitcher { trigger: trig > 0 and A33 < 1, };\nE34 @DSwitcher { trigger: trig > 0 and A34 < 1, };\nE35 @DSwitcher { trigger: trig > 0 and A35 < 1, };\nE36 @DSwitcher { trigger: trig > 0 and A36 < 1, };\nE37 @DSwitcher { trigger: trig > 0 and A37 < 1, };\nE38 @DSwitcher { trigger: trig > 0 and A38 < 1, };\nE39 @DSwitcher { trigger: trig > 0 and A39 < 1, };\nE40 @DSwitcher { trigger: trig > 0 and A40 < 1, };\nE41 @DSwitcher { trigger: trig > 0 and A41 < 1, };\nE42 @DSwitcher { trigger: trig > 0 and A42 < 1, };\nE43 @DSwitcher { trigger: trig > 0 and A43 < 1, };\nE44 @DSwitcher { trigger: trig > 0 and A44 < 1, };\nE45 @DSwitcher { trigger: trig > 0 and A45 < 1, };\nE46 @DSwitcher { trigger: trig > 0 and A46 < 1, };\nE47 @DSwitcher { trigger: trig > 0 and A47 < 1, };\nE48 @DSwitcher { trigger: trig > 0 and A48 < 1, };\nE49 @DSwitcher { trigger: trig > 0 and A49 < 1, };\nE50 @DSwitcher { trigger: trig > 0 and A50 < 1, };\nE51 @DSwitcher { trigger: trig > 0 and A51 < 1, };\nE52 @DSwitcher { trigger: trig > 0 and A52 < 1, };\nE53 @DSwitcher { trigger: trig > 0 and A53 < 1, };\nE54 @DSwitcher { trigger: trig > 0 and A54 < 1, };\nE55 @DSwitcher { trigger: trig > 0 and A55 < 1, };\nE56 @DSwitcher { trigger: trig > 0 and A56 < 1, };\nE57 @DSwitcher { trigger: trig > 0 and A57 < 1, };\nE58 @DSwitcher { trigger: trig > 0 and A58 < 1, };\nE59 @DSwitcher { trigger: trig > 0 and A59 < 1, };\nE60 @DSwitcher { trigger: trig > 0 and A60 < 1, };\nE61 @DSwitcher { trigger: trig > 0 and A61 < 1, };\nE62 @DSwitcher { trigger: trig > 0 and A62 < 1, };\nE63 @DSwitcher { trigger: trig > 0 and A63 < 1, };\nE64 @DSwitcher { trigger: trig > 0 and A64 < 1, };\nE65 @DSwitcher { trigger: trig > 0 and A65 < 1, };\nE66 @DSwitcher { trigger: trig > 0 and A66 < 1, };\nE67 @DSwitcher { trigger: trig > 0 and A67 < 1, };\nE68 @DSwitcher { trigger: trig > 0 and A68 < 1, };\nE69 @DSwitcher { trigger: trig > 0 and A69 < 1, };\nE70 @DSwitcher { trigger: trig > 0 and A70 < 1, };\nE71 @DSwitcher { trigger: trig > 0 and A71 < 1, };\nE72 @DSwitcher { trigger: trig > 0 and A72 < 1, };\nE73 @DSwitcher { trigger: trig > 0 and A73 < 1, };\nE74 @DSwitcher { trigger: trig > 0 and A74 < 1, };\nE75 @DSwitcher { trigger: trig > 0 and A75 < 1, };\nE76 @DSwitcher { trigger: trig > 0 and A76 < 1, };\nE77 @DSwitcher { trigger: trig > 0 and A77 < 1, };\nE78 @DSwitcher { trigger: trig > 0 and A78 < 1, };\nE79 @DSwitcher { trigger: trig > 0 and A79 < 1, };\nE80 @DSwitcher { trigger: trig > 0 and A80 < 1, };\nE81 @DSwitcher { trigger: trig > 0 and A81 < 1, };\nE82 @DSwitcher { trigger: trig > 0 and A82 < 1, };\nE83 @DSwitcher { trigger: trig > 0 and A83 < 1, };\nE84 @DSwitcher { trigger: trig > 0 and A84 < 1, };\nE85 @DSwitcher { trigger: trig > 0 and A85 < 1, };\nE86 @DSwitcher { trigger: trig > 0 and A86 < 1, };\nE87 @DSwitcher { trigger: trig > 0 and A87 < 1, };\nE88 @DSwitcher { trigger: trig > 0 and A88 < 1, };\nE89 @DSwitcher { trigger: trig > 0 and A89 < 1, };\nE90 @DSwitcher { trigger: trig > 0 and A90 < 1, };\nE91 @DSwitcher { trigger: trig > 0 and A91 < 1, };\nE92 @DSwitcher { trigger: trig > 0 and A92 < 1, };\nE93 @DSwitcher { trigger: trig > 0 and A93 < 1, };\nE94 @DSwitcher { trigger: trig > 0 and A94 < 1, };\nE95 @DSwitcher { trigger: trig > 0 and A95 < 1, };\nE96 @DSwitcher { trigger: trig > 0 and A96 < 1, };\nE97 @DSwitcher { trigger: trig > 0 and A97 < 1, };\nE98 @DSwitcher { trigger: trig > 0 and A98 < 1, };\nE99 @DSwitcher { trigger: trig > 0 and A99 < 1, };\nEb0 @DSwitcher { trigger: trig > 0 and B0 < 1, };\nEb1 @DSwitcher { trigger: trig > 0 and B1 < 1, };\nEb2 @DSwitcher { trigger: trig > 0 and B2 < 1, };\nEb3 @DSwitcher { trigger: trig > 0 and B3 < 1, };\nEb4 @DSwitcher { trigger: trig > 0 and B4 < 1, };\nEb5 @DSwitcher { trigger: trig > 0 and B5 < 1, };\nEb6 @DSwitcher { trigger: trig > 0 and B6 < 1, };\nEb7 @DSwitcher { trigger: trig > 0 and B7 < 1, };\nEb8 @DSwitcher { trigger: trig > 0 and B8 < 1, };\nEb9 @DSwitcher { trigger: trig > 0 and B9 < 1, };\nEb10 @DSwitcher { trigger: trig > 0 and B10 < 1, };\nEb11 @DSwitcher { trigger: trig > 0 and B11 < 1, };\nEb12 @DSwitcher { trigger: trig > 0 and B12 < 1, };\nEb13 @DSwitcher { trigger: trig > 0 and B13 < 1, };\nEb14 @DSwitcher { trigger: trig > 0 and B14 < 1, };\nEb15 @DSwitcher { trigger: trig > 0 and B15 < 1, };\nEb16 @DSwitcher { trigger: trig > 0 and B16 < 1, };\nEb17 @DSwitcher { trigger: trig > 0 and B17 < 1, };\nEb18 @DSwitcher { trigger: trig > 0 and B18 < 1, };\nEb19 @DSwitcher { trigger: trig > 0 and B19 < 1, };\nEb20 @DSwitcher { trigger: trig > 0 and B20 < 1, };\nEb21 @DSwitcher { trigger: trig > 0 and B21 < 1, };\nEb22 @DSwitcher { trigger: trig > 0 and B22 < 1, };\nEb23 @DSwitcher { trigger: trig > 0 and B23 < 1, };\nEb24 @DSwitcher { trigger: trig > 0 and B24 < 1, };\nEb25 @DSwitcher { trigger: trig > 0 and B25 < 1, };\nEb26 @DSwitcher { trigger: trig > 0 and B26 < 1, };\nEb27 @DSwitcher { trigger: trig > 0 and B27 < 1, };\nEb28 @DSwitcher { trigger: trig > 0 and B28 < 1, };\nEb29 @DSwitcher { trigger: trig > 0 and B29 < 1, };\nEb30 @DSwitcher { trigger: trig > 0 and B30 < 1, };\nEb31 @DSwitcher { trigger: trig > 0 and B31 < 1, };\nEb32 @DSwitcher { trigger: trig > 0 and B32 < 1, };\nEb33 @DSwitcher { trigger: trig > 0 and B33 < 1, };\nEb34 @DSwitcher { trigger: trig > 0 and B34 < 1, };\nEb35 @DSwitcher { trigger: trig > 0 and B35 < 1, };\nEb36 @DSwitcher { trigger: trig > 0 and B36 < 1, };\nEb37 @DSwitcher { trigger: trig > 0 and B37 < 1, };\nEb38 @DSwitcher { trigger: trig > 0 and B38 < 1, };\nEb39 @DSwitcher { trigger: trig > 0 and B39 < 1, };\nEb40 @DSwitcher { trigger: trig > 0 and B40 < 1, };\nEb41 @DSwitcher { trigger: trig > 0 and B41 < 1, };\nEb42 @DSwitcher { trigger: trig > 0 and B42 < 1, };\nEb43 @DSwitcher { trigger: trig > 0 and B43 < 1, };\nEb44 @DSwitcher { trigger: trig > 0 and B44 < 1, };\nEb45 @DSwitcher { trigger: trig > 0 and B45 < 1, };\nEb46 @DSwitcher { trigger: trig > 0 and B46 < 1, };\nEb47 @DSwitcher { trigger: trig > 0 and B47 < 1, };\nEb48 @DSwitcher { trigger: trig > 0 and B48 < 1, };\nEb49 @DSwitcher { trigger: trig > 0 and B49 < 1, };\nEb50 @DSwitcher { trigger: trig > 0 and B50 < 1, };\nEb51 @DSwitcher { trigger: trig > 0 and B51 < 1, };\nEb52 @DSwitcher { trigger: trig > 0 and B52 < 1, };\nEb53 @DSwitcher { trigger: trig > 0 and B53 < 1, };\nEb54 @DSwitcher { trigger: trig > 0 and B54 < 1, };\nEb55 @DSwitcher { trigger: trig > 0 and B55 < 1, };\nEb56 @DSwitcher { trigger: trig > 0 and B56 < 1, };\nEb57 @DSwitcher { trigger: trig > 0 and B57 < 1, };\nEb58 @DSwitcher { trigger: trig > 0 and B58 < 1, };\nEb59 @DSwitcher { trigger: trig > 0 and B59 < 1, };\nEb60 @DSwitcher { trigger: trig > 0 and B60 < 1, };\nEb61 @DSwitcher { trigger: trig > 0 and B61 < 1, };\nEb62 @DSwitcher { trigger: trig > 0 and B62 < 1, };\nEb63 @DSwitcher { trigger: trig > 0 and B63 < 1, };\nEb64 @DSwitcher { trigger: trig > 0 and B64 < 1, };\nEb65 @DSwitcher { trigger: trig > 0 and B65 < 1, };\nEb66 @DSwitcher { trigger: trig > 0 and B66 < 1, };\nEb67 @DSwitcher { trigger: trig > 0 and B67 < 1, };\nEb68 @DSwitcher { trigger: trig > 0 and B68 < 1, };\nEb69 @DSwitcher { trigger: trig > 0 and B69 < 1, };\nEb70 @DSwitcher { trigger: trig > 0 and B70 < 1, };\nEb71 @DSwitcher { trigger: trig > 0 and B71 < 1, };\nEb72 @DSwitcher { trigger: trig > 0 and B72 < 1, };\nEb73 @DSwitcher { trigger: trig > 0 and B73 < 1, };\nEb74 @DSwitcher { trigger: trig > 0 and B74 < 1, };\nEb75 @DSwitcher { trigger: trig > 0 and B75 < 1, };\nEb76 @DSwitcher { trigger: trig > 0 and B76 < 1, };\nEb77 @DSwitcher { trigger: trig > 0 and B77 < 1, };\nEb78 @DSwitcher { trigger: trig > 0 and B78 < 1, };\nEb79 @DSwitcher { trigger: trig > 0 and B79 < 1, };\nEb80 @DSwitcher { trigger: trig > 0 and B80 < 1, };\nEb81 @DSwitcher { trigger: trig > 0 and B81 < 1, };\nEb82 @DSwitcher { trigger: trig > 0 and B82 < 1, };\nEb83 @DSwitcher { trigger: trig > 0 and B83 < 1, };\nEb84 @DSwitcher { trigger: trig > 0 and B84 < 1, };\nEb85 @DSwitcher { trigger: trig > 0 and B85 < 1, };\nEb86 @DSwitcher { trigger: trig > 0 and B86 < 1, };\nEb87 @DSwitcher { trigger: trig > 0 and B87 < 1, };\nEb88 @DSwitcher { trigger: trig > 0 and B88 < 1, };\nEb89 @DSwitcher { trigger: trig > 0 and B89 < 1, };\nEb90 @DSwitcher { trigger: trig > 0 and B90 < 1, };\nEb91 @DSwitcher { trigger: trig > 0 and B91 < 1, };\nEb92 @DSwitcher { trigger: trig > 0 and B92 < 1, };\nEb93 @DSwitcher { trigger: trig > 0 and B93 < 1, };\nEb94 @DSwitcher { trigger: trig > 0 and B94 < 1, };\nEb95 @DSwitcher { trigger: trig > 0 and B95 < 1, };\nEb96 @DSwitcher { trigger: trig > 0 and B96 < 1, };\nEb97 @DSwitcher { trigger: trig > 0 and B97 < 1, };\nEb98 @DSwitcher { trigger: trig > 0 and B98 < 1, };\nEb99 @DSwitcher { trigger: trig > 0 and B99 < 1, };\n_E0 @DSwitcher { trigger: abs(Asum - Bsum) > 100, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a reaction modified by an extent conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (sub2__sub1__s1)\r\n* 1 parameter (extentconv)\r\n* 1 compartment (sub2__sub1__C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| sub2__sub1__J0: -> sub2__sub1__s1 | $extentconv * 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species sub2__sub1__s1 | $1$ | variable |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial volume of compartment 'sub2__sub1__C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nextentconv @Const { } = 1000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a reaction modified by an extent conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Amount, comp:ExtentConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection. The species and compartment are replaced in the top-level model.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 1 parameter (extentconv)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| sub2__sub1__J0: -> s1 | $extentconv * 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $1$ | variable |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, } .= 1 / C;\n\nextentconv @Const { } = 1000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a reaction modified by an extent conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:Submodel\r\ntestTags: Amount, HasOnlySubstanceUnits, comp:ExtentConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection. The species and compartment from the top-level model are replaced by the submodel elements.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 1 parameter (extentconv)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| sub2__sub1__J0: -> s1 | $extentconv * 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $1$ | variable |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, } .= 1 / C;\n\nextentconv @Const { } = 1000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Replacements in external models\r\ncomponentTags: Compartment, Reaction, Species, comp:Deletion, comp:ExternalModelDefinition, comp:ModelDefinition, comp:Port, comp:ReplacedBy, comp:ReplacedElement, comp:Submodel\r\ntestTags: Amount, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n In this modified example from the specification, an external model is referenced by both a ReplacedBy and a ReplacedElement.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 4 species (S, A__E, D, A__ES)\r\n* 1 compartment (comp)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| A__J0: S + A__E -> A__ES | $(S + A__E) / A__ES$ |\r\n| A__J1: A__ES -> A__E + D | $A__ES / (A__E + D)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S | $1$ | variable |\r\n| Initial concentration of species A__E | $1$ | variable |\r\n| Initial concentration of species D | $1$ | variable |\r\n| Initial concentration of species A__ES | $1$ | variable |\r\n| Initial volume of compartment 'comp' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ncomp @Compartment { boundary: true, } .= 1;\n\nS @Species { compartment: comp, } .= 5;\nD @Species { compartment: comp, } .= 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An element in an external model submodel as the target of a replacedBy element.\r\ncomponentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedBy, comp:SBaseRef, comp:Submodel\r\ntestTags: Amount, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n In this model, an element is replaced by an element in a submodel of an external model.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 4 species (S, A__submod1__E, D, A__submod1__ES)\r\n* 1 compartment (comp)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* | *Fast* |\r\n| A__submod1__J0: S + A__submod1__E -> A__submod1__ES | $(S + A__submod1__E) / A__submod1__ES$ | fast |\r\n| A__submod1__J1: A__submod1__ES -> A__submod1__E + D | $A__submod1__ES / (A__submod1__E + D)$ | fast |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S | $10$ | variable |\r\n| Initial concentration of species A__submod1__E | $1$ | variable |\r\n| Initial concentration of species D | $15$ | variable |\r\n| Initial concentration of species A__submod1__ES | $1$ | variable |\r\n| Initial volume of compartment 'comp' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ncomp @Compartment { boundary: true, } .= 1;\n\nS @Species { compartment: comp, } .= 5;\nD @Species { compartment: comp, } .= 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: External models with submodels with replaced elements.\r\ncomponentTags: Compartment, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Amount, comp:SubmodelOutput\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n In this modification of a model from the specification, an external model has submodels referenced by replacedElements.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 4 species (S, D, A__submod1__E, A__submod1__ES)\r\n* 1 compartment (comp)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| A__submod1__J0: S + A__submod1__E -> A__submod1__ES | $(S + A__submod1__E) / A__submod1__ES$ |\r\n| A__submod1__J1: A__submod1__ES -> A__submod1__E + D | $A__submod1__ES / (A__submod1__E + D)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S | $5$ | variable |\r\n| Initial concentration of species D | $10$ | variable |\r\n| Initial concentration of species A__submod1__E | $1$ | variable |\r\n| Initial concentration of species A__submod1__ES | $1$ | variable |\r\n| Initial volume of compartment 'comp' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ncomp @Compartment { boundary: true, } .= 1;\n\nS @Species { compartment: comp, } .= 5;\nD @Species { compartment: comp, } .= 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a reaction modified by a time conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Amount, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The reaction in the submodel must be converted by the time conversion factor, separated by a level of submodel indirection. The species and compartment are replaced in the top-level model.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 1 parameter (timeconv)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| sub2__sub1__J0: -> s1 | $(1 / timeconv) * 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $0$ | variable |\r\n| Initial value of parameter timeconv | $100$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, } .= 0 / C;\n\ntimeconv @Const { } = 100;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a reaction modified by a time conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Amount, comp:TimeConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The reaction in the submodel must be converted by the time conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 1 parameter (timeconv)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| sub2__sub1__J0: -> s1 | $(1 / timeconv) * 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $0$ | variable |\r\n| Initial value of parameter timeconv | $100$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, } .= 0 / C;\n\ntimeconv @Const { } = 100;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a reaction modified by an extent conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Amount, comp:ExtentConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The reaction in the submodel must be converted by the extent conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 1 parameter (extentconv)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| sub2__sub1__J0: -> s1 | $extentconv * 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species s1 | $0$ | variable |\r\n| Initial value of parameter extentconv | $1000$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, } .= 0 / C;\n\nextentconv @Const { } = 1000;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a species modified by a conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Amount, comp:ConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The reaction in the replaced species must be converted by the conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 1 parameter (cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| sub2__sub1__J0: -> s1 | $10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species s1 | $2$ | variable |\r\n| Initial value of parameter cf | $10$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, } .= 2;\n\ncf @Const { } = 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species and a compartment both under control of a rate rule.\r\ncomponentTags: AssignmentRule, Compartment, FunctionDefinition, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. One of the rate rules is a function definition, just to ensure that is considered.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $getPointFour()$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe model contains the following function definition:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | getPointFour | | $0.4$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\n","completion":"\ngetPointFour #defineFunction { arguments: [], math: 0.4, };\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\n\nS1 @Species { compartment: C1, } .= 0;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := getPointFour();\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species and a compartment both under control of a rate rule, then modified by an event.\r\ncomponentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by an event partway through the simulation, affecting things all over again.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time >= 0.45$ | $S1 = 0.2$ |]\r\n\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0.4$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\n\nS1 @Species { compartment: C1, } .= 0;\nS1 [_E0]= 0.2;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0.4;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\n_E0 @DSwitcher { trigger: t >= 0.45, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species and a compartment both under control of a rate rule, and affected by an event.\r\ncomponentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Partway through the simulation, an event changes the level of the compartment, forcing yet another change.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time >= 0.45$ | $C1 = 0.2$ |]\r\n\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0.4$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\nC1 [_E0]= 0.2;\n\nS1 @Species { compartment: C1, } .= 0;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0.4;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\n_E0 @DSwitcher { trigger: t >= 0.45, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species and a compartment both under control of a rate rule, and affected by an event.\r\ncomponentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n NOTE: This test is a more complicated version of test 1779. If this isn't passing, make sure you pass test 1779 first, as it is likely that the issue here is actually reflective of the more fundamental issue tested in that test (i.e. the simultaneous assignment to a species concentration and compartment).\r\n \r\n A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Partway through the simulation, an event changes the level of the species and of the compartment, forcing yet another change.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time >= 0.45$ | $S1 = 0.2$ |\r\n| | | $C1 = 0.2$ |]\r\n\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0.4$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\nC1 [E0]= 0.2;\n\nS1 @Species { compartment: C1, } .= 0;\nS1 [E0]= 0.2;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0.4;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\nE0 @DSwitcher { trigger: t >= 0.45, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species and a compartment both under control of a rate rule, modified by an event at t0.\r\ncomponentTags: AssignmentRule, Compartment, EventNoDelay, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, EventT0Firing, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. The species concentration is changed by an event at t0.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $S1 > -1$ | false | $S1 = 0$ |]\r\n\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0.4$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\n\nS1 @Species { compartment: C1, } .= 1;\nS1 [E0]= 0;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0.4;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\nE0 @DSwitcher { trigger: S1 > (-1), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species and a compartment both under control of a rate rule,that affects an event priority.\r\ncomponentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Two other simultaneous events fire, with the priority of one equal to S1, and the priority of the other equal to a value between the concentration of S1 and the amount of S1, to ensure that the order is correct.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 2 parameters (x, x2)\r\n* 1 compartment (C1)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 0.45$ | $S1$ | $x2 = 3$ |\r\n| E1 | $time > 0.45$ | $0.15$ | $x2 = 5$ |]\r\n\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0.4$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial value of parameter x2 | $0$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\n\nS1 @Species { compartment: C1, } .= 0;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0.4;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\nx2 @Record { } .= 0;\nx2 [E0]= 3;\nx2 [E1]= 5;\n\nE0 @DSwitcher { trigger: t > 0.45, };\nE1 @DSwitcher { trigger: t > 0.45, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species and a compartment both under control of a rate rule,with an initial assignment to the species.\r\ncomponentTags: AssignmentRule, Compartment, InitialAssignment, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Its concentration is set with an initial assignment (not its amount).\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0.4$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3 / 2$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\n\nS1 @Species { compartment: C1, } .= 3 / 2;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0.4;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species and a compartment both under control of a rate rule,with an initial assignment to the species and compartment.\r\ncomponentTags: AssignmentRule, Compartment, InitialAssignment, Parameter, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\n A species in a non-unity compartment under control of a rate rule, and the species is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is affected by the rate of change. That value then gets assigned to the parameter 'x', since we typically only require Species output in amounts. Its concentration is set with an initial assignment (not its amount), and the compartment itself also has an initial assignment.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $0.4$ |\r\n| Rate | C1 | $0.2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $3 / 2$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $1 / 2$ | variable |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 1 / 2;\n\nS1 @Species { compartment: C1, } .= 3 / 2;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := 0.4;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.2;\n\nx @Record { };\nx := S1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two simultaneous events with a priority using a delay.\r\ncomponentTags: CSymbolDelay, EventNoDelay, EventPriority, Parameter, RateRule\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, two events fire simultaneously, with the priority of one being set using the delay function for another parameter, making its priority lower, and therefore firing second.\r\n\r\nThe model contains:\r\n* 2 parameters (P1, P2)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $P1 > 1.5$ | $delay(P1, 1)$ | $P2 = 3$ |\r\n| E1 | $P1 > 1.5$ | $1$ | $P2 = 5$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | P1 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $0$ | variable |\r\n| Initial value of parameter P2 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP1_proc @Process { actors: = P1, };\nP1_proc := 1;\n\nP1 @Record { } .= 0;\nP2 @Record { } .= 0;\nP2 [E0]= 3;\nP2 [E1]= 5;\n\nE0 @DSwitcher { trigger: P1 > 1.5, };\nE1 @DSwitcher { trigger: P1 > 1.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Uncommon MathML used in event priorities.\r\ncomponentTags: CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: NonConstantParameter, UncommonMathML\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n The model tests the various unusual mathematical constructs in event priorities, essentially comparing them to 0.55 to see which is greater.\r\n\r\nThe model contains:\r\n* 53 parameters (P0, P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P20, P21, P22, P23, P24, P25, P26, P27, P28, P29, P30, P31, P32, P33, P34, P35, P36, P37, P38, P39, P40, P41, P42, P43, P44, P45, P46, P47, P48, P49, P50, P51, P52)\r\n\r\nThere are 106 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 1.5$ | $exponentiale$ | $P0 = 2$ |\r\n| E1 | $time > 1.5$ | $exp(exponentiale)$ | $P1 = 2$ |\r\n| E2 | $time > 1.5$ | $abs(-1)$ | $P2 = 2$ |\r\n| E3 | $time > 1.5$ | $abs(1)$ | $P3 = 2$ |\r\n| E4 | $time > 1.5$ | $acos(-1)$ | $P4 = 2$ |\r\n| E5 | $time > 1.5$ | $acos(0.5)$ | $P5 = 2$ |\r\n| E6 | $time > 1.5$ | $asin(1)$ | $P6 = 2$ |\r\n| E7 | $time > 1.5$ | $asin(-0.5)$ | $P7 = 2$ |\r\n| E8 | $time > 1.5$ | $atan(2.8)$ | $P8 = 2$ |\r\n| E9 | $time > 1.5$ | $atan(-7.09)$ | $P9 = 2$ |\r\n| E10 | $time > 1.5$ | $ceil(0.5)$ | $P10 = 2$ |\r\n| E11 | $time > 1.5$ | $ceil(3.55)$ | $P11 = 2$ |\r\n| E12 | $time > 1.5$ | $ceil(-4.6)$ | $P12 = 2$ |\r\n| E13 | $time > 1.5$ | $cos(9.1)$ | $P13 = 2$ |\r\n| E14 | $time > 1.5$ | $cos(-0.22)$ | $P14 = 2$ |\r\n| E15 | $time > 1.5$ | $exp(0)$ | $P15 = 2$ |\r\n| E16 | $time > 1.5$ | $exp(1)$ | $P16 = 2$ |\r\n| E17 | $time > 1.5$ | $exp(0.77)$ | $P17 = 2$ |\r\n| E18 | $time > 1.5$ | $floor(-4.6)$ | $P18 = 2$ |\r\n| E19 | $time > 1.5$ | $floor(9.1)$ | $P19 = 2$ |\r\n| E20 | $time > 1.5$ | $ln(0.2)$ | $P20 = 2$ |\r\n| E21 | $time > 1.5$ | $ln(1)$ | $P21 = 2$ |\r\n| E22 | $time > 1.5$ | $log10(0.2)$ | $P22 = 2$ |\r\n| E23 | $time > 1.5$ | $log10(1)$ | $P23 = 2$ |\r\n| E24 | $time > 1.5$ | $1^2$ | $P24 = 2$ |\r\n| E25 | $time > 1.5$ | $2^2$ | $P25 = 2$ |\r\n| E26 | $time > 1.5$ | $1.4^5.1$ | $P26 = 2$ |\r\n| E27 | $time > 1.5$ | $4^2$ | $P27 = 2$ |\r\n| E28 | $time > 1.5$ | $3.1^2$ | $P28 = 2$ |\r\n| E29 | $time > 1.5$ | $sqrt(4)$ | $P29 = 2$ |\r\n| E30 | $time > 1.5$ | $sqrt(7.4)$ | $P30 = 2$ |\r\n| E31 | $time > 1.5$ | $sin(2.1)$ | $P31 = 2$ |\r\n| E32 | $time > 1.5$ | $sin(0)$ | $P32 = 2$ |\r\n| E33 | $time > 1.5$ | $sin(-5.9)$ | $P33 = 2$ |\r\n| E34 | $time > 1.5$ | $tan(0)$ | $P34 = 2$ |\r\n| E35 | $time > 1.5$ | $tan(1.11)$ | $P35 = 2$ |\r\n| E36 | $time > 1.5$ | $tan(-6)$ | $P36 = 2$ |\r\n| E37 | $time > 1.5$ | $sec(0.5)$ | $P37 = 2$ |\r\n| E38 | $time > 1.5$ | $csc(4.5)$ | $P38 = 2$ |\r\n| E39 | $time > 1.5$ | $cot(0.2)$ | $P39 = 2$ |\r\n| E40 | $time > 1.5$ | $sinh(0.3)$ | $P40 = 2$ |\r\n| E41 | $time > 1.5$ | $cosh(1.7)$ | $P41 = 2$ |\r\n| E42 | $time > 1.5$ | $arcsec(2.3)$ | $P42 = 2$ |\r\n| E43 | $time > 1.5$ | $arccsc(1.1)$ | $P43 = 2$ |\r\n| E44 | $time > 1.5$ | $arccot(-0.1)$ | $P44 = 2$ |\r\n| E45 | $time > 1.5$ | $arcsinh(99)$ | $P45 = 2$ |\r\n| E46 | $time > 1.5$ | $arccosh(1.34)$ | $P46 = 2$ |\r\n| E47 | $time > 1.5$ | $arctanh(-0.7)$ | $P47 = 2$ |\r\n| E48 | $time > 1.5$ | $arcsech(0.42)$ | $P48 = 2$ |\r\n| E49 | $time > 1.5$ | $arccsch(0.01)$ | $P49 = 2$ |\r\n| E50 | $time > 1.5$ | $arccoth(8.2)$ | $P50 = 2$ |\r\n| E51 | $time > 1.5$ | $times()$ | $P51 = 2$ |\r\n| E52 | $time > 1.5$ | $plus()$ | $P52 = 2$ |\r\n| Ep0 | $time > 1.5$ | $0.55$ | $P0 = 3$ |\r\n| Ep1 | $time > 1.5$ | $0.55$ | $P1 = 3$ |\r\n| Ep2 | $time > 1.5$ | $0.55$ | $P2 = 3$ |\r\n| Ep3 | $time > 1.5$ | $0.55$ | $P3 = 3$ |\r\n| Ep4 | $time > 1.5$ | $0.55$ | $P4 = 3$ |\r\n| Ep5 | $time > 1.5$ | $0.55$ | $P5 = 3$ |\r\n| Ep6 | $time > 1.5$ | $0.55$ | $P6 = 3$ |\r\n| Ep7 | $time > 1.5$ | $0.55$ | $P7 = 3$ |\r\n| Ep8 | $time > 1.5$ | $0.55$ | $P8 = 3$ |\r\n| Ep9 | $time > 1.5$ | $0.55$ | $P9 = 3$ |\r\n| Ep10 | $time > 1.5$ | $0.55$ | $P10 = 3$ |\r\n| Ep11 | $time > 1.5$ | $0.55$ | $P11 = 3$ |\r\n| Ep12 | $time > 1.5$ | $0.55$ | $P12 = 3$ |\r\n| Ep13 | $time > 1.5$ | $0.55$ | $P13 = 3$ |\r\n| Ep14 | $time > 1.5$ | $0.55$ | $P14 = 3$ |\r\n| Ep15 | $time > 1.5$ | $0.55$ | $P15 = 3$ |\r\n| Ep16 | $time > 1.5$ | $0.55$ | $P16 = 3$ |\r\n| Ep17 | $time > 1.5$ | $0.55$ | $P17 = 3$ |\r\n| Ep18 | $time > 1.5$ | $0.55$ | $P18 = 3$ |\r\n| Ep19 | $time > 1.5$ | $0.55$ | $P19 = 3$ |\r\n| Ep20 | $time > 1.5$ | $0.55$ | $P20 = 3$ |\r\n| Ep21 | $time > 1.5$ | $0.55$ | $P21 = 3$ |\r\n| Ep22 | $time > 1.5$ | $0.55$ | $P22 = 3$ |\r\n| Ep23 | $time > 1.5$ | $0.55$ | $P23 = 3$ |\r\n| Ep24 | $time > 1.5$ | $0.55$ | $P24 = 3$ |\r\n| Ep25 | $time > 1.5$ | $0.55$ | $P25 = 3$ |\r\n| Ep26 | $time > 1.5$ | $0.55$ | $P26 = 3$ |\r\n| Ep27 | $time > 1.5$ | $0.55$ | $P27 = 3$ |\r\n| Ep28 | $time > 1.5$ | $0.55$ | $P28 = 3$ |\r\n| Ep29 | $time > 1.5$ | $0.55$ | $P29 = 3$ |\r\n| Ep30 | $time > 1.5$ | $0.55$ | $P30 = 3$ |\r\n| Ep31 | $time > 1.5$ | $0.55$ | $P31 = 3$ |\r\n| Ep32 | $time > 1.5$ | $0.55$ | $P32 = 3$ |\r\n| Ep33 | $time > 1.5$ | $0.55$ | $P33 = 3$ |\r\n| Ep34 | $time > 1.5$ | $0.55$ | $P34 = 3$ |\r\n| Ep35 | $time > 1.5$ | $0.55$ | $P35 = 3$ |\r\n| Ep36 | $time > 1.5$ | $0.55$ | $P36 = 3$ |\r\n| Ep37 | $time > 1.5$ | $0.55$ | $P37 = 3$ |\r\n| Ep38 | $time > 1.5$ | $0.55$ | $P38 = 3$ |\r\n| Ep39 | $time > 1.5$ | $0.55$ | $P39 = 3$ |\r\n| Ep40 | $time > 1.5$ | $0.55$ | $P40 = 3$ |\r\n| Ep41 | $time > 1.5$ | $0.55$ | $P41 = 3$ |\r\n| Ep42 | $time > 1.5$ | $0.55$ | $P42 = 3$ |\r\n| Ep43 | $time > 1.5$ | $0.55$ | $P43 = 3$ |\r\n| Ep44 | $time > 1.5$ | $0.55$ | $P44 = 3$ |\r\n| Ep45 | $time > 1.5$ | $0.55$ | $P45 = 3$ |\r\n| Ep46 | $time > 1.5$ | $0.55$ | $P46 = 3$ |\r\n| Ep47 | $time > 1.5$ | $0.55$ | $P47 = 3$ |\r\n| Ep48 | $time > 1.5$ | $0.55$ | $P48 = 3$ |\r\n| Ep49 | $time > 1.5$ | $0.55$ | $P49 = 3$ |\r\n| Ep50 | $time > 1.5$ | $0.55$ | $P50 = 3$ |\r\n| Ep51 | $time > 1.5$ | $0.55$ | $P51 = 3$ |\r\n| Ep52 | $time > 1.5$ | $0.55$ | $P52 = 3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P0 | $0$ | variable |\r\n| Initial value of parameter P1 | $0$ | variable |\r\n| Initial value of parameter P2 | $0$ | variable |\r\n| Initial value of parameter P3 | $0$ | variable |\r\n| Initial value of parameter P4 | $0$ | variable |\r\n| Initial value of parameter P5 | $0$ | variable |\r\n| Initial value of parameter P6 | $0$ | variable |\r\n| Initial value of parameter P7 | $0$ | variable |\r\n| Initial value of parameter P8 | $0$ | variable |\r\n| Initial value of parameter P9 | $0$ | variable |\r\n| Initial value of parameter P10 | $0$ | variable |\r\n| Initial value of parameter P11 | $0$ | variable |\r\n| Initial value of parameter P12 | $0$ | variable |\r\n| Initial value of parameter P13 | $0$ | variable |\r\n| Initial value of parameter P14 | $0$ | variable |\r\n| Initial value of parameter P15 | $0$ | variable |\r\n| Initial value of parameter P16 | $0$ | variable |\r\n| Initial value of parameter P17 | $0$ | variable |\r\n| Initial value of parameter P18 | $0$ | variable |\r\n| Initial value of parameter P19 | $0$ | variable |\r\n| Initial value of parameter P20 | $0$ | variable |\r\n| Initial value of parameter P21 | $0$ | variable |\r\n| Initial value of parameter P22 | $0$ | variable |\r\n| Initial value of parameter P23 | $0$ | variable |\r\n| Initial value of parameter P24 | $0$ | variable |\r\n| Initial value of parameter P25 | $0$ | variable |\r\n| Initial value of parameter P26 | $0$ | variable |\r\n| Initial value of parameter P27 | $0$ | variable |\r\n| Initial value of parameter P28 | $0$ | variable |\r\n| Initial value of parameter P29 | $0$ | variable |\r\n| Initial value of parameter P30 | $0$ | variable |\r\n| Initial value of parameter P31 | $0$ | variable |\r\n| Initial value of parameter P32 | $0$ | variable |\r\n| Initial value of parameter P33 | $0$ | variable |\r\n| Initial value of parameter P34 | $0$ | variable |\r\n| Initial value of parameter P35 | $0$ | variable |\r\n| Initial value of parameter P36 | $0$ | variable |\r\n| Initial value of parameter P37 | $0$ | variable |\r\n| Initial value of parameter P38 | $0$ | variable |\r\n| Initial value of parameter P39 | $0$ | variable |\r\n| Initial value of parameter P40 | $0$ | variable |\r\n| Initial value of parameter P41 | $0$ | variable |\r\n| Initial value of parameter P42 | $0$ | variable |\r\n| Initial value of parameter P43 | $0$ | variable |\r\n| Initial value of parameter P44 | $0$ | variable |\r\n| Initial value of parameter P45 | $0$ | variable |\r\n| Initial value of parameter P46 | $0$ | variable |\r\n| Initial value of parameter P47 | $0$ | variable |\r\n| Initial value of parameter P48 | $0$ | variable |\r\n| Initial value of parameter P49 | $0$ | variable |\r\n| Initial value of parameter P50 | $0$ | variable |\r\n| Initial value of parameter P51 | $0$ | variable |\r\n| Initial value of parameter P52 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP0 @Record { } .= 0;\nP0 [E0]= 2;\nP0 [Ep0]= 3;\nP1 @Record { } .= 0;\nP1 [E1]= 2;\nP1 [Ep1]= 3;\nP2 @Record { } .= 0;\nP2 [E2]= 2;\nP2 [Ep2]= 3;\nP3 @Record { } .= 0;\nP3 [E3]= 2;\nP3 [Ep3]= 3;\nP4 @Record { } .= 0;\nP4 [E4]= 2;\nP4 [Ep4]= 3;\nP5 @Record { } .= 0;\nP5 [E5]= 2;\nP5 [Ep5]= 3;\nP6 @Record { } .= 0;\nP6 [E6]= 2;\nP6 [Ep6]= 3;\nP7 @Record { } .= 0;\nP7 [E7]= 2;\nP7 [Ep7]= 3;\nP8 @Record { } .= 0;\nP8 [E8]= 2;\nP8 [Ep8]= 3;\nP9 @Record { } .= 0;\nP9 [E9]= 2;\nP9 [Ep9]= 3;\nP10 @Record { } .= 0;\nP10 [E10]= 2;\nP10 [Ep10]= 3;\nP11 @Record { } .= 0;\nP11 [E11]= 2;\nP11 [Ep11]= 3;\nP12 @Record { } .= 0;\nP12 [E12]= 2;\nP12 [Ep12]= 3;\nP13 @Record { } .= 0;\nP13 [E13]= 2;\nP13 [Ep13]= 3;\nP14 @Record { } .= 0;\nP14 [E14]= 2;\nP14 [Ep14]= 3;\nP15 @Record { } .= 0;\nP15 [E15]= 2;\nP15 [Ep15]= 3;\nP16 @Record { } .= 0;\nP16 [E16]= 2;\nP16 [Ep16]= 3;\nP17 @Record { } .= 0;\nP17 [E17]= 2;\nP17 [Ep17]= 3;\nP18 @Record { } .= 0;\nP18 [E18]= 2;\nP18 [Ep18]= 3;\nP19 @Record { } .= 0;\nP19 [E19]= 2;\nP19 [Ep19]= 3;\nP20 @Record { } .= 0;\nP20 [E20]= 2;\nP20 [Ep20]= 3;\nP21 @Record { } .= 0;\nP21 [E21]= 2;\nP21 [Ep21]= 3;\nP22 @Record { } .= 0;\nP22 [E22]= 2;\nP22 [Ep22]= 3;\nP23 @Record { } .= 0;\nP23 [E23]= 2;\nP23 [Ep23]= 3;\nP24 @Record { } .= 0;\nP24 [E24]= 2;\nP24 [Ep24]= 3;\nP25 @Record { } .= 0;\nP25 [E25]= 2;\nP25 [Ep25]= 3;\nP26 @Record { } .= 0;\nP26 [E26]= 2;\nP26 [Ep26]= 3;\nP27 @Record { } .= 0;\nP27 [E27]= 2;\nP27 [Ep27]= 3;\nP28 @Record { } .= 0;\nP28 [E28]= 2;\nP28 [Ep28]= 3;\nP29 @Record { } .= 0;\nP29 [E29]= 2;\nP29 [Ep29]= 3;\nP30 @Record { } .= 0;\nP30 [E30]= 2;\nP30 [Ep30]= 3;\nP31 @Record { } .= 0;\nP31 [E31]= 2;\nP31 [Ep31]= 3;\nP32 @Record { } .= 0;\nP32 [E32]= 2;\nP32 [Ep32]= 3;\nP33 @Record { } .= 0;\nP33 [E33]= 2;\nP33 [Ep33]= 3;\nP34 @Record { } .= 0;\nP34 [E34]= 2;\nP34 [Ep34]= 3;\nP35 @Record { } .= 0;\nP35 [E35]= 2;\nP35 [Ep35]= 3;\nP36 @Record { } .= 0;\nP36 [E36]= 2;\nP36 [Ep36]= 3;\nP37 @Record { } .= 0;\nP37 [E37]= 2;\nP37 [Ep37]= 3;\nP38 @Record { } .= 0;\nP38 [E38]= 2;\nP38 [Ep38]= 3;\nP39 @Record { } .= 0;\nP39 [E39]= 2;\nP39 [Ep39]= 3;\nP40 @Record { } .= 0;\nP40 [E40]= 2;\nP40 [Ep40]= 3;\nP41 @Record { } .= 0;\nP41 [E41]= 2;\nP41 [Ep41]= 3;\nP42 @Record { } .= 0;\nP42 [E42]= 2;\nP42 [Ep42]= 3;\nP43 @Record { } .= 0;\nP43 [E43]= 2;\nP43 [Ep43]= 3;\nP44 @Record { } .= 0;\nP44 [E44]= 2;\nP44 [Ep44]= 3;\nP45 @Record { } .= 0;\nP45 [E45]= 2;\nP45 [Ep45]= 3;\nP46 @Record { } .= 0;\nP46 [E46]= 2;\nP46 [Ep46]= 3;\nP47 @Record { } .= 0;\nP47 [E47]= 2;\nP47 [Ep47]= 3;\nP48 @Record { } .= 0;\nP48 [E48]= 2;\nP48 [Ep48]= 3;\nP49 @Record { } .= 0;\nP49 [E49]= 2;\nP49 [Ep49]= 3;\nP50 @Record { } .= 0;\nP50 [E50]= 2;\nP50 [Ep50]= 3;\nP51 @Record { } .= 0;\nP51 [E51]= 2;\nP51 [Ep51]= 3;\nP52 @Record { } .= 0;\nP52 [E52]= 2;\nP52 [Ep52]= 3;\n\nE0 @DSwitcher { trigger: t > 1.5, };\nE1 @DSwitcher { trigger: t > 1.5, };\nE2 @DSwitcher { trigger: t > 1.5, };\nE3 @DSwitcher { trigger: t > 1.5, };\nE4 @DSwitcher { trigger: t > 1.5, };\nE5 @DSwitcher { trigger: t > 1.5, };\nE6 @DSwitcher { trigger: t > 1.5, };\nE7 @DSwitcher { trigger: t > 1.5, };\nE8 @DSwitcher { trigger: t > 1.5, };\nE9 @DSwitcher { trigger: t > 1.5, };\nE10 @DSwitcher { trigger: t > 1.5, };\nE11 @DSwitcher { trigger: t > 1.5, };\nE12 @DSwitcher { trigger: t > 1.5, };\nE13 @DSwitcher { trigger: t > 1.5, };\nE14 @DSwitcher { trigger: t > 1.5, };\nE15 @DSwitcher { trigger: t > 1.5, };\nE16 @DSwitcher { trigger: t > 1.5, };\nE17 @DSwitcher { trigger: t > 1.5, };\nE18 @DSwitcher { trigger: t > 1.5, };\nE19 @DSwitcher { trigger: t > 1.5, };\nE20 @DSwitcher { trigger: t > 1.5, };\nE21 @DSwitcher { trigger: t > 1.5, };\nE22 @DSwitcher { trigger: t > 1.5, };\nE23 @DSwitcher { trigger: t > 1.5, };\nE24 @DSwitcher { trigger: t > 1.5, };\nE25 @DSwitcher { trigger: t > 1.5, };\nE26 @DSwitcher { trigger: t > 1.5, };\nE27 @DSwitcher { trigger: t > 1.5, };\nE28 @DSwitcher { trigger: t > 1.5, };\nE29 @DSwitcher { trigger: t > 1.5, };\nE30 @DSwitcher { trigger: t > 1.5, };\nE31 @DSwitcher { trigger: t > 1.5, };\nE32 @DSwitcher { trigger: t > 1.5, };\nE33 @DSwitcher { trigger: t > 1.5, };\nE34 @DSwitcher { trigger: t > 1.5, };\nE35 @DSwitcher { trigger: t > 1.5, };\nE36 @DSwitcher { trigger: t > 1.5, };\nE37 @DSwitcher { trigger: t > 1.5, };\nE38 @DSwitcher { trigger: t > 1.5, };\nE39 @DSwitcher { trigger: t > 1.5, };\nE40 @DSwitcher { trigger: t > 1.5, };\nE41 @DSwitcher { trigger: t > 1.5, };\nE42 @DSwitcher { trigger: t > 1.5, };\nE43 @DSwitcher { trigger: t > 1.5, };\nE44 @DSwitcher { trigger: t > 1.5, };\nE45 @DSwitcher { trigger: t > 1.5, };\nE46 @DSwitcher { trigger: t > 1.5, };\nE47 @DSwitcher { trigger: t > 1.5, };\nE48 @DSwitcher { trigger: t > 1.5, };\nE49 @DSwitcher { trigger: t > 1.5, };\nE50 @DSwitcher { trigger: t > 1.5, };\nE51 @DSwitcher { trigger: t > 1.5, };\nE52 @DSwitcher { trigger: t > 1.5, };\nEp0 @DSwitcher { trigger: t > 1.5, };\nEp1 @DSwitcher { trigger: t > 1.5, };\nEp2 @DSwitcher { trigger: t > 1.5, };\nEp3 @DSwitcher { trigger: t > 1.5, };\nEp4 @DSwitcher { trigger: t > 1.5, };\nEp5 @DSwitcher { trigger: t > 1.5, };\nEp6 @DSwitcher { trigger: t > 1.5, };\nEp7 @DSwitcher { trigger: t > 1.5, };\nEp8 @DSwitcher { trigger: t > 1.5, };\nEp9 @DSwitcher { trigger: t > 1.5, };\nEp10 @DSwitcher { trigger: t > 1.5, };\nEp11 @DSwitcher { trigger: t > 1.5, };\nEp12 @DSwitcher { trigger: t > 1.5, };\nEp13 @DSwitcher { trigger: t > 1.5, };\nEp14 @DSwitcher { trigger: t > 1.5, };\nEp15 @DSwitcher { trigger: t > 1.5, };\nEp16 @DSwitcher { trigger: t > 1.5, };\nEp17 @DSwitcher { trigger: t > 1.5, };\nEp18 @DSwitcher { trigger: t > 1.5, };\nEp19 @DSwitcher { trigger: t > 1.5, };\nEp20 @DSwitcher { trigger: t > 1.5, };\nEp21 @DSwitcher { trigger: t > 1.5, };\nEp22 @DSwitcher { trigger: t > 1.5, };\nEp23 @DSwitcher { trigger: t > 1.5, };\nEp24 @DSwitcher { trigger: t > 1.5, };\nEp25 @DSwitcher { trigger: t > 1.5, };\nEp26 @DSwitcher { trigger: t > 1.5, };\nEp27 @DSwitcher { trigger: t > 1.5, };\nEp28 @DSwitcher { trigger: t > 1.5, };\nEp29 @DSwitcher { trigger: t > 1.5, };\nEp30 @DSwitcher { trigger: t > 1.5, };\nEp31 @DSwitcher { trigger: t > 1.5, };\nEp32 @DSwitcher { trigger: t > 1.5, };\nEp33 @DSwitcher { trigger: t > 1.5, };\nEp34 @DSwitcher { trigger: t > 1.5, };\nEp35 @DSwitcher { trigger: t > 1.5, };\nEp36 @DSwitcher { trigger: t > 1.5, };\nEp37 @DSwitcher { trigger: t > 1.5, };\nEp38 @DSwitcher { trigger: t > 1.5, };\nEp39 @DSwitcher { trigger: t > 1.5, };\nEp40 @DSwitcher { trigger: t > 1.5, };\nEp41 @DSwitcher { trigger: t > 1.5, };\nEp42 @DSwitcher { trigger: t > 1.5, };\nEp43 @DSwitcher { trigger: t > 1.5, };\nEp44 @DSwitcher { trigger: t > 1.5, };\nEp45 @DSwitcher { trigger: t > 1.5, };\nEp46 @DSwitcher { trigger: t > 1.5, };\nEp47 @DSwitcher { trigger: t > 1.5, };\nEp48 @DSwitcher { trigger: t > 1.5, };\nEp49 @DSwitcher { trigger: t > 1.5, };\nEp50 @DSwitcher { trigger: t > 1.5, };\nEp51 @DSwitcher { trigger: t > 1.5, };\nEp52 @DSwitcher { trigger: t > 1.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A boundary species with an assignment rule with no math.\r\ncomponentTags: AssignmentRule, Compartment, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, NoMathML, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the initial amount of a boundary species is 2, with an assignment rule to change it that doesn't have any mathML, leaving the value at 2.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> 2S2 | $0.1$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S1 | $$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { boundary: true, compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = 2*S2, };\nJ0 := 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A boundary species with an initial assignment with no math.\r\ncomponentTags: Compartment, InitialAssignment, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, NoMathML, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the initial amount of a boundary species is 2, with an initial assignment to change it that doesn't have any mathML, leaving the value at 2.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> 2S2 | $0.1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { boundary: true, compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = 2*S2, };\nJ0 := 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases.\r\ncomponentTags: AssignmentRule, CSymbolTime, EventNoDelay, EventPriority, Parameter, RateRule\r\ntestTags: EventIsNotPersistent, InitialValueReassigned, NonConstantParameter, RandomEventExecution\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the parameters Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A final parameter, 'error' checks to make sure neither Q nor R are chosen more frequently than the other--if the difference gets higher than 0.2, it triggers. Note: The 'errorLow' and 'errorHigh' parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner. This test is a repeat and synthesis of tests 952 and 962, with the additional wrinkle of the triggers being set via a variable under control of a rate rule.\r\n\r\nThe model contains:\r\n* 7 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh)\r\n\r\nThere are 5 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ |\r\n| | | | | $Q = Q + 0.01$ |\r\n| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ |\r\n| | | | | $R = R + 0.01$ |\r\n| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ |\r\n| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ |\r\n| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |]\r\n\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | S | $Q + R$ |\r\n| Rate | reset | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter S | $Q + R$ | variable |\r\n| Initial value of parameter Q | $0$ | variable |\r\n| Initial value of parameter R | $0$ | variable |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter maxdiff | $0$ | variable |\r\n| Initial value of parameter errorLow | $0$ | variable |\r\n| Initial value of parameter errorHigh | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nreset_proc @Process { actors: = reset, };\nreset_proc := 1;\n\nS @Record { };\nS := Q + R;\nQ @Record { } .= 0;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 0;\nR [Rinc]= R + 0.01;\nreset @Record { } .= 0;\nreset [Qinc]= 0;\nreset [Rinc]= 0;\nmaxdiff @Record { } .= 0;\nmaxdiff [maxcheck]= abs(Q - R);\nerrorLow @Record { } .= 0;\nerrorLow [error_check]= 1;\nerrorHigh @Record { } .= 0;\nerrorHigh [error_check2]= 1;\n\nQinc @DSwitcher { trigger: reset >= 0.01, };\nRinc @DSwitcher { trigger: reset >= 0.01, };\nmaxcheck @DSwitcher { trigger: abs(Q - R) > maxdiff, };\nerror_check @DSwitcher { trigger: t >= 99 and maxdiff < 0.2, };\nerror_check2 @DSwitcher { trigger: maxdiff >= 4, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Competing events with the same priority, jointly causing a parameter to monotonically increase, checking to make sure the two events are not exactly evenly distributed. NOTE: STOCHASTIC TEST. Your software may fail periodically; it is only supposed to succeed in the majority of cases.\r\ncomponentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, RateRule, Species\r\ntestTags: EventIsNotPersistent, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, RandomEventExecution, VolumeConcentrationRates\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n This model contains two events with the same trigger, the same effective priority, both set 'persistent=false', and both of which disable the trigger of the other. This means that every .01 seconds, one fires and the other does not, at random, and increases the stoichiometries Q or R, respectively. A third parameter, S, is assigned the value of Q+R, meaning that it doesn't matter which one fires; S will increase monotonically. A species S2 is controlled by a rate rule for its concentration based on Q-R, which should be close to zero for the duration of the simulation. Its compartment is also under control of a rate rule, making the amount of S2 dependent on those two different rate rules. Three other parameters (errorHigh, errorLow, and errorS2), check to make sure neither Q nor R are chosen more or less frequently than the other, and that the species S2 doesn't get too extreme (the reaction in which it appears should be balanced, on average). Note: The error parameters are a stochastic test, and may not always remain at '0' for all runs. If your software fails, try running it again with a new random number seed, and it may succeed. The values were chosen to be reasonable in the vast majority of cases, but still high enough to reveal problems in software that tends to pick both events either evenly or in an unbalanced manner.\r\n\r\nThe model contains:\r\n* 1 species (S2)\r\n* 9 parameters (S, Q, R, reset, maxdiff, errorLow, errorHigh, errorS2, S2_det)\r\n* 1 compartment (C1)\r\n\r\nThere are 6 events:\r\n\r\n[{width:40em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Persistent* | *Event Assignments* |\r\n| Qinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ |\r\n| | | | | $Q = Q + 0.01$ |\r\n| Rinc | $reset >= 0.01$ | $1$ | false | $reset = 0$ |\r\n| | | | | $R = R + 0.01$ |\r\n| maxcheck | $abs(Q - R) > maxdiff$ | (unset) | true | $maxdiff = abs(Q - R)$ |\r\n| error_check | $(time >= 99) && (maxdiff < 0.2)$ | (unset) | true | $errorLow = 1$ |\r\n| error_check2 | $maxdiff >= 4$ | (unset) | true | $errorHigh = 1$ |\r\n| error_check3 | $abs(S2) >= 250$ | (unset) | true | $errorS2 = 1$ |]\r\n\r\n\r\nThere are 4 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S2 | $Q - R$ |\r\n| Rate | C1 | $0.002$ |\r\n| Assignment | S | $Q + R$ |\r\n| Rate | reset | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S2 | $0$ | variable |\r\n| Initial value of parameter S | $Q + R$ | variable |\r\n| Initial value of parameter Q | $1$ | variable |\r\n| Initial value of parameter R | $1$ | variable |\r\n| Initial value of parameter reset | $0$ | variable |\r\n| Initial value of parameter maxdiff | $0$ | variable |\r\n| Initial value of parameter errorLow | $0$ | variable |\r\n| Initial value of parameter errorHigh | $0$ | variable |\r\n| Initial value of parameter errorS2 | $0$ | variable |\r\n| Initial value of parameter S2_det | $0$ | variable |\r\n| Initial volume of compartment 'C1' | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 1;\n\nS2 @Species { compartment: C1, } .= 0;\n\nS2_proc @Process { actors: = S2, };\nS2_proc := Q - R;\nC1_proc @Process { actors: = C1, };\nC1_proc := 0.002;\nreset_proc @Process { actors: = reset, };\nreset_proc := 1;\n\nS @Record { };\nS := Q + R;\nQ @Record { } .= 1;\nQ [Qinc]= Q + 0.01;\nR @Record { } .= 1;\nR [Rinc]= R + 0.01;\nreset @Record { } .= 0;\nreset [Qinc]= 0;\nreset [Rinc]= 0;\nmaxdiff @Record { } .= 0;\nmaxdiff [maxcheck]= abs(Q - R);\nerrorLow @Record { } .= 0;\nerrorLow [error_check]= 1;\nerrorHigh @Record { } .= 0;\nerrorHigh [error_check2]= 1;\nerrorS2 @Record { } .= 0;\nerrorS2 [error_check3]= 1;\nS2_det @Record { } .= 0;\n\nQinc @DSwitcher { trigger: reset >= 0.01, };\nRinc @DSwitcher { trigger: reset >= 0.01, };\nmaxcheck @DSwitcher { trigger: abs(Q - R) > maxdiff, };\nerror_check @DSwitcher { trigger: t >= 99 and maxdiff < 0.2, };\nerror_check2 @DSwitcher { trigger: maxdiff >= 4, };\nerror_check3 @DSwitcher { trigger: abs(S2) >= 250, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species reference for a boundary species that has the same ID as a local parameter.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a local parameter has the same ID as a boundary species (but another species is present in the model as well).\r\n\r\nThe model contains:\r\n* 2 species (k0, S2)\r\n* 1 local parameter (J0.k0)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: k0 -> S2 | $1 / k0$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species k0 | $2$ | variable |\r\n| Initial amount of species S2 | $0$ | variable |\r\n| Initial value of local parameter 'J0.k0' | $3$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nk0 @Species { boundary: true, compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 0 / C;\n\nJ0 @Reaction { actors: k0 = S2, };\nJ0 := 1 / k0__J0_local;\n\nk0__J0_local @Const { } = 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors for substance-only species.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors are set for species set to be substance-only (hasOnlySubstanceUnits=true).\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 2;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\nS2 @Species { compartment: C, isAmount: true, } .= 3;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species conversion factor for substance-only species.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a species conversion factor is set for species set to be substance-only (hasOnlySubstanceUnits=true).\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 2;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\nS2 @Species { compartment: C, isAmount: true, } .= 3;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A model conversion factor for substance-only species.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n This model has a model conversion factor for species set to be substance-only (hasOnlySubstanceUnits=true).\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (m_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial volume of compartment 'C' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 2;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\nS2 @Species { compartment: C, isAmount: true, } .= 3;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors whose IDs are duplicated by local parameters.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors IDs are duplicated by local parameters.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 2 local parameters (J0.m_cf, J0.s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $m_cf + s1_cf$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial value of local parameter 'J0.m_cf' | $0.003$ | constant |\r\n| Initial value of local parameter 'J0.s1_cf' | $0.007$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := m_cf__J0_local + s1_cf__J0_local;\n\nm_cf__J0_local @Const { } = 0.003;\ns1_cf__J0_local @Const { } = 0.007;\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species conversion factor whose ID is duplicated by local parameters.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a species conversion factors ID is duplicated by a local parameter.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (s1_cf)\r\n* 2 local parameters (J0.m_cf, J0.s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $m_cf + s1_cf$ |]\r\n\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial value of local parameter 'J0.m_cf' | $0.003$ | constant |\r\n| Initial value of local parameter 'J0.s1_cf' | $0.007$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := m_cf__J0_local + s1_cf__J0_local;\n\nm_cf__J0_local @Const { } = 0.003;\ns1_cf__J0_local @Const { } = 0.007;\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A model conversion factor whose ID is duplicated by a local parameter.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a model conversion factor ID is duplicated by a local parameter.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (m_cf)\r\n* 2 local parameters (J0.m_cf, J0.s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $m_cf + s1_cf$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of local parameter 'J0.m_cf' | $0.003$ | constant |\r\n| Initial value of local parameter 'J0.s1_cf' | $0.007$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := m_cf__J0_local + s1_cf__J0_local;\n\nm_cf__J0_local @Const { } = 0.003;\ns1_cf__J0_local @Const { } = 0.007;\nm_cf @Const { } = 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An event with avogadro in the trigger.\r\ncomponentTags: CSymbolAvogadro, CSymbolTime, EventNoDelay, Parameter\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the avogadro csymbol is used in an event trigger.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| _E0 | $time > (avogadro / 6.022e23)$ | $p1 = 3$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1 @Record { } .= 1;\np1 [_E0]= 3;\n\n_E0 @DSwitcher { trigger: t > 6.02214076e+23 / (6.022e+23), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An event with avogadro in the priority.\r\ncomponentTags: CSymbolAvogadro, CSymbolTime, EventNoDelay, EventPriority, Parameter\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the avogadro csymbol is used in an event priority, determining which of two simultaneous events fires first.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time >= 2.5$ | $1$ | $p1 = 3$ |\r\n| E1 | $time >= 2.5$ | $avogadro / 6.022e23$ | $p1 = 5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1 @Record { } .= 1;\np1 [E0]= 3;\np1 [E1]= 5;\n\nE0 @DSwitcher { trigger: t >= 2.5, };\nE1 @DSwitcher { trigger: t >= 2.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An event with avogadro in the trigger.\r\ncomponentTags: CSymbolAvogadro, EventNoDelay, Parameter\r\ntestTags: EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the avogadro csymbol is used in an event trigger, which evaluates to 'true' at t0, and firing only because it's set initialValue=false.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $avogadro > 6.022e23$ | false | $p1 = 5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1 @Record { } .= 1;\np1 [E0]= 5;\n\nE0 @DSwitcher { trigger: 6.02214076e+23 > (6.022e+23), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An event with avogadro in an event assignment.\r\ncomponentTags: CSymbolAvogadro, CSymbolTime, EventNoDelay, Parameter\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the avogadro csymbol is used as the assignment value in an event.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time > 1.5$ | $p1 = avogadro$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1 @Record { } .= 1;\np1 [E0]= 6.02214076e+23;\n\nE0 @DSwitcher { trigger: t > 1.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A rate rule that uses avogadro.\r\ncomponentTags: CSymbolAvogadro, Parameter, RateRule\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nIn this model, the avogadro csymbol is used in a rate rule.\r\n\r\nThe model contains:\r\n* 1 parameter (p1)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | p1 | $avogadro / 1e23$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter p1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\np1_proc @Process { actors: = p1, };\np1_proc := 6.02214076e+23 / (1e+23);\n\np1 @Record { } .= 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors for species only affected by rate rules.\r\ncomponentTags: Compartment, Parameter, RateRule, Species\r\ntestTags: Amount, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors are set for species, but those species only change due to rate rules, which means the conversion factors are not used (as they only affect reactions).\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 1 compartment (C)\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $-0.01$ |\r\n| Rate | S2 | $0.01$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := (-0.01);\nS2_proc @Process { actors: = S2, };\nS2_proc := 0.01;\n\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species conversion factor for species only affected by rate rules.\r\ncomponentTags: Compartment, Parameter, RateRule, Species\r\ntestTags: Amount, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a species conversion factor is set for species, but those species only change due to rate rules, which means the conversion factor is not used (as they only affect reactions).\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (s1_cf)\r\n* 1 compartment (C)\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $-0.01$ |\r\n| Rate | S2 | $0.01$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := (-0.01);\nS2_proc @Process { actors: = S2, };\nS2_proc := 0.01;\n\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model conversion factor for species only affected by rate rules.\r\ncomponentTags: Compartment, Parameter, RateRule, Species\r\ntestTags: Amount, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a model conversion factor is set for species, but those species only change due to rate rules, which means the conversion factor is not used (as they only affect reactions).\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 1 compartment (C)\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere are 2 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $-0.01$ |\r\n| Rate | S2 | $0.01$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := (-0.01);\nS2_proc @Process { actors: = S2, };\nS2_proc := 0.01;\n\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors for event-modified species.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors are set for species reset partway through the simulation by an event.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time >= 4.5$ | $S2 = 3$ |\r\n| | | $S1 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS1 [E0]= 2;\nS2 @Species { compartment: C, } .= 3 / C;\nS2 [E0]= 3;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\nE0 @DSwitcher { trigger: t >= 4.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Species conversion factor for event-modified species.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, species conversion factor set for species reset partway through the simulation by an event.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time >= 4.5$ | $S2 = 3$ |\r\n| | | $S1 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS1 [E0]= 2;\nS2 @Species { compartment: C, } .= 3 / C;\nS2 [E0]= 3;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\ns1_cf @Const { } = 5;\n\nE0 @DSwitcher { trigger: t >= 4.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model conversion factors for event-modified species.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model conversion factor set for species reset partway through the simulation by an event.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (m_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time >= 4.5$ | $S2 = 3$ |\r\n| | | $S1 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS1 [E0]= 2;\nS2 @Species { compartment: C, } .= 3 / C;\nS2 [E0]= 3;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\n\nE0 @DSwitcher { trigger: t >= 4.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors for simultaneous events.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors are set for species reset partway through the simulation by two simultaneous events, whose priorities involve the species.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 3.5$ | $S1$ | $S2 = 3$ |\r\n| | | | $S1 = 1$ |\r\n| E1 | $time > 3.5$ | $1.82$ | $S2 = 4$ |\r\n| | | | $S1 = 4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS1 [E0]= 1;\nS1 [E1]= 4;\nS2 @Species { compartment: C, } .= 3 / C;\nS2 [E0]= 3;\nS2 [E1]= 4;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\nE0 @DSwitcher { trigger: t > 3.5, };\nE1 @DSwitcher { trigger: t > 3.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species conversion factor for simultaneous events.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a species conversion factor is set for species reset partway through the simulation by two simultaneous events, whose priorities involve the species.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 3.5$ | $S1$ | $S2 = 3$ |\r\n| | | | $S1 = 1$ |\r\n| E1 | $time > 3.5$ | $1.82$ | $S2 = 4$ |\r\n| | | | $S1 = 4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS1 [E0]= 1;\nS1 [E1]= 4;\nS2 @Species { compartment: C, } .= 3 / C;\nS2 [E0]= 3;\nS2 [E1]= 4;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\ns1_cf @Const { } = 5;\n\nE0 @DSwitcher { trigger: t > 3.5, };\nE1 @DSwitcher { trigger: t > 3.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors for simultaneous events.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors are set for species reset partway through the simulation by two simultaneous events, whose priorities involve the species.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 3.5$ | $S2$ | $S2 = 3$ |\r\n| | | | $S1 = 1$ |\r\n| E1 | $time > 3.5$ | $3.013$ | $S2 = 4$ |\r\n| | | | $S1 = 4$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS1 [E0]= 1;\nS1 [E1]= 4;\nS2 @Species { compartment: C, } .= 3 / C;\nS2 [E0]= 3;\nS2 [E1]= 4;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\nE0 @DSwitcher { trigger: t > 3.5, };\nE1 @DSwitcher { trigger: t > 3.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors for events that fire at t0.\r\ncomponentTags: Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, EventT0Firing\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors are set for species reset at t0 by an event.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $S1 > 0.9$ | false | $S2 = 3$ |\r\n| | | | $S1 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $0$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1 / C;\nS1 [E0]= 2;\nS2 @Species { compartment: C, } .= 0 / C;\nS2 [E0]= 3;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\nE0 @DSwitcher { trigger: S1 > 0.9, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species conversion factor for events that fire at t0.\r\ncomponentTags: Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, EventT0Firing\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a species conversion factor is set for species reset at t0 by an event.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $S1 > 0.9$ | false | $S2 = 3$ |\r\n| | | | $S1 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $0$ | variable |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1 / C;\nS1 [E0]= 2;\nS2 @Species { compartment: C, } .= 0 / C;\nS2 [E0]= 3;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\ns1_cf @Const { } = 5;\n\nE0 @DSwitcher { trigger: S1 > 0.9, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model conversion factor for events that fire at t0.\r\ncomponentTags: Compartment, EventNoDelay, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, EventT0Firing\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a model conversion factor is set for species reset at t0 by an event.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (m_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\n\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $S1 > 0.9$ | false | $S2 = 3$ |\r\n| | | | $S1 = 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $1$ | variable |\r\n| Initial amount of species S2 | $0$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1 / C;\nS1 [E0]= 2;\nS2 @Species { compartment: C, } .= 0 / C;\nS2 [E0]= 3;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\n\nE0 @DSwitcher { trigger: S1 > 0.9, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A function definition in an event that fires at t0.\r\ncomponentTags: EventNoDelay, FunctionDefinition, Parameter\r\ntestTags: EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the event assignment of an event that fires at t0 uses a function defintion.\r\n\r\nThe model contains:\r\n* 1 parameter (P1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $P1 > 0.9$ | false | $P1 = getThree()$ |]\r\n\r\nThe model contains the following function definition:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | getThree | | $3$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\ngetThree #defineFunction { arguments: [], math: 3, };\n\nt @TimeScale { };\n\nP1 @Record { } .= 1;\nP1 [E0]= getThree();\n\nE0 @DSwitcher { trigger: P1 > 0.9, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A function definition in an event that fires at t0.\r\ncomponentTags: EventNoDelay, FunctionDefinition, Parameter\r\ntestTags: EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the trigger of an event that fires at t0 uses a function defintion.\r\n\r\nThe model contains:\r\n* 1 parameter (P1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $P1 > getPointNine()$ | false | $P1 = 3$ |]\r\n\r\nThe model contains the following function definition:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | getPointNine | | $0.9$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\ngetPointNine #defineFunction { arguments: [], math: 0.9, };\n\nt @TimeScale { };\n\nP1 @Record { } .= 1;\nP1 [E0]= 3;\n\nE0 @DSwitcher { trigger: P1 > getPointNine(), };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A function definition in an event that fires at t0.\r\ncomponentTags: EventNoDelay, FunctionDefinition, Parameter\r\ntestTags: EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the assignment of an event that fires at t0 uses a function defintion.\r\n\r\nThe model contains:\r\n* 1 parameter (P1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $P1 > 0.9$ | false | $P1 = addTo(P1, 2)$ |]\r\n\r\nThe model contains the following function definition:\r\n\r\n[{width:30em,margin: 1em auto}| *Id* | *Arguments* | *Formula* |\r\n | addTo | x, y | $x + y$ |\r\n]\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\naddTo #defineFunction { arguments: [x, y], math: x + y, };\n\nt @TimeScale { };\n\nP1 @Record { } .= 1;\nP1 [E0]= addTo(P1, 2);\n\nE0 @DSwitcher { trigger: P1 > 0.9, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An event that fires at t0 that uses a parameter in its own assignment.\r\ncomponentTags: EventNoDelay, Parameter\r\ntestTags: EventT0Firing, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, an event that fires at t0 uses a parameter in its own assignment.\r\n\r\nThe model contains:\r\n* 1 parameter (P1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $1$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP1 @Record { } .= 1;\nP1 [E0]= P1 + 2;\n\nE0 @DSwitcher { trigger: P1 > 0.9, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An event that fires at t0 that uses a parameter in its own assignment.\r\ncomponentTags: EventNoDelay, InitialAssignment, Parameter\r\ntestTags: EventT0Firing, InitialValueReassigned, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, an event that fires at t0 uses a parameter in its own assignment. Also, its 'value' attribute would not trigger the event, but its initial assignment will.\r\n\r\nThe model contains:\r\n* 1 parameter (P1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $2$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP1 @Record { } .= 2;\nP1 [E0]= P1 + 2;\n\nE0 @DSwitcher { trigger: P1 > 0.9, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An event that fires at t0 that uses a parameter in its own assignment.\r\ncomponentTags: EventNoDelay, InitialAssignment, Parameter\r\ntestTags: EventT0Firing, InitialValueReassigned, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, an event that fires at t0 uses a parameter in its own assignment. Also, its 'value' attribute and its initial assignment will trigger the event, but both are different values.\r\n\r\nThe model contains:\r\n* 1 parameter (P1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $2$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP1 @Record { } .= 2;\nP1 [E0]= P1 + 2;\n\nE0 @DSwitcher { trigger: P1 > 0.9, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An event that fires at t0 that uses a parameter in its own assignment.\r\ncomponentTags: EventNoDelay, InitialAssignment, Parameter\r\ntestTags: EventT0Firing, InitialValueReassigned, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, an event that would fire at t0, and use a parameter in its own assignment. However, though its 'value' attribute would trigger the event, its initial assignment will not, meaning the event should not be triggered.\r\n\r\nThe model contains:\r\n* 1 parameter (P1)\r\n\r\nThere is one event:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *initialValue* | *Event Assignments* |\r\n| E0 | $P1 > 0.9$ | false | $P1 = P1 + 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter P1 | $0$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nP1 @Record { } .= 0;\nP1 [E0]= P1 + 2;\n\nE0 @DSwitcher { trigger: P1 > 0.9, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two simultaneous events whose priorities involve a substance-only species.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, RateRule, Species\r\ntestTags: Amount, BoundaryCondition, HasOnlySubstanceUnits, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, two simultaneous events have similar priorities, with one being greater than the other because of the actual value of the substance-only speces. If misinterpreted, the two events will fire in the wrong order..\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time >= 2.5$ | $S1$ | $S1 = 5$ |\r\n| E1 | $time >= 2.5$ | $7.4$ | $S1 = 10$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | S1 | $-1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $10$ | variable |\r\n| Initial volume of compartment 'C' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 2;\n\nS1 @Species { compartment: C, isAmount: true, } .= 10;\nS1 [E0]= 5;\nS1 [E1]= 10;\n\nS1_proc @Process { actors: = S1, };\nS1_proc := (-1);\n\nE0 @DSwitcher { trigger: t >= 2.5, };\nE1 @DSwitcher { trigger: t >= 2.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Two simultaneous events with a priority with the same ID as a local parameter.\r\ncomponentTags: CSymbolTime, Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species\r\ntestTags: Amount, LocalParameters, NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, the two simultaneous events fire in one order because of the priorities, but would fire in the wrong order if a local parameter was confused for the global parameter.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (k1)\r\n* 1 local parameter (J0.k1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $k1$ |]\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $time > 2.5$ | $k1$ | $k1 = 5$ |\r\n| E1 | $time > 2.5$ | $2.5$ | $k1 = 10$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial value of parameter k1 | $2$ | variable |\r\n| Initial value of local parameter 'J0.k1' | $3$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 0;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := k1__J0_local;\n\nk1 @Record { } .= 2;\nk1 [E0]= 5;\nk1 [E1]= 10;\n\nk1__J0_local @Const { } = 3;\n\nE0 @DSwitcher { trigger: t > 2.5, };\nE1 @DSwitcher { trigger: t > 2.5, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors affecting a reaction with boundary conditions.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors affect a reaction with boundary species.\r\n\r\nThe model contains:\r\n* 4 species (S1, S2, S3, S4)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S3 + S1 -> S2 + S4 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\nThe conversion factor for the species 'S3' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial amount of species S3 | $2$ | variable |\r\n| Initial amount of species S4 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\nS3 @Species { boundary: true, compartment: C, } .= 2 / C;\nS4 @Species { boundary: true, compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S3 + S1 = S2 + S4, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species conversion factor affecting a reaction with boundary conditions.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a species conversion factor affects a reaction with boundary species.\r\n\r\nThe model contains:\r\n* 4 species (S1, S2, S3, S4)\r\n* 1 parameter (s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S3 + S1 -> S2 + S4 | $0.01$ |]\r\n\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\nThe conversion factor for the species 'S3' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial amount of species S3 | $2$ | variable |\r\n| Initial amount of species S4 | $3$ | variable |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\nS3 @Species { boundary: true, compartment: C, } .= 2 / C;\nS4 @Species { boundary: true, compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S3 + S1 = S2 + S4, };\nJ0 := 0.01;\n\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model conversion factor affecting a reaction with boundary conditions.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, ConversionFactors\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a model conversion factor affects a reaction with boundary species.\r\n\r\nThe model contains:\r\n* 4 species (S1, S2, S3, S4)\r\n* 1 parameter (m_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S3 + S1 -> S2 + S4 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial amount of species S3 | $2$ | variable |\r\n| Initial amount of species S4 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\nS3 @Species { boundary: true, compartment: C, } .= 2 / C;\nS4 @Species { boundary: true, compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S3 + S1 = S2 + S4, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors affecting a reaction with local parameters.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors affect a reaction with local parameters that shadow the conversion factor IDs.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 2 local parameters (J0.m_cf, J0.s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $m_cf * s1_cf * 0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial value of local parameter 'J0.m_cf' | $1$ | constant |\r\n| Initial value of local parameter 'J0.s1_cf' | $1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := m_cf__J0_local * s1_cf__J0_local * 0.01;\n\nm_cf__J0_local @Const { } = 1;\ns1_cf__J0_local @Const { } = 1;\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species conversion factor affecting a reaction with local parameters.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a species conversion factor affects a reaction with local parameters that shadow the conversion factor ID.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (s1_cf)\r\n* 2 local parameters (J0.m_cf, J0.s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $m_cf * s1_cf * 0.01$ |]\r\n\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter s1_cf | $5$ | constant |\r\n| Initial value of local parameter 'J0.m_cf' | $1$ | constant |\r\n| Initial value of local parameter 'J0.s1_cf' | $1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := m_cf__J0_local * s1_cf__J0_local * 0.01;\n\nm_cf__J0_local @Const { } = 1;\ns1_cf__J0_local @Const { } = 1;\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model conversion factor affecting a reaction with local parameters.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a model conversion factor affects a reaction with local parameters that shadow the conversion factor ID.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (m_cf)\r\n* 2 local parameters (J0.m_cf, J0.s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $m_cf * s1_cf * 0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $3$ | constant |\r\n| Initial value of local parameter 'J0.m_cf' | $1$ | constant |\r\n| Initial value of local parameter 'J0.s1_cf' | $1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := m_cf__J0_local * s1_cf__J0_local * 0.01;\n\nm_cf__J0_local @Const { } = 1;\ns1_cf__J0_local @Const { } = 1;\nm_cf @Const { } = 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A local parameter that shadows a boundary species.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a local parameter shadows a boundary species in that reaction.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 local parameter (J0.S1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of local parameter 'J0.S1' | $0.1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { boundary: true, compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := S1__J0_local;\n\nS1__J0_local @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A reaction with a local parameter named 'avogadro'.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a local parameter is given the id 'avogadro', which the kinetic law references.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 local parameter (J0.avogadro)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $avogadro$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | variable |\r\n| Initial value of local parameter 'J0.avogadro' | $0.1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := avogadro__J0_local;\n\navogadro__J0_local @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A parameter with the id 'avogadro'\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a parameter named 'avogadro' is used in a kinetic law.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (avogadro)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $avogadro$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | variable |\r\n| Initial value of parameter avogadro | $0.1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := avogadro;\n\navogadro @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A reaction with a local parameter named 'avogadro'.\r\ncomponentTags: CSymbolAvogadro, Compartment, Reaction, Species\r\ntestTags: Amount, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a local parameter is given the id 'avogadro', and the kinetic law references both it and the avogadro csymbol.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 local parameter (J0.avogadro)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $avogadro / avogadro$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | variable |\r\n| Initial value of local parameter 'J0.avogadro' | $1e+24$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := 6.02214076e+23 / avogadro__J0_local;\n\navogadro__J0_local @Const { } = 1e+24;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A parameter named 'avogadro' as well as the csymbol avogadro.\r\ncomponentTags: CSymbolAvogadro, Compartment, Parameter, Reaction, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a parameter is given the id 'avogadro', and the kinetic law references both it and the avogadro csymbol.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (avogadro)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $avogadro / avogadro$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | variable |\r\n| Initial value of parameter avogadro | $1e+24$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := 6.02214076e+23 / avogadro;\n\navogadro @Const { } = 1e+24;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A local parameter shadowing a species reference in an event priority.\r\ncomponentTags: Compartment, EventNoDelay, EventPriority, Parameter, Reaction, Species\r\ntestTags: Amount, HasOnlySubstanceUnits, LocalParameters, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a local parameter shadows a species reference. That ID is used in an event priority, and refers to the species reference.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (k0)\r\n* 1 local parameter (J1.S1_stoich)\r\n* 1 compartment (C)\r\n* 1 species reference (S1_stoich)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: 2S1 -> | $0.01$ |\r\n| J1: -> S2 | $S1_stoich$ |]\r\n\r\n\r\nThere are 2 events:\r\n\r\n[{width:35em,margin: 1em auto}| *Event* | *Trigger* | *Priority* | *Event Assignments* |\r\n| E0 | $S1 < 1.885$ | $1$ | $k0 = 4$ |\r\n| E1 | $S1 < 1.885$ | $S1_stoich$ | $k0 = 6$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter k0 | $0$ | variable |\r\n| Initial value of local parameter 'J1.S1_stoich' | $0.01$ | constant |\r\n| Initial volume of compartment 'C' | $2$ | constant |\r\n| Initial value of species reference 'S1_stoich' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 2;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\nS2 @Species { compartment: C, isAmount: true, } .= 3;\n\nJ0 @Reaction { actors: 2*S1 = , };\nJ0 := 0.01;\nJ1 @Reaction { actors: = S2, };\nJ1 := S1_stoich__J1_local;\n\nk0 @Record { } .= 0;\nk0 [E0]= 4;\nk0 [E1]= 6;\n\nS1_stoich__J1_local @Const { } = 0.01;\n\nE0 @DSwitcher { trigger: S1 < 1.885, };\nE1 @DSwitcher { trigger: S1 < 1.885, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model and species conversion factors set with avogadro.\r\ncomponentTags: CSymbolAvogadro, Compartment, InitialAssignment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, model and species conversion factors are set via an initial assignment with the avogadro csymbol.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 parameters (m_cf, s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $avogadro / 1e24$ | constant |\r\n| Initial value of parameter s1_cf | $avogadro / 1.5e24$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Species conversion factor set with avogadro.\r\ncomponentTags: CSymbolAvogadro, Compartment, InitialAssignment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nREVOLUTION!!!!\r\n \r\nIn this model, a species conversion factor is set via an initial assignment with the avogadro csymbol.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (s1_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the species 'S1' is 's1_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter s1_cf | $avogadro / 1.5e24$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\ns1_cf @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Model conversion factor set with avogadro.\r\ncomponentTags: CSymbolAvogadro, Compartment, InitialAssignment, Parameter, Reaction, Species\r\ntestTags: Amount, ConversionFactors, InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a model conversion factor is set via an initial assignment with the avogadro csymbol.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 1 parameter (m_cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: S1 -> S2 | $0.01$ |]\r\n\r\nThe conversion factor for the model is 'm_cf'\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of parameter m_cf | $avogadro / 1e24$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nThe species' initial quantities are given in terms of substance units to\r\nmake it easier to use the model in a discrete stochastic simulator, but\r\ntheir symbols represent their values in concentration units where they\r\nappear in expressions.\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 3 / C;\n\nJ0 @Reaction { actors: S1 = S2, };\nJ0 := 0.01;\n\nm_cf @Const { } = 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A hierarchical model with a species modified by a conversion factor.\r\ncomponentTags: Compartment, Parameter, Reaction, Species, comp:ExternalModelDefinition, comp:ReplacedElement, comp:SBaseRef, comp:Submodel\r\ntestTags: Amount, comp:ConversionFactor\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Numeric\r\npackagesPresent: comp\r\n\r\n The species in the replaced submodel must be converted by the conversion factor, separated by a level of submodel indirection, and in an external model. The species and compartment are replaced in the top-level model. An extension of test 1477, which doesn't have the conversion factor for the species.\r\n\r\nThe 'flattened' version of this hierarchical model contains:\r\n* 1 species (s1)\r\n* 1 parameter (cf)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| sub2__sub1__J0: -> s1 | $10 / (s1 / cf)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species s1 | $2$ | variable |\r\n| Initial value of parameter cf | $10$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\ns1 @Species { compartment: C, } .= 2;\n\ncf @Const { } = 10;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species concentration and its compartment assigned to by the same event.\r\ncomponentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A species in a non-unity compartment is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is used in all situations, including the event assignment. However, another event assignment in the same event is to the volume of that species' compartment. Both assignments are made based on the current state of the model, and *not* of of the state of the model after any one of the assignments. As a result, the assignment to S1 should set the amount of S1 to 0.1. The simultaneous assignment of 0.2 to the compartment means that the concentration of S1 ends up being 0.5 (0.1/0.2). This is counter-intuitive, since the concentration of S1 was just assigned to be 0.2! But it is a consequence of S1's concentration being derived instead of atomic.\r\n\r\nThis test is a simpler variant of 01506, when it was realized some of the subtleties of that test were complicated by the rate rules.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time >= 0.45$ | $S1 = 0.2$ |\r\n| | | $C1 = 0.2$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $2$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\nC1 [E0]= 0.2;\n\nS1 @Species { boundary: true, compartment: C1, } .= 2;\nS1 [E0]= 0.2;\n\nx @Record { };\nx := S1;\n\nE0 @DSwitcher { trigger: t >= 0.45, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A species concentration and its compartment assigned to by the same event.\r\ncomponentTags: AssignmentRule, CSymbolTime, Compartment, EventNoDelay, Parameter, Species\r\ntestTags: Amount, BoundaryCondition, InitialValueReassigned, NonConstantCompartment, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n This model is a duplicate of 01779, with the event assignments reversed. This should make no difference in the results.\r\n\r\n To recap model 1779: a species in a non-unity compartment is set 'hasOnlySubstanceUnits=false', meaning that the species concentration is used in all situations, including the event assignment. However, another event assignment in the same event is to the volume of that species' compartment. Both assignments are made based on the current state of the model, and *not* of of the state of the model after any one of the assignments. As a result, the assignment to S1 should set the amount of S1 to 0.1. The simultaneous assignment of 0.2 to the compartment means that the concentration of S1 ends up being 0.5 (0.1/0.2). This is counter-intuitive, since the concentration of S1 was just assigned to be 0.2! But it is a consequence of S1's concentration being derived instead of atomic.\r\n\r\n This test is a simpler variant of 01506, when it was realized some of the subtleties of that test were complicated by the rate rules.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 parameter (x)\r\n* 1 compartment (C1)\r\n\r\nThere is one event:\r\n\r\n[{width:30em,margin: 1em auto}| *Event* | *Trigger* | *Event Assignments* |\r\n| E0 | $time >= 0.45$ | $C1 = 0.2$ |\r\n| | | $S1 = 0.2$ |]\r\n\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $2$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial volume of compartment 'C1' | $0.5$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC1 @Compartment { } .= 0.5;\nC1 [E0]= 0.2;\n\nS1 @Species { boundary: true, compartment: C1, } .= 2;\nS1 [E0]= 0.2;\n\nx @Record { };\nx := S1;\n\nE0 @DSwitcher { trigger: t >= 0.45, };\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An initial assignment with an nary relational element.\r\ncomponentTags: InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In MathML, it is legal to have 3+ arguments to relational elements such as less than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. This test is based on test 01209, except that it will fail if the interpreter mistakenly checks only the first and last arguments of the 'lt' function.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $piecewise(1, 1 < 3 < 2, 3)$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nx @Record { } .= ((1 < 3) ? 1 : 3);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: An assignment rule with an nary relational element.\r\ncomponentTags: AssignmentRule, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the result of the 'piecewise' test. This test is based on test 01210, with the difference that it will fail if the interpreter mistakenly checks only the first and last arguments of the 'gt' function.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | x | $piecewise(1, 2 > 0 > 1, 3)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $piecewise(1, 2 > 0 > 1, 3)$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx @Record { };\nx := ((2 > 0) ? 1 : 3);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A rate rule with an nary relational element.\r\ncomponentTags: Parameter, RateRule\r\ntestTags: NonConstantParameter\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In MathML, it is legal to have 3+ arguments to relational elements such as greater than. This model checks to make sure interpreters notice the third argument, which changes the rate rule from 1 to 0. This test is based on test 01215, with the difference that it will fail if the interpreter mistakenly checks only the first and last arguments of the 'gt' function.\r\n\r\nThe model contains:\r\n* 1 parameter (x)\r\n\r\nThere is one rule:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Rate | x | $piecewise(1, 2 > 0 > 1, 0)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter x | $3$ | variable |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nx_proc @Process { actors: = x, };\nx_proc := ((2 > 0) ? 1 : 0);\n\nx @Record { } .= 3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Test that L1 and L2 reactions default to fast=false.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, DefaultValue\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5\r\ngeneratedBy: Numeric\r\npackagesPresent: \r\n\r\nIn this very simple model, a reaction is present that, if it was set 'fast=true', would immediately go to 1.0, but goes there asymptotically instead. This tests to ensure that in L2 and L1 model reactions with no explicit 'fast' flag, the default value of 'false' is used.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $1 * (1 - S1)$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $0$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 0;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := 1 * (1 - S1);\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Default values for species boundaryCondition\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, BoundaryCondition, DefaultValue\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In SBML L1 and L2, the value for a species 'boundaryCondition' attribute defaults to 'false'. This model tests that this value is correctly assumed, in a model where S1 has no 'boundaryCondition' attribute, S2 has it set to 'true', and S3 has it set to 'false'. S1 should follow S3, and not S2.\r\n \r\nThe model contains:\r\n* 3 species (S1, S2, S3)\r\n* 1 compartment (C)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $1$ |\r\n| J1: -> S2 | $1$ |\r\n| J2: -> S3 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $2$ | variable |\r\n| Initial concentration of species S2 | $2$ | variable |\r\n| Initial concentration of species S3 | $2$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 2;\nS2 @Species { boundary: true, compartment: C, } .= 2;\nS3 @Species { compartment: C, } .= 2;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := 1;\nJ1 @Reaction { actors: = S2, };\nJ1 := 1;\nJ2 @Reaction { actors: = S3, };\nJ2 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Default values for species boundaryCondition\r\ncomponentTags: AssignmentRule, Compartment, Parameter, Species\r\ntestTags: Amount, DefaultValue, HasOnlySubstanceUnits, InitialValueReassigned, NonConstantParameter, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In SBML L1 and L2, the value for a species 'hasOnlySubstanceUnits' attribute defaults to 'false'. This model tests that this value is correctly assumed, in a model where S1 has no 'hasOnlySubstanceUnits' attribute, S2 has it set to 'false', and S3 has it set to 'true'. S1 should follow S2, and not S3.\r\n\r\nThe model contains:\r\n* 3 species (S1, S2, S3)\r\n* 3 parameters (x, y, z)\r\n* 1 compartment (C)\r\n\r\nThere are 3 rules:\r\n\r\n[{width:30em,margin: 1em auto}| *Type* | *Variable* | *Formula* |\r\n| Assignment | z | $S3$ |\r\n| Assignment | y | $S2$ |\r\n| Assignment | x | $S1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $2$ | variable |\r\n| Initial amount of species S3 | $2$ | variable |\r\n| Initial value of parameter x | $S1$ | variable |\r\n| Initial value of parameter y | $S2$ | variable |\r\n| Initial value of parameter z | $S3$ | variable |\r\n| Initial volume of compartment 'C' | $3$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 3;\n\nS1 @Species { compartment: C, } .= 2 / C;\nS2 @Species { compartment: C, } .= 2 / C;\nS3 @Species { compartment: C, isAmount: true, } .= 2;\n\nx @Record { };\nx := S1;\ny @Record { };\ny := S2;\nz @Record { };\nz := S3;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Default values for species boundaryCondition\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, DefaultValue, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In SBML L2, the value for a speciesReference 'stoichiometry' attribute defaults to '1'. This model tests that this value is correctly assumed, in a model where the first speciesReference has no 'stoichiometry' attribute, the second has it set to '2', and the third has it set to '1'. The first should follow the third.\r\n\r\nThe model contains:\r\n* 3 species (S1, S2, S3)\r\n* 1 compartment (C)\r\n\r\nThere are 3 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J0: -> S1 | $1$ |\r\n| J1: -> 2S2 | $1$ |\r\n| J2: -> S3 | $1$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | variable |\r\n| Initial concentration of species S2 | $1$ | variable |\r\n| Initial concentration of species S3 | $1$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, } .= 1;\nS2 @Species { compartment: C, } .= 1;\nS3 @Species { compartment: C, } .= 1;\n\nJ0 @Reaction { actors: = S1, };\nJ0 := 1;\nJ1 @Reaction { actors: = 2*S2, };\nJ1 := 1;\nJ2 @Reaction { actors: = S3, };\nJ2 := 1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A local parameter shadowing its own reaction's ID.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, HasOnlySubstanceUnits, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a local parameter shadows the ID of the reaction it is in. Its kinetic law, therefore, is actually OK and not a circular reference.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 local parameter (J1.J1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $J1 * 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial value of local parameter 'J1.J1' | $0.1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := J1__J1_local * 2;\n\nJ1__J1_local @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A local parameter shadowing a species reference from its own reaction.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, HasOnlySubstanceUnits, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, a local parameter shadows the ID of a species reference from the reaction it is in. This is valid even in SBML L2, where you cannot reference a species reference ID anywhere... because it's not being referenced.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 local parameter (J1.S1_stoich)\r\n* 1 compartment (C)\r\n* 1 species reference (S1_stoich)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: -> S1 | $S1_stoich * 2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial value of local parameter 'J1.S1_stoich' | $0.1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial value of species reference 'S1_stoich' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\n\nJ1 @Reaction { actors: = S1, };\nJ1 := S1_stoich__J1_local * 2;\n\nS1_stoich__J1_local @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A local parameter shadowing two species references from its own reaction.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, HasOnlySubstanceUnits, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, two local parameters shadow the ID of species references from the reaction they are in.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 2 local parameters (J1.S1_stoich, J1.S2_stoich)\r\n* 1 compartment (C)\r\n* 2 species references (S1_stoich, S2_stoich)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: S1 -> S2 | $S1_stoich * S2_stoich * 20$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of local parameter 'J1.S1_stoich' | $0.1$ | constant |\r\n| Initial value of local parameter 'J1.S2_stoich' | $0.1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial value of species reference 'S1_stoich' | $1$ | constant |\r\n| Initial value of species reference 'S2_stoich' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\nS2 @Species { compartment: C, isAmount: true, } .= 3;\n\nJ1 @Reaction { actors: S1 = S2, };\nJ1 := S1_stoich__J1_local * S2_stoich__J1_local * 20;\n\nS1_stoich__J1_local @Const { } = 0.1;\nS2_stoich__J1_local @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Local parameters shadowing two species references and the reaction ID of their own reaction.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, HasOnlySubstanceUnits, LocalParameters\r\ntestType: TimeCourse\r\nlevels: 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In this model, local parameters shadow the ID of species references from the reaction they are in, as well as the ID of the reaction itself.\r\n\r\nThe model contains:\r\n* 2 species (S1, S2)\r\n* 3 local parameters (J1.S1_stoich, J1.S2_stoich, J1.J1)\r\n* 1 compartment (C)\r\n* 2 species references (S1_stoich, S2_stoich)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J1: S1 -> S2 | $S1_stoich * S2_stoich * J1 * 200$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial amount of species S1 | $2$ | variable |\r\n| Initial amount of species S2 | $3$ | variable |\r\n| Initial value of local parameter 'J1.S1_stoich' | $0.1$ | constant |\r\n| Initial value of local parameter 'J1.S2_stoich' | $0.1$ | constant |\r\n| Initial value of local parameter 'J1.J1' | $0.1$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial value of species reference 'S1_stoich' | $1$ | constant |\r\n| Initial value of species reference 'S2_stoich' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nS1 @Species { compartment: C, isAmount: true, } .= 2;\nS2 @Species { compartment: C, isAmount: true, } .= 3;\n\nJ1 @Reaction { actors: S1 = S2, };\nJ1 := S1_stoich__J1_local * S2_stoich__J1_local * J1__J1_local * 200;\n\nS1_stoich__J1_local @Const { } = 0.1;\nS2_stoich__J1_local @Const { } = 0.1;\nJ1__J1_local @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Parameters with different capitalizations.\r\ncomponentTags: Parameter\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A simple model to ensure that the simulator is case-sensitive.\r\n\r\nThe model contains:\r\n* 3 parameters (param, Param, pArAm)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter param | $3$ | constant |\r\n| Initial value of parameter Param | $4$ | constant |\r\n| Initial value of parameter pArAm | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nparam @Const { } = 3;\nParam @Const { } = 4;\npArAm @Const { } = 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Species with different capitalizations.\r\ncomponentTags: Compartment, Species\r\ntestTags: Amount\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A simple model to ensure that the simulator is case-sensitive.\r\n\r\nThe model contains:\r\n* 3 species (spec, Spec, sPeC)\r\n* 1 compartment (C)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species spec | $3$ | variable |\r\n| Initial concentration of species Spec | $4$ | variable |\r\n| Initial concentration of species sPeC | $5$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\n\nspec @Species { compartment: C, } .= 3;\nSpec @Species { compartment: C, } .= 4;\nsPeC @Species { compartment: C, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Compartments with different capitalizations.\r\ncomponentTags: Compartment\r\ntestTags: MultiCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A simple model to ensure that the simulator is case-sensitive.\r\n\r\nThe model contains:\r\n* 3 compartments (comp, Comp, cOmP)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial volume of compartment 'comp' | $3$ | constant |\r\n| Initial volume of compartment 'Comp' | $4$ | constant |\r\n| Initial volume of compartment 'cOmP' | $5$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ncomp @Compartment { boundary: true, } .= 3;\nComp @Compartment { boundary: true, } .= 4;\ncOmP @Compartment { boundary: true, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Species in compartments with different capitalizations.\r\ncomponentTags: Compartment, Species\r\ntestTags: Amount, MultiCompartment, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A simple model to ensure that the simulator is case-sensitive.\r\n\r\nThe model contains:\r\n* 3 species (spec, Spec, sPeC)\r\n* 2 compartments (C, c)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species spec | $3$ | variable |\r\n| Initial concentration of species Spec | $4$ | variable |\r\n| Initial concentration of species sPeC | $5$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial volume of compartment 'c' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\nc @Compartment { boundary: true, } .= 2;\n\nspec @Species { compartment: C, } .= 3;\nSpec @Species { compartment: c, } .= 4;\nsPeC @Species { compartment: C, } .= 5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Species in reactions with different capitalizations.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: Amount, MultiCompartment, NonUnityCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A simple model to ensure that the simulator is case-sensitive.\r\n\r\nThe model contains:\r\n* 3 species (spec, Spec, sPeC)\r\n* 2 compartments (C, c)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J: -> spec | $1$ |\r\n| j: -> Spec + 2sPeC | $2$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species spec | $3$ | variable |\r\n| Initial concentration of species Spec | $4$ | variable |\r\n| Initial concentration of species sPeC | $5$ | variable |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial volume of compartment 'c' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\nc @Compartment { boundary: true, } .= 2;\n\nspec @Species { compartment: C, } .= 3;\nSpec @Species { compartment: c, } .= 4;\nsPeC @Species { compartment: C, } .= 5;\n\nJ @Reaction { actors: = spec, };\nJ := 1;\nj @Reaction { actors: = Spec + 2*sPeC, };\nj := 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Species in reactions with different capitalizations.\r\ncomponentTags: Compartment, Parameter, Reaction, Species\r\ntestTags: Amount, MultiCompartment, NonUnityCompartment, NonUnityStoichiometry\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n A simple model to ensure that the simulator is case-sensitive.\r\n\r\nThe model contains:\r\n* 3 species (spec, Spec, sPeC)\r\n* 2 parameters (K, k)\r\n* 2 compartments (C, c)\r\n\r\nThere are 2 reactions:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J: -> spec | $K$ |\r\n| j: -> Spec + 2sPeC | $k$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species spec | $3$ | variable |\r\n| Initial concentration of species Spec | $4$ | variable |\r\n| Initial concentration of species sPeC | $5$ | variable |\r\n| Initial value of parameter K | $1$ | constant |\r\n| Initial value of parameter k | $2$ | constant |\r\n| Initial volume of compartment 'C' | $1$ | constant |\r\n| Initial volume of compartment 'c' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 1;\nc @Compartment { boundary: true, } .= 2;\n\nspec @Species { compartment: C, } .= 3;\nSpec @Species { compartment: c, } .= 4;\nsPeC @Species { compartment: C, } .= 5;\n\nJ @Reaction { actors: = spec, };\nJ := K;\nj @Reaction { actors: = Spec + 2*sPeC, };\nj := k;\n\nK @Const { } = 1;\nk @Const { } = 2;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: A reaction with a species in a 0-dimensional compartment.\r\ncomponentTags: Compartment, Reaction, Species\r\ntestTags: 0D-Compartment, Amount, NonUnityCompartment\r\ntestType: TimeCourse\r\nlevels: 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\n In SBML L3v2, there were special rules for when a compartment had a spatialDimensions of 0. Those rules were removed for SMBL L3, so a model with a 0D compartment now behaves exactly the same as if the compartment had some other dimensionality. This model tests a non-unity compartment in a reaction, and gives the species an initial concentration, to ensure the compartment's size is being properly handled.\r\n\r\nThe model contains:\r\n* 1 species (S1)\r\n* 1 compartment (C)\r\n\r\nThere is one reaction:\r\n\r\n[{width:30em,margin: 1em auto}| *Reaction* | *Rate* |\r\n| J: -> S1 | $1.5$ |]\r\n\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial concentration of species S1 | $1$ | variable |\r\n| Initial volume of compartment 'C' | $2$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nC @Compartment { boundary: true, } .= 0;\n\nS1 @Species { compartment: C, isAmount: true, } .= 1 * C;\n\nJ @Reaction { actors: = S1, };\nJ := 1.5;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Test SBML IDs named 'inf'\r\ncomponentTags: Parameter\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis tests whether parameters named 'inf' are properly handled by the simulator.\r\n\r\nThe model contains:\r\n* 3 parameters (INF, Inf, inf)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter INF | $10$ | constant |\r\n| Initial value of parameter Inf | $1$ | constant |\r\n| Initial value of parameter inf | $0.1$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nINF @Const { } = 10;\nInf @Const { } = 1;\ninf @Const { } = 0.1;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Test SBML IDs named 'inf'\r\ncomponentTags: InitialAssignment, Parameter\r\ntestTags: InitialValueReassigned\r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis tests whether parameters named 'inf' are properly handled by the simulator when assigned as values to other parameters.\r\n\r\nThe model contains:\r\n* 7 parameters (INF, Inf, inf, a, b, c, d)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter INF | $10$ | constant |\r\n| Initial value of parameter Inf | $1$ | constant |\r\n| Initial value of parameter inf | $0.1$ | constant |\r\n| Initial value of parameter a | $INF$ | constant |\r\n| Initial value of parameter b | $Inf$ | constant |\r\n| Initial value of parameter c | $inf$ | constant |\r\n| Initial value of parameter d | $INF$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\nvolume #defineUnit { units: litre, };\narea #defineUnit { units: metre^2, };\nlength #defineUnit { units: metre, };\nsubstance #defineUnit { units: mole, };\ntime #defineUnit { units: second, };\n\nt @TimeScale { };\n\nINF @Record { } .= 10;\nInf @Record { } .= 1;\ninf @Record { } .= 0.1;\na @Record { } .= INF;\nb @Record { } .= Inf;\nc @Record { } .= inf;\nd @Record { } .= Infinity;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Test SBML IDs named 'true'\r\ncomponentTags: Parameter\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis tests whether parameters named 'true' are properly handled by the simulator when assigned as values to other parameters.\r\n\r\nThe model contains:\r\n* 3 parameters (true, True, TRUE)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter true | $10$ | constant |\r\n| Initial value of parameter True | $20$ | constant |\r\n| Initial value of parameter TRUE | $30$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\ntrue @Const { } = 10;\nTrue @Const { } = 20;\nTRUE @Const { } = 30;\n\n"} +{"prompt":"Create Heta model\n\r\ncategory: Test\r\nsynopsis: Test SBML IDs named 'false'\r\ncomponentTags: Parameter\r\ntestTags: \r\ntestType: TimeCourse\r\nlevels: 1.2, 2.1, 2.2, 2.3, 2.4, 2.5, 3.1, 3.2\r\ngeneratedBy: Analytic\r\npackagesPresent: \r\n\r\nThis tests whether parameters named 'false' are properly handled by the simulator.\r\n\r\nThe model contains:\r\n* 3 parameters (false, False, FALSE)\r\nThe initial conditions are as follows:\r\n\r\n[{width:35em,margin: 1em auto}| | *Value* | *Constant* |\r\n| Initial value of parameter false | $4$ | constant |\r\n| Initial value of parameter False | $5$ | constant |\r\n| Initial value of parameter FALSE | $6$ | constant |]\r\n\r\nNote: The test data for this model was generated from an analytical\r\nsolution of the system of equations.\r\n\r\n","completion":"\n\nt @TimeScale { };\n\nfalse @Const { } = 4;\nFalse @Const { } = 5;\nFALSE @Const { } = 6;\n\n"} diff --git a/latest/summary.json b/latest/summary.json index 370acdb15..a149c9b12 100644 --- a/latest/summary.json +++ b/latest/summary.json @@ -1,7 +1,7 @@ { "hetaCompilerVersion": "0.8.3", - "started": "Thu Jun 13 12:33:20 UTC 2024", - "totalCasesCount": "100", + "started": "Thu Jun 13 14:24:45 UTC 2024", + "totalCasesCount": "1821", "cases": [ {"id": "00001", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00002", "l2v5RetCode": 0, "l3v2RetCode": 0}, @@ -29,7 +29,7 @@ {"id": "00024", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00025", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00026", "l2v5RetCode": 0, "l3v2RetCode": 0}, - {"id": "00027", "l2v5RetCode": 0, "l3v2RetCode": 2}, + {"id": "00027", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00028", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00029", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00030", "l2v5RetCode": 0, "l3v2RetCode": 0}, @@ -59,7 +59,7 @@ {"id": "00054", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00055", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00056", "l2v5RetCode": 0, "l3v2RetCode": 0}, - {"id": "00057", "l2v5RetCode": 0, "l3v2RetCode": 2}, + {"id": "00057", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00058", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00059", "l2v5RetCode": 0, "l3v2RetCode": 9}, {"id": "00060", "l2v5RetCode": 0, "l3v2RetCode": 0}, @@ -102,7 +102,1728 @@ {"id": "00097", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00098", "l2v5RetCode": 0, "l3v2RetCode": 0}, {"id": "00099", "l2v5RetCode": 0, "l3v2RetCode": 0}, - {"id": "00100", "l2v5RetCode": 0, "l3v2RetCode": 0} + {"id": "00100", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00101", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00102", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00103", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00104", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00105", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00106", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00107", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00108", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00109", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00110", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00111", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00112", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00113", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00114", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00115", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00116", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00117", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00118", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00119", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00120", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00121", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00122", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00123", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00124", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00125", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00126", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00127", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00128", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00129", "l2v5RetCode": 2, "l3v2RetCode": 9}, + {"id": "00130", "l2v5RetCode": 2, "l3v2RetCode": 9}, + {"id": "00131", "l2v5RetCode": 2, "l3v2RetCode": 9}, + {"id": "00132", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00133", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00134", "l2v5RetCode": 0, "l3v2RetCode": 9}, + {"id": "00135", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00136", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00137", "l2v5RetCode": 0, "l3v2RetCode": 0}, + {"id": "00138", 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